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	788351	788351	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:788351delT	uc009vjn.1	+						LOC643837_uc001abp.1_Intron|LOC643837_uc001abq.1_Intron|LOC643837_uc009vjo.1_Intron|LOC643837_uc001abr.1_Intron					Homo sapiens cDNA: FLJ23220 fis, clone ADSU01957.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	850328	850329	+	3'UTR	INS	-	A	A	rs79575748		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:850328_850329insA	uc001abu.1	+	2										Homo sapiens cDNA FLJ31924 fis, clone NT2RP7005468.																														---	---	---	---
GNB1	2782	broad.mit.edu	37	1	1761184	1761185	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1761184_1761185insT	uc001aif.2	-						GNB1_uc009vky.2_Intron	NM_002074	NP_002065			guanine nucleotide-binding protein, beta-1						cellular response to glucagon stimulus|energy reserve metabolic process|muscarinic acetylcholine receptor signaling pathway|platelet activation|Ras protein signal transduction|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|GTPase binding|signal transducer activity				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	1869565	1869566	+	IGR	DEL	CA	-	-	rs144908957		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1869565_1869566delCA								TMEM52 (18825 upstream) : KIAA1751 (15186 downstream)																																			---	---	---	---
PRKCZ	5590	broad.mit.edu	37	1	2091678	2091681	+	Intron	DEL	GTGT	-	-	rs59846504		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2091678_2091681delGTGT	uc001aiq.2	+						PRKCZ_uc001air.2_Intron|PRKCZ_uc010nyw.1_Intron|PRKCZ_uc001ais.2_Intron|PRKCZ_uc009vla.2_Intron|PRKCZ_uc010nyx.1_Intron	NM_002744	NP_002735			protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	2371882	2371882	+	IGR	DEL	T	-	-	rs111269301		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2371882delT								PEX10 (27872 upstream) : PLCH2 (35872 downstream)																																			---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3328152	3328152	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3328152delC	uc001akf.2	+	9	1471	c.1391delC	c.(1390-1392)ACCfs	p.T464fs	PRDM16_uc001akc.2_Frame_Shift_Del_p.T464fs|PRDM16_uc001akd.2_Frame_Shift_Del_p.T464fs|PRDM16_uc001ake.2_Frame_Shift_Del_p.T464fs|PRDM16_uc009vlh.2_Frame_Shift_Del_p.T165fs	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1	464	Pro-rich.				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								---	---	---	---
DFFB	1677	broad.mit.edu	37	1	3801134	3801134	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3801134delT	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	4013582	4013583	+	RNA	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4013582_4013583delAG	uc001ali.1	+	3		c.1502_1503delAG								Homo sapiens cDNA FLJ42718 fis, clone BRAMY3010411.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	4110158	4110159	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4110158_4110159delAG								LOC100133612 (276281 upstream) : LOC284661 (361952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	4576648	4576648	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4576648delT								LOC284661 (91904 upstream) : AJAP1 (138457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	4707423	4707425	+	IGR	DEL	TGA	-	-	rs139953979		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4707423_4707425delTGA								LOC284661 (222679 upstream) : AJAP1 (7680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5137705	5137705	+	IGR	DEL	A	-	-	rs35236862		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5137705delA								AJAP1 (293855 upstream) : NPHP4 (785165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5695337	5695338	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5695337_5695338insC	uc001alp.1	-											Homo sapiens cDNA FLJ43088 fis, clone BRTHA3025826.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	5788943	5788944	+	IGR	INS	-	TGC	TGC	rs144196249	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5788943_5788944insTGC								AJAP1 (945093 upstream) : NPHP4 (133926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5830192	5830192	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5830192delA								AJAP1 (986342 upstream) : NPHP4 (92678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5863326	5863327	+	IGR	INS	-	ACAC	ACAC	rs150846684	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5863326_5863327insACAC								None (None upstream) : NPHP4 (59543 downstream)																																			---	---	---	---
RPL22	6146	broad.mit.edu	37	1	6257785	6257785	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6257785delT	uc001amd.2	-	2	90	c.44delA	c.(43-45)AAGfs	p.K15fs	RPL22_uc001ame.2_Frame_Shift_Del_p.K15fs	NM_000983	NP_000974	P35268	RL22_HUMAN	ribosomal protein L22 proprotein	15					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	heparin binding|RNA binding|structural constituent of ribosome				0	Ovarian(185;0.0634)	all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)				T	RUNX1	AML|CML								---	---	---	---
PLEKHG5	57449	broad.mit.edu	37	1	6552527	6552527	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6552527delC	uc001ano.1	-						PLEKHG5_uc001ann.1_Intron|PLEKHG5_uc001anq.1_Intron|PLEKHG5_uc001anp.1_Intron|PLEKHG5_uc009vmb.1_5'Flank|PLEKHG5_uc001anl.1_5'Flank|PLEKHG5_uc001anm.1_5'Flank	NM_001042663	NP_001036128			pleckstrin homology domain containing family G						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
PHF13	148479	broad.mit.edu	37	1	6678202	6678202	+	Intron	DEL	T	-	-	rs113955558		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6678202delT	uc001aob.3	+							NM_153812	NP_722519			PHD finger protein 13						cell division|chromatin modification|mitotic chromosome condensation	nucleoplasm	chromatin binding|methylated histone residue binding|zinc ion binding				0	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;1.46e-33)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.19e-07)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|STAD - Stomach adenocarcinoma(132;0.0165)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	6869090	6869090	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6869090delT	uc001aoi.2	+						CAMTA1_uc001aoh.2_Intron	NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	6894337	6894337	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6894337delT	uc001aoi.2	+						CAMTA1_uc001aoh.2_Intron	NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7547087	7547088	+	Intron	INS	-	A	A	rs137965883	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7547087_7547088insA	uc001aoi.2	+							NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7601093	7601094	+	Intron	INS	-	G	G	rs143905763	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7601093_7601094insG	uc001aoi.2	+							NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7793277	7793277	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7793277delA	uc001aoi.2	+						CAMTA1_uc010nzv.1_Intron|CAMTA1_uc001aok.3_Intron	NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	8257131	8257132	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8257131_8257132delTT								ERRFI1 (170738 upstream) : SLC45A1 (127258 downstream)																																			---	---	---	---
RERE	473	broad.mit.edu	37	1	8798353	8798353	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8798353delT	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)														---	---	---	---
SLC2A7	155184	broad.mit.edu	37	1	9075048	9075048	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9075048delC	uc009vmo.1	-							NM_207420	NP_997303			intestinal facilitative glucose transporter 7							integral to membrane|plasma membrane	sugar transmembrane transporter activity				0	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
SLC2A5	6518	broad.mit.edu	37	1	9142608	9142608	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9142608delA	uc010oab.1	-							NM_003039	NP_003030			solute carrier family 2 (facilitated						carbohydrate metabolic process	integral to membrane|plasma membrane	fructose transmembrane transporter activity|glucose transmembrane transporter activity			pancreas(2)|ovary(1)	3	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	9231983	9231985	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9231983_9231985delAAA	uc009vmq.2	-											EF609116																														---	---	---	---
TMEM201	199953	broad.mit.edu	37	1	9668821	9668823	+	Intron	DEL	AGA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9668821_9668823delAGA	uc001apz.2	+							NM_001130924	NP_001124396			transmembrane protein 201 isoform 1							integral to membrane|nuclear inner membrane					0	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
CTNNBIP1	56998	broad.mit.edu	37	1	9954581	9954581	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9954581delT	uc001aqk.1	-						CTNNBIP1_uc001aql.1_Intron	NM_020248	NP_064633			catenin, beta interacting protein 1						anterior/posterior pattern formation|branching involved in ureteric bud morphogenesis|negative regulation of mesenchymal cell proliferation|negative regulation of protein binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of smooth muscle cell proliferation|negative regulation of transcription initiation from RNA polymerase II promoter|negative regulation of Wnt receptor signaling pathway|positive regulation of monocyte differentiation|positive regulation of osteoblast differentiation|regulation of vascular permeability involved in acute inflammatory response|Wnt receptor signaling pathway	Axin-APC-beta-catenin-GSK3B complex|cytosol|nucleus	armadillo repeat domain binding|beta-catenin binding				0		all_lung(284;1.82e-05)|Lung NSC(185;3.08e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|Colorectal(212;7.32e-08)|COAD - Colon adenocarcinoma(227;1.73e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000912)|KIRC - Kidney renal clear cell carcinoma(229;0.00112)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
LZIC	84328	broad.mit.edu	37	1	9996736	9996736	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9996736delA	uc001aqm.2	-						LZIC_uc001aqn.2_Intron|LZIC_uc001aqo.2_Intron|LZIC_uc009vmr.2_Intron|LZIC_uc010oah.1_Intron	NM_032368	NP_115744			leucine zipper and CTNNBIP1 domain containing								beta-catenin 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;5.29e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;0.000242)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.00842)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10100680	10100680	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10100680delT	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron	NM_001105562	NP_001099032			ubiquitination factor E4B isoform 1						apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10108852	10108852	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10108852delA	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron	NM_001105562	NP_001099032			ubiquitination factor E4B isoform 1						apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10177642	10177642	+	Frame_Shift_Del	DEL	A	-	-	rs143511579	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10177642delA	uc001aqs.3	+	8	2035	c.1322delA	c.(1321-1323)GAAfs	p.E441fs	UBE4B_uc001aqr.3_Frame_Shift_Del_p.E312fs|UBE4B_uc010oai.1_RNA|UBE4B_uc010oaj.1_5'UTR	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1	441					apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10193944	10193945	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10193944_10193945insA	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron|UBE4B_uc001aqt.1_Intron	NM_001105562	NP_001099032			ubiquitination factor E4B isoform 1						apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10211221	10211222	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10211221_10211222delAA	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron|UBE4B_uc001aqt.1_Intron	NM_001105562	NP_001099032			ubiquitination factor E4B isoform 1						apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10387560	10387562	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10387560_10387562delAAA	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)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10389797	10389797	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10389797delA	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)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10408017	10408017	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10408017delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	10892136	10892136	+	IGR	DEL	T	-	-	rs72643257		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10892136delT								CASZ1 (35429 upstream) : C1orf127 (114397 downstream)																																			---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11206366	11206366	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11206366delG	uc001asd.2	-							NM_004958	NP_004949			FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29																		---	---	---	---
UBIAD1	29914	broad.mit.edu	37	1	11347986	11347986	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11347986delA	uc001asg.2	+	2						NM_013319	NP_037451			UbiA prenyltransferase domain containing 1						menaquinone biosynthetic process	endoplasmic reticulum membrane|integral to membrane|mitochondrion|nucleus	prenyltransferase activity				0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.012)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.52e-06)|COAD - Colon adenocarcinoma(227;0.000254)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0487)														---	---	---	---
CLCN6	1185	broad.mit.edu	37	1	11888700	11888700	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11888700delC	uc001ate.3	+						CLCN6_uc009vnh.1_Intron|CLCN6_uc010oat.1_Intron|CLCN6_uc010oau.1_Intron	NM_001286	NP_001277			chloride channel 6 isoform ClC-6a						cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	11937662	11937663	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11937662_11937663insT								NPPB (18670 upstream) : KIAA2013 (42461 downstream)																																			---	---	---	---
KIAA2013	90231	broad.mit.edu	37	1	11987127	11987130	+	5'Flank	DEL	AAAA	-	-	rs144379384		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11987127_11987130delAAAA	uc001atk.2	-						KIAA2013_uc001atl.1_5'Flank	NM_138346	NP_612355			hypothetical protein LOC90231 precursor							integral to membrane				ovary(1)	1	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PLOD1	5351	broad.mit.edu	37	1	12000485	12000485	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12000485delC	uc001atm.2	+						PLOD1_uc010obb.1_Intron	NM_000302	NP_000293			lysyl hydroxylase 1 precursor						epidermis development|hydroxylysine biosynthetic process|protein modification process|response to hypoxia	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein homodimerization activity			ovary(2)|breast(1)	3	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Minoxidil(DB00350)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
TNFRSF8	943	broad.mit.edu	37	1	12198204	12198204	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12198204delA	uc001atq.2	+						TNFRSF8_uc010obc.1_Intron|TNFRSF8_uc001atr.2_Intron|TNFRSF8_uc001ats.2_Intron	NM_001243	NP_001234			tumor necrosis factor receptor superfamily,						cellular response to mechanical stimulus|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of TRAIL biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	cytoplasm|integral to membrane|plasma membrane				skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	5	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12385320	12385320	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12385320delT	uc001atv.2	+						VPS13D_uc001atw.2_Intron|VPS13D_uc001atx.2_Intron|VPS13D_uc001aty.1_Intron	NM_015378	NP_056193			vacuolar protein sorting 13D isoform 1						protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	12592376	12592376	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12592376delT								VPS13D (20280 upstream) : DHRS3 (35564 downstream)																																			---	---	---	---
DHRS3	9249	broad.mit.edu	37	1	12643614	12643615	+	Intron	INS	-	ATCC	ATCC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12643614_12643615insATCC	uc001auc.2	-						DHRS3_uc001aub.2_Intron|DHRS3_uc009vnm.2_Intron|DHRS3_uc001aud.3_Intron|DHRS3_uc001aue.1_Intron	NM_004753	NP_004744			dehydrogenase/reductase (SDR family) member 3						retinol metabolic process|visual perception	integral to membrane	electron carrier activity|NADP-retinol dehydrogenase activity|nucleotide binding			skin(1)	1	Ovarian(185;0.249)	Lung NSC(185;4.11e-05)|all_lung(284;4.58e-05)|Renal(390;0.000147)|Colorectal(325;0.000585)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|Colorectal(212;9.25e-07)|COAD - Colon adenocarcinoma(227;0.000326)|BRCA - Breast invasive adenocarcinoma(304;0.000344)|Kidney(185;0.00235)|KIRC - Kidney renal clear cell carcinoma(229;0.00656)|STAD - Stomach adenocarcinoma(313;0.00798)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	12743831	12743831	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12743831delT								AADACL4 (16735 upstream) : AADACL3 (32287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	12747800	12747800	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12747800delA								AADACL4 (20704 upstream) : AADACL3 (28318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14018349	14018350	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14018349_14018350delAC								PDPN (73899 upstream) : PRDM2 (8385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14248128	14248128	+	IGR	DEL	T	-	-	rs74848873		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14248128delT								PRDM2 (96556 upstream) : KAZ (677085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14474290	14474290	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14474290delA								PRDM2 (322718 upstream) : KAZ (450923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14824319	14824319	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14824319delA								PRDM2 (672747 upstream) : KAZ (100894 downstream)																																			---	---	---	---
KAZ	23254	broad.mit.edu	37	1	15100674	15100674	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15100674delG	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron	NM_201628	NP_963922			kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0																		---	---	---	---
FHAD1	114827	broad.mit.edu	37	1	15601465	15601466	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15601465_15601466delTT	uc001awb.2	+						FHAD1_uc001awa.1_Intron	NM_052929	NP_443161			forkhead-associated (FHA) phosphopeptide binding											skin(1)	1																		---	---	---	---
CASP9	842	broad.mit.edu	37	1	15824855	15824856	+	Intron	DEL	TT	-	-	rs34667779		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15824855_15824856delTT	uc001awn.2	-						CASP9_uc001awm.1_Intron|CASP9_uc001awo.2_Intron|CASP9_uc001awp.2_Intron|CASP9_uc009voi.2_Intron|CASP9_uc010obm.1_Intron|CASP9_uc001awq.2_Intron	NM_001229	NP_001220			caspase 9 isoform alpha preproprotein						activation of caspase activity by cytochrome c|induction of apoptosis by intracellular signals|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol	cysteine-type endopeptidase activity|enzyme activator activity|protein binding			central_nervous_system(1)|kidney(1)	2		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)														---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16189262	16189262	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16189262delT	uc001axk.1	+							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	16433234	16433234	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16433234delT								FAM131C (33107 upstream) : EPHA2 (17598 downstream)																																			---	---	---	---
EPHA2	1969	broad.mit.edu	37	1	16458077	16458077	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16458077delA	uc001aya.1	-							NM_004431	NP_004422			ephrin receptor EphA2 precursor						activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus	focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane	ATP binding|ephrin receptor activity|protein binding			lung(3)|central_nervous_system(3)|stomach(2)|ovary(2)	10		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	16502814	16502815	+	IGR	INS	-	TC	TC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16502814_16502815insTC								EPHA2 (20250 upstream) : ARHGEF19 (21784 downstream)																																			---	---	---	---
FBXO42	54455	broad.mit.edu	37	1	16584179	16584179	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16584179delT	uc001ayg.2	-						FBXO42_uc001ayf.2_Intron	NM_018994	NP_061867			F-box protein 42											upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)														---	---	---	---
FBXO42	54455	broad.mit.edu	37	1	16617177	16617177	+	Intron	DEL	A	-	-	rs34993877		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16617177delA	uc001ayg.2	-						FBXO42_uc001ayf.2_Intron	NM_018994	NP_061867			F-box protein 42											upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17098017	17098018	+	Intron	DEL	AG	-	-	rs72381779		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17098017_17098018delAG	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17098863	17098863	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17098863delA	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17123680	17123680	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17123680delT	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17217650	17217650	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17217650delT	uc009voy.1	+						uc001azs.1_5'Flank					Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
PADI2	11240	broad.mit.edu	37	1	17408925	17408926	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17408925_17408926delAG	uc001baf.2	-						PADI2_uc010ocm.1_Intron|PADI2_uc001bag.1_Intron	NM_007365	NP_031391			peptidyl arginine deiminase, type II						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity			ovary(3)|pancreas(1)|central_nervous_system(1)|skin(1)	6		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)													---	---	---	---
ARHGEF10L	55160	broad.mit.edu	37	1	17977824	17977824	+	Intron	DEL	G	-	-	rs114507852	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17977824delG	uc001ban.2	+						ARHGEF10L_uc009vpe.1_Intron|ARHGEF10L_uc001bao.2_Intron|ARHGEF10L_uc001bap.2_Intron|ARHGEF10L_uc001baq.2_Intron|ARHGEF10L_uc010ocs.1_Intron|ARHGEF10L_uc001bar.2_Intron|ARHGEF10L_uc009vpf.2_Intron	NM_018125	NP_060595			Rho guanine nucleotide exchange factor (GEF)						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	18376124	18376125	+	IGR	INS	-	ATA	ATA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18376124_18376125insATA								ACTL8 (222568 upstream) : IGSF21 (58115 downstream)																																			---	---	---	---
IGSF21	84966	broad.mit.edu	37	1	18480776	18480776	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18480776delT	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)														---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19423487	19423488	+	Intron	DEL	TT	-	-	rs36041876		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19423487_19423488delTT	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	19455704	19455704	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19455704delA	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)														---	---	---	---
KIAA0090	23065	broad.mit.edu	37	1	19560550	19560551	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19560550_19560551delAC	uc001bbo.2	-						KIAA0090_uc001bbp.2_Intron|KIAA0090_uc001bbq.2_Intron|KIAA0090_uc001bbr.2_Intron	NM_015047	NP_055862			hypothetical protein LOC23065 precursor							integral to membrane	protein binding			ovary(1)	1		Colorectal(325;0.000147)|Renal(390;0.000469)|Breast(348;0.00366)|all_lung(284;0.00519)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;3.84e-05)|Kidney(64;0.000191)|KIRC - Kidney renal clear cell carcinoma(64;0.00274)|GBM - Glioblastoma multiforme(114;0.005)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0656)														---	---	---	---
CAPZB	832	broad.mit.edu	37	1	19770656	19770656	+	Intron	DEL	A	-	-	rs79896581		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19770656delA	uc010ocz.1	-						CAPZB_uc001bce.2_Intron|CAPZB_uc009vpk.2_Intron	NM_004930	NP_004921			F-actin capping protein beta subunit						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement	cytosol|F-actin capping protein complex|WASH complex	actin binding				0		Colorectal(325;3.93e-05)|Renal(390;0.000147)|all_lung(284;0.000169)|Lung NSC(340;0.000202)|Breast(348;0.000496)|Ovarian(437;0.00428)|Myeloproliferative disorder(586;0.0262)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Kidney(64;8.63e-06)|BRCA - Breast invasive adenocarcinoma(304;4.06e-05)|KIRC - Kidney renal clear cell carcinoma(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000525)|STAD - Stomach adenocarcinoma(196;0.00779)|READ - Rectum adenocarcinoma(331;0.103)|Lung(427;0.173)														---	---	---	---
CAPZB	832	broad.mit.edu	37	1	19770957	19770957	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19770957delA	uc010ocz.1	-						CAPZB_uc001bce.2_Intron|CAPZB_uc009vpk.2_Intron	NM_004930	NP_004921			F-actin capping protein beta subunit						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement	cytosol|F-actin capping protein complex|WASH complex	actin binding				0		Colorectal(325;3.93e-05)|Renal(390;0.000147)|all_lung(284;0.000169)|Lung NSC(340;0.000202)|Breast(348;0.000496)|Ovarian(437;0.00428)|Myeloproliferative disorder(586;0.0262)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Kidney(64;8.63e-06)|BRCA - Breast invasive adenocarcinoma(304;4.06e-05)|KIRC - Kidney renal clear cell carcinoma(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000525)|STAD - Stomach adenocarcinoma(196;0.00779)|READ - Rectum adenocarcinoma(331;0.103)|Lung(427;0.173)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	20164825	20164825	+	IGR	DEL	T	-	-	rs112196639		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20164825delT								RNF186 (23054 upstream) : OTUD3 (44063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	20425863	20425863	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20425863delA								PLA2G5 (7470 upstream) : PLA2G2D (12578 downstream)																																			---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21191489	21191490	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21191489_21191490delAA	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron	NM_003760	NP_003751			eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21260999	21260999	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21260999delA	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron	NM_003760	NP_003751			eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21307743	21307746	+	Intron	DEL	ATTT	-	-	rs74258939		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21307743_21307746delATTT	uc001bec.2	-						EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beg.2_Intron|EIF4G3_uc010odk.1_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751			eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21665437	21665438	+	Intron	INS	-	T	T	rs139982914	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21665437_21665438insT	uc001bem.2	-							NM_001113348	NP_001106819			endothelin converting enzyme 1 isoform 4						bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	21689913	21689913	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21689913delT								ECE1 (17879 upstream) : NBPF3 (76718 downstream)																																			---	---	---	---
NBPF3	84224	broad.mit.edu	37	1	21806303	21806304	+	Intron	INS	-	TA	TA	rs140026006	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21806303_21806304insTA	uc001ber.2	+						NBPF3_uc001bes.2_Intron|NBPF3_uc009vqb.2_Intron|NBPF3_uc010odm.1_Intron	NM_032264	NP_115640			neuroblastoma breakpoint family, member 3							cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
RAP1GAP	5909	broad.mit.edu	37	1	21980037	21980040	+	Intron	DEL	CTTC	-	-	rs35417076	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21980037_21980040delCTTC	uc001bex.2	-						RAP1GAP_uc001bew.2_5'Flank|RAP1GAP_uc001bey.2_Intron	NM_002885	NP_002876			RAP1 GTPase activating protein isoform c						regulation of Ras GTPase activity|signal transduction	cytosol|Golgi membrane|membrane fraction	GTPase activator activity|GTPase activity|protein homodimerization activity|Ras GTPase binding			breast(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)														---	---	---	---
USP48	84196	broad.mit.edu	37	1	22032081	22032081	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22032081delA	uc001bfb.2	-						USP48_uc001bfa.2_Intron|USP48_uc010odq.1_Intron|USP48_uc009vqc.2_Intron|USP48_uc001bfc.2_Intron|USP48_uc001bfd.1_5'Flank	NM_032236	NP_115612			ubiquitin specific protease 48 isoform a						ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)														---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22214279	22214279	+	Intron	DEL	C	-	-	rs114537356	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22214279delC	uc001bfj.2	-						HSPG2_uc009vqd.2_Intron|HSPG2_uc009vqe.1_Intron	NM_005529	NP_005520			heparan sulfate proteoglycan 2 precursor						angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	22345314	22345314	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22345314delT								CELA3A (6281 upstream) : HSPC157 (6393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22591872	22591873	+	IGR	DEL	GC	-	-	rs67400059		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22591872_22591873delGC								WNT4 (121487 upstream) : ZBTB40 (186471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22663019	22663022	+	IGR	DEL	CATC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22663019_22663022delCATC								WNT4 (192634 upstream) : ZBTB40 (115322 downstream)																																			---	---	---	---
ZBTB40	9923	broad.mit.edu	37	1	22778140	22778140	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22778140delA	uc001bft.2	+						ZBTB40_uc001bfu.2_5'Flank|ZBTB40_uc009vqi.1_5'Flank	NM_001083621	NP_001077090			zinc finger and BTB domain containing 40						bone mineralization|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	22996397	22996398	+	IGR	DEL	GC	-	-	rs10588615		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22996397_22996398delGC								C1QB (8369 upstream) : EPHB2 (40933 downstream)																																			---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23122777	23122777	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23122777delG	uc009vqj.1	+						EPHB2_uc001bge.2_Intron|EPHB2_uc001bgf.2_Intron|EPHB2_uc010odu.1_Intron	NM_017449	NP_059145			ephrin receptor EphB2 isoform 1 precursor						axon guidance	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)										Hereditary_Prostate_Cancer				---	---	---	---
LUZP1	7798	broad.mit.edu	37	1	23466446	23466449	+	Intron	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23466446_23466449delAAAA	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)														---	---	---	---
LUZP1	7798	broad.mit.edu	37	1	23505281	23505281	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23505281delT	uc001bgm.1	-							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	23529416	23529416	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23529416delT								HTR1D (8194 upstream) : HNRNPR (106861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	23531098	23531098	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23531098delT								HTR1D (9876 upstream) : HNRNPR (105179 downstream)																																			---	---	---	---
HNRNPR	10236	broad.mit.edu	37	1	23636875	23636875	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23636875delT	uc001bgr.3	-	11					HNRNPR_uc001bgo.2_3'UTR|HNRNPR_uc001bgp.3_3'UTR|HNRNPR_uc009vqk.2_3'UTR|HNRNPR_uc001bgs.3_3'UTR|HNRNPR_uc010odw.1_3'UTR|HNRNPR_uc010odx.1_3'UTR|HNRNPR_uc009vql.2_3'UTR	NM_005826	NP_005817			heterogeneous nuclear ribonucleoprotein R							catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)														---	---	---	---
HMGCL	3155	broad.mit.edu	37	1	24146974	24146974	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24146974delT	uc001bib.2	-						HMGCL_uc010oec.1_Intron|HMGCL_uc009vqr.2_Intron|HMGCL_uc001bic.2_Intron|HMGCL_uc009vqs.1_Intron|HMGCL_uc001bid.1_Intron	NM_000191	NP_000182			3-hydroxy-3-methylglutaryl CoA lyase isoform 1						acetoacetic acid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA lyase activity|metal ion binding			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)														---	---	---	---
FUCA1	2517	broad.mit.edu	37	1	24173070	24173070	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24173070delT	uc001bie.2	-							NM_000147	NP_000138			fucosidase, alpha-L-1, tissue precursor						fucose metabolic process|glycosaminoglycan catabolic process	lysosome	alpha-L-fucosidase activity|cation binding			breast(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)														---	---	---	---
FUCA1	2517	broad.mit.edu	37	1	24175455	24175456	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24175455_24175456insT	uc001bie.2	-							NM_000147	NP_000138			fucosidase, alpha-L-1, tissue precursor						fucose metabolic process|glycosaminoglycan catabolic process	lysosome	alpha-L-fucosidase activity|cation binding			breast(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)														---	---	---	---
CNR2	1269	broad.mit.edu	37	1	24236906	24236906	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24236906delA	uc001bif.2	-							NM_001841	NP_001832			cannabinoid receptor 2 (macrophage)						behavior|G-protein signaling, coupled to cyclic nucleotide second messenger|immune response|inflammatory response	dendrite|integral to plasma membrane|perikaryon	cannabinoid receptor activity			skin(2)|central_nervous_system(1)	3		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Nabilone(DB00486)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	24560742	24560742	+	IGR	DEL	C	-	-	rs35708272		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24560742delC								LOC284632 (22562 upstream) : GRHL3 (85139 downstream)																																			---	---	---	---
NIPAL3	57185	broad.mit.edu	37	1	24774046	24774046	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24774046delA	uc001bjh.2	+						NIPAL3_uc010oek.1_Intron|NIPAL3_uc001bjg.2_Intron|NIPAL3_uc009vrc.2_Intron	NM_020448	NP_065181			NIPA-like domain containing 3							integral to membrane					0																		---	---	---	---
RCAN3	11123	broad.mit.edu	37	1	24857940	24857940	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24857940delT	uc001bjj.2	+						RCAN3_uc009vrd.2_Intron|RCAN3_uc009vre.2_Intron|RCAN3_uc009vrf.2_Intron|RCAN3_uc009vrg.2_Intron	NM_013441	NP_038469			Down syndrome critical region gene 1-like 2						anatomical structure morphogenesis|calcium-mediated signaling		nucleotide binding|RNA binding|troponin I binding				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)														---	---	---	---
MAN1C1	57134	broad.mit.edu	37	1	26095882	26095883	+	Intron	DEL	AC	-	-	rs71928501		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26095882_26095883delAC	uc001bkm.2	+						MAN1C1_uc009vry.1_Intron	NM_020379	NP_065112			mannosidase, alpha, class 1C, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(1)	1		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)														---	---	---	---
MAN1C1	57134	broad.mit.edu	37	1	26108577	26108578	+	Intron	DEL	AG	-	-	rs2280998	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26108577_26108578delAG	uc001bkm.2	+						MAN1C1_uc009vry.1_Intron|MAN1C1_uc001bkn.2_Intron	NM_020379	NP_065112			mannosidase, alpha, class 1C, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(1)	1		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)														---	---	---	---
PAQR7	164091	broad.mit.edu	37	1	26195624	26195624	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26195624delA	uc001bkx.2	-							NM_178422	NP_848509			progestin and adipoQ receptor family member VII						cell differentiation|multicellular organismal development|oogenesis	integral to membrane|plasma membrane	receptor activity|steroid binding			breast(3)	3		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.16e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000724)|BRCA - Breast invasive adenocarcinoma(304;0.000965)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0136)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RPS6KA1	6195	broad.mit.edu	37	1	26854645	26854646	+	5'Flank	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26854645_26854646delTT	uc001bmr.1	+							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	27012228	27012228	+	IGR	DEL	A	-	-	rs79112076		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27012228delA								RPS6KA1 (110708 upstream) : ARID1A (10294 downstream)																																			---	---	---	---
FAM46B	115572	broad.mit.edu	37	1	27335398	27335398	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27335398delT	uc010ofj.1	-							NM_052943	NP_443175			hypothetical protein LOC115572											central_nervous_system(1)	1		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
SLC9A1	6548	broad.mit.edu	37	1	27442227	27442227	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27442227delA	uc001bnm.2	-						SLC9A1_uc010ofk.1_Intron|SLC9A1_uc001bnn.2_Intron	NM_003047	NP_003038			solute carrier family 9, isoform A1						regulation of pH	integral to membrane	sodium:hydrogen antiporter activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	27493769	27493769	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27493769delT								SLC9A1 (12318 upstream) : WDTC1 (67238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	27540661	27540661	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27540661delA								SLC9A1 (59210 upstream) : WDTC1 (20346 downstream)																																			---	---	---	---
WDTC1	23038	broad.mit.edu	37	1	27633952	27633952	+	3'UTR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27633952delC	uc001bno.2	+	16					WDTC1_uc001bnp.1_Intron|WDTC1_uc001bnq.2_3'UTR	NM_015023	NP_055838			WD and tetratricopeptide repeats 1								protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)														---	---	---	---
RPA2	6118	broad.mit.edu	37	1	28243617	28243618	+	5'Flank	INS	-	CTT	CTT	rs112146684		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28243617_28243618insCTT	uc001bpe.1	-						RPA2_uc001bpd.1_5'Flank|RPA2_uc010ofp.1_5'Flank	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	28353272	28353272	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28353272delA	uc001bpi.1	-						EYA3_uc010ofs.1_Intron|EYA3_uc010oft.1_Intron|EYA3_uc001bpj.2_Intron|EYA3_uc001bpk.1_Intron|EYA3_uc010ofu.1_Intron	NM_001990	NP_001981			eyes absent 3						anatomical structure morphogenesis|double-strand break repair|histone dephosphorylation|multicellular organismal development|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|transcription, DNA-dependent|visual perception	cytoplasm	metal ion binding|protein binding|protein tyrosine phosphatase activity			ovary(2)|skin(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28817970	28817970	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	29132940	29132940	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29132940delA								YTHDF2 (36654 upstream) : OPRD1 (5714 downstream)																																			---	---	---	---
OPRD1	4985	broad.mit.edu	37	1	29180906	29180906	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29180906delT	uc001brf.1	+							NM_000911	NP_000902			opioid receptor, delta 1						immune response|protein import into nucleus, translocation	integral to plasma membrane	delta-opioid receptor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Butorphanol(DB00611)|Codeine(DB00318)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Loperamide(DB00836)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pimozide(DB01100)|Propoxyphene(DB00647)													---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29257000	29257000	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29257000delT	uc001brl.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Intron	NM_004437	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29338635	29338635	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29338635delT	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29375226	29375226	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29375226delT	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29389165	29389168	+	Intron	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29389165_29389168delTTTT	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc001brk.2_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29398221	29398222	+	Intron	INS	-	AC	AC	rs139632969	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29398221_29398222insAC	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
PTPRU	10076	broad.mit.edu	37	1	29602360	29602360	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29602360delT	uc001bru.2	+						PTPRU_uc001brv.2_Intron|PTPRU_uc001brw.2_Intron|PTPRU_uc009vtq.2_Intron|PTPRU_uc009vtr.2_Intron	NM_005704	NP_005695			protein tyrosine phosphatase, receptor type, U						canonical Wnt receptor signaling pathway|cell differentiation|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transmembrane receptor protein tyrosine phosphatase signaling pathway	cell-cell junction|integral to plasma membrane	beta-catenin binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(3)|ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	7		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	30133223	30133223	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30133223delT								PTPRU (479908 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30234176	30234177	+	IGR	INS	-	GAGACACG	GAGACACG	rs139592478	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30234176_30234177insGAGACACG								PTPRU (580861 upstream) : MATN1 (949949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30367692	30367693	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30367692_30367693insT								PTPRU (714377 upstream) : MATN1 (816433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30421581	30421582	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30421581_30421582delCA								PTPRU (768266 upstream) : MATN1 (762544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	31338507	31338509	+	IGR	DEL	AAA	-	-	rs111732336		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31338507_31338509delAAA								LAPTM5 (107824 upstream) : SDC3 (3804 downstream)																																			---	---	---	---
SDC3	9672	broad.mit.edu	37	1	31365290	31365293	+	Intron	DEL	GAAT	-	-	rs71916891		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31365290_31365293delGAAT	uc001bse.2	-							NM_014654	NP_055469			syndecan 3							integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PUM1	9698	broad.mit.edu	37	1	31508603	31508603	+	Intron	DEL	A	-	-	rs78545282		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31508603delA	uc001bsi.1	-						PUM1_uc001bsh.1_Intron|PUM1_uc001bsj.1_Intron|PUM1_uc010oga.1_Intron|PUM1_uc001bsk.1_Intron|PUM1_uc010ogb.1_Intron	NM_014676	NP_055491			pumilio 1 isoform 2						cellular membrane organization|post-Golgi vesicle-mediated transport|regulation of translation	cytosol	RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	31580928	31580929	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31580928_31580929delTT								PUM1 (42165 upstream) : NKAIN1 (71664 downstream)																																			---	---	---	---
NKAIN1	79570	broad.mit.edu	37	1	31660705	31660705	+	Intron	DEL	A	-	-	rs111493842		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31660705delA	uc010ogd.1	-						NKAIN1_uc001bsn.2_Intron|NKAIN1_uc010ogc.1_Intron	NM_024522	NP_078798			Na+/K+ transporting ATPase interacting 1							integral to membrane|plasma membrane				ovary(1)	1		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|Breast(348;0.141)|all_neural(195;0.146)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0184)|READ - Rectum adenocarcinoma(331;0.148)														---	---	---	---
SNRNP40	9410	broad.mit.edu	37	1	31740385	31740386	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31740385_31740386insT	uc001bso.2	-						SNRNP40_uc009vtt.2_Intron|SNRNP40_uc010oge.1_Intron	NM_004814	NP_004805			WD repeat domain 57 (U5 snRNP specific)							catalytic step 2 spliceosome|cytoplasm|nucleoplasm|small nucleolar ribonucleoprotein complex|U5 snRNP	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	31869273	31869274	+	IGR	INS	-	TC	TC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31869273_31869274insTC								FABP3 (23350 upstream) : SERINC2 (13774 downstream)																																			---	---	---	---
COL16A1	1307	broad.mit.edu	37	1	32119201	32119202	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32119201_32119202insG	uc001btk.1	-	70	4975_4976	c.4610_4611insC	c.(4609-4611)CCAfs	p.P1537fs	COL16A1_uc001bti.1_Frame_Shift_Ins_p.P151fs|COL16A1_uc001btj.1_Frame_Shift_Ins_p.P1335fs	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor	1537	Triple-helical region 1 (COL1) with 2 imperfections.				cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)														---	---	---	---
TMEM39B	55116	broad.mit.edu	37	1	32567704	32567705	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32567704_32567705insT	uc010ogv.1	+						TMEM39B_uc001bue.3_Intron|TMEM39B_uc001buf.3_Intron|TMEM39B_uc010ogw.1_Intron	NM_018056	NP_060526			transmembrane protein 39B							integral to membrane					0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)																---	---	---	---
KPNA6	23633	broad.mit.edu	37	1	32575088	32575088	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32575088delT	uc001bug.2	+						KPNA6_uc001buh.2_Intron|KPNA6_uc010ogx.1_Intron	NM_012316	NP_036448			karyopherin alpha 6						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)																---	---	---	---
KPNA6	23633	broad.mit.edu	37	1	32602779	32602779	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32602779delT	uc001bug.2	+						KPNA6_uc001buh.2_Intron|KPNA6_uc010ogx.1_Intron	NM_012316	NP_036448			karyopherin alpha 6						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)																---	---	---	---
ZNF362	149076	broad.mit.edu	37	1	33760658	33760658	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33760658delC	uc001bxc.1	+							NM_152493	NP_689706			zinc finger protein 362						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)														OREG0013342	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	1	33782169	33782170	+	Intron	INS	-	TAGGTGCC	TAGGTGCC	rs141453070	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33782169_33782170insTAGGTGCC	uc001bxd.1	-							NM_001080438	NP_001073907			RecName: Full=Alpha 1,3-galactosyltransferase 2;          Short=A3galt2;          EC=2.4.1.87; AltName: Full=Isoglobotriaosylceramide synthase; AltName: Full=iGb3 synthase;          Short=iGb3S; Flags: Precursor;																														---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34321786	34321786	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34321786delG	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)																---	---	---	---
HMGB4	127540	broad.mit.edu	37	1	34330367	34330367	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34330367delA	uc001bxp.2	+	2					CSMD2_uc001bxm.1_Intron|CSMD2_uc001bxn.1_Intron|HMGB4_uc001bxq.2_3'UTR	NM_145205	NP_660206			HMG2 like isoform 1							nucleus	DNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34368004	34368004	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34368004delA	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)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34441088	34441089	+	Intron	DEL	AC	-	-	rs72360466		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34441088_34441089delAC	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128			CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	34779011	34779011	+	IGR	DEL	T	-	-	rs74790109		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34779011delT								C1orf94 (94282 upstream) : MIR552 (356189 downstream)																																			---	---	---	---
EIF2C4	192670	broad.mit.edu	37	1	36282442	36282442	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36282442delA	uc001bzj.1	+							NM_017629	NP_060099			eukaryotic translation initiation factor 2C, 4						mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
EIF2C4	192670	broad.mit.edu	37	1	36298020	36298020	+	Intron	DEL	T	-	-	rs111531043		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36298020delT	uc001bzj.1	+							NM_017629	NP_060099			eukaryotic translation initiation factor 2C, 4						mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
EIF2C1	26523	broad.mit.edu	37	1	36358976	36358976	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36358976delA	uc001bzl.2	+						EIF2C1_uc001bzk.2_Intron|EIF2C1_uc009vuy.2_5'Flank	NM_012199	NP_036331			eukaryotic translation initiation factor 2C, 1						negative regulation of translation involved in gene silencing by miRNA|nuclear-transcribed mRNA catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|polysome	protein binding|RNA binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
EIF2C3	192669	broad.mit.edu	37	1	36476506	36476506	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36476506delA	uc001bzp.2	+						EIF2C3_uc001bzq.2_Intron	NM_024852	NP_079128			eukaryotic translation initiation factor 2C, 3						mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
CSF3R	1441	broad.mit.edu	37	1	36950450	36950450	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36950450delT	uc001caw.1	-						CSF3R_uc001cav.1_5'Flank|CSF3R_uc001cax.1_5'Flank|CSF3R_uc001cay.1_5'Flank	NM_000760	NP_000751			colony stimulating factor 3 receptor isoform a						cell adhesion|defense response	extracellular region|integral to plasma membrane	cytokine receptor activity			central_nervous_system(2)|ovary(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	37520891	37520891	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37520891delT								GRIK3 (21047 upstream) : ZC3H12A (419228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38129993	38129993	+	IGR	DEL	A	-	-	rs11302733		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38129993delA								RSPO1 (29502 upstream) : C1orf109 (17257 downstream)																																			---	---	---	---
CDCA8	55143	broad.mit.edu	37	1	38165240	38165240	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38165240delA	uc001cbr.2	+						CDCA8_uc001cbs.2_Intron|CDCA8_uc010oih.1_Intron	NM_018101	NP_060571			cell division cycle associated 8						cell division|chromosome organization|mitotic metaphase|mitotic prometaphase	chromosome passenger complex|chromosome, centromeric region|cytosol|nucleolus|spindle	protein binding			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
CDCA8	55143	broad.mit.edu	37	1	38170966	38170966	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38170966delT	uc001cbr.2	+						CDCA8_uc001cbs.2_Intron|CDCA8_uc010oih.1_Intron	NM_018101	NP_060571			cell division cycle associated 8						cell division|chromosome organization|mitotic metaphase|mitotic prometaphase	chromosome passenger complex|chromosome, centromeric region|cytosol|nucleolus|spindle	protein binding			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
MTF1	4520	broad.mit.edu	37	1	38301123	38301123	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38301123delT	uc001cce.1	-						MTF1_uc009vvj.1_Intron	NM_005955	NP_005946			metal-regulatory transcription factor 1							nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
SF3A3	10946	broad.mit.edu	37	1	38446098	38446098	+	Intron	DEL	A	-	-	rs113844754		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38446098delA	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	38505447	38505448	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38505447_38505448delGT								UTP11L (14951 upstream) : POU3F1 (4075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39009729	39009730	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39009729_39009730delTG								POU3F1 (497279 upstream) : RRAGC (295285 downstream)																																			---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39772947	39772947	+	Intron	DEL	T	-	-	rs112097056		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39772947delT	uc010ois.1	+						MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc009vvq.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	40295409	40295409	+	IGR	DEL	A	-	-	rs111329818		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40295409delA								BMP8B (40876 upstream) : TRIT1 (11299 downstream)																																			---	---	---	---
TRIT1	54802	broad.mit.edu	37	1	40319885	40319885	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40319885delT	uc010oiz.1	-						TRIT1_uc001cec.3_5'Flank|TRIT1_uc001ced.3_5'Flank|TRIT1_uc001cee.3_5'Flank|TRIT1_uc001cef.3_5'Flank|TRIT1_uc001ceg.3_5'Flank|TRIT1_uc001ceh.3_5'Flank|TRIT1_uc009vvv.2_5'Flank|TRIT1_uc001cei.3_5'Flank|TRIT1_uc001ceq.2_Intron|TRIT1_uc001cek.2_Intron|TRIT1_uc009vvx.2_Intron|TRIT1_uc001cel.2_Intron|TRIT1_uc001cem.2_Intron|TRIT1_uc001cen.2_Intron|TRIT1_uc001ceo.2_Intron|TRIT1_uc001cep.2_Intron|TRIT1_uc010oja.1_5'Flank	NM_017646	NP_060116			tRNA isopentenyltransferase 1 precursor						tRNA processing	mitochondrion	ATP binding|metal ion binding|tRNA dimethylallyltransferase activity			ovary(1)	1	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	40411075	40411075	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40411075delT								MYCL1 (43388 upstream) : MFSD2A (9709 downstream)																																			---	---	---	---
MFSD2A	84879	broad.mit.edu	37	1	40429116	40429116	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
PPT1	5538	broad.mit.edu	37	1	40540188	40540188	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40540188delG	uc001cfb.2	-						PPT1_uc010ojf.1_Intron|PPT1_uc010ojg.1_Intron|PPT1_uc009vwa.2_Intron	NM_000310	NP_000301			palmitoyl-protein thioesterase 1 isoform 1						brain development|cofactor metabolic process|cofactor transport|DNA fragmentation involved in apoptotic nuclear change|lysosomal lumen acidification|membrane raft organization|negative regulation of cell growth|negative regulation of neuron apoptosis|neuron development|pinocytosis|positive regulation of pinocytosis|positive regulation of receptor-mediated endocytosis|protein depalmitoylation|protein transport|receptor-mediated endocytosis|regulation of synapse structure and activity|sphingolipid catabolic process|visual perception	axon|cytosol|Golgi apparatus|lysosome|membrane fraction|membrane raft|nucleus|synaptic vesicle	palmitoyl-(protein) hydrolase activity|palmitoyl-CoA hydrolase activity			ovary(1)	1	Lung NSC(20;3.43e-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;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
NFYC	4802	broad.mit.edu	37	1	41172842	41172842	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41172842delA	uc001cfx.3	+						NFYC_uc010ojm.1_Intron|NFYC_uc009vwd.2_Intron|NFYC_uc001cfz.2_Intron|NFYC_uc010ojn.1_Intron|NFYC_uc001cfy.3_Intron|NFYC_uc001cgc.2_Intron|NFYC_uc001cgb.2_5'Flank	NM_001142588	NP_001136060			nuclear transcription factor Y, gamma isoform 1						protein folding|regulation of transcription from RNA polymerase II promoter	CCAAT-binding factor complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)|kidney(1)	3	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	41345058	41345058	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41345058delT								CITED4 (17040 upstream) : CTPS (99949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	41419060	41419061	+	IGR	INS	-	C	C	rs116209334	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41419060_41419061insC								CITED4 (91042 upstream) : CTPS (25946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	41740769	41740769	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41740769delT								SCMH1 (32981 upstream) : EDN2 (203680 downstream)																																			---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42031633	42031633	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42031633delT	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron|HIVEP3_uc001cgy.2_Intron	NM_024503	NP_078779			human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42122600	42122600	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42122600delA	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron	NM_024503	NP_078779			human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
CCDC30	728621	broad.mit.edu	37	1	43021760	43021760	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43021760delT	uc009vwk.1	+						CCDC30_uc001chm.2_Intron|CCDC30_uc001chn.2_Intron|CCDC30_uc010oju.1_Intron|CCDC30_uc001chp.2_Intron	NM_001080850	NP_001074319			coiled-coil domain containing 30												0																		---	---	---	---
LEPRE1	64175	broad.mit.edu	37	1	43220198	43220198	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43220198delT	uc001chv.2	-						LEPRE1_uc001chw.2_Intron|LEPRE1_uc001chx.3_Intron	NM_022356	NP_071751			leprecan 1 isoform 1						negative regulation of cell proliferation	endoplasmic reticulum|proteinaceous extracellular matrix	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			ovary(3)|lung(1)	4	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
TIE1	7075	broad.mit.edu	37	1	43772910	43772910	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43772910delC	uc001ciu.2	+	5	817	c.738delC	c.(736-738)TGCfs	p.C246fs	TIE1_uc010okd.1_Frame_Shift_Del_p.C246fs|TIE1_uc010oke.1_Frame_Shift_Del_p.C201fs|TIE1_uc009vwq.2_Intron|TIE1_uc010okf.1_5'UTR|TIE1_uc010okg.1_5'UTR|TIE1_uc010okc.1_Frame_Shift_Del_p.C246fs	NM_005424	NP_005415	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and	246	Extracellular (Potential).|EGF-like 1.				mesoderm development	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	43842362	43842363	+	IGR	INS	-	GT	GT	rs145846251	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43842362_43842363insGT								ELOVL1 (8663 upstream) : MED8 (7225 downstream)																																			---	---	---	---
KIAA0467	23334	broad.mit.edu	37	1	43907817	43907817	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43907817delG	uc001cjk.1	+							NM_015284	NP_056099			hypothetical protein LOC23334							peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44216554	44216554	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44216554delA	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)																---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44251688	44251688	+	Intron	DEL	T	-	-	rs112668946		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44251688delT	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	44699078	44699078	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44699078delT	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	44877627	44877627	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44877627delT	uc001clv.1	+						RNF220_uc001clw.1_Intron	NM_018150	NP_060620			ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
RNF220	55182	broad.mit.edu	37	1	44880511	44880511	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44880511delT	uc001clv.1	+						RNF220_uc001clw.1_Intron	NM_018150	NP_060620			ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
KIF2C	11004	broad.mit.edu	37	1	45227279	45227280	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45227279_45227280insA	uc001cmg.3	+						KIF2C_uc010olb.1_Intron|KIF2C_uc010olc.1_Intron|KIF2C_uc001cmh.3_Intron	NM_006845	NP_006836			kinesin family member 2C						blood coagulation|cell division|cell proliferation|chromosome segregation|establishment or maintenance of microtubule cytoskeleton polarity|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|kinesin complex|microtubule|nucleus	ATP binding|centromeric DNA binding|microtubule motor activity|microtubule plus-end binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
KIF2C	11004	broad.mit.edu	37	1	45229850	45229851	+	Intron	DEL	TA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45229850_45229851delTA	uc001cmg.3	+						KIF2C_uc010olb.1_Intron|KIF2C_uc010olc.1_Intron|KIF2C_uc001cmh.3_Intron	NM_006845	NP_006836			kinesin family member 2C						blood coagulation|cell division|cell proliferation|chromosome segregation|establishment or maintenance of microtubule cytoskeleton polarity|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|kinesin complex|microtubule|nucleus	ATP binding|centromeric DNA binding|microtubule motor activity|microtubule plus-end binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	45245946	45245948	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45245946_45245948delTTT								RPS8 (1535 upstream) : BEST4 (3311 downstream)																																			---	---	---	---
EIF2B3	8891	broad.mit.edu	37	1	45423433	45423434	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45423433_45423434insA	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)																	---	---	---	---
UROD	7389	broad.mit.edu	37	1	45479967	45479967	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45479967delT	uc001cna.1	+						HECTD3_uc009vxk.2_5'Flank|HECTD3_uc010olh.1_5'Flank|UROD_uc001cnb.1_Intron|UROD_uc010olj.1_3'UTR|UROD_uc001cnc.1_Intron	NM_000374	NP_000365			uroporphyrinogen decarboxylase							cytosol|microtubule cytoskeleton|nucleus	uroporphyrinogen decarboxylase activity				0	Acute lymphoblastic leukemia(166;0.155)													Porphyria_Cutanea_Tarda_Type_II		OREG0013449	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	46003358	46003359	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46003358_46003359insT								PRDX1 (15749 upstream) : AKR1A1 (13139 downstream)																																			---	---	---	---
NASP	4678	broad.mit.edu	37	1	46059702	46059702	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46059702delA	uc001coi.1	+						NASP_uc010olq.1_Intron|NASP_uc001coh.1_Intron|NASP_uc001coj.1_Intron|NASP_uc010olr.1_Intron	NM_002482	NP_002473			nuclear autoantigenic sperm protein isoform 2						blastocyst development|cell cycle|cell proliferation|DNA replication|histone exchange|protein transport	cytoplasm|nucleus	Hsp90 protein binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)																	---	---	---	---
GPBP1L1	60313	broad.mit.edu	37	1	46106254	46106254	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46106254delA	uc001coq.2	-							NM_021639	NP_067652			GC-rich promoter binding protein 1-like 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
MAST2	23139	broad.mit.edu	37	1	46299542	46299542	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46299542delT	uc001cov.2	+						MAST2_uc001cow.2_Intron	NM_015112	NP_055927			microtubule associated serine/threonine kinase						regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|stomach(2)|breast(1)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)																	---	---	---	---
PIK3R3	8503	broad.mit.edu	37	1	46609327	46609327	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46609327delT	uc010olw.1	-							NM_003629	NP_003620			phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
RAD54L	8438	broad.mit.edu	37	1	46736036	46736037	+	Intron	DEL	AA	-	-	rs80223375		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46736036_46736037delAA	uc009vye.2	+						RAD54L_uc001cpl.2_Intron|RAD54L_uc001cpm.1_Intron	NM_001142548	NP_001136020			RAD54-like protein						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					---	---	---	---
KIAA0494	9813	broad.mit.edu	37	1	47166628	47166629	+	Intron	INS	-	GAGA	GAGA	rs72283851		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47166628_47166629insGAGA	uc001cqk.3	-						KIAA0494_uc010omh.1_Intron|KIAA0494_uc010omj.1_Intron|KIAA0494_uc001cql.1_Intron	NM_014774	NP_055589			hypothetical protein LOC9813								calcium ion binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
CYP4A11	1579	broad.mit.edu	37	1	47400667	47400668	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47400667_47400668delAG	uc001cqp.3	-						CYP4A11_uc001cqq.2_Intron|CYP4A11_uc010omm.1_Intron	NM_000778	NP_000769			cytochrome P450, family 4, subfamily A,						long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|oxygen binding			ovary(2)|skin(2)	4					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	48537688	48537688	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48537688delT								FOXD2 (631326 upstream) : SKINTL (29699 downstream)																																			---	---	---	---
SPATA6	54558	broad.mit.edu	37	1	48878299	48878300	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48878299_48878300delTT	uc001crr.1	-						SPATA6_uc001crs.1_Intron|SPATA6_uc010omv.1_Intron|SPATA6_uc001crt.2_Intron	NM_019073	NP_061946			spermatogenesis associated 6 precursor						cell differentiation|multicellular organismal development|spermatogenesis	extracellular region				ovary(1)	1																		---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49073295	49073295	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49073295delC	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49426753	49426754	+	Intron	DEL	GT	-	-	rs71797948		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49426753_49426754delGT	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49453991	49453991	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49453991delG	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	50389290	50389290	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50389290delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	51501563	51501564	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51501563_51501564delCA								CDKN2C (61256 upstream) : C1orf185 (66342 downstream)														p.0?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	1	51540268	51540271	+	IGR	DEL	GTGT	-	-	rs112763372		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51540268_51540271delGTGT								CDKN2C (99961 upstream) : C1orf185 (27635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	51668698	51668698	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51668698delA								C1orf185 (54946 upstream) : RNF11 (33247 downstream)																																			---	---	---	---
EPS15	2060	broad.mit.edu	37	1	51889671	51889671	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51889671delA	uc001csq.1	-						EPS15_uc009vyz.1_Intron|EPS15_uc001csp.3_5'Flank	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	51908976	51908976	+	Intron	DEL	A	-	-	rs67017631		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51908976delA	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								---	---	---	---
OSBPL9	114883	broad.mit.edu	37	1	52139738	52139739	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52139738_52139739delTT	uc001cst.2	+						OSBPL9_uc001css.2_Intron|OSBPL9_uc001csx.2_Intron|OSBPL9_uc009vza.2_Intron|OSBPL9_uc001csu.2_Intron|OSBPL9_uc001csv.2_Intron|OSBPL9_uc001csw.2_Intron	NM_024586	NP_078862			oxysterol binding protein-like 9 isoform e						lipid transport		lipid binding			central_nervous_system(1)	1																		---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52669755	52669756	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52669755_52669756delTT	uc001cto.2	+						ZFYVE9_uc001ctn.2_Intron|ZFYVE9_uc001ctp.2_Intron	NM_004799	NP_004790			zinc finger, FYVE domain containing 9 isoform 3						endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity			ovary(2)|lung(2)|central_nervous_system(2)|skin(2)	8																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52937901	52937901	+	Intron	DEL	A	-	-	rs78098408		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52937901delA	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron|ZCCHC11_uc009vze.1_Intron|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cub.2_Intron	NM_015269	NP_056084			zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
ZYG11B	79699	broad.mit.edu	37	1	53219705	53219705	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53219705delT	uc001cuj.2	+						ZYG11B_uc009vzg.2_Intron|ZYG11B_uc010onj.1_Intron	NM_024646	NP_078922			zyg-11 homolog B								protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
SCP2	6342	broad.mit.edu	37	1	53436211	53436211	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53436211delT	uc001cur.1	+						SCP2_uc001cus.1_Intron|SCP2_uc010ono.1_Intron|SCP2_uc010onp.1_Intron|SCP2_uc009vzi.1_Intron|SCP2_uc001cuq.1_Intron	NM_002979	NP_002970			sterol carrier protein 2 isoform 1 proprotein						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|lipid transport	mitochondrion|nucleus|peroxisomal matrix	propanoyl-CoA C-acyltransferase activity|propionyl-CoA C2-trimethyltridecanoyltransferase activity|protein binding|sterol binding			breast(1)	1																		---	---	---	---
SCP2	6342	broad.mit.edu	37	1	53459392	53459392	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53459392delA	uc001cur.1	+						SCP2_uc001cus.1_RNA|SCP2_uc010ono.1_Intron|SCP2_uc010onp.1_Intron|SCP2_uc009vzi.1_Intron|SCP2_uc001cuq.1_3'UTR	NM_002979	NP_002970			sterol carrier protein 2 isoform 1 proprotein						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|lipid transport	mitochondrion|nucleus|peroxisomal matrix	propanoyl-CoA C-acyltransferase activity|propionyl-CoA C2-trimethyltridecanoyltransferase activity|protein binding|sterol binding			breast(1)	1																		---	---	---	---
GLIS1	148979	broad.mit.edu	37	1	53978042	53978042	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53978042delA	uc001cvr.1	-							NM_147193	NP_671726			GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
GLIS1	148979	broad.mit.edu	37	1	53992200	53992201	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53992200_53992201delAC	uc001cvr.1	-							NM_147193	NP_671726			GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
GLIS1	148979	broad.mit.edu	37	1	54116263	54116265	+	Intron	DEL	AAA	-	-	rs67086203		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54116263_54116265delAAA	uc001cvr.1	-							NM_147193	NP_671726			GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	54450311	54450311	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54450311delA								LRRC42 (16472 upstream) : LDLRAD1 (24195 downstream)																																			---	---	---	---
C1orf83	127428	broad.mit.edu	37	1	54526625	54526625	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54526625delA	uc001cwt.1	+						C1orf83_uc001cwu.1_Intron	NM_153035	NP_694580			hypothetical protein LOC127428						transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
SSBP3	23648	broad.mit.edu	37	1	54750443	54750443	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54750443delA	uc001cxe.2	-						SSBP3_uc001cxf.2_Intron|SSBP3_uc001cxg.2_Intron|uc001cxi.1_5'Flank	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	54811835	54811835	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54811835delA	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	54834892	54834892	+	Intron	DEL	G	-	-	rs72185393		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54834892delG	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																		---	---	---	---
ACOT11	26027	broad.mit.edu	37	1	55079052	55079052	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55079052delA	uc001cxm.1	+						FAM151A_uc001cxn.2_Intron	NM_015547	NP_056362			thioesterase, adipose associated isoform BFIT1						fatty acid metabolic process|intracellular signal transduction|response to cold		acyl-CoA thioesterase activity|carboxylesterase activity			central_nervous_system(1)	1																		---	---	---	---
C1orf177	163747	broad.mit.edu	37	1	55289703	55289703	+	Intron	DEL	T	-	-	rs112534990		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55289703delT	uc001cyb.3	+						C1orf177_uc001cya.3_Intron	NM_001110533	NP_001104003			hypothetical protein LOC163747 isoform 2												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	56788488	56788488	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56788488delT								None (None upstream) : PPAP2B (171945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	57087000	57087000	+	IGR	DEL	A	-	-	rs68128960		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57087000delA								PPAP2B (41743 upstream) : PRKAA2 (23990 downstream)																																			---	---	---	---
C8B	732	broad.mit.edu	37	1	57404565	57404565	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57404565delA	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	57526516	57526516	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57526516delT	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57537755	57537755	+	Intron	DEL	C	-	-	rs12718424	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57537755delC	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58585082	58585082	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58585082delG	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58602761	58602761	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58602761delA	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58915420	58915422	+	Intron	DEL	GGC	-	-	rs112776161		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58915420_58915422delGGC	uc001cyt.1	-							NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
MYSM1	114803	broad.mit.edu	37	1	59160290	59160290	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59160290delA	uc009wab.1	-						MYSM1_uc001czd.2_Intron	NM_001085487	NP_001078956			Myb-like, SWIRM and MPN domains 1						histone deubiquitination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin remodeling complex	DNA binding|histone binding|metal ion binding|metallopeptidase activity|transcription coactivator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(1)	1	all_cancers(7;9.36e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	59316407	59316410	+	Intron	DEL	TGTG	-	-	rs72459420		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59316407_59316410delTGTG	uc001czf.2	+						uc010oop.1_Intron					Homo sapiens cDNA FLJ30588 fis, clone BRAWH2008128.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	59443023	59443024	+	IGR	INS	-	T	T	rs143652758	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59443023_59443024insT								JUN (193238 upstream) : LOC729467 (154586 downstream)																																			---	---	---	---
FGGY	55277	broad.mit.edu	37	1	59792395	59792395	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59792395delT	uc001czi.3	+						FGGY_uc001czg.2_Intron|FGGY_uc001czh.2_Intron|FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron	NM_018291	NP_060761			FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)																	---	---	---	---
C1orf87	127795	broad.mit.edu	37	1	60475688	60475688	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60475688delT	uc001czs.1	-						C1orf87_uc001czr.1_5'Flank	NM_152377	NP_689590			hypothetical protein LOC127795								calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	60927009	60927009	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60927009delA								C1orf87 (387583 upstream) : NFIA (615937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	61533034	61533034	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61533034delT								C1orf87 (993608 upstream) : NFIA (9912 downstream)																																			---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61572892	61572892	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61572892delT	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron	NM_001134673	NP_001128145			nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	62102393	62102393	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62102393delA								NFIA (173934 upstream) : TM2D1 (44326 downstream)																																			---	---	---	---
TM2D1	83941	broad.mit.edu	37	1	62189461	62189461	+	Intron	DEL	A	-	-	rs147863719		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62189461delA	uc001czz.1	-							NM_032027	NP_114416			beta-amyloid binding protein precursor						apoptosis					ovary(1)	1																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62364078	62364078	+	Intron	DEL	T	-	-	rs113964723		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62364078delT	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	62631352	62631352	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62631352delA	uc009wag.2	+							NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
DOCK7	85440	broad.mit.edu	37	1	62939787	62939787	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62939787delT	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc001dam.2_Intron|DOCK7_uc010oov.1_Intron|DOCK7_uc001dar.1_Intron	NM_033407	NP_212132			dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2																		---	---	---	---
DOCK7	85440	broad.mit.edu	37	1	62941104	62941104	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62941104delA	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc001dam.2_Intron|DOCK7_uc010oov.1_Intron|DOCK7_uc001dar.1_Intron	NM_033407	NP_212132			dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2																		---	---	---	---
DOCK7	85440	broad.mit.edu	37	1	63024585	63024586	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63024585_63024586delTT	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc001dam.2_5'Flank	NM_033407	NP_212132			dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2																		---	---	---	---
ATG4C	84938	broad.mit.edu	37	1	63284744	63284744	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63284744delA	uc001dat.2	+	5	625	c.463delA	c.(463-465)AAAfs	p.K155fs	ATG4C_uc001dau.2_Frame_Shift_Del_p.K155fs	NM_178221	NP_835739	Q96DT6	ATG4C_HUMAN	APG4 autophagy 4 homolog C isoform 8	155					autophagic vacuole assembly|protein targeting to membrane|proteolysis	cytosol|extracellular region	cysteine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	63350942	63350942	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63350942delA								ATG4C (20893 upstream) : FOXD3 (437788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	63472457	63472457	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63472457delT								ATG4C (142408 upstream) : FOXD3 (316273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	64909546	64909547	+	IGR	INS	-	AAT	AAT	rs72501002	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64909546_64909547insAAT								UBE2U (199519 upstream) : CACHD1 (26929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	64909761	64909761	+	IGR	DEL	A	-	-	rs60097680	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64909761delA								UBE2U (199734 upstream) : CACHD1 (26715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	65479077	65479078	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65479077_65479078insA								JAK1 (46458 upstream) : MIR101-1 (45039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	65714337	65714340	+	IGR	DEL	TTTT	-	-	rs67894604		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65714337_65714340delTTTT								AK3L1 (21164 upstream) : DNAJC6 (5808 downstream)																																			---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66293154	66293154	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66293154delA	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.2_Intron	NM_001037341	NP_001032418			phosphodiesterase 4B isoform 1						signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)													---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66689366	66689366	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66689366delC	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.2_Intron|PDE4B_uc001dcp.2_Intron	NM_001037341	NP_001032418			phosphodiesterase 4B isoform 1						signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)													---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67046176	67046177	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67046176_67046177insT	uc001dcr.2	+							NM_032291	NP_115667			SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67098850	67098850	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67098850delT	uc001dcr.2	+							NM_032291	NP_115667			SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67206944	67206944	+	Intron	DEL	T	-	-	rs76751942		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67206944delT	uc001dcr.2	+						SGIP1_uc010opd.1_Intron|SGIP1_uc001dcs.2_Intron|SGIP1_uc001dct.2_Intron|SGIP1_uc009wat.2_Intron|SGIP1_uc001dcu.2_Intron	NM_032291	NP_115667			SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
IL23R	149233	broad.mit.edu	37	1	67688236	67688236	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67688236delT	uc001ddo.2	+						IL23R_uc009waz.2_Intron|IL23R_uc001ddp.2_Intron|IL23R_uc010opi.1_Intron|IL23R_uc010opj.1_Intron|IL23R_uc010opk.1_Intron|IL23R_uc010opl.1_Intron|IL23R_uc010opm.1_Intron|IL23R_uc001ddq.2_Intron|IL23R_uc010opn.1_Intron|IL23R_uc001ddr.2_Intron|IL23R_uc010opo.1_Intron|IL23R_uc010opp.1_Intron|IL23R_uc010opq.1_Intron|IL23R_uc010opr.1_Intron|IL23R_uc010ops.1_Intron|IL23R_uc010opt.1_Intron|IL23R_uc010opu.1_Intron|IL23R_uc010opv.1_Intron|IL23R_uc010opw.1_Intron|IL23R_uc010opx.1_Intron|IL23R_uc010opy.1_Intron|IL23R_uc010opz.1_Intron|IL23R_uc010oqa.1_Intron|IL23R_uc010oqb.1_Intron|IL23R_uc010oqc.1_Intron|IL23R_uc010oqd.1_Intron|IL23R_uc010oqe.1_Intron|IL23R_uc010oqf.1_Intron|IL23R_uc010oqg.1_Intron|IL23R_uc010oqh.1_Intron|IL23R_uc001dds.2_Intron|IL23R_uc001ddt.2_Intron	NM_144701	NP_653302			interleukin 23 receptor precursor						inflammatory response|negative regulation of interleukin-10 production|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of interleukin-12 production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|response to interferon-gamma|response to lipopolysaccharide	interleukin-23 receptor complex	receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	68163717	68163717	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68163717delT								GADD45A (9698 upstream) : GNG12 (3432 downstream)																																			---	---	---	---
GNG12	55970	broad.mit.edu	37	1	68235500	68235505	+	Intron	DEL	CACACT	-	-	rs113880063		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68235500_68235505delCACACT	uc001dea.1	-							NM_018841	NP_061329			G-protein gamma-12 subunit precursor						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	68516707	68516707	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68516707delC	uc001deb.1	+						uc001dec.1_Intron|DIRAS3_uc001ded.2_5'Flank					Homo sapiens cDNA FLJ38762 fis, clone KIDNE2013801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	68822053	68822053	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68822053delT								WLS (123800 upstream) : RPE65 (72454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69786220	69786220	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69786220delT								DEPDC1 (823421 upstream) : LRRC7 (246648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69836714	69836714	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69836714delT								DEPDC1 (873915 upstream) : LRRC7 (196154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69837051	69837051	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69837051delT								DEPDC1 (874252 upstream) : LRRC7 (195817 downstream)																																			---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70236349	70236349	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70236349delA	uc001dep.2	+						LRRC7_uc001deo.1_Intron|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	70287576	70287577	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70287576_70287577delAA	uc001dep.2	+						LRRC7_uc001deo.1_Intron|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	70742436	70742436	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70742436delA	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																		---	---	---	---
PTGER3	5733	broad.mit.edu	37	1	71467255	71467255	+	Intron	DEL	T	-	-	rs145102255		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71467255delT	uc001dfg.1	-						PTGER3_uc001dfh.1_Intron|PTGER3_uc001dfi.1_Intron|PTGER3_uc001dfj.1_Intron|PTGER3_uc001dfk.1_Intron|PTGER3_uc001dfl.1_Intron|PTGER3_uc009wbm.1_Intron|PTGER3_uc001dfm.1_Intron|PTGER3_uc001dfn.2_Intron|PTGER3_uc009wbn.1_Intron|PTGER3_uc009wbo.2_Intron|PTGER3_uc001dfo.2_Intron|PTGER3_uc001dfp.1_Intron	NM_198714	NP_942007			prostaglandin E receptor 3, subtype EP3 isoform						cell death|positive regulation of fever generation|transcription, DNA-dependent	integral to plasma membrane|nuclear envelope	ligand-dependent nuclear receptor activity|prostaglandin E receptor activity			pancreas(1)|lung(1)|skin(1)	3					Bimatoprost(DB00905)													---	---	---	---
PTGER3	5733	broad.mit.edu	37	1	71502522	71502522	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71502522delA	uc001dfg.1	-						PTGER3_uc001dfh.1_Intron|PTGER3_uc001dfi.1_Intron|PTGER3_uc001dfj.1_Intron|PTGER3_uc001dfk.1_Intron|PTGER3_uc001dfl.1_Intron|PTGER3_uc009wbm.1_Intron|PTGER3_uc001dfm.1_Intron|PTGER3_uc001dfn.2_Intron|PTGER3_uc009wbn.1_Intron|PTGER3_uc009wbo.2_Intron|PTGER3_uc001dfo.2_Intron|PTGER3_uc001dfp.1_Intron|PTGER3_uc001dfq.2_Intron	NM_198714	NP_942007			prostaglandin E receptor 3, subtype EP3 isoform						cell death|positive regulation of fever generation|transcription, DNA-dependent	integral to plasma membrane|nuclear envelope	ligand-dependent nuclear receptor activity|prostaglandin E receptor activity			pancreas(1)|lung(1)|skin(1)	3					Bimatoprost(DB00905)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	71627981	71627981	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71627981delT	uc001dfu.1	+											Homo sapiens cDNA clone IMAGE:6592429, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	71748904	71748904	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71748904delT								ZRANB2 (202159 upstream) : NEGR1 (119722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	71785700	71785700	+	IGR	DEL	C	-	-	rs111896458		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71785700delC								ZRANB2 (238955 upstream) : NEGR1 (82926 downstream)																																			---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72469240	72469240	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72469240delA	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	73551941	73551942	+	IGR	DEL	TT	-	-	rs71692862		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73551941_73551942delTT								NEGR1 (803536 upstream) : LRRIQ3 (939762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	74300084	74300084	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74300084delA								None (None upstream) : LRRIQ3 (191620 downstream)																																			---	---	---	---
LRRIQ3	127255	broad.mit.edu	37	1	74539193	74539194	+	Intron	INS	-	AAAC	AAAC	rs150618239	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74539193_74539194insAAAC	uc001dfy.3	-						LRRIQ3_uc001dfz.3_Intron	NM_001105659	NP_001099129			leucine-rich repeats and IQ motif containing 3											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	75521766	75521766	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75521766delA								TYW3 (289408 upstream) : LHX8 (72353 downstream)																																			---	---	---	---
ACADM	34	broad.mit.edu	37	1	76195141	76195142	+	Intron	DEL	TT	-	-	rs143414020		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76195141_76195142delTT	uc001dgw.3	+						ACADM_uc010orc.1_Intron|ACADM_uc010ord.1_Intron|ACADM_uc009wbp.2_Intron|ACADM_uc009wbr.2_Intron|ACADM_uc010ore.1_Intron|ACADM_uc010orf.1_Intron|ACADM_uc001dgx.3_Intron	NM_000016	NP_000007			medium-chain acyl-CoA dehydrogenase isoform a						carnitine biosynthetic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|medium-chain fatty acid catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|identical protein binding|medium-chain-acyl-CoA dehydrogenase activity			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	76531677	76531677	+	IGR	DEL	A	-	-	rs67654727		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76531677delA								ASB17 (133561 upstream) : ST6GALNAC3 (8712 downstream)																																			---	---	---	---
ST6GALNAC5	81849	broad.mit.edu	37	1	77438025	77438025	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77438025delG	uc001dhi.2	+						ST6GALNAC5_uc010ori.1_Intron|ST6GALNAC5_uc009wbw.2_Intron	NM_030965	NP_112227			sialyltransferase 7E						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			pancreas(1)|skin(1)	2																		---	---	---	---
FUBP1	8880	broad.mit.edu	37	1	78432648	78432648	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78432648delA	uc001dii.2	-						FUBP1_uc001dih.3_Intron|FUBP1_uc010orm.1_Intron	NM_003902	NP_003893			far upstream element-binding protein						transcription from RNA polymerase II promoter	nucleus	protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			central_nervous_system(2)|lung(1)	3																		---	---	---	---
DNAJB4	11080	broad.mit.edu	37	1	78447006	78447007	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78447006_78447007insT	uc010orn.1	+						FUBP1_uc001dih.3_5'Flank|FUBP1_uc001dii.2_5'Flank|FUBP1_uc010orm.1_5'Flank	NM_007034	NP_008965			DnaJ (Hsp40) homolog, subfamily B, member 4						protein folding|response to heat|response to unfolded protein	cytoplasm|plasma membrane	heat shock protein binding|unfolded protein binding				0																		---	---	---	---
GIPC2	54810	broad.mit.edu	37	1	78566626	78566629	+	Intron	DEL	ACAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78566626_78566629delACAC	uc001dik.2	+							NM_017655	NP_060125			PDZ domain protein GIPC2							cytoplasm				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	78632837	78632838	+	IGR	INS	-	A	A	rs145699801	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78632837_78632838insA								GIPC2 (29726 upstream) : MGC27382 (62445 downstream)																																			---	---	---	---
MGC27382	149047	broad.mit.edu	37	1	78753517	78753517	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78753517delT	uc001dil.1	+						MGC27382_uc009wcc.2_Intron					Homo sapiens cDNA FLJ34438 fis, clone HLUNG2001144.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	79132207	79132207	+	IGR	DEL	A	-	-	rs149208484		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79132207delA								IFI44 (2446 upstream) : ELTD1 (223244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	79711320	79711323	+	IGR	DEL	CACA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79711320_79711323delCACA								ELTD1 (238825 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	79970832	79970832	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79970832delT								ELTD1 (498337 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	80343103	80343104	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80343103_80343104insA								ELTD1 (870608 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	80465646	80465646	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80465646delA								ELTD1 (993151 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	81693956	81693956	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81693956delA								None (None upstream) : LPHN2 (77889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	82533065	82533065	+	IGR	DEL	A	-	-	rs76219319		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82533065delA								LPHN2 (74959 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	82603189	82603189	+	IGR	DEL	A	-	-	rs35495371		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82603189delA								LPHN2 (145083 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83037971	83037974	+	IGR	DEL	CGCA	-	-	rs61710375		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83037971_83037974delCGCA								LPHN2 (579865 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83254573	83254574	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83254573_83254574insT								LPHN2 (796467 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	84259638	84259638	+	Intron	DEL	A	-	-	rs111685871		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84259638delA	uc001diz.3	-											Homo sapiens cDNA clone IMAGE:4815396.																														---	---	---	---
TTLL7	79739	broad.mit.edu	37	1	84349674	84349674	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84349674delA	uc001djc.2	-						TTLL7_uc001djb.2_Intron|TTLL7_uc001djd.2_Intron|TTLL7_uc001dje.2_Intron|TTLL7_uc001djf.2_Intron|TTLL7_uc001djg.2_Intron	NM_024686	NP_078962			tubulin tyrosine ligase-like family, member 7						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	84745037	84745037	+	IGR	DEL	T	-	-	rs71706750		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84745037delT								PRKACB (40858 upstream) : SAMD13 (19012 downstream)																																			---	---	---	---
WDR63	126820	broad.mit.edu	37	1	85574027	85574027	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85574027delT	uc001dkt.2	+						WDR63_uc009wcl.2_Intron	NM_145172	NP_660155			WD repeat domain 63											upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	85753754	85753755	+	Intron	INS	-	TG	TG	rs149179661	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85753754_85753755insTG	uc001dla.1	+											Homo sapiens cDNA FLJ43735 fis, clone TESTI2005280.																														---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	86018016	86018016	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86018016delA	uc001dlc.2	-							NM_001134445	NP_001127917			dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)													---	---	---	---
CYR61	3491	broad.mit.edu	37	1	86047289	86047289	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86047289delA	uc001dle.2	+						CYR61_uc001dlg.2_5'Flank|CYR61_uc009wcp.1_5'Flank	NM_001554	NP_001545			cysteine-rich, angiogenic inducer, 61 precursor						cell proliferation|chemotaxis|positive regulation of BMP signaling pathway|positive regulation of cell migration|positive regulation of osteoblast differentiation|positive regulation of osteoblast proliferation|positive regulation of protein kinase activity|positive regulation of protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell growth|regulation of ERK1 and ERK2 cascade|wound healing, spreading of cells	extracellular region	heparin binding|insulin-like growth factor binding			central_nervous_system(1)	1				all cancers(265;0.0216)|Epithelial(280;0.0441)												OREG0013583	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CLCA4	22802	broad.mit.edu	37	1	87029572	87029572	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87029572delT	uc009wcs.2	+						CLCA4_uc009wct.2_Intron|CLCA4_uc009wcu.2_Intron	NM_012128	NP_036260			chloride channel accessory 4							apical plasma membrane|extracellular region|integral to plasma membrane	chloride channel activity			ovary(2)	2		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)														---	---	---	---
CLCA4	22802	broad.mit.edu	37	1	87031503	87031504	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87031503_87031504insA	uc009wcs.2	+	6	798_799	c.754_755insA	c.(754-756)GAAfs	p.E252fs	CLCA4_uc009wct.2_Frame_Shift_Ins_p.E15fs|CLCA4_uc009wcu.2_Frame_Shift_Ins_p.E72fs	NM_012128	NP_036260	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	252						apical plasma membrane|extracellular region|integral to plasma membrane	chloride channel activity			ovary(2)	2		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)														---	---	---	---
SH3GLB1	51100	broad.mit.edu	37	1	87196188	87196188	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87196188delT	uc001dlw.2	+						SH3GLB1_uc001dlx.2_Intron|SH3GLB1_uc001dly.2_Intron|SH3GLB1_uc001dlz.2_Intron	NM_016009	NP_057093			SH3-containing protein SH3GLB1						anti-apoptosis|filopodium assembly|signal transduction	Golgi membrane|mitochondrial outer membrane	cytoskeletal adaptor activity|protein homodimerization activity|SH3 domain binding				0		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	87278434	87278435	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87278434_87278435insA								SH3GLB1 (64568 upstream) : SEP15 (49695 downstream)																																			---	---	---	---
LMO4	8543	broad.mit.edu	37	1	87806074	87806074	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87806074delA	uc001dmi.2	+						LMO4_uc001dmj.2_Intron	NM_006769	NP_006760			LIM domain only 4						neural tube closure|transcription from RNA polymerase II promoter	transcription factor complex	sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding				0		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	88072788	88072788	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88072788delA								LMO4 (258185 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88396786	88396786	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88396786delA								LMO4 (582183 upstream) : PKN2 (753136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88708846	88708846	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88708846delA								LMO4 (894243 upstream) : PKN2 (441076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88917895	88917895	+	IGR	DEL	T	-	-	rs35116163		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88917895delT								None (None upstream) : PKN2 (232027 downstream)																																			---	---	---	---
PKN2	5586	broad.mit.edu	37	1	89206848	89206848	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89206848delA	uc001dmn.2	+	2	568	c.226delA	c.(226-228)AAAfs	p.K76fs	PKN2_uc001dmm.1_Frame_Shift_Del_p.K76fs|PKN2_uc010osp.1_Frame_Shift_Del_p.K76fs|PKN2_uc010osq.1_Intron|PKN2_uc009wcv.2_Frame_Shift_Del_p.K76fs	NM_006256	NP_006247	Q16513	PKN2_HUMAN	protein kinase N2	76	REM 1.				signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)														---	---	---	---
LOC400759	400759	broad.mit.edu	37	1	89886531	89886532	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89886531_89886532insA	uc009wcy.1	+							NR_003133				Homo sapiens cDNA, FLJ17004.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	90657614	90657614	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90657614delA								ZNF326 (163520 upstream) : BARHL2 (519966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91671798	91671799	+	IGR	INS	-	G	G	rs139715838	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91671798_91671799insG								ZNF644 (184127 upstream) : HFM1 (54525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91725244	91725244	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91725244delA								ZNF644 (237573 upstream) : HFM1 (1080 downstream)																																			---	---	---	---
HFM1	164045	broad.mit.edu	37	1	91807337	91807337	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91807337delA	uc001doa.3	-						HFM1_uc009wdb.2_Intron|HFM1_uc010osu.1_Intron|HFM1_uc001dob.3_Intron|HFM1_uc010osv.1_Intron	NM_001017975	NP_001017975			HFM1 protein								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)														---	---	---	---
CDC7	8317	broad.mit.edu	37	1	91982620	91982620	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91982620delA	uc001doe.2	+						CDC7_uc001dof.2_Intron|CDC7_uc010osw.1_Intron|CDC7_uc009wdc.2_Intron|CDC7_uc009wdd.2_Intron	NM_003503	NP_003494			cell division cycle 7						cell cycle checkpoint|cell division|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|positive regulation of cell proliferation|regulation of S phase	cytoplasm|nucleoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|large_intestine(1)|ovary(1)|central_nervous_system(1)	5		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	92066062	92066062	+	IGR	DEL	A	-	-	rs144829580		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92066062delA								CDC7 (74742 upstream) : HSP90B3P (34506 downstream)																																			---	---	---	---
BTBD8	284697	broad.mit.edu	37	1	92552748	92552748	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92552748delT	uc001doo.2	+						BTBD8_uc010otc.1_Intron	NM_183242	NP_899065			BTB (POZ) domain containing 8							nucleus				ovary(1)	1		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)														---	---	---	---
BTBD8	284697	broad.mit.edu	37	1	92568324	92568324	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92568324delT	uc001doo.2	+						BTBD8_uc010otc.1_Intron	NM_183242	NP_899065			BTB (POZ) domain containing 8							nucleus				ovary(1)	1		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	92654424	92654424	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92654424delG								KIAA1107 (4145 upstream) : C1orf146 (29149 downstream)																																			---	---	---	---
RPAP2	79871	broad.mit.edu	37	1	92775138	92775143	+	Intron	DEL	ACATAC	-	-	rs141456963		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92775138_92775143delACATAC	uc001dot.2	+						RPAP2_uc009wdh.2_Intron	NM_024813	NP_079089			RNA polymerase II associated protein 2							integral to membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	92877904	92877904	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92877904delT								RPAP2 (24172 upstream) : GFI1 (62415 downstream)																																			---	---	---	---
RPL5	6125	broad.mit.edu	37	1	93301569	93301569	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93301569delT	uc001doz.2	+						FAM69A_uc001dpc.2_Intron|RPL5_uc001dpa.2_Intron|RPL5_uc001dpb.2_Intron|RPL5_uc001dpd.2_5'Flank|SNORD21_uc001dpe.2_5'Flank	NM_000969	NP_000960			ribosomal protein L5						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	5S rRNA binding|protein binding|structural constituent of ribosome				0		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)														---	---	---	---
MTF2	22823	broad.mit.edu	37	1	93583423	93583423	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93583423delA	uc009wdj.2	+						MTF2_uc001dph.2_Intron|MTF2_uc010oth.1_Intron|MTF2_uc009wdk.2_Intron|MTF2_uc001dpi.3_Intron|MTF2_uc010oti.1_Intron|MTF2_uc001dpj.3_Intron|MTF2_uc001dpl.3_Intron	NM_007358	NP_031384			metal response element binding transcription							nucleus	DNA binding|zinc ion binding			ovary(2)	2		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	93773672	93773672	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93773672delT	uc001dps.2	-											Homo sapiens cDNA FLJ42965 fis, clone BRSTN2014751.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	93802436	93802436	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93802436delT	uc001dps.2	-						uc001dpt.1_Intron					Homo sapiens cDNA FLJ42965 fis, clone BRSTN2014751.																														---	---	---	---
BCAR3	8412	broad.mit.edu	37	1	94157326	94157326	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94157326delA	uc001dqb.2	-							NM_003567	NP_003558			breast cancer antiestrogen resistance 3						response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)														---	---	---	---
DNTTIP2	30836	broad.mit.edu	37	1	94335644	94335644	+	Intron	DEL	A	-	-	rs150209724		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94335644delA	uc001dqf.2	-						DNTTIP2_uc010otm.1_Intron	NM_014597	NP_055412			deoxynucleotidyltransferase, terminal,						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)														---	---	---	---
ABCA4	24	broad.mit.edu	37	1	94467355	94467356	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94467355_94467356insA	uc001dqh.2	-						ABCA4_uc001dqi.1_Frame_Shift_Ins_p.W233fs	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)														---	---	---	---
ARHGAP29	9411	broad.mit.edu	37	1	94649050	94649050	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94649050delA	uc001dqj.3	-						ARHGAP29_uc009wdq.1_Intron|ARHGAP29_uc001dqk.2_Intron	NM_004815	NP_004806			PTPL1-associated RhoGAP 1						Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)														---	---	---	---
ARHGAP29	9411	broad.mit.edu	37	1	94668131	94668131	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94668131delT	uc001dqj.3	-	11	1481	c.1112delA	c.(1111-1113)AAGfs	p.K371fs	ARHGAP29_uc009wdq.1_RNA|ARHGAP29_uc001dql.2_Frame_Shift_Del_p.K371fs	NM_004815	NP_004806	Q52LW3	RHG29_HUMAN	PTPL1-associated RhoGAP 1	371	Potential.				Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	95398358	95398358	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95398358delA								CNN3 (5623 upstream) : ALG14 (49921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96198254	96198254	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96198254delA								RWDD3 (485481 upstream) : PTBP2 (988921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96293772	96293773	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96293772_96293773insT								RWDD3 (580999 upstream) : PTBP2 (893402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96989103	96989104	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96989103_96989104delAA								None (None upstream) : PTBP2 (198071 downstream)																																			---	---	---	---
DPYD	1806	broad.mit.edu	37	1	98349487	98349487	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98349487delA	uc001drv.2	-						DPYD_uc010oub.1_Intron|DPYD_uc001drw.2_Intron	NM_000110	NP_000101			dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	98823796	98823796	+	IGR	DEL	A	-	-	rs67144963		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98823796delA								MIR137 (312069 upstream) : SNX7 (303440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	100068921	100068922	+	IGR	INS	-	T	T	rs10634520		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100068921_100068922insT								LPPR4 (293785 upstream) : PALMD (42509 downstream)																																			---	---	---	---
FRRS1	391059	broad.mit.edu	37	1	100214596	100214596	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100214596delT	uc001dsh.1	-							NM_001013660	NP_001013682			stromal cell derived factor receptor 2 homolog						electron transport chain|transport	integral to membrane	ferric-chelate reductase activity|metal ion binding			skin(1)	1		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)														---	---	---	---
SLC35A3	23443	broad.mit.edu	37	1	100480714	100480716	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100480714_100480716delAAA	uc001dsp.1	+						SLC35A3_uc001dsq.1_Intron|SLC35A3_uc009wdy.1_Intron|SLC35A3_uc001dsr.1_Intron|SLC35A3_uc001dss.1_Intron	NM_012243	NP_036375			solute carrier family 35 member 3A						UDP-N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	sugar:hydrogen symporter activity|UDP-N-acetylglucosamine transmembrane transporter activity				0		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.124)|all cancers(265;0.198)|Lung(183;0.199)														---	---	---	---
SASS6	163786	broad.mit.edu	37	1	100551005	100551005	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100551005delA	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)														---	---	---	---
CDC14A	8556	broad.mit.edu	37	1	100876574	100876574	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100876574delT	uc001dtg.3	+						CDC14A_uc009web.2_Intron|CDC14A_uc010oui.1_Intron|CDC14A_uc001dte.3_Intron|CDC14A_uc001dtf.2_Intron|CDC14A_uc009wed.1_Intron|CDC14A_uc009wee.2_Intron	NM_003672	NP_003663			CDC14 homolog A isoform 1						cell cycle|cell division|cell proliferation	centrosome|nucleus|spindle	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			large_intestine(1)	1		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)														---	---	---	---
EXTL2	2135	broad.mit.edu	37	1	101339425	101339425	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101339425delA	uc001dtk.1	-	5					EXTL2_uc001dtl.1_3'UTR|EXTL2_uc010ouk.1_3'UTR|EXTL2_uc001dtm.1_3'UTR	NM_001439	NP_001430			exostoses-like 2						N-acetylglucosamine metabolic process|UDP-N-acetylgalactosamine metabolic process	extracellular region|integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,4-N-acetylgalactosaminyltransferase activity|glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1		all_epithelial(167;2.48e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0425)|all cancers(265;0.0628)|COAD - Colon adenocarcinoma(174;0.148)|Colorectal(144;0.167)|Lung(183;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	102246115	102246115	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102246115delA								S1PR1 (539039 upstream) : OLFM3 (22012 downstream)																																			---	---	---	---
OLFM3	118427	broad.mit.edu	37	1	102296516	102296516	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102296516delT	uc001duf.2	-						OLFM3_uc001dug.2_Intron|OLFM3_uc001duh.2_Intron|OLFM3_uc001dui.2_Intron|OLFM3_uc001duj.2_Intron|OLFM3_uc001due.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	102477865	102477866	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102477865_102477866delTT								OLFM3 (15075 upstream) : COL11A1 (864158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	103189822	103189822	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103189822delT								OLFM3 (727032 upstream) : COL11A1 (152202 downstream)																																			---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103473925	103473926	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103473925_103473926insA	uc001dul.2	-						COL11A1_uc001duk.2_Intron|COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Intron	NM_001854	NP_001845			alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	105244853	105244853	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105244853delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105554767	105554768	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105554767_105554768delTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	107038724	107038724	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107038724delA								None (None upstream) : PRMT6 (560543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	107478897	107478898	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107478897_107478898insA								None (None upstream) : PRMT6 (120369 downstream)																																			---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	107859081	107859081	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107859081delC	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_Intron	NM_001113226	NP_001106697			netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)														---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108254035	108254035	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108254035delT	uc001dvk.1	-						VAV3_uc010ouw.1_Intron|VAV3_uc001dvl.1_Intron|VAV3_uc010oux.1_Intron	NM_006113	NP_006104			vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)														---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108288027	108288028	+	Intron	INS	-	C	C	rs146750974	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108288027_108288028insC	uc001dvk.1	-						VAV3_uc010ouw.1_Intron|VAV3_uc001dvl.1_Intron|VAV3_uc010oux.1_Intron	NM_006113	NP_006104			vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)														---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108338683	108338684	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108338683_108338684delTT	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	109063728	109063728	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109063728delC								NBPF6 (50469 upstream) : FAM102B (39243 downstream)																																			---	---	---	---
PRPF38B	55119	broad.mit.edu	37	1	109242695	109242695	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109242695delT	uc001dvv.3	+	6					PRPF38B_uc001dvw.3_3'UTR|PRPF38B_uc010ouz.1_3'UTR	NM_018061	NP_060531			PRP38 pre-mRNA processing factor 38 (yeast)						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)														---	---	---	---
KIAA1324	57535	broad.mit.edu	37	1	109680801	109680801	+	Intron	DEL	A	-	-	rs67421721		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109680801delA	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	109758494	109758495	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109758494_109758495delTT	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	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	109784407	109784408	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109784407_109784408delTT								SARS (3622 upstream) : CELSR2 (8233 downstream)																																			---	---	---	---
SLC6A17	388662	broad.mit.edu	37	1	110714812	110714812	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110714812delG	uc009wfq.2	+	3	878	c.417delG	c.(415-417)CTGfs	p.L139fs		NM_001010898	NP_001010898	Q9H1V8	S6A17_HUMAN	solute carrier family 6, member 17	139	Cytoplasmic (Potential).				alanine transport|glycine transport|leucine transport|proline transport	cell junction|integral to plasma membrane|synaptic vesicle membrane	neurotransmitter:sodium symporter activity			ovary(1)|pancreas(1)	2		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	111473611	111473611	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111473611delT								CD53 (31054 upstream) : C1orf103 (16202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	111485686	111485686	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111485686delA								CD53 (43129 upstream) : C1orf103 (4127 downstream)																																			---	---	---	---
CEPT1	10390	broad.mit.edu	37	1	111693751	111693752	+	Intron	DEL	TT	-	-	rs28735146		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111693751_111693752delTT	uc001eah.1	+						CEPT1_uc001eag.2_Intron|CEPT1_uc001eai.1_Intron|CEPT1_uc001eaj.1_Intron	NM_001007794	NP_001007795			choline/ethanolaminephosphotransferase							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	diacylglycerol cholinephosphotransferase activity|ethanolaminephosphotransferase activity|metal ion binding				0		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	111925093	111925093	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111925093delA								C1orf88 (29454 upstream) : OVGP1 (31845 downstream)																																			---	---	---	---
WDR77	79084	broad.mit.edu	37	1	111990820	111990821	+	Intron	INS	-	T	T	rs141616266	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111990820_111990821insT	uc001ebb.2	-						WDR77_uc010owd.1_Intron|WDR77_uc010owe.1_Intron|ATP5F1_uc009wgf.1_5'Flank|ATP5F1_uc001ebc.2_5'Flank|ATP5F1_uc001ebd.3_5'Flank	NM_024102	NP_077007			WD repeat domain 77						ncRNA metabolic process|spliceosomal snRNP assembly	cytosol|nucleus	ligand-dependent nuclear receptor transcription coactivator activity|protein binding				0		all_cancers(81;0.000902)|all_epithelial(167;0.00056)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)														---	---	---	---
KCND3	3752	broad.mit.edu	37	1	112321259	112321259	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112321259delC	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)														---	---	---	---
ST7L	54879	broad.mit.edu	37	1	113067471	113067471	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113067471delA	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)														---	---	---	---
CAPZA1	829	broad.mit.edu	37	1	113201624	113201624	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113201624delT	uc001ecj.1	+							NM_006135	NP_006126			F-actin capping protein alpha-1 subunit						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex|WASH complex	actin binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
RHOC	389	broad.mit.edu	37	1	113246218	113246218	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113246218delG	uc001ecp.1	-						RHOC_uc001ecq.1_Intron|RHOC_uc001ecr.1_Intron|RHOC_uc009wgk.1_Intron	NM_001042679	NP_001036144			ras homolog gene family, member C precursor						axon guidance|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity|signal transducer activity			ovary(1)	1	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
LRIG2	9860	broad.mit.edu	37	1	113635953	113635953	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113635953delT	uc001edf.1	+						LRIG2_uc009wgn.1_Intron	NM_014813	NP_055628			leucine-rich repeats and immunoglobulin-like							cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	113673970	113673970	+	IGR	DEL	T	-	-	rs147199256	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113673970delT								LRIG2 (6628 upstream) : MAGI3 (259505 downstream)																																			---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	114064741	114064742	+	Intron	INS	-	T	T	rs139186643	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114064741_114064742insT	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)														---	---	---	---
PHTF1	10745	broad.mit.edu	37	1	114268597	114268597	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114268597delA	uc009wgp.1	-						PHTF1_uc001edn.2_Intron|PHTF1_uc010own.1_Intron|PHTF1_uc001edp.2_Intron	NM_006608	NP_006599			putative homeodomain transcription factor 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
BCL2L15	440603	broad.mit.edu	37	1	114429118	114429118	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114429118delA	uc001edw.2	-						uc001edv.1_Intron|BCL2L15_uc001edx.2_Intron|BCL2L15_uc001edy.2_Intron|BCL2L15_uc001edz.1_Intron	NM_001010922	NP_001010922			pro-apoptotic Bcl-2 protein						apoptosis					ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.95e-08)|all_epithelial(167;9.95e-08)|all_lung(203;1.31e-05)|Lung NSC(69;2.46e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
AP4B1	10717	broad.mit.edu	37	1	114441526	114441526	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114441526delA	uc001eeb.2	-						uc001edv.1_Intron|AP4B1_uc001eec.2_Intron|AP4B1_uc001eed.2_Intron|AP4B1_uc010owp.1_Intron|AP4B1_uc001eea.1_Intron|AP4B1_uc001eee.1_5'Flank	NM_006594	NP_006585			adaptor-related protein complex 4, beta 1						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|soluble fraction|trans-Golgi network	protein binding|protein transporter activity			ovary(3)|central_nervous_system(1)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
CSDE1	7812	broad.mit.edu	37	1	115263051	115263051	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115263051delA	uc001efk.2	-						CSDE1_uc001efi.2_Intron|CSDE1_uc001efj.2_Intron|CSDE1_uc001efl.2_Intron|CSDE1_uc001efm.2_Intron|CSDE1_uc009wgv.2_Intron|CSDE1_uc001efn.2_Intron	NM_001007553	NP_001007554			upstream of NRAS isoform 1						male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	115893304	115893305	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115893304_115893305delAC								NGF (12447 upstream) : VANGL1 (291269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	116091552	116091553	+	IGR	DEL	AT	-	-	rs150311168	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116091552_116091553delAT								NGF (210695 upstream) : VANGL1 (93021 downstream)																																			---	---	---	---
CASQ2	845	broad.mit.edu	37	1	116288783	116288783	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116288783delT	uc001efx.3	-						CASQ2_uc010owu.1_Intron	NM_001232	NP_001223			cardiac calsequestrin 2 precursor						heart development|striated muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	116457811	116457811	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116457811delG								NHLH2 (74064 upstream) : SLC22A15 (61308 downstream)																																			---	---	---	---
SLC22A15	55356	broad.mit.edu	37	1	116588492	116588492	+	Intron	DEL	T	-	-	rs149958210		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116588492delT	uc001egb.3	+							NM_018420	NP_060890			solute carrier family 22, member 15						ion transport	integral to membrane	transmembrane transporter activity			large_intestine(2)	2	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	117412977	117412977	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117412977delC								CD2 (101127 upstream) : PTGFRN (39712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118196857	118196858	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118196857_118196858insT								FAM46C (25847 upstream) : GDAP2 (209250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118783632	118783632	+	IGR	DEL	A	-	-	rs35305224		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118783632delA								SPAG17 (55784 upstream) : TBX15 (642034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	119061798	119061798	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119061798delT								SPAG17 (333950 upstream) : TBX15 (363868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	119824199	119824199	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119824199delA								WARS2 (140904 upstream) : HAO2 (87203 downstream)																																			---	---	---	---
HMGCS2	3158	broad.mit.edu	37	1	120291856	120291856	+	Intron	DEL	T	-	-	rs80164653		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120291856delT	uc001eid.2	-						HMGCS2_uc010oxj.1_Intron|HMGCS2_uc001eie.2_Intron	NM_005518	NP_005509			hydroxymethylglutaryl-CoA synthase 2 isoform 1						acetoacetic acid biosynthetic process|cholesterol biosynthetic process|isoprenoid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA synthase activity			ovary(2)	2	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)														---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120560007	120560008	+	Intron	INS	-	A	A	rs138352700	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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				---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120560538	120560538	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120560538delA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719			notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)				N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	1	142607456	142607457	+	IGR	INS	-	AACA	AACA	rs147601859	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142607456_142607457insAACA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142642817	142642818	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142642817_142642818insT	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143125255	143125255	+	Intron	DEL	A	-	-	rs149679425		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143125255delA	uc001eiw.1	+						uc001ejf.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143418339	143418340	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143418339_143418340delCT								None (None upstream) : LOC100286793 (229299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143459861	143459861	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143459861delT	uc001ejn.1	-											Homo sapiens cDNA clone IMAGE:30343207.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143504763	143504764	+	IGR	INS	-	A	A	rs150986294	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143504763_143504764insA								None (None upstream) : LOC100286793 (142875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143534548	143534549	+	IGR	INS	-	C	C	rs150523668		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143534548_143534549insC								None (None upstream) : LOC100286793 (113090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143541201	143541202	+	IGR	INS	-	G	G	rs140228887	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143541201_143541202insG								None (None upstream) : LOC100286793 (106437 downstream)																																			---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144852877	144852877	+	Intron	DEL	T	-	-	rs71909310		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144852877delT	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145220306	145220307	+	Intron	INS	-	T	T	rs150855626		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145220306_145220307insT	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	145550427	145550427	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145550427delA	uc001emp.3	+						ANKRD35_uc010oyx.1_Intron|ANKRD35_uc001eob.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145587859	145587860	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145587859_145587860delTT	uc001emp.3	+						NUDT17_uc001eoe.2_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145804698	145804698	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145804698delA	uc001emp.3	+						GPR89A_uc001eor.2_Intron|GPR89A_uc010ozb.1_Intron|GPR89A_uc001eos.2_Intron|GPR89A_uc001eot.2_Intron|GPR89A_uc010ozc.1_Intron|GPR89A_uc010ozd.1_Intron|GPR89A_uc010oze.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	146804761	146804761	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146804761delA	uc001epp.2	-											Homo sapiens cDNA clone IMAGE:5266739.																														---	---	---	---
BCL9	607	broad.mit.edu	37	1	147087679	147087680	+	Frame_Shift_Del	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147087679_147087680delAC	uc001epq.2	+	7	1377_1378	c.637_638delAC	c.(637-639)ACAfs	p.T213fs	BCL9_uc010ozr.1_Frame_Shift_Del_p.T139fs	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	213					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								---	---	---	---
Unknown	0	broad.mit.edu	37	1	148538283	148538283	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148538283delT								NBPF14 (191492 upstream) : NBPF15 (19986 downstream)																																			---	---	---	---
NBPF15	284565	broad.mit.edu	37	1	148558602	148558602	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148558602delT	uc001esc.2	+						NBPF15_uc001esb.1_Intron	NM_173638	NP_775909			hypothetical protein LOC284565							cytoplasm					0	all_hematologic(923;0.032)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	148679944	148679944	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148679944delC								PPIAL4E (35151 upstream) : NBPF16 (59498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149026370	149026371	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149026370_149026371delTT								LOC645166 (73316 upstream) : LOC388692 (253105 downstream)																																			---	---	---	---
FCGR1C	100132417	broad.mit.edu	37	1	149377284	149377285	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149377284_149377285delTC	uc010pbh.1	+							NR_027484				Homo sapiens cDNA FLJ77773 complete cds, highly similar to Homo sapiens Fc fragment of IgG, high affinity Ia, receptor (CD64) (FCGR1A), mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	150161641	150161641	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150161641delT								PLEKHO1 (29825 upstream) : ANP32E (29077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	150284737	150284738	+	IGR	INS	-	TT	TT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150284737_150284738insTT								MRPS21 (3919 upstream) : PRPF3 (9190 downstream)																																			---	---	---	---
PRPF3	9129	broad.mit.edu	37	1	150314981	150314982	+	Intron	INS	-	AC	AC	rs147409085	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150314981_150314982insAC	uc001eum.3	+						PRPF3_uc009wlp.2_Intron|PRPF3_uc010pca.1_Intron|PRPF3_uc010pcb.1_Intron|PRPF3_uc009wlq.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)														---	---	---	---
ADAMTSL4	54507	broad.mit.edu	37	1	150523469	150523469	+	Intron	DEL	T	-	-	rs78880005		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150523469delT	uc001eux.2	+						ADAMTSL4_uc009wlv.1_3'UTR|ADAMTSL4_uc001euw.2_Intron|ADAMTSL4_uc009wlw.2_Intron|ADAMTSL4_uc010pcg.1_Intron|hsa-mir-4257|MI0015856_5'Flank	NM_019032	NP_061905			thrombospondin repeat containing 1 isoform 1						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	150538858	150538858	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150538858delT								ADAMTSL4 (5448 upstream) : MCL1 (8179 downstream)																																			---	---	---	---
FAM63A	55793	broad.mit.edu	37	1	150974465	150974465	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150974465delT	uc001ewf.2	-						FAM63A_uc001ewc.2_Intron|FAM63A_uc010pcm.1_Intron|FAM63A_uc001ewd.2_Intron|FAM63A_uc001ewe.2_Intron|FAM63A_uc010pcn.1_Intron|FAM63A_uc001ewg.2_Intron	NM_018379	NP_001156731			hypothetical protein LOC55793 isoform 1								protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
PRUNE	58497	broad.mit.edu	37	1	150990219	150990220	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150990219_150990220insA	uc001ewh.1	+						PRUNE_uc001ewi.1_Intron|PRUNE_uc010pco.1_Intron|PRUNE_uc001ewj.1_Intron	NM_021222	NP_067045			prune							cytoplasm|focal adhesion|nucleus	inorganic diphosphatase activity|manganese ion binding|protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
PI4KB	5298	broad.mit.edu	37	1	151302218	151302218	+	5'Flank	DEL	A	-	-	rs76978699		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151302218delA	uc001ext.2	-						PI4KB_uc001exu.2_5'Flank|PI4KB_uc010pcw.1_5'Flank|PI4KB_uc009wmq.1_5'Flank	NM_002651	NP_002642			catalytic phosphatidylinositol 4-kinase beta						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|receptor-mediated endocytosis	endosome|Golgi apparatus|mitochondrial outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum membrane	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			ovary(2)|skin(2)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	151334629	151334631	+	IGR	DEL	AGA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151334629_151334631delAGA								RFX5 (14860 upstream) : SELENBP1 (2150 downstream)																																			---	---	---	---
POGZ	23126	broad.mit.edu	37	1	151386959	151386959	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151386959delT	uc001eyd.1	-						POGZ_uc001eye.1_Intron|POGZ_uc010pdb.1_Intron|POGZ_uc001eyf.1_Intron|POGZ_uc010pdc.1_Intron|POGZ_uc009wmv.1_Intron|POGZ_uc010pdd.1_Intron	NM_015100	NP_055915			pogo transposable element with ZNF domain						cell division|kinetochore assembly|mitotic sister chromatid cohesion|regulation of transcription, DNA-dependent	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	151463570	151463570	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151463570delT								POGZ (31638 upstream) : CGN (20292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	152074392	152074393	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152074392_152074393delAA								TCHHL1 (12852 upstream) : TCHH (4400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	152146011	152146012	+	IGR	INS	-	TT	TT	rs141866722	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152146011_152146012insTT								RPTN (14307 upstream) : HRNR (38546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	152787476	152787476	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152787476delT								LCE1B (1891 upstream) : LCE1A (12473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	153215597	153215599	+	IGR	DEL	CAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153215597_153215599delCAC								LELP1 (38003 upstream) : LOR (16580 downstream)																																			---	---	---	---
INTS3	65123	broad.mit.edu	37	1	153718823	153718824	+	Intron	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153718823_153718824insG	uc009wom.2	+						INTS3_uc001fct.2_Intron|INTS3_uc001fcu.2_Intron|INTS3_uc001fcv.2_Intron	NM_023015	NP_075391			integrator complex subunit 3						DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
GATAD2B	57459	broad.mit.edu	37	1	153791121	153791121	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153791121delA	uc001fdb.3	-							NM_020699	NP_065750			GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
DENND4B	9909	broad.mit.edu	37	1	153916853	153916853	+	5'UTR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153916853delC	uc001fdd.1	-	2						NM_014856	NP_055671			DENN/MADD domain containing 4B											ovary(1)	1	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
SLC39A1	27173	broad.mit.edu	37	1	153934362	153934362	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153934362delA	uc001fdh.2	-						SLC39A1_uc001fdi.2_Intron|SLC39A1_uc001fdj.2_Intron|SLC39A1_uc001fdk.2_Intron|SLC39A1_uc010pee.1_Intron|SLC39A1_uc001fdl.2_Intron	NM_014437	NP_055252			solute carrier family 39 (zinc transporter),							endoplasmic reticulum membrane|integral to membrane|membrane fraction|plasma membrane	zinc ion transmembrane transporter activity				0	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)	Colorectal(1306;0.019)														---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	153994528	153994528	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153994528delT	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	154013068	154013068	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154013068delT	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)															---	---	---	---
C1orf43	25912	broad.mit.edu	37	1	154180574	154180574	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154180574delA	uc001fei.2	-						C1orf189_uc001fee.1_5'Flank|C1orf43_uc001fef.1_Intron|C1orf43_uc001feg.2_Intron|C1orf43_uc001feh.2_Intron|C1orf43_uc001fej.2_Intron|C1orf43_uc009wos.1_Intron	NM_001098616	NP_001092086			hypothetical protein LOC25912 isoform 3							integral to membrane	coenzyme binding|oxidoreductase activity				0	all_lung(78;1.98e-30)|Lung NSC(65;2.87e-28)|Hepatocellular(266;0.0877)																	---	---	---	---
UBE2Q1	55585	broad.mit.edu	37	1	154522742	154522742	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154522742delT	uc001fff.1	-	13						NM_017582	NP_060052			ubiquitin-conjugating enzyme E2Q								ATP binding|protein binding|ubiquitin-protein ligase activity				0	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
KCNN3	3782	broad.mit.edu	37	1	154739161	154739161	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154739161delT	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron	NM_002249	NP_002240			small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)															---	---	---	---
KCNN3	3782	broad.mit.edu	37	1	154819681	154819681	+	Intron	DEL	C	-	-	rs147821402	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154819681delC	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron|KCNN3_uc009wox.1_Intron	NM_002249	NP_002240			small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)															---	---	---	---
FLAD1	80308	broad.mit.edu	37	1	154952936	154952936	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154952936delA	uc001fgf.1	+						FLAD1_uc001fgc.2_5'Flank|FLAD1_uc001fgd.1_5'Flank|FLAD1_uc001fge.1_5'Flank|FLAD1_uc001fgg.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	155091631	155091631	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155091631delA								EFNA3 (31625 upstream) : EFNA1 (8718 downstream)																																			---	---	---	---
MUC1	4582	broad.mit.edu	37	1	155161732	155161732	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155161732delG	uc010pft.1	-	2	467	c.401delC	c.(400-402)CCAfs	p.P134fs	RAG1AP1_uc010pey.1_Intron|MUC1_uc001fhy.2_5'Flank|MUC1_uc001fhz.2_5'Flank|MUC1_uc010pfb.1_Intron|MUC1_uc010pfc.1_Intron|MUC1_uc009wph.2_Intron|MUC1_uc010pfd.1_Intron|MUC1_uc010pfe.1_Intron|MUC1_uc010pff.1_Intron|MUC1_uc009wpi.2_Intron|MUC1_uc010pfg.1_Intron|MUC1_uc010pfh.1_Intron|MUC1_uc010pfi.1_Intron|MUC1_uc010pfj.1_Intron|MUC1_uc010pfk.1_Intron|MUC1_uc010pfl.1_Intron|MUC1_uc001fin.2_Intron|MUC1_uc009wpk.2_Intron|MUC1_uc001fip.2_Intron|MUC1_uc009wqg.2_Intron|MUC1_uc009wpo.2_Intron|MUC1_uc009wps.2_Intron|MUC1_uc009wpt.2_Intron|MUC1_uc001fic.2_Intron|MUC1_uc009wpu.2_Intron|MUC1_uc009wpq.2_Intron|MUC1_uc009wpv.2_Intron|MUC1_uc001fim.2_Intron|MUC1_uc001fib.2_Intron|MUC1_uc009wpw.2_Intron|MUC1_uc001fie.2_Intron|MUC1_uc009wpr.2_Intron|MUC1_uc001fig.2_Intron|MUC1_uc001fif.2_Intron|MUC1_uc009wpx.2_Intron|MUC1_uc001fid.2_Intron|MUC1_uc009wpj.2_Intron|MUC1_uc001fij.2_Intron|MUC1_uc009wpy.2_Intron|MUC1_uc010pfm.1_Intron|MUC1_uc001fiq.2_Intron|MUC1_uc009wpz.2_Intron|MUC1_uc010pfn.1_Intron|MUC1_uc009wqa.2_Intron|MUC1_uc010pfo.1_Intron|MUC1_uc010pfp.1_Intron|MUC1_uc001fii.2_Intron|MUC1_uc001fih.2_Intron|MUC1_uc001fia.2_Intron|MUC1_uc009wqc.2_Intron|MUC1_uc009wqd.2_Intron|MUC1_uc009wqb.2_Intron|MUC1_uc010pfq.1_Intron|MUC1_uc010pfr.1_Intron|MUC1_uc001fit.2_Intron|MUC1_uc009wqe.2_Intron|MUC1_uc001fil.2_Intron|MUC1_uc009wpm.2_Intron|MUC1_uc009wpp.2_Intron|MUC1_uc010pfs.1_Intron|MUC1_uc001fik.2_Intron|MUC1_uc001fio.2_Intron|MUC1_uc009wqf.2_Intron|MUC1_uc009wpl.2_Intron|MUC1_uc009wpn.2_Intron|MUC1_uc001fis.1_Intron|uc009wqh.2_5'Flank|MUC1_uc001fiv.1_Frame_Shift_Del_p.P143fs|MUC1_uc001fiw.1_Frame_Shift_Del_p.P134fs			P15941	MUC1_HUMAN	SubName: Full=MUC1 isoform M13;	134	Extracellular (Potential).|42 X 20 AA approximate tandem repeats of P-A-P-G-S-T-A-P-P-A-H-G-V-T-S-A-P-D-T-R.|4.			P -> Q (in Ref. 16; AAA35757).		apical plasma membrane|cell surface|cytoplasm|extracellular region|integral to plasma membrane|nucleus	protein binding			large_intestine(1)|pancreas(1)|breast(1)|skin(1)	4	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)					T	IGH@	B-NHL								---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155308000	155308000	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155308000delT	uc009wqq.2	-	27	9178	c.8698delA	c.(8698-8700)ACAfs	p.T2900fs	RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Frame_Shift_Del_p.T2895fs	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	2900					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155339238	155339239	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155339238_155339239delAA	uc009wqq.2	-						RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155500534	155500534	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155500534delA	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron|ASH1L_uc009wqr.1_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	155571854	155571854	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155571854delT								LOC645676 (38122 upstream) : MSTO1 (8153 downstream)																																			---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155720557	155720557	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155720557delT	uc001flz.2	-						MSTO2P_uc010pgp.1_RNA|GON4L_uc001flx.1_Intron|GON4L_uc009wrg.1_Intron|GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron	NM_001037533	NP_001032622			gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
SEMA4A	64218	broad.mit.edu	37	1	156138345	156138346	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156138345_156138346delTC	uc001fnl.2	+						SEMA4A_uc009wrq.2_Intron|SEMA4A_uc001fnm.2_Intron|SEMA4A_uc001fnn.2_Intron|SEMA4A_uc001fno.2_Intron	NM_022367	NP_071762			semaphorin B precursor						axon guidance	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)																	---	---	---	---
PMF1	11243	broad.mit.edu	37	1	156184542	156184542	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156184542delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	156318667	156318667	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156318667delA								C1orf182 (1884 upstream) : RHBG (20336 downstream)																																			---	---	---	---
IQGAP3	128239	broad.mit.edu	37	1	156499845	156499846	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156499845_156499846delCA	uc001fpf.2	-							NM_178229	NP_839943			IQ motif containing GTPase activating protein 3						small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)|skin(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
MRPL24	79590	broad.mit.edu	37	1	156708604	156708604	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156708604delT	uc001fpw.1	-						MRPL24_uc001fpx.1_Intron	NM_024540	NP_078816			mitochondrial ribosomal protein L24 precursor						translation	mitochondrion|ribosome	structural constituent of ribosome				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
NTRK1	4914	broad.mit.edu	37	1	156788788	156788789	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156788788_156788789delTG	uc001fqf.1	+						SH2D2A_uc001fqc.1_5'Flank|SH2D2A_uc009wsh.2_5'Flank|SH2D2A_uc001fqd.2_5'Flank|SH2D2A_uc001fqe.2_5'Flank|SH2D2A_uc010phs.1_5'Flank|NTRK1_uc009wsi.1_Intron	NM_001007792	NP_001007793			neurotrophic tyrosine kinase, receptor, type 1						activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(9)|ovary(6)|stomach(1)|central_nervous_system(1)	17	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Imatinib(DB00619)			T	TPM3|TPR|TFG	papillary thyroid					TSP Lung(10;0.080)			---	---	---	---
PEAR1	375033	broad.mit.edu	37	1	156865712	156865712	+	Intron	DEL	T	-	-	rs71856291		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156865712delT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	157159255	157159255	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157159255delT								ETV3 (50872 upstream) : FCRL5 (323913 downstream)																																			---	---	---	---
FCRL1	115350	broad.mit.edu	37	1	157774037	157774037	+	Intron	DEL	C	-	-	rs71658497		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157774037delC	uc001frg.2	-						FCRL1_uc001frf.2_5'Flank|FCRL1_uc001frh.2_Intron|FCRL1_uc001fri.2_Intron|FCRL1_uc001frj.2_Intron	NM_052938	NP_443170			Fc receptor-like 1 isoform 1 precursor							integral to membrane|plasma membrane	receptor activity			skin(4)|ovary(3)	7	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	157951861	157951862	+	IGR	DEL	GG	-	-	rs60104291		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157951861_157951862delGG								CD5L (140227 upstream) : KIRREL (11201 downstream)																																			---	---	---	---
KIRREL	55243	broad.mit.edu	37	1	157970908	157970908	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157970908delT	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)																	---	---	---	---
C1orf204	284677	broad.mit.edu	37	1	159821951	159821954	+	Intron	DEL	AGAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159821951_159821954delAGAC	uc001fug.1	-						C1orf204_uc001fuf.1_Intron	NM_001134233	NP_001127705			hypothetical protein LOC284677							integral to membrane					0																		---	---	---	---
IGSF9	57549	broad.mit.edu	37	1	159900128	159900128	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159900128delC	uc001fur.2	-	15	2113	c.1915delG	c.(1915-1917)GTAfs	p.V639fs	IGSF9_uc001fuq.2_Frame_Shift_Del_p.V623fs|IGSF9_uc001fup.2_5'UTR	NM_001135050	NP_001128522	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9 isoform a	639	Fibronectin type-III 2.|Extracellular (Potential).					cell junction|integral to membrane|synapse				ovary(2)|central_nervous_system(2)|large_intestine(1)	5	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160076051	160076052	+	IGR	DEL	AA	-	-	rs67254354		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160076051_160076052delAA								IGSF8 (7433 upstream) : ATP1A2 (9468 downstream)																																			---	---	---	---
CASQ1	844	broad.mit.edu	37	1	160164263	160164264	+	Intron	INS	-	CA	CA	rs150057122		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160164263_160164264insCA	uc010pja.1	+							NM_001231	NP_001222			calsequestrin 1							mitochondrial matrix|sarcoplasmic reticulum lumen|smooth endoplasmic reticulum	calcium ion binding			central_nervous_system(1)	1	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
DCAF8	50717	broad.mit.edu	37	1	160250305	160250305	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160250305delT	uc010pjc.1	-						PEX19_uc010pje.1_Intron|PEX19_uc001fvs.2_Intron|PEX19_uc001fvt.2_Intron	NM_015726	NP_056541			DDB1 and CUL4 associated factor 8							CUL4 RING ubiquitin ligase complex	protein binding			skin(2)	2																		---	---	---	---
F11R	50848	broad.mit.edu	37	1	160991569	160991569	+	5'Flank	DEL	A	-	-	rs12567886	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160991569delA	uc009wtt.2	-						F11R_uc010pjv.1_5'Flank|F11R_uc001fxe.3_5'Flank|F11R_uc009wtu.2_5'Flank|F11R_uc010pjw.1_Intron|F11R_uc001fxf.3_Intron	NM_016946	NP_058642			F11 receptor precursor						blood coagulation|inflammatory response|interspecies interaction between organisms|leukocyte migration|tight junction assembly	integral to membrane|tight junction				ovary(2)	2	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)															---	---	---	---
DEDD	9191	broad.mit.edu	37	1	161093498	161093498	+	Intron	DEL	T	-	-	rs112931699		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161093498delT	uc001fxz.2	-						NIT1_uc001fxw.2_Intron|DEDD_uc009wty.2_Intron|DEDD_uc001fya.2_Intron|DEDD_uc001fyb.2_Intron|DEDD_uc010pkb.1_Intron|DEDD_uc001fyc.2_Intron	NM_001039712	NP_001034801			death effector domain-containing protein						apoptosis|induction of apoptosis via death domain receptors|negative regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding				0	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)															---	---	---	---
NDUFS2	4720	broad.mit.edu	37	1	161175957	161175957	+	Intron	DEL	A	-	-	rs137870116		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161175957delA	uc001fyv.2	+						NDUFS2_uc010pki.1_Intron|NDUFS2_uc001fyw.2_Intron|NDUFS2_uc010pkj.1_Intron|NDUFS2_uc001fyx.2_Intron|NDUFS2_uc001fyy.1_Intron	NM_004550	NP_004541			NADH dehydrogenase (ubiquinone) Fe-S protein 2						mitochondrial electron transport, NADH to ubiquinone|response to oxidative stress|transport	mitochondrial respiratory chain complex I	4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NAD binding|NADH dehydrogenase (ubiquinone) activity|protein binding|quinone binding			skin(1)	1	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		NADH(DB00157)													---	---	---	---
TOMM40L	84134	broad.mit.edu	37	1	161195710	161195719	+	5'Flank	DEL	TTTTTTTTTT	-	-	rs71641244		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161195710_161195719delTTTTTTTTTT	uc001fzd.2	+						APOA2_uc001fzb.1_5'Flank|APOA2_uc001fzc.1_5'Flank|TOMM40L_uc010pkk.1_5'Flank|TOMM40L_uc010pkl.1_5'Flank|TOMM40L_uc009wue.2_5'Flank|TOMM40L_uc009wuf.1_5'Flank|TOMM40L_uc001fze.2_5'Flank	NM_032174	NP_115550			translocase of outer mitochondrial membrane 40						protein transport	mitochondrial outer membrane|pore complex	porin activity|voltage-gated anion channel activity			large_intestine(1)	1	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)															---	---	---	---
NR1I3	9970	broad.mit.edu	37	1	161206997	161206998	+	Intron	DEL	TT	-	-	rs66782410		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161206997_161206998delTT	uc001fzx.2	-						TOMM40L_uc009wuf.1_Intron|NR1I3_uc001fzf.2_Intron|NR1I3_uc001fzg.2_Intron|NR1I3_uc001fzh.2_Intron|NR1I3_uc001fzi.2_Intron|NR1I3_uc001fzj.2_Intron|NR1I3_uc001fzk.2_Intron|NR1I3_uc001fzl.2_Intron|NR1I3_uc001fzm.2_Intron|NR1I3_uc001fzn.2_Intron|NR1I3_uc009wug.2_Intron|NR1I3_uc001fzp.2_Intron|NR1I3_uc001fzo.2_Intron|NR1I3_uc001fzq.2_Intron|NR1I3_uc001fzr.2_Intron|NR1I3_uc001fzs.2_Intron|NR1I3_uc001fzt.2_Intron|NR1I3_uc001fzu.2_Intron|NR1I3_uc001fzv.2_Intron|NR1I3_uc001fzw.2_Intron|NR1I3_uc001fzy.2_Intron|NR1I3_uc001fzz.2_Intron|NR1I3_uc001gaa.2_Intron|NR1I3_uc001gab.2_Intron|NR1I3_uc001gac.2_Intron|NR1I3_uc010pkm.1_Intron|NR1I3_uc010pkn.1_Intron	NM_001077480	NP_001070948			constitutive androstane receptor isoform 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	androgen receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity|transcription coactivator activity|zinc ion binding			ovary(1)|skin(1)	2	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)															---	---	---	---
ATF6	22926	broad.mit.edu	37	1	161928711	161928711	+	3'UTR	DEL	T	-	-	rs74579405		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161928711delT	uc001gbr.2	+	16					ATF6_uc001gbs.2_RNA	NM_007348	NP_031374			activating transcription factor 6						positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|skin(1)	3	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)															---	---	---	---
NOS1AP	9722	broad.mit.edu	37	1	162049017	162049017	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162049017delT	uc001gbv.2	+						NOS1AP_uc010pkr.1_Intron|NOS1AP_uc010pks.1_Intron|NOS1AP_uc001gbw.2_Intron	NM_014697	NP_055512			nitric oxide synthase 1 (neuronal) adaptor						regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)															---	---	---	---
SH2D1B	117157	broad.mit.edu	37	1	162372704	162372704	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162372704delT	uc001gbz.1	-						SH2D1B_uc001gca.1_Intron	NM_053282	NP_444512			SH2 domain containing 1B											pancreas(1)	1	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	164036359	164036359	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164036359delT								NUF2 (710806 upstream) : PBX1 (492443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164289082	164289082	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164289082delG								NUF2 (963529 upstream) : PBX1 (239720 downstream)																																			---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164534660	164534661	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164534660_164534661delAC	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
Unknown	0	broad.mit.edu	37	1	165672291	165672292	+	Intron	INS	-	A	A	rs4657469	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165672291_165672292insA	uc001gdi.2	+											Homo sapiens carbonic anhydrase XIV (CA14) pseudogene, mRNA (cDNA clone IMAGE:4643256).																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	166171584	166171587	+	IGR	DEL	TAAT	-	-	rs147292459		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166171584_166171587delTAAT								FAM78B (35378 upstream) : FMO9P (401566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	166754541	166754541	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166754541delT								FMO9P (160070 upstream) : POGK (54183 downstream)																																			---	---	---	---
TADA1	117143	broad.mit.edu	37	1	166838514	166838514	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166838514delA	uc001gdw.2	-						TADA1_uc009wve.2_Intron	NM_053053	NP_444281			transcriptional adaptor 1-like						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(1)	1																		---	---	---	---
POU2F1	5451	broad.mit.edu	37	1	167374616	167374617	+	Intron	DEL	AA	-	-	rs113014888		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167374616_167374617delAA	uc001gec.2	+						POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron|POU2F1_uc001gef.2_Intron|POU2F1_uc001geg.2_Intron|POU2F1_uc009wvg.1_Intron	NM_002697	NP_002688			POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5																		---	---	---	---
CD247	919	broad.mit.edu	37	1	167428377	167428377	+	Intron	DEL	T	-	-	rs111653505		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167428377delT	uc001gei.3	-						CD247_uc001gej.3_Intron|CD247_uc001gek.2_Intron	NM_198053	NP_932170			T-cell receptor zeta chain isoform 1 precursor						interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)															---	---	---	---
ADCY10	55811	broad.mit.edu	37	1	167827181	167827181	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167827181delT	uc001ger.2	-						ADCY10_uc009wvk.2_Intron|ADCY10_uc010plj.1_Intron|ADCY10_uc009wvl.2_Intron	NM_018417	NP_060887			adenylate cyclase 10						intracellular signal transduction|spermatogenesis	cytoskeleton|cytosol|perinuclear region of cytoplasm|plasma membrane|soluble fraction	adenylate cyclase activity|ATP binding|magnesium ion binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
TBX19	9095	broad.mit.edu	37	1	168216312	168216312	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168216312delT	uc001gfj.3	+						ANKRD36BP1_uc010plo.1_RNA|uc001gfk.1_5'Flank	NM_005149	NP_005140			T-box 19						anatomical structure morphogenesis	nucleus	DNA binding				0	all_hematologic(923;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	168764777	168764777	+	IGR	DEL	T	-	-	rs71996077		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168764777delT								MGC4473 (2657 upstream) : ATP1B1 (311170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	169012265	169012265	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169012265delA								MGC4473 (250145 upstream) : ATP1B1 (63682 downstream)																																			---	---	---	---
C1orf114	57821	broad.mit.edu	37	1	169366387	169366387	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)																	---	---	---	---
SELP	6403	broad.mit.edu	37	1	169590332	169590333	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169590332_169590333delTG	uc001ggi.3	-						SELP_uc001ggh.2_5'Flank|SELP_uc009wvr.2_Intron	NM_003005	NP_002996			selectin P precursor						platelet activation|platelet degranulation|positive regulation of platelet activation	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane fraction|platelet alpha granule membrane|platelet dense granule membrane|soluble fraction	fucose binding|glycosphingolipid binding|heparin binding|lipopolysaccharide binding|oligosaccharide binding|sialic acid binding			ovary(2)|skin(2)	4	all_hematologic(923;0.208)				Clopidogrel(DB00758)|Heparin(DB01109)|Tirofiban(DB00775)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	169607072	169607072	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169607072delA								SELP (7695 upstream) : C1orf112 (24173 downstream)																																			---	---	---	---
C1orf112	55732	broad.mit.edu	37	1	169727753	169727753	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169727753delA	uc001ggj.2	+											Homo sapiens cDNA FLJ10706 fis, clone NT2RP3000852.												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	170226292	170226293	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170226292_170226293delTT								METTL11B (89369 upstream) : LOC284688 (14254 downstream)																																			---	---	---	---
PRRX1	5396	broad.mit.edu	37	1	170676287	170676287	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170676287delA	uc001ghf.2	+						PRRX1_uc001ghe.2_Intron	NM_022716	NP_073207			paired mesoderm homeobox 1 isoform pmx-1b							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	170771652	170771652	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170771652delT								PRRX1 (63112 upstream) : C1orf129 (132960 downstream)																																			---	---	---	---
FMO6P	388714	broad.mit.edu	37	1	171120946	171120960	+	Intron	DEL	TGATGTTTAACTGCT	-	-	rs146400497	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171120946_171120960delTGATGTTTAACTGCT	uc001ghj.1	+							NR_002601				SubName: Full=Putative uncharacterized protein FMO6P;												0																		---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171476170	171476170	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171476170delC	uc010pmg.1	+						BAT2L2_uc001ghq.1_Intron|BAT2L2_uc001ghr.1_Intron	NM_015172	NP_055987			HBxAg transactivated protein 2								protein C-terminus binding				0																		---	---	---	---
DNM3	26052	broad.mit.edu	37	1	171810057	171810058	+	5'Flank	INS	-	A	A	rs145553951	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171810057_171810058insA	uc001gie.2	+						DNM3_uc001gid.3_5'Flank|DNM3_uc009wwb.2_5'Flank|DNM3_uc001gif.2_5'Flank	NM_015569	NP_056384			dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	172486437	172486440	+	IGR	DEL	TGTG	-	-	rs113844905		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172486437_172486440delTGTG								C1orf105 (48472 upstream) : C1orf9 (15820 downstream)																																			---	---	---	---
TNFSF4	7292	broad.mit.edu	37	1	173176050	173176050	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173176050delA	uc001giw.2	-						TNFSF4_uc001giv.2_5'Flank	NM_003326	NP_003317			tumor necrosis factor (ligand) superfamily,						acute inflammatory response|cellular response to lipopolysaccharide|cellular response to prostaglandin E stimulus|chemokine (C-C motif) ligand 11 production|defense response to nematode|interleukin-4-dependent isotype switching to IgE isotypes|memory T cell activation|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of regulatory T cell differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of T-helper 1 cell differentiation|negative regulation of transcription, DNA-dependent|positive regulation of alpha-beta T cell proliferation|positive regulation of B cell activation|positive regulation of immunoglobulin mediated immune response|positive regulation of immunoglobulin secretion|positive regulation of inflammatory response|positive regulation of interferon-gamma production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-13 production|positive regulation of interleukin-4 production|positive regulation of interleukin-6 production|positive regulation of memory T cell differentiation|positive regulation of T cell cytokine production|positive regulation of T-helper 2 cell differentiation|positive regulation of type 2 immune response|response to virus|signal transduction|T-helper 2 cell activation	cell surface|extracellular space|integral to plasma membrane	cytokine activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	173217493	173217493	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173217493delA	uc001gix.1	-											Homo sapiens cDNA FLJ45305 fis, clone BRHIP3004193.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	173323160	173323160	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173323160delA	uc001gix.1	-											Homo sapiens cDNA FLJ45305 fis, clone BRHIP3004193.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	173352014	173352015	+	Intron	DEL	CA	-	-	rs35738368		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173352014_173352015delCA	uc001gix.1	-											Homo sapiens cDNA FLJ45305 fis, clone BRHIP3004193.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	173413496	173413496	+	Intron	DEL	C	-	-	rs113950576		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173413496delC	uc001gix.1	-						uc010pmp.1_Intron					Homo sapiens cDNA FLJ45305 fis, clone BRHIP3004193.																														---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173930702	173930702	+	Intron	DEL	A	-	-	rs71715802		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173930702delA	uc001gju.3	-						RC3H1_uc010pms.1_Intron|RC3H1_uc001gjv.2_Intron|RC3H1_uc010pmt.1_Intron	NM_172071	NP_742068			roquin						cytoplasmic mRNA processing body assembly|negative regulation of activated T cell proliferation|negative regulation of B cell proliferation|negative regulation of germinal center formation|negative regulation of T-helper cell differentiation|nuclear-transcribed mRNA catabolic process|regulation of mRNA stability|regulation of T cell receptor signaling pathway	cytoplasmic mRNA processing body|stress granule	mRNA 3'-UTR binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	174090014	174090015	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174090014_174090015delTT								RC3H1 (127804 upstream) : RABGAP1L (38619 downstream)																																			---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174272417	174272417	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174272417delA	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	174321293	174321294	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174321293_174321294delTC	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	174914708	174914708	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174914708delT	uc001gjx.2	+						RABGAP1L_uc001gkb.3_Intron|RABGAP1L_uc001gkc.3_Intron|RABGAP1L_uc001gkd.3_Intron|RABGAP1L_uc001gke.3_Intron|RABGAP1L_uc001gkf.2_Intron|RABGAP1L_uc001gkg.2_Intron|RABGAP1L_uc001gkh.3_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
TNN	63923	broad.mit.edu	37	1	175080160	175080160	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175080160delA	uc001gkl.1	+							NM_022093	NP_071376			tenascin N precursor						cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)														---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	175958359	175958359	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175958359delA	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_Intron|RFWD2_uc001gkt.1_Intron	NM_022457	NP_071902			ring finger and WD repeat domain 2 isoform a						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	176145160	176145160	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176145160delA	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc001gkt.1_Intron	NM_022457	NP_071902			ring finger and WD repeat domain 2 isoform a						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
PAPPA2	60676	broad.mit.edu	37	1	176590810	176590810	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176590810delT	uc001gkz.2	+						PAPPA2_uc001gky.1_Intron|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																		---	---	---	---
RASAL2	9462	broad.mit.edu	37	1	178305057	178305058	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178305057_178305058delAA	uc001glq.2	+						RASAL2_uc009wxb.2_Intron	NM_170692	NP_733793			RAS protein activator like 2 isoform 2						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	178589967	178589968	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178589967_178589968delAG								C1orf220 (71943 upstream) : RALGPS2 (104332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	178688275	178688275	+	IGR	DEL	G	-	-	rs928155	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178688275delG								C1orf220 (170251 upstream) : RALGPS2 (6025 downstream)																																			---	---	---	---
RALGPS2	55103	broad.mit.edu	37	1	178885457	178885457	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178885457delT	uc001glz.2	+						RALGPS2_uc010pnb.1_Intron	NM_152663	NP_689876			Ral GEF with PH domain and SH3 binding motif 2						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity|protein binding				0																		---	---	---	---
TDRD5	163589	broad.mit.edu	37	1	179604781	179604781	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179604781delT	uc001gnf.1	+						TDRD5_uc010pnp.1_Intron|TDRD5_uc001gnh.1_Intron	NM_173533	NP_775804			tudor domain containing 5						DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	180508792	180508792	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180508792delT								ACBD6 (36770 upstream) : XPR1 (92354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	180562696	180562696	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180562696delA								ACBD6 (90674 upstream) : XPR1 (38450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	180571321	180571321	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180571321delA								ACBD6 (99299 upstream) : XPR1 (29825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	180595550	180595550	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180595550delA								ACBD6 (123528 upstream) : XPR1 (5596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	181028303	181028303	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	182102240	182102240	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182102240delT								ZNF648 (71393 upstream) : GLUL (249429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182263543	182263543	+	IGR	DEL	A	-	-	rs35039146		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182263543delA								ZNF648 (232696 upstream) : GLUL (88126 downstream)																																			---	---	---	---
C1orf14	81626	broad.mit.edu	37	1	182908681	182908681	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182908681delA	uc001gpu.2	-	4	1063	c.778delT	c.(778-780)TATfs	p.Y260fs	C1orf14_uc001gpv.2_Frame_Shift_Del_p.Y141fs|C1orf14_uc010pnz.1_Frame_Shift_Del_p.Y118fs|C1orf14_uc001gpw.2_5'UTR	NM_030933	NP_112195	Q9BZQ2	SHP1L_HUMAN	chromosome 1 open reading frame 14	332											0				Colorectal(1306;1.64e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00267)														---	---	---	---
LAMC1	3915	broad.mit.edu	37	1	183063519	183063519	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183063519delT	uc001gpy.3	+						LAMC1_uc001gpx.2_Intron	NM_002293	NP_002284			laminin, gamma 1 precursor						axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent			ovary(3)|large_intestine(1)|kidney(1)	5					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
RGL1	23179	broad.mit.edu	37	1	183775705	183775705	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183775705delT	uc001gqo.2	+						RGL1_uc010pof.1_Intron|RGL1_uc001gqm.2_Intron|RGL1_uc010pog.1_Intron|RGL1_uc010poh.1_Intron|RGL1_uc010poi.1_Intron	NM_015149	NP_055964			ral guanine nucleotide dissociation						cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	protein binding|Ral guanyl-nucleotide exchange factor activity			breast(5)|ovary(4)|lung(2)	11																		---	---	---	---
GLT25D2	23127	broad.mit.edu	37	1	183972513	183972514	+	Intron	INS	-	C	C	rs148438872	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183972513_183972514insC	uc001gqr.2	-						GLT25D2_uc010poj.1_Intron|GLT25D2_uc001gqs.2_Intron	NM_015101	NP_055916			glycosyltransferase 25 domain containing 2						lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	184147036	184147036	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184147036delT								TSEN15 (103695 upstream) : C1orf21 (209114 downstream)																																			---	---	---	---
C1orf21	81563	broad.mit.edu	37	1	184562767	184562767	+	Intron	DEL	T	-	-	rs56072514		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184562767delT	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	184622655	184622656	+	IGR	DEL	GT	-	-	rs112791294		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184622655_184622656delGT								C1orf21 (24500 upstream) : EDEM3 (36971 downstream)																																			---	---	---	---
EDEM3	80267	broad.mit.edu	37	1	184717583	184717583	+	Intron	DEL	A	-	-	rs143405729		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184717583delA	uc010pok.1	-						EDEM3_uc010pol.1_Intron|EDEM3_uc010pom.1_Intron|EDEM3_uc001gqy.2_Intron	NM_025191	NP_079467			ER degradation enhancer, mannosidase alpha-like						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding			skin(1)	1																		---	---	---	---
FAM129A	116496	broad.mit.edu	37	1	184920650	184920650	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184920650delT	uc001gra.2	-						FAM129A_uc009wyh.1_Intron|FAM129A_uc009wyi.1_Intron	NM_052966	NP_443198			niban protein isoform 2						negative regulation of protein phosphorylation|positive regulation of protein phosphorylation|positive regulation of translation|response to endoplasmic reticulum stress	cytoplasm|nucleus|plasma membrane				ovary(3)|skin(1)	4																		---	---	---	---
C1orf26	54823	broad.mit.edu	37	1	185162600	185162600	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185162600delT	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988			hypothetical protein LOC54823												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	185622973	185622973	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185622973delT								IVNS1ABP (336512 upstream) : HMCN1 (80710 downstream)																																			---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185882149	185882149	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185882149delT	uc001grq.1	+							NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186063360	186063362	+	Intron	DEL	TTG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186063360_186063362delTTG	uc001grq.1	+							NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186076225	186076225	+	Intron	DEL	T	-	-	rs79076408		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186076225delT	uc001grq.1	+							NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186089103	186089103	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186089103delT	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	186341675	186341675	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186341675delA	uc001grv.2	-						TPR_uc010pop.1_Intron	NM_003292	NP_003283			nuclear pore complex-associated protein TPR						carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)				T	NTRK1	papillary thyroid								---	---	---	---
PLA2G4A	5321	broad.mit.edu	37	1	186899204	186899205	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186899204_186899205delGA	uc001gsc.2	+						PLA2G4A_uc010pos.1_Intron	NM_024420	NP_077734			cytosolic phospholipase A2, group IVA						phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			lung(2)|breast(1)	3					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	187521497	187521497	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187521497delA								PLA2G4A (563392 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189767877	189767877	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189767877delA								None (None upstream) : FAM5C (298920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	190045714	190045714	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190045714delT								None (None upstream) : FAM5C (21083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	190618806	190618817	+	IGR	DEL	TTCCTTCCTTCT	-	-	rs150632663		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190618806_190618817delTTCCTTCCTTCT								FAM5C (172047 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192053588	192053588	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192053588delT								None (None upstream) : RGS18 (74004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192064232	192064232	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192064232delT								None (None upstream) : RGS18 (63360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192113665	192113665	+	IGR	DEL	A	-	-	rs34725257		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192113665delA								None (None upstream) : RGS18 (13927 downstream)																																			---	---	---	---
RGS18	64407	broad.mit.edu	37	1	192128012	192128012	+	Intron	DEL	A	-	-	rs28417375		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
UCHL5	51377	broad.mit.edu	37	1	193018711	193018711	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193018711delT	uc001gsm.2	-						UCHL5_uc001gsn.2_Intron|UCHL5_uc001gso.2_Intron|UCHL5_uc010pov.1_Intron|UCHL5_uc001gsp.2_Intron|UCHL5_uc001gsq.2_Intron|UCHL5_uc010pow.1_Intron|UCHL5_uc010pox.1_Intron	NM_015984	NP_057068			ubiquitin carboxyl-terminal hydrolase L5						DNA recombination|DNA repair|protein deubiquitination|regulation of proteasomal protein catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytosol|Ino80 complex|proteasome complex	endopeptidase inhibitor activity|omega peptidase activity|proteasome binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	193513000	193513000	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193513000delA								CDC73 (289060 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193738542	193738542	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193738542delT								CDC73 (514602 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193802090	193802105	+	IGR	DEL	TCCCTCCTTCCCTCCC	-	-	rs71522475		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193802090_193802105delTCCCTCCTTCCCTCCC								CDC73 (578150 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194231206	194231206	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194231206delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195222170	195222170	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195222170delA								None (None upstream) : KCNT2 (972743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195333542	195333544	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195333542_195333544delAAA								None (None upstream) : KCNT2 (861369 downstream)																																			---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196288816	196288817	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196288816_196288817insT	uc001gtd.1	-						KCNT2_uc009wyt.1_Intron|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc001gth.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																		---	---	---	---
CFHR5	81494	broad.mit.edu	37	1	196951808	196951808	+	Intron	DEL	A	-	-	rs71993683		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196951808delA	uc001gts.3	+							NM_030787	NP_110414			complement factor H-related 5 precursor						complement activation, alternative pathway	extracellular region				breast(1)|skin(1)	2																		---	---	---	---
CFHR5	81494	broad.mit.edu	37	1	196974025	196974025	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196974025delT	uc001gts.3	+							NM_030787	NP_110414			complement factor H-related 5 precursor						complement activation, alternative pathway	extracellular region				breast(1)|skin(1)	2																		---	---	---	---
ASPM	259266	broad.mit.edu	37	1	197107384	197107384	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197107384delG	uc001gtu.2	-						ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606			asp (abnormal spindle)-like, microcephaly						mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6																		---	---	---	---
ZBTB41	360023	broad.mit.edu	37	1	197163159	197163159	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197163159delT	uc001gtx.1	-						ZBTB41_uc009wyz.1_Intron	NM_194314	NP_919290			zinc finger and BTB domain containing 41						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197341842	197341843	+	Intron	INS	-	A	A	rs144652368		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197341842_197341843insA	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron|CRB1_uc010ppc.1_Intron|CRB1_uc010ppd.1_Intron	NM_201253	NP_957705			crumbs homolog 1 precursor						cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197411573	197411573	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197411573delA	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Intron|CRB1_uc001gub.1_3'UTR	NM_201253	NP_957705			crumbs homolog 1 precursor						cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9																		---	---	---	---
NEK7	140609	broad.mit.edu	37	1	198247004	198247004	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198247004delT	uc001gun.3	+							NM_133494	NP_598001			NIMA-related kinase 7							cytoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|lung(1)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	198600058	198600058	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198600058delA								ATP6V1G3 (89983 upstream) : PTPRC (8079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199379592	199379592	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199379592delT								MIR181A1 (551310 upstream) : NR5A2 (617178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199383321	199383322	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199383321_199383322delAA								MIR181A1 (555039 upstream) : NR5A2 (613448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199631300	199631300	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199631300delA								MIR181A1 (803018 upstream) : NR5A2 (365470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	200448142	200448142	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200448142delA								ZNF281 (68976 upstream) : KIF14 (72483 downstream)																																			---	---	---	---
KIF14	9928	broad.mit.edu	37	1	200584999	200584999	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200584999delT	uc010ppk.1	-						KIF14_uc010ppj.1_Intron	NM_014875	NP_055690			kinesin family member 14						microtubule-based movement	cytoplasm|microtubule|nucleus|spindle	ATP binding|microtubule motor activity|protein binding			breast(3)|ovary(2)|skin(2)	7																		---	---	---	---
DDX59	83479	broad.mit.edu	37	1	200627887	200627887	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200627887delA	uc009wzk.2	-						DDX59_uc010ppl.1_Intron	NM_001031725	NP_001026895			DEAD (Asp-Glu-Ala-Asp) box polypeptide 59							intracellular	ATP binding|ATP-dependent helicase activity|metal ion binding|RNA binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	200643975	200643975	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200643975delT								DDX59 (4849 upstream) : CAMSAP1L1 (64711 downstream)																																			---	---	---	---
CAMSAP1L1	23271	broad.mit.edu	37	1	200822407	200822407	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200822407delA	uc001gvl.2	+	14	3910	c.3640delA	c.(3640-3642)AAAfs	p.K1214fs	CAMSAP1L1_uc001gvk.2_Frame_Shift_Del_p.K1203fs|CAMSAP1L1_uc001gvm.2_Frame_Shift_Del_p.K1187fs	NM_203459	NP_982284	Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein	1214						cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4																		---	---	---	---
CACNA1S	779	broad.mit.edu	37	1	201047355	201047355	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201047355delT	uc001gvv.2	-							NM_000069	NP_000060			calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
CACNA1S	779	broad.mit.edu	37	1	201077234	201077237	+	Intron	DEL	TTTT	-	-	rs111404229		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201077234_201077237delTTTT	uc001gvv.2	-							NM_000069	NP_000060			calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201624977	201624977	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201624977delT	uc001gwu.2	+							NM_020443	NP_065176			neuron navigator 1						cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	201997689	201997689	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201997689delA								ELF3 (11383 upstream) : GPR37L1 (94340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	202028052	202028052	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202028052delT								ELF3 (41746 upstream) : GPR37L1 (63977 downstream)																																			---	---	---	---
UBE2T	29089	broad.mit.edu	37	1	202300886	202300886	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202300886delA	uc001gxx.3	-	7						NM_014176	NP_054895			ubiquitin-conjugating enzyme E2T						DNA repair|protein K11-linked ubiquitination|protein K27-linked ubiquitination|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|protein K63-linked ubiquitination	nucleoplasm	ATP binding|ubiquitin-protein ligase activity				0																		---	---	---	---
KDM5B	10765	broad.mit.edu	37	1	202748607	202748607	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202748607delA	uc001gyf.2	-						KDM5B_uc009xag.2_Intron|KDM5B_uc001gyg.1_Intron	NM_006618	NP_006609			jumonji, AT rich interactive domain 1B						negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	202784593	202784593	+	IGR	DEL	T	-	-	rs71709459		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202784593delT								KDM5B (7044 upstream) : LOC148709 (46289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203543516	203543516	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203543516delT								OPTC (65439 upstream) : ATP2B4 (52412 downstream)																																			---	---	---	---
REN	5972	broad.mit.edu	37	1	204137579	204137581	+	5'Flank	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204137579_204137581delTTT	uc001haq.2	-							NM_000537	NP_000528			renin preproprotein						angiotensin maturation|regulation of MAPKKK cascade	extracellular space|membrane	aspartic-type endopeptidase activity			skin(3)|central_nervous_system(1)	4	all_cancers(21;0.00965)|Breast(84;0.116)|all_epithelial(62;0.157)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)		Aliskiren(DB01258)|Remikiren(DB00212)													---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204414335	204414338	+	Intron	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204414335_204414338delAAAA	uc001haw.2	-						PIK3C2B_uc010pqv.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	204774411	204774411	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204774411delT								MDM4 (96750 upstream) : NFASC (23371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	205050907	205050907	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205050907delA								CNTN2 (3771 upstream) : TMEM81 (1351 downstream)																																			---	---	---	---
DSTYK	25778	broad.mit.edu	37	1	205181200	205181201	+	5'Flank	INS	-	AT	AT	rs138217803	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205181200_205181201insAT	uc001hbw.2	-						DSTYK_uc001hbx.2_5'Flank	NM_015375	NP_056190			receptor interacting protein kinase 5 isoform 1							cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	205259736	205259736	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205259736delA								TMCC2 (17266 upstream) : NUAK2 (11457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	205431018	205431018	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205431018delA	uc001hco.1	+											Homo sapiens cDNA FLJ38314 fis, clone FCBBF3022765.																														---	---	---	---
CTSE	1510	broad.mit.edu	37	1	206331336	206331337	+	3'UTR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206331336_206331337delAC	uc001hdu.2	+	9					CTSE_uc001hdv.2_3'UTR|CTSE_uc010prs.1_3'UTR	NM_001910	NP_001901			cathepsin E isoform a preproprotein						antigen processing and presentation of exogenous peptide antigen via MHC class II|digestion|proteolysis	endosome	aspartic-type endopeptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.0754)															---	---	---	---
SRGAP2	23380	broad.mit.edu	37	1	206583141	206583144	+	Intron	DEL	AAAA	-	-	rs113368415		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206583141_206583144delAAAA	uc001hdy.2	+						SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron|SRGAP2_uc010prv.1_Intron	NM_015326	NP_056141			SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)																	---	---	---	---
IKBKE	9641	broad.mit.edu	37	1	206664440	206664440	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206664440delT	uc001hdz.1	+						IKBKE_uc009xbv.1_Intron|IKBKE_uc001hea.1_Intron	NM_014002	NP_054721			IKK-related kinase epsilon						DNA damage response, signal transduction resulting in induction of apoptosis|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane|PML body	ATP binding|IkappaB kinase activity|NF-kappaB-inducing kinase activity|protein binding			ovary(3)|lung(3)|central_nervous_system(1)|skin(1)	8	Breast(84;0.137)															OREG0014171	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RASSF5	83593	broad.mit.edu	37	1	206696345	206696345	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206696345delA	uc001hed.2	+						RASSF5_uc001hec.1_Intron|RASSF5_uc001hee.2_Intron	NM_182663	NP_872604			Ras association (RalGDS/AF-6) domain family 5						apoptosis|intracellular signal transduction	cytoplasm|microtubule	metal ion binding|protein binding			ovary(1)	1	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
DYRK3	8444	broad.mit.edu	37	1	206809454	206809454	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206809454delG	uc001hej.2	+						DYRK3_uc001hek.2_Intron|DYRK3_uc001hei.2_Intron	NM_003582	NP_003573			dual-specificity tyrosine-(Y)-phosphorylation						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	207273438	207273439	+	IGR	DEL	TA	-	-	rs72516622		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207273438_207273439delTA								C4BPB (103 upstream) : C4BPA (4072 downstream)																																			---	---	---	---
CR1	1378	broad.mit.edu	37	1	207675264	207675264	+	Intron	DEL	T	-	-	rs71818668		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207675264delT	uc001hfy.2	+						CR1_uc009xcl.1_Intron|CR1_uc001hfx.2_Intron|CR1_uc010psg.1_Intron|CR1_uc009xcj.1_Intron|CR1_uc009xck.1_Intron	NM_000573	NP_000564			complement receptor 1 isoform F precursor						complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3																		---	---	---	---
CR1	1378	broad.mit.edu	37	1	207685948	207685948	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207685948delT	uc001hfy.2	+						CR1_uc009xcl.1_Intron|CR1_uc001hfx.2_Intron|CR1_uc009xcj.1_Intron|CR1_uc009xck.1_Intron	NM_000573	NP_000564			complement receptor 1 isoform F precursor						complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3																		---	---	---	---
CR1	1378	broad.mit.edu	37	1	207804107	207804107	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207804107delT	uc001hfy.2	+						CR1_uc001hfx.2_Intron	NM_000573	NP_000564			complement receptor 1 isoform F precursor						complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3																		---	---	---	---
CR1L	1379	broad.mit.edu	37	1	207821520	207821523	+	Intron	DEL	ACAC	-	-	rs67025648		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207821520_207821523delACAC	uc001hga.3	+						CR1L_uc001hfz.2_Intron	NM_175710	NP_783641			complement component (3b/4b) receptor 1-like							cytoplasm|extracellular region|membrane					0																		---	---	---	---
CR1L	1379	broad.mit.edu	37	1	207877673	207877673	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207877673delA	uc001hga.3	+						CR1L_uc001hfz.2_Intron|CR1L_uc001hgb.1_Intron	NM_175710	NP_783641			complement component (3b/4b) receptor 1-like							cytoplasm|extracellular region|membrane					0																		---	---	---	---
PLXNA2	5362	broad.mit.edu	37	1	208235418	208235418	+	Intron	DEL	A	-	-	rs77592655		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208235418delA	uc001hgz.2	-							NM_025179	NP_079455			plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	208793161	208793161	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208793161delA								PLXNA2 (375496 upstream) : LOC642587 (809007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	208959275	208959275	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208959275delA								PLXNA2 (541610 upstream) : LOC642587 (642893 downstream)																																			---	---	---	---
G0S2	50486	broad.mit.edu	37	1	209846652	209846652	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209846652delA	uc001hhi.3	+							NM_015714	NP_056529			G0/G1switch 2						cell cycle						0				OV - Ovarian serous cystadenocarcinoma(81;0.041)														---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	210945373	210945373	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210945373delA	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872			potassium voltage-gated channel, subfamily H,						myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)														---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	211093539	211093539	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211093539delA	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872			potassium voltage-gated channel, subfamily H,						myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)														---	---	---	---
RCOR3	55758	broad.mit.edu	37	1	211433416	211433416	+	5'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211433416delT	uc001hig.2	+	1					RCOR3_uc010psv.1_Intron|RCOR3_uc001hie.2_Intron|RCOR3_uc010psw.1_Intron|RCOR3_uc001hif.2_Intron	NM_018254	NP_060724			REST corepressor 3 isoform d						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	211814459	211814459	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211814459delA	uc001hip.1	+											full-length cDNA clone CS0DK012YI08 of HeLa cells Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
TMEM206	55248	broad.mit.edu	37	1	212563772	212563772	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212563772delA	uc001hjc.3	-						TMEM206_uc010pte.1_Intron	NM_018252	NP_060722			transmembrane protein 206							integral to membrane				breast(1)	1				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)														---	---	---	---
VASH2	79805	broad.mit.edu	37	1	213132244	213132244	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213132244delT	uc001hjy.2	+						VASH2_uc001hju.2_Intron|VASH2_uc001hjv.2_Intron|VASH2_uc001hjx.2_Intron|VASH2_uc010ptn.1_Intron|VASH2_uc001hjw.2_Intron	NM_001136475	NP_001129947			vasohibin 2 isoform 3						positive regulation of angiogenesis|positive regulation of endothelial cell proliferation	cytoplasm					0				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	213209587	213209589	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213209587_213209589delTTT								ANGEL2 (20419 upstream) : RPS6KC1 (14999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	213997069	213997070	+	Intron	INS	-	CACACA	CACACA	rs145197951	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213997069_213997070insCACACA	uc001hkf.1	-											Homo sapiens cDNA FLJ34932 fis, clone NT2RP7005631.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	214451096	214451097	+	IGR	DEL	AC	-	-	rs34184221		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214451096_214451097delAC								PROX1 (241336 upstream) : SMYD2 (3468 downstream)																																			---	---	---	---
PTPN14	5784	broad.mit.edu	37	1	214582213	214582213	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214582213delA	uc001hkk.1	-						PTPN14_uc010pty.1_Intron	NM_005401	NP_005392			protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	214757818	214757818	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214757818delT								PTPN14 (33176 upstream) : CENPF (18714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	214998516	214998517	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214998516_214998517insT								CENPF (160604 upstream) : KCNK2 (180368 downstream)																																			---	---	---	---
KCNK2	3776	broad.mit.edu	37	1	215342531	215342531	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215342531delT	uc001hkq.2	+						KCNK2_uc001hko.2_Intron|KCNK2_uc009xdm.2_Intron|KCNK2_uc001hkp.2_Intron|KCNK2_uc010pua.1_Intron|KCNK2_uc001hkr.3_Intron	NM_001017425	NP_001017425			potassium channel, subfamily K, member 2 isoform								outward rectifier potassium channel activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	215476355	215476356	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215476355_215476356delAA								KCNK2 (65920 upstream) : KCTD3 (264379 downstream)																																			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215814143	215814144	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215814143_215814144delAA	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215840097	215840097	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215840097delA	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	216778722	216778722	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216778722delA	uc001hkw.1	-						ESRRG_uc001hky.1_Intron|ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron|ESRRG_uc001hkx.1_Intron|ESRRG_uc009xdo.1_Intron|ESRRG_uc001hle.1_Intron	NM_001438	NP_001429			estrogen-related receptor gamma isoform 1						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	217522877	217522877	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217522877delT								ESRRG (211780 upstream) : GPATCH2 (80957 downstream)																																			---	---	---	---
GPATCH2	55105	broad.mit.edu	37	1	217801060	217801060	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217801060delA	uc001hlf.1	-						GPATCH2_uc001hlg.3_Intron	NM_018040	NP_060510			G patch domain containing 2							intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)														---	---	---	---
TGFB2	7042	broad.mit.edu	37	1	218520021	218520021	+	5'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218520021delT	uc001hlm.2	+	1					TGFB2_uc001hll.2_5'UTR|TGFB2_uc001hln.2_5'UTR|TGFB2_uc010pue.1_RNA|TGFB2_uc001hlo.2_RNA	NM_003238	NP_003229			transforming growth factor, beta 2 isoform 2						activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway	axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen	beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding				0				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	218982418	218982418	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218982418delT								TGFB2 (364459 upstream) : LYPLAL1 (364774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219589900	219589900	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219589900delT								LYPLAL1 (203694 upstream) : SLC30A10 (268869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219799272	219799272	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219799272delA								LYPLAL1 (413066 upstream) : SLC30A10 (59497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	220605352	220605353	+	IGR	INS	-	CT	CT	rs144538242	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220605352_220605353insCT								RAB3GAP2 (159509 upstream) : MARK1 (96215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221001465	221001465	+	5'Flank	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221001465delC	uc001hmu.2	+											Homo sapiens cDNA clone IMAGE:5298101.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	221208272	221208273	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221208272_221208273delGT								HLX (149874 upstream) : LOC400804 (294997 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221522932	221522932	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221522932delA								LOC400804 (13294 upstream) : DUSP10 (351834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221790484	221790484	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221790484delT								LOC400804 (280846 upstream) : DUSP10 (84282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222048636	222048636	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222048636delT								DUSP10 (133175 upstream) : HHIPL2 (646966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222285354	222285354	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222285354delT								DUSP10 (369893 upstream) : HHIPL2 (410248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222606231	222606231	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222606231delA								DUSP10 (690770 upstream) : HHIPL2 (89371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	223214105	223214105	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223214105delT								DISP1 (34770 upstream) : TLR5 (69479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	223222802	223222803	+	IGR	DEL	TG	-	-	rs72020592		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223222802_223222803delTG								DISP1 (43467 upstream) : TLR5 (60781 downstream)																																			---	---	---	---
FBXO28	23219	broad.mit.edu	37	1	224339744	224339744	+	Intron	DEL	A	-	-	rs35662577		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224339744delA	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	224412853	224412853	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224412853delT								DEGS1 (31713 upstream) : NVL (2184 downstream)																																			---	---	---	---
NVL	4931	broad.mit.edu	37	1	224485290	224485290	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224485290delA	uc001hok.2	-						NVL_uc001hol.2_Intron|NVL_uc010pvd.1_Intron|NVL_uc010pve.1_Intron|NVL_uc010pvf.1_Intron	NM_002533	NP_002524			nuclear VCP-like isoform 1							aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	224525544	224525546	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224525544_224525546delTTT								NVL (7672 upstream) : CNIH4 (19049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	224743881	224743882	+	IGR	DEL	TT	-	-	rs112250509		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224743881_224743882delTT								WDR26 (122149 upstream) : CNIH3 (60297 downstream)																																			---	---	---	---
DNAH14	127602	broad.mit.edu	37	1	225311428	225311428	+	Intron	DEL	T	-	-	rs111645895		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225311428delT	uc001how.2	+							NM_001373	NP_001364			dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
LBR	3930	broad.mit.edu	37	1	225595602	225595602	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225595602delA	uc001hoy.2	-						LBR_uc001hoz.2_Intron|LBR_uc001hpa.1_Intron	NM_002296	NP_002287			lamin B receptor						cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	225919146	225919146	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225919146delT	uc001hpe.1	+											Homo sapiens cDNA FLJ42062 fis, clone SYNOV2005673.																														---	---	---	---
ACBD3	64746	broad.mit.edu	37	1	226347062	226347062	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226347062delA	uc001hpy.2	-							NM_022735	NP_073572			acyl-Coenzyme A binding domain containing 3						steroid biosynthetic process|transport	Golgi membrane|integral to membrane|mitochondrion	fatty-acyl-CoA binding|protein binding				0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.121)														---	---	---	---
LIN9	286826	broad.mit.edu	37	1	226465694	226465694	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226465694delT	uc001hqa.2	-						LIN9_uc001hqb.2_Intron|LIN9_uc001hqc.2_Intron|LIN9_uc009xel.1_Intron	NM_173083	NP_775106			lin-9 homolog						cell cycle|DNA replication	nucleoplasm					0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)														---	---	---	---
C1orf95	375057	broad.mit.edu	37	1	226759253	226759253	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226759253delT	uc010pvn.1	+							NM_001003665	NP_001003665			hypothetical protein LOC375057							integral to membrane				ovary(1)	1	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)														---	---	---	---
ITPKB	3707	broad.mit.edu	37	1	226855528	226855529	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226855528_226855529delTG	uc010pvo.1	-							NM_002221	NP_002212			1D-myo-inositol-trisphosphate 3-kinase B								ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)																---	---	---	---
PSEN2	5664	broad.mit.edu	37	1	227057753	227057753	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227057753delA	uc009xeo.1	+						PSEN2_uc009xep.1_5'Flank	NM_000447	NP_000438			presenilin 2 isoform 1						amyloid precursor protein catabolic process|anti-apoptosis|apoptosis|beta-amyloid metabolic process|calcium ion transport|induction of apoptosis by extracellular signals|intracellular signal transduction|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity	apical plasma membrane|axon|cell cortex|cell surface|centrosome|ciliary rootlet|dendritic shaft|endoplasmic reticulum membrane|Golgi membrane|growth cone|integral to plasma membrane|kinetochore|lysosomal membrane|membrane raft|mitochondrial inner membrane|neuromuscular junction|neuronal cell body|nuclear inner membrane|perinuclear region of cytoplasm|Z disc	aspartic-type endopeptidase activity|protein binding			lung(2)	2		Prostate(94;0.0771)																---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227207603	227207603	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227207603delT	uc001hqr.2	-						CDC42BPA_uc001hqq.2_Intron|CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron|CDC42BPA_uc001hqp.2_Intron|CDC42BPA_uc001hqt.2_Intron	NM_003607	NP_003598			CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227214936	227214936	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227214936delA	uc001hqr.2	-						CDC42BPA_uc001hqq.2_Intron|CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron|CDC42BPA_uc001hqp.2_Intron|CDC42BPA_uc001hqt.2_Intron|CDC42BPA_uc001hqu.1_Intron	NM_003607	NP_003598			CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
ZNF678	339500	broad.mit.edu	37	1	227867980	227867981	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227867980_227867981delGT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	228104039	228104040	+	IGR	DEL	AT	-	-	rs36005011		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228104039_228104040delAT								PRSS38 (69870 upstream) : WNT9A (5125 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229131073	229131073	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229131073delA								RHOU (248664 upstream) : RAB4A (275806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229193791	229193791	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229193791delT								RHOU (311382 upstream) : RAB4A (213088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230652559	230652560	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230652559_230652560insT								PGBD5 (139192 upstream) : COG2 (125642 downstream)																																			---	---	---	---
GNPAT	8443	broad.mit.edu	37	1	231384314	231384314	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231384314delA	uc001hup.3	+						GNPAT_uc009xfo.1_Intron|GNPAT_uc009xfp.2_Intron	NM_014236	NP_055051			glyceronephosphate O-acyltransferase						ether lipid biosynthetic process|fatty acid metabolic process|organ morphogenesis	peroxisomal matrix|peroxisomal membrane	glycerone-phosphate O-acyltransferase activity			ovary(3)|breast(1)	4	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)																---	---	---	---
C1orf124	83932	broad.mit.edu	37	1	231477078	231477078	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231477078delT	uc001hur.2	+						C1orf124_uc001hus.2_Intron|C1orf124_uc001hut.2_Intron	NM_032018	NP_114407			hypothetical protein LOC83932 isoform a						DNA repair	nuclear speck	DNA binding|metal ion binding				0	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	231493394	231493394	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231493394delT								C1orf124 (3406 upstream) : EGLN1 (6103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	233532399	233532408	+	IGR	DEL	CACATACACT	-	-	rs138085878		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233532399_233532408delCACATACACT								KIAA1804 (11506 upstream) : KCNK1 (217342 downstream)																																			---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234456146	234456146	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234456146delA	uc001hwa.1	+						SLC35F3_uc001hvy.1_Intron	NM_173508	NP_775779			solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
TARBP1	6894	broad.mit.edu	37	1	234531127	234531127	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234531127delA	uc001hwd.2	-							NM_005646	NP_005637			TAR RNA binding protein 1						regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)|skin(1)	3	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	234755793	234755793	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234755793delA								IRF2BP2 (10522 upstream) : TOMM20 (516867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	234835364	234835364	+	IGR	DEL	A	-	-	rs35338033		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234835364delA								IRF2BP2 (90093 upstream) : TOMM20 (437296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	234854001	234854002	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234854001_234854002delAA	uc001hwi.1	+											Homo sapiens cDNA FLJ46067 fis, clone TESOP2002110.																														---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235378863	235378866	+	Intron	DEL	TGTG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235378863_235378866delTGTG	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_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)															---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235464025	235464025	+	Intron	DEL	T	-	-	rs111362486		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235464025delT	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwu.1_Intron	NM_016374	NP_057458			AT rich interactive domain 4B isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)															---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235486200	235486201	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235486200_235486201delGA	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwu.1_Intron	NM_016374	NP_057458			AT rich interactive domain 4B isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)															---	---	---	---
GGPS1	9453	broad.mit.edu	37	1	235505913	235505913	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235505913delA	uc001hwv.2	+	4	813	c.729delA	c.(727-729)ATAfs	p.I243fs	GGPS1_uc001hww.2_Frame_Shift_Del_p.I243fs|GGPS1_uc001hwx.2_Frame_Shift_Del_p.I189fs|GGPS1_uc001hwy.2_Frame_Shift_Del_p.I243fs	NM_001037277	NP_001032354	O95749	GGPPS_HUMAN	geranylgeranyl diphosphate synthase 1 isoform A	243					cholesterol biosynthetic process|isoprenoid biosynthetic process	cytosol|soluble fraction	dimethylallyltranstransferase activity|farnesyltranstransferase activity|geranyltranstransferase activity|metal ion binding			central_nervous_system(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;1.39e-05)															---	---	---	---
TBCE	6905	broad.mit.edu	37	1	235558864	235558865	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235558864_235558865delTT	uc001hwz.1	+						TBCE_uc010pxq.1_Intron|TBCE_uc001hxa.1_Intron|TBCE_uc010pxr.1_Intron|TBCE_uc001hxb.1_Intron	NM_003193	NP_003184			beta-tubulin cofactor E						'de novo' posttranslational protein folding|post-chaperonin tubulin folding pathway	cytoplasm|microtubule|nucleus|plasma membrane	chaperone binding				0	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;2.56e-05)															---	---	---	---
TBCE	6905	broad.mit.edu	37	1	235605324	235605325	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235605324_235605325delTT	uc001hwz.1	+						TBCE_uc001hxa.1_Intron|TBCE_uc010pxr.1_Intron|TBCE_uc001hxb.1_Intron	NM_003193	NP_003184			beta-tubulin cofactor E						'de novo' posttranslational protein folding|post-chaperonin tubulin folding pathway	cytoplasm|microtubule|nucleus|plasma membrane	chaperone binding				0	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;2.56e-05)															---	---	---	---
B3GALNT2	148789	broad.mit.edu	37	1	235643717	235643717	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235643717delA	uc001hxc.2	-						B3GALNT2_uc001hxd.1_Intron	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	235843730	235843730	+	Intron	DEL	T	-	-	rs111680478		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235843730delT	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	235855688	235855688	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235855688delT	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	235875502	235875502	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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				---	---	---	---
Unknown	0	broad.mit.edu	37	1	236075518	236075518	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236075518delT								LYST (28578 upstream) : NID1 (63623 downstream)																																			---	---	---	---
NID1	4811	broad.mit.edu	37	1	236180604	236180604	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236180604delT	uc001hxo.2	-						NID1_uc009xgd.2_Intron	NM_002508	NP_002499			nidogen 1 precursor						cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	236272585	236272585	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236272585delA								NID1 (44104 upstream) : GPR137B (33247 downstream)																																			---	---	---	---
ERO1LB	56605	broad.mit.edu	37	1	236393400	236393400	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236393400delT	uc001hxt.2	-							NM_019891	NP_063944			endoplasmic reticulum oxidoreductin 1-Lbeta						electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	236504218	236504218	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236504218delT								ERO1LB (58879 upstream) : EDARADD (53462 downstream)																																			---	---	---	---
HEATR1	55127	broad.mit.edu	37	1	236758371	236758377	+	Intron	DEL	CTTTTTG	-	-	rs141691343		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236758371_236758377delCTTTTTG	uc001hyd.1	-							NM_018072	NP_060542			protein BAP28						rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	237145043	237145043	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237145043delA								MTR (77763 upstream) : RYR2 (60659 downstream)																																			---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237392069	237392069	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237392069delA	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	237732389	237732389	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237732389delG	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	237750019	237750019	+	Intron	DEL	T	-	-	rs145371760	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237750019delT	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	237875201	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237875200_237875201delTT	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	238001367	238001367	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238001367delA								RYR2 (4079 upstream) : LOC100130331 (24108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	238019833	238019833	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238019833delA								RYR2 (22545 upstream) : LOC100130331 (5642 downstream)																																			---	---	---	---
LOC100130331	100130331	broad.mit.edu	37	1	238055780	238055781	+	Intron	DEL	AC	-	-	rs35927061		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238055780_238055781delAC	uc010pyc.1	+						ZP4_uc001hym.2_5'Flank	NR_027247				Homo sapiens mRNA; cDNA DKFZp434B2115 (from clone DKFZp434B2115).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	238273030	238273031	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238273030_238273031delAC								LOC100130331 (181413 upstream) : LOC339535 (370655 downstream)																																			---	---	---	---
LOC339535	339535	broad.mit.edu	37	1	238649467	238649468	+	5'Flank	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238649467_238649468delTT	uc001hyn.2	-							NR_015407				Homo sapiens cDNA clone IMAGE:5186761.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	238846632	238846633	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238846632_238846633delAC								LOC339535 (197315 upstream) : CHRM3 (703232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239001078	239001079	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239001078_239001079delTT								LOC339535 (351761 upstream) : CHRM3 (548786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239363360	239363360	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239363360delA								LOC339535 (714043 upstream) : CHRM3 (186505 downstream)																																			---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	239826233	239826234	+	Intron	DEL	CC	-	-	rs10541656		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239826233_239826234delCC	uc001hyp.2	+						CHRM3_uc001hyo.1_Intron	NM_000740	NP_000731			cholinergic receptor, muscarinic 3						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)													---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240289665	240289665	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240289665delC	uc010pyd.1	+						FMN2_uc010pye.1_Intron	NM_020066	NP_064450			formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)															---	---	---	---
GREM2	64388	broad.mit.edu	37	1	240754073	240754073	+	Intron	DEL	T	-	-	rs72107251		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240754073delT	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	241504905	241504906	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241504905_241504906delAG	uc001hyv.2	-						RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915			regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)															---	---	---	---
KMO	8564	broad.mit.edu	37	1	241754064	241754067	+	Intron	DEL	ATAG	-	-	rs144025018		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241754064_241754067delATAG	uc009xgp.2	+							NM_003679	NP_003670			kynurenine 3-monooxygenase						pyridine nucleotide biosynthetic process|response to salt stress	cytosol|integral to membrane|mitochondrial outer membrane	electron carrier activity|flavin adenine dinucleotide binding|kynurenine 3-monooxygenase activity|NAD(P)H oxidase activity			ovary(2)	2	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)															---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242253557	242253557	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242253557delA	uc001hzn.1	-						PLD5_uc001hzl.3_Intron|PLD5_uc001hzm.3_Intron|PLD5_uc001hzo.1_Intron					RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	243267740	243267740	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243267740delA	uc001hzq.1	-											Homo sapiens cDNA FLJ52610 complete cds.																														---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243434124	243434125	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243434124_243434125delTT	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron	NM_006642	NP_006633			serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)														---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243578147	243578148	+	Intron	INS	-	TGTG	TGTG	rs138136583	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243578147_243578148insTGTG	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron|SDCCAG8_uc001hzx.2_Intron	NM_006642	NP_006633			serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)														---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243587523	243587523	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243587523delT	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron|SDCCAG8_uc001hzx.2_Intron	NM_006642	NP_006633			serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)														---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243643906	243643906	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243643906delA	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron|SDCCAG8_uc001hzx.2_Intron	NM_006642	NP_006633			serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)														---	---	---	---
AKT3	10000	broad.mit.edu	37	1	243830903	243830903	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243830903delA	uc001iab.1	-						AKT3_uc001hzz.1_Intron	NM_005465	NP_005456			AKT3 kinase isoform 1						signal transduction	Golgi apparatus|nucleus|plasma membrane	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|lung(1)|breast(1)|central_nervous_system(1)	4	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)															---	---	---	---
AKT3	10000	broad.mit.edu	37	1	243963292	243963292	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243963292delT	uc001iab.1	-						AKT3_uc001hzz.1_Intron	NM_005465	NP_005456			AKT3 kinase isoform 1						signal transduction	Golgi apparatus|nucleus|plasma membrane	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|lung(1)|breast(1)|central_nervous_system(1)	4	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	244088798	244088799	+	Intron	DEL	TG	-	-	rs35949199		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244088798_244088799delTG	uc001iac.2	+											Homo sapiens cDNA clone IMAGE:5244187.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	244205265	244205266	+	Intron	DEL	AC	-	-	rs144715676		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244205265_244205266delAC	uc001iac.2	+											Homo sapiens cDNA clone IMAGE:5244187.																														---	---	---	---
ZNF238	10472	broad.mit.edu	37	1	244214668	244214668	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244214668delT	uc001iae.2	+						ZNF238_uc001iad.3_5'UTR|ZNF238_uc001iaf.1_5'Flank	NM_006352	NP_006343			zinc finger protein 238 isoform 2						negative regulation of transcription from RNA polymerase II promoter|skeletal muscle tissue development	nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|pancreas(2)	5	all_cancers(71;6.42e-05)|all_epithelial(71;7e-05)|Breast(184;0.0333)|Ovarian(71;0.0619)|all_lung(81;0.089)|all_neural(11;0.101)|Lung NSC(105;0.123)		all cancers(7;1.35e-08)|GBM - Glioblastoma multiforme(7;1e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00223)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	244950962	244950962	+	IGR	DEL	A	-	-	rs78562541		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244950962delA								PPPDE1 (78630 upstream) : FAM36A (47677 downstream)																																			---	---	---	---
FAM36A	116228	broad.mit.edu	37	1	245005229	245005230	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245005229_245005230insT	uc001iar.2	+						FAM36A_uc001ias.2_Intron|FAM36A_uc001iat.2_Intron|NCRNA00201_uc001iav.2_RNA	NM_198076	NP_932342			hypothetical protein LOC116228							integral to membrane					0	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	245057661	245057661	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245057661delT								HNRNPU (29834 upstream) : EFCAB2 (75510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	245094995	245094995	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245094995delT								HNRNPU (67168 upstream) : EFCAB2 (38176 downstream)																																			---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246186844	246186844	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246186844delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246314672	246314672	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246314672delT	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
TFB2M	64216	broad.mit.edu	37	1	246711983	246711984	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246711983_246711984insA	uc001ibn.2	-						TFB2M_uc010pys.1_Intron	NM_022366	NP_071761			transcription factor B2, mitochondrial						positive regulation of transcription, DNA-dependent|transcription initiation from mitochondrial promoter	mitochondrial nucleoid	protein binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity|transcription cofactor activity			ovary(1)	1	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)															---	---	---	---
CNST	163882	broad.mit.edu	37	1	246778473	246778473	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246778473delA	uc001ibp.2	+						CNST_uc001ibo.3_Intron	NM_152609	NP_689822			hypothetical protein LOC163882 isoform 1						positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0																		---	---	---	---
AHCTF1	25909	broad.mit.edu	37	1	247062420	247062420	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247062420delT	uc001ibu.1	-						AHCTF1_uc001ibv.1_Intron|AHCTF1_uc009xgs.1_Intron	NM_015446	NP_056261			transcription factor ELYS						cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)															---	---	---	---
ZNF695	57116	broad.mit.edu	37	1	247125999	247125999	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247125999delT	uc001ibx.2	-						ZNF695_uc001ica.2_Intron|ZNF695_uc009xgt.1_Intron|ZNF695_uc001iby.2_Intron					RecName: Full=Zinc finger protein 695; AltName: Full=Zinc finger protein SBZF3;						regulation of transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)															---	---	---	---
ZNF124	7678	broad.mit.edu	37	1	247316435	247316435	+	Intron	DEL	A	-	-	rs34244288		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247316435delA	uc001ici.2	-											Homo sapiens cDNA FLJ30085 fis, clone BGGI12001714, highly similar to Homo sapiens zinc finger protein 124 (HZF-16) (ZNF124), mRNA.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)															---	---	---	---
ZNF124	7678	broad.mit.edu	37	1	247317420	247317421	+	Intron	DEL	AC	-	-	rs67344627		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247317420_247317421delAC	uc001ici.2	-											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)															---	---	---	---
C1orf150	148823	broad.mit.edu	37	1	247719791	247719791	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247719791delT	uc001idf.2	+						C1orf150_uc009xgw.2_Intron|C1orf150_uc001ida.3_Intron|C1orf150_uc001idb.3_Intron|C1orf150_uc009xgx.2_Intron	NM_145278	NP_660321			hypothetical protein LOC148823												0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0241)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	248011098	248011098	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248011098delA								OR11L1 (5900 upstream) : TRIM58 (9403 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	170921	170922	+	IGR	DEL	CG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170921_170922delCG								FAM110C (124536 upstream) : SH3YL1 (47216 downstream)																																			---	---	---	---
SH3YL1	26751	broad.mit.edu	37	2	244568	244569	+	Intron	INS	-	AAAG	AAAG	rs150436981	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:244568_244569insAAAG	uc002qvx.2	-						SH3YL1_uc002qvy.2_Intron|SH3YL1_uc002qvz.2_Intron|SH3YL1_uc002qwa.2_Intron|SH3YL1_uc010ewe.2_Intron|SH3YL1_uc002qwc.1_Intron|SH3YL1_uc002qvu.2_Intron|SH3YL1_uc002qvv.2_Intron|SH3YL1_uc002qvw.2_Intron|uc002qwb.2_5'Flank	NM_015677	NP_056492			SH3 domain containing, Ysc84-like 1 isoform 1											ovary(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	329266	329266	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:329266delA								FAM150B (40958 upstream) : TMEM18 (338709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	833758	833758	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:833758delT	uc002qwn.1	-						uc002qwo.1_Intron					Homo sapiens cDNA clone IMAGE:5174186.																														---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	971333	971334	+	Intron	INS	-	A	A	rs150179332	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:971333_971334insA	uc002qwq.2	+						SNTG2_uc002qwp.2_Intron|SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841			syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)														---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	1005410	1005411	+	Intron	DEL	AT	-	-	rs34239516		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1005410_1005411delAT	uc002qwq.2	+						SNTG2_uc002qwp.2_Intron|SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841			syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)														---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	1249054	1249054	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1249054delA	uc002qwq.2	+						SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841			syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	1585966	1585967	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1585966_1585967delCT								TPO (39468 upstream) : PXDN (49693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	1600517	1600518	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1600517_1600518delCA								TPO (54019 upstream) : PXDN (35142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	1632895	1632895	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1632895delA								TPO (86397 upstream) : PXDN (2765 downstream)																																			---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1870746	1870747	+	Intron	DEL	GA	-	-	rs34873420		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1870746_1870747delGA	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	3185496	3185496	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3185496delG								MYT1L (850451 upstream) : TSSC1 (7245 downstream)																																			---	---	---	---
TSSC1	7260	broad.mit.edu	37	2	3380777	3380777	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3380777delG	uc002qxj.2	-						TTC15_uc002qxm.1_5'Flank|TTC15_uc002qxn.1_5'Flank|TTC15_uc002qxl.1_5'Flank	NM_003310	NP_003301			tumor suppressing subtransferable candidate 1								protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)														---	---	---	---
TTC15	51112	broad.mit.edu	37	2	3478694	3478694	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3478694delA	uc002qxm.1	+						TTC15_uc002qxn.1_Intron|TTC15_uc010ewm.1_Intron	NM_016030	NP_057114			tetratricopeptide repeat domain 15								binding			ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	3921233	3921233	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3921233delT								ALLC (170975 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	3935740	3935741	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3935740_3935741insT								ALLC (185482 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4017578	4017578	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4017578delC	uc002qyg.3	-						uc002qyh.1_Intron					Homo sapiens cDNA clone IMAGE:5297607.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	4432003	4432003	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4432003delT								ALLC (681745 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4610192	4610192	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4610192delT								ALLC (859934 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4708248	4708248	+	IGR	DEL	A	-	-	rs79251280	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4708248delA								ALLC (957990 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4775624	4775626	+	IGR	DEL	AAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4775624_4775626delAAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5363878	5363879	+	IGR	INS	-	G	G	rs150905455	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5363878_5363879insG								None (None upstream) : SOX11 (468920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5521147	5521149	+	IGR	DEL	AAA	-	-	rs72555159		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5521147_5521149delAAA								None (None upstream) : SOX11 (311650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5694993	5694994	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5694993_5694994delTT								None (None upstream) : SOX11 (137805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6315488	6315488	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6315488delA								LOC400940 (187124 upstream) : CMPK2 (665015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6588481	6588481	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6588481delA								LOC400940 (460117 upstream) : CMPK2 (392022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6909172	6909173	+	Intron	DEL	GT	-	-	rs78895990		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6909172_6909173delGT	uc002qym.1	-											Homo sapiens cDNA FLJ42418 fis, clone BLADE2001987.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	7533260	7533260	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7533260delA								RNF144A (348953 upstream) : LOC339788 (529298 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	7592023	7592024	+	IGR	DEL	TT	-	-	rs112955523		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7592023_7592024delTT								RNF144A (407716 upstream) : LOC339788 (470534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8210651	8210651	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8210651delA	uc010eww.1	-											Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	8386630	8386630	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8386630delT	uc010eww.1	-						uc002qyy.1_Intron					Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	8472235	8472236	+	IGR	DEL	AA	-	-	rs113722828		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8472235_8472236delAA								LOC339788 (355258 upstream) : ID2 (347104 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8839640	8839640	+	IGR	DEL	T	-	-	rs113933559		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8839640delT								ID2 (15059 upstream) : KIDINS220 (26050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	9932173	9932174	+	IGR	INS	-	AGCAG	AGCAG	rs149677969	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9932173_9932174insAGCAG								YWHAQ (161067 upstream) : TAF1B (51397 downstream)																																			---	---	---	---
GRHL1	29841	broad.mit.edu	37	2	10101687	10101687	+	Intron	DEL	T	-	-	rs138724700		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10101687delT	uc002raa.2	+						GRHL1_uc002rab.2_Intron|GRHL1_uc002rad.2_Intron|GRHL1_uc010yjb.1_Intron	NM_198182	NP_937825			grainyhead-like 1						cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	10276089	10276089	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10276089delT								RRM2 (4543 upstream) : C2orf48 (5420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	10411594	10411596	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10411594_10411596delAAA								C2orf48 (59738 upstream) : HPCAL1 (31444 downstream)																																			---	---	---	---
ATP6V1C2	245973	broad.mit.edu	37	2	10885485	10885485	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10885485delT	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)														---	---	---	---
ATP6V1C2	245973	broad.mit.edu	37	2	10922664	10922665	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10922664_10922665delAA	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)														---	---	---	---
ROCK2	9475	broad.mit.edu	37	2	11380141	11380141	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11380141delA	uc002rbd.1	-							NM_004850	NP_004841			Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)														---	---	---	---
ROCK2	9475	broad.mit.edu	37	2	11466356	11466356	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11466356delA	uc002rbd.1	-							NM_004850	NP_004841			Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	11550331	11550332	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11550331_11550332insT								ROCK2 (65620 upstream) : E2F6 (34170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	11645976	11645976	+	IGR	DEL	A	-	-	rs148976924	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11645976delA								E2F6 (39679 upstream) : GREB1 (28266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	12122645	12122645	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12122645delT								LPIN1 (155114 upstream) : TRIB2 (734353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	12166714	12166715	+	Intron	INS	-	A	A	rs139685127	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12166714_12166715insA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12547255	12547255	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12547255delT	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	13217141	13217141	+	IGR	DEL	A	-	-	rs72233385		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13217141delA								TRIB2 (334285 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	14148036	14148036	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14148036delT								None (None upstream) : FAM84A (624820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	14397668	14397668	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14397668delA	uc002rby.2	-											Homo sapiens cDNA clone IMAGE:5263003.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	14435372	14435372	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14435372delA	uc002rby.2	-											Homo sapiens cDNA clone IMAGE:5263003.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	14488809	14488810	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14488809_14488810delGA	uc002rby.2	-											Homo sapiens cDNA clone IMAGE:5263003.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	14625251	14625251	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14625251delA								None (None upstream) : FAM84A (147605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	14886526	14886526	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14886526delC								FAM84A (95593 upstream) : NBAS (420506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	15015988	15015988	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15015988delA								FAM84A (225055 upstream) : NBAS (291044 downstream)																																			---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15534568	15534569	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15534568_15534569insA	uc002rcc.1	-						NBAS_uc010exl.1_Intron|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993			neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15657661	15657662	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15657661_15657662delAC	uc002rcc.1	-						NBAS_uc002rcd.1_Intron	NM_015909	NP_056993			neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15664923	15664923	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15664923delT	uc002rcc.1	-						NBAS_uc002rcd.1_Intron	NM_015909	NP_056993			neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	15884342	15884342	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15884342delT								DDX1 (113118 upstream) : MYCNOS (195678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16343884	16343885	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16343884_16343885delTT								MYCN (256756 upstream) : FAM49A (390016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16407935	16407935	+	IGR	DEL	T	-	-	rs78167150		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16407935delT								MYCN (320807 upstream) : FAM49A (325966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16639955	16639955	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16639955delT								MYCN (552827 upstream) : FAM49A (93946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16690593	16690595	+	IGR	DEL	GAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16690593_16690595delGAA								MYCN (603465 upstream) : FAM49A (43306 downstream)																																			---	---	---	---
FAM49A	81553	broad.mit.edu	37	2	16841703	16841703	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16841703delA	uc002rck.1	-							NM_030797	NP_110424			family with sequence similarity 49, member A							intracellular					0	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		GBM - Glioblastoma multiforme(3;0.00969)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	16860303	16860303	+	IGR	DEL	T	-	-	rs72135623		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16860303delT								FAM49A (13207 upstream) : RAD51AP2 (831683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17259049	17259049	+	IGR	DEL	T	-	-	rs113111159		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17259049delT								FAM49A (411953 upstream) : RAD51AP2 (432937 downstream)																																			---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17860044	17860044	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	18147266	18147266	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18147266delT								KCNS3 (33042 upstream) : NT5C1B (588725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19043092	19043092	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19043092delT								NT5C1B (272254 upstream) : OSR1 (508155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19092836	19092837	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19092836_19092837delTG								NT5C1B (321998 upstream) : OSR1 (458410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19549557	19549558	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19549557_19549558delTG								NT5C1B (778719 upstream) : OSR1 (1689 downstream)																																	OREG0014466	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	2	19861828	19861828	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19861828delA								OSR1 (303456 upstream) : TTC32 (234690 downstream)																																			---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20141611	20141611	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	20260839	20260841	+	IGR	DEL	TTG	-	-	rs7561613	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20260839_20260841delTTG								LAPTM4A (9050 upstream) : SDC1 (139717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	20282232	20282232	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20282232delT								LAPTM4A (30443 upstream) : SDC1 (118326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	20592898	20592899	+	IGR	INS	-	CAA	CAA	rs141258393	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20592898_20592899insCAA								PUM2 (42435 upstream) : RHOB (53936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	20689138	20689138	+	IGR	DEL	T	-	-	rs67372923		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20689138delT								RHOB (39938 upstream) : HS1BP3 (128426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	21148888	21148889	+	IGR	INS	-	A	A	rs151010582	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21148888_21148889insA								C2orf43 (126061 upstream) : APOB (75413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	22175838	22175838	+	IGR	DEL	T	-	-	rs72002614		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22175838delT								APOB (908893 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23386639	23386639	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23386639delT								None (None upstream) : KLHL29 (368816 downstream)																																			---	---	---	---
KLHL29	114818	broad.mit.edu	37	2	23797075	23797075	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23797075delT	uc002reg.2	+						KLHL29_uc002ref.2_Intron					RecName: Full=Kelch-like protein 29; AltName: Full=Kelch repeat and BTB domain-containing protein 9;											ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	23935645	23935645	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23935645delA								KLHL29 (4164 upstream) : ATAD2B (35896 downstream)																																			---	---	---	---
ATAD2B	54454	broad.mit.edu	37	2	24009146	24009146	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24009146delT	uc002rek.3	-						ATAD2B_uc010yki.1_Intron|ATAD2B_uc002rei.3_Intron|ATAD2B_uc002rej.3_Intron	NM_017552	NP_060022			ATPase family, AAA domain containing 2B								ATP binding|nucleoside-triphosphatase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
UBXN2A	165324	broad.mit.edu	37	2	24209969	24209969	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24209969delA	uc010exy.2	+						UBXN2A_uc002rem.2_Intron|UBXN2A_uc002ren.2_Intron|UBXN2A_uc010ykj.1_Intron	NM_181713	NP_859064			UBX domain containing 4												0																		---	---	---	---
LOC375190	375190	broad.mit.edu	37	2	24333636	24333636	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24333636delC	uc002rew.2	+											SubName: Full=Putative uncharacterized protein C2orf84;												0																		---	---	---	---
LOC375190	375190	broad.mit.edu	37	2	24345197	24345197	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24345197delA	uc010ykl.1	+						LOC375190_uc002rew.2_Intron|LOC375190_uc002rfb.2_5'Flank|PFN4_uc002rfa.1_Intron	NM_001145710	NP_001139182			hypothetical protein LOC375190												0																		---	---	---	---
ITSN2	50618	broad.mit.edu	37	2	24553436	24553436	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24553436delA	uc002rfe.2	-						ITSN2_uc002rff.2_Intron|ITSN2_uc002rfg.2_Intron|ITSN2_uc010eyd.2_Intron	NM_006277	NP_006268			intersectin 2 isoform 1						endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
ITSN2	50618	broad.mit.edu	37	2	24553641	24553642	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24553641_24553642delTT	uc002rfe.2	-						ITSN2_uc002rff.2_Intron|ITSN2_uc002rfg.2_Intron|ITSN2_uc010eyd.2_Intron	NM_006277	NP_006268			intersectin 2 isoform 1						endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
ADCY3	109	broad.mit.edu	37	2	25118498	25118498	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25118498delT	uc002rfs.3	-						ADCY3_uc010ykm.1_Intron	NM_004036	NP_004027			adenylate cyclase 3						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)																	---	---	---	---
DTNB	1838	broad.mit.edu	37	2	25642422	25642422	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25642422delA	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_uc002rgp.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	25803427	25803427	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25803427delA	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)																	---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	26090153	26090154	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26090153_26090154delTT	uc002rgs.2	-							NM_018263	NP_060733			additional sex combs like 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	26105867	26105867	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26105867delA								ASXL2 (4555 upstream) : KIF3C (43588 downstream)																																			---	---	---	---
HADHA	3030	broad.mit.edu	37	2	26423952	26423952	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26423952delA	uc002rgy.2	-						HADHA_uc010yks.1_Intron	NM_000182	NP_000173			mitochondrial trifunctional protein, alpha						fatty acid beta-oxidation	fatty acid beta-oxidation multienzyme complex|mitochondrial nucleoid|nucleolus	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acetyltransferase activity|coenzyme binding|enoyl-CoA hydratase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				NADH(DB00157)													---	---	---	---
CENPA	1058	broad.mit.edu	37	2	27015954	27015954	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27015954delA	uc002rhr.2	+						CENPA_uc002rht.2_Intron|CENPA_uc002rhs.2_Intron	NM_001809	NP_001800			centromere protein A isoform a						CenH3-containing nucleosome assembly at centromere|establishment of mitotic spindle orientation|interspecies interaction between organisms|kinetochore assembly|mitotic prometaphase|protein localization to chromosome, centromeric region	condensed nuclear chromosome kinetochore|cytosol|nucleoplasm|nucleosome	chromatin binding|DNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
DPYSL5	56896	broad.mit.edu	37	2	27133202	27133202	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27133202delT	uc002rhu.3	+						DPYSL5_uc002rhv.3_Intron	NM_020134	NP_064519			dihydropyrimidinase-like 5						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
EMILIN1	11117	broad.mit.edu	37	2	27300532	27300532	+	5'Flank	DEL	T	-	-	rs66572633		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27300532delT	uc002rii.3	+						EMILIN1_uc010eyq.1_5'Flank	NM_007046	NP_008977			elastin microfibril interfacer 1 precursor						cell adhesion	collagen				pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
PPM1G	5496	broad.mit.edu	37	2	27606853	27606855	+	In_Frame_Del	DEL	TCT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27606853_27606855delTCT	uc002rkl.2	-	7	1037_1039	c.930_932delAGA	c.(928-933)GAAGAG>GAG	p.310_311EE>E	PPM1G_uc002rkm.2_In_Frame_Del_p.91_92EE>E	NM_002707	NP_002698	O15355	PPM1G_HUMAN	protein phosphatase 1G	310_311	Asp/Glu-rich (acidic).|Poly-Glu.				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)																	---	---	---	---
SLC4A1AP	22950	broad.mit.edu	37	2	27887946	27887946	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27887946delT	uc002rlk.3	+						SUPT7L_uc002rlh.1_5'Flank|SUPT7L_uc002rli.1_5'Flank|SUPT7L_uc010ymf.1_5'Flank|SUPT7L_uc002rlj.1_5'Flank|SUPT7L_uc010ezh.1_5'Flank	NM_018158	NP_060628			solute carrier family 4 (anion exchanger),							cytoplasm|nucleus	double-stranded RNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
MRPL33	9553	broad.mit.edu	37	2	27997475	27997475	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27997475delT	uc002rlm.1	+						MRPL33_uc002rln.1_Intron	NM_004891	NP_004882			mitochondrial ribosomal protein L33 isoform a						translation	mitochondrion|ribosome	structural constituent of ribosome				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BRE	9577	broad.mit.edu	37	2	28221023	28221023	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28221023delA	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)																	---	---	---	---
PLB1	151056	broad.mit.edu	37	2	28853567	28853567	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28853567delG	uc002rmb.1	+						PLB1_uc010ezj.1_Intron|PLB1_uc002rme.1_Intron|PLB1_uc002rmf.1_Intron	NM_153021	NP_694566			phospholipase B1 precursor						lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	28946534	28946534	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28946534delA								PLB1 (79921 upstream) : PPP1CB (28078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	28949864	28949864	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28949864delA								PLB1 (83251 upstream) : PPP1CB (24748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	29310784	29310784	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29310784delT								C2orf71 (13657 upstream) : CLIP4 (9787 downstream)																																			---	---	---	---
ALK	238	broad.mit.edu	37	2	29456860	29456860	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29456860delT	uc002rmy.2	-							NM_004304	NP_004295			anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	31979880	31979880	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31979880delA								SRD5A2 (173840 upstream) : MEMO1 (113016 downstream)																																			---	---	---	---
MEMO1	51072	broad.mit.edu	37	2	32144925	32144926	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32144925_32144926delGT	uc002rnx.2	-						MEMO1_uc010ymu.1_Intron|MEMO1_uc010ezq.2_Intron|MEMO1_uc002rny.2_Intron|MEMO1_uc002rnz.2_Intron|MEMO1_uc010ymv.1_Intron	NM_015955	NP_057039			mediator of cell motility 1 isoform 1						regulation of microtubule-based process	cytosol|nucleus				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	32538074	32538074	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32538074delC								YIPF4 (6417 upstream) : BIRC6 (44022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	32577445	32577449	+	IGR	DEL	GATGG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32577445_32577449delGATGG								YIPF4 (45788 upstream) : BIRC6 (4647 downstream)																																			---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32707476	32707476	+	Intron	DEL	T	-	-	rs71446071	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32707476delT	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33220251	33220251	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33220251delA	uc002ros.2	+							NM_206943	NP_996826			latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33236673	33236673	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33236673delT	uc002ros.2	+							NM_206943	NP_996826			latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	33793126	33793126	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33793126delA								RASGRP3 (3329 upstream) : FAM98A (15603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34041814	34041814	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34041814delT								MYADML (88530 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34203677	34203677	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34203677delT								MYADML (250393 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34774990	34774990	+	IGR	DEL	T	-	-	rs113041307		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34774990delT								MYADML (821706 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34793727	34793727	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34793727delT								MYADML (840443 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35108702	35108702	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35108702delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36313403	36313404	+	IGR	INS	-	CA	CA	rs150653508	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36313403_36313404insCA								None (None upstream) : CRIM1 (269993 downstream)																																			---	---	---	---
CRIM1	51232	broad.mit.edu	37	2	36696456	36696456	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36696456delT	uc002rpd.2	+							NM_016441	NP_057525			cysteine-rich motor neuron 1 precursor						nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)																---	---	---	---
CRIM1	51232	broad.mit.edu	37	2	36777378	36777380	+	3'UTR	DEL	TTT	-	-	rs10707574		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36777378_36777380delTTT	uc002rpd.2	+	17						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)																---	---	---	---
HEATR5B	54497	broad.mit.edu	37	2	37217758	37217758	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37217758delT	uc002rpp.1	-						HEATR5B_uc002rpo.1_Intron|HEATR5B_uc010ezy.1_Intron	NM_019024	NP_061897			HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)																---	---	---	---
HEATR5B	54497	broad.mit.edu	37	2	37232692	37232692	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37232692delA	uc002rpp.1	-						HEATR5B_uc002rpo.1_5'Flank|HEATR5B_uc010ezy.1_Intron	NM_019024	NP_061897			HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)																---	---	---	---
HEATR5B	54497	broad.mit.edu	37	2	37274321	37274321	+	Intron	DEL	A	-	-	rs79873393		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37274321delA	uc002rpp.1	-							NM_019024	NP_061897			HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)																---	---	---	---
CCDC75	253635	broad.mit.edu	37	2	37315480	37315480	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)																---	---	---	---
EIF2AK2	5610	broad.mit.edu	37	2	37349982	37349982	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37349982delA	uc010ynh.1	-						EIF2AK2_uc010fab.1_Intron|EIF2AK2_uc010yng.1_Intron|EIF2AK2_uc010fac.2_Intron|EIF2AK2_uc010fad.2_Intron	NM_002759	NP_002750			eukaryotic translation initiation factor 2-alpha						evasion by virus of host immune response|modulation by virus of host cellular process|negative regulation of osteoblast proliferation|protein autophosphorylation|response to virus|viral infectious cycle	cytosol	ATP binding|double-stranded RNA binding|eukaryotic translation initiation factor 2alpha kinase activity|protein binding|protein phosphatase type 2A regulator activity			ovary(2)|lung(2)|pancreas(1)	5		all_hematologic(82;0.248)																---	---	---	---
CEBPZ	10153	broad.mit.edu	37	2	37438027	37438027	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)																---	---	---	---
C2orf56	55471	broad.mit.edu	37	2	37469850	37469850	+	Intron	DEL	A	-	-	rs142499241	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37469850delA	uc002rqa.3	+						C2orf56_uc010ynj.1_Intron|C2orf56_uc002rqc.3_Intron|C2orf56_uc010ynk.1_Intron|C2orf56_uc010ynl.1_Intron|C2orf56_uc010fah.2_Intron	NM_144736	NP_653337			hypothetical protein LOC55471 isoform 1						mitochondrial respiratory chain complex I assembly	mitochondrion	enzyme binding|methyltransferase activity			central_nervous_system(1)	1		all_hematologic(82;0.21)																---	---	---	---
ATL2	64225	broad.mit.edu	37	2	38536778	38536778	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38536778delA	uc002rqq.2	-						ATL2_uc010ynm.1_Intron|ATL2_uc010ynn.1_Intron|ATL2_uc010yno.1_Intron|ATL2_uc002rqs.2_Intron|ATL2_uc002rqr.2_Intron	NM_001135673	NP_001129145			atlastin GTPase 2 isoform 2						endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
ATL2	64225	broad.mit.edu	37	2	38570334	38570334	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38570334delT	uc002rqq.2	-						ATL2_uc010ynm.1_Intron|ATL2_uc010ynn.1_Intron|ATL2_uc010yno.1_Intron|ATL2_uc002rqs.2_Intron|ATL2_uc002rqr.2_Intron	NM_001135673	NP_001129145			atlastin GTPase 2 isoform 2						endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	38615164	38615167	+	IGR	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38615164_38615167delTTTT								ATL2 (10732 upstream) : HNRPLL (175161 downstream)																																			---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39262297	39262297	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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				---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39326030	39326030	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39326030delA	uc002rrk.3	-						SOS1_uc010ynr.1_Intron	NM_005633	NP_005624			son of sevenless homolog 1						apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)												Noonan_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	39731331	39731331	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39731331delA	uc002rrq.2	+						uc002rrr.1_Intron					Homo sapiens cDNA FLJ33477 fis, clone BRAMY2002604.																														---	---	---	---
TMEM178	130733	broad.mit.edu	37	2	39905103	39905103	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39905103delA	uc002rrt.2	+						TMEM178_uc010fam.1_Intron	NM_152390	NP_689603			transmembrane protein 178 precursor							integral to membrane					0		all_hematologic(82;0.248)																---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40677435	40677435	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40677435delT	uc002rsa.2	-						SLC8A1_uc002rsd.3_Intron|SLC8A1_uc010fan.1_Intron|SLC8A1_uc002rsc.1_Intron	NM_001112802	NP_001106273			solute carrier family 8 (sodium/calcium						cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	40928308	40928309	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40928308_40928309insG								SLC8A1 (188733 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41384162	41384162	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41384162delA								SLC8A1 (644587 upstream) : PKDCC (890999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41934507	41934507	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41934507delC								None (None upstream) : PKDCC (340654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42267135	42267136	+	IGR	INS	-	A	A	rs139548699	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42267135_42267136insA								None (None upstream) : PKDCC (8025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42382758	42382758	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42382758delA								PKDCC (97092 upstream) : EML4 (13732 downstream)																																			---	---	---	---
EML4	27436	broad.mit.edu	37	2	42523618	42523619	+	Intron	DEL	TC	-	-	rs67244705		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42523618_42523619delTC	uc002rsi.2	+						EML4_uc010fap.2_Intron|EML4_uc002rsj.2_Intron	NM_019063	NP_061936			echinoderm microtubule associated protein like 4						microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250								T	ALK	NSCLC								---	---	---	---
COX7A2L	9167	broad.mit.edu	37	2	42578275	42578275	+	3'UTR	DEL	A	-	-	rs71682791		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42578275delA	uc002rsk.2	-	3					COX7A2L_uc002rsl.2_RNA	NM_004718	NP_004709			cytochrome c oxidase subunit VIIa polypeptide 2						respiratory electron transport chain	mitochondrial respiratory chain	cytochrome-c oxidase activity|electron carrier activity				0																		---	---	---	---
COX7A2L	9167	broad.mit.edu	37	2	42584625	42584625	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42584625delT	uc002rsk.2	-						COX7A2L_uc002rsl.2_Intron	NM_004718	NP_004709			cytochrome c oxidase subunit VIIa polypeptide 2						respiratory electron transport chain	mitochondrial respiratory chain	cytochrome-c oxidase activity|electron carrier activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	43377184	43377185	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43377184_43377185delTG								HAAO (357433 upstream) : ZFP36L2 (72357 downstream)																																			---	---	---	---
THADA	63892	broad.mit.edu	37	2	43569354	43569354	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43569354delA	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron	NM_001083953	NP_001077422			thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)																---	---	---	---
THADA	63892	broad.mit.edu	37	2	43613462	43613462	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43613462delT	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron	NM_001083953	NP_001077422			thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)																---	---	---	---
THADA	63892	broad.mit.edu	37	2	43755132	43755132	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43755132delA	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron|THADA_uc010fat.1_Intron|THADA_uc002rta.2_Intron	NM_001083953	NP_001077422			thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)																---	---	---	---
THADA	63892	broad.mit.edu	37	2	43807860	43807860	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43807860delA	uc002rsw.3	-						THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc002rsz.2_Intron|THADA_uc002rta.2_Intron|THADA_uc002rtb.1_Intron|THADA_uc002rtc.3_Intron|THADA_uc002rtd.2_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)																---	---	---	---
PLEKHH2	130271	broad.mit.edu	37	2	43984562	43984562	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43984562delT	uc010yny.1	+							NM_172069	NP_742066			pleckstrin homology domain containing, family H							cytoplasm|cytoskeleton|integral to membrane	binding			skin(2)|central_nervous_system(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
ABCG8	64241	broad.mit.edu	37	2	44078049	44078049	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44078049delA	uc002rtq.2	+						ABCG8_uc010yoa.1_Intron	NM_022437	NP_071882			ATP-binding cassette sub-family G member 8						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
ABCG8	64241	broad.mit.edu	37	2	44101418	44101418	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44101418delA	uc002rtq.2	+						ABCG8_uc010yoa.1_Intron	NM_022437	NP_071882			ATP-binding cassette sub-family G member 8						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
PREPL	9581	broad.mit.edu	37	2	44573572	44573572	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44573572delA	uc002ruf.2	-						PREPL_uc002rug.2_Intron|PREPL_uc002ruh.2_Intron|PREPL_uc010fax.2_Intron|PREPL_uc002rui.3_Intron|PREPL_uc002ruj.1_Intron|PREPL_uc002ruk.1_Intron	NM_006036	NP_006027			prolyl endopeptidase-like isoform C						proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	45253171	45253171	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45253171delC								SIX2 (16628 upstream) : SRBD1 (362649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45296696	45296697	+	IGR	INS	-	G	G	rs71394806		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45296696_45296697insG								SIX2 (60153 upstream) : SRBD1 (319123 downstream)																																			---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45744979	45744979	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45744979delT	uc002rus.2	-						SRBD1_uc010yoc.1_Intron	NM_018079	NP_060549			S1 RNA binding domain 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)															---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45748426	45748427	+	Intron	DEL	AC	-	-	rs72451454		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45748426_45748427delAC	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	45869193	45869196	+	IGR	DEL	AAAG	-	-	rs139764727		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45869193_45869196delAAAG								SRBD1 (30760 upstream) : PRKCE (9847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45869228	45869229	+	IGR	INS	-	G	G	rs145922094	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45869228_45869229insG								SRBD1 (30795 upstream) : PRKCE (9814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45872173	45872173	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45872173delT								SRBD1 (33740 upstream) : PRKCE (6870 downstream)																																			---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	46217798	46217799	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46217798_46217799delTT	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	46385332	46385332	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46385332delG	uc002rut.2	+							NM_005400	NP_005391			protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)															---	---	---	---
TTC7A	57217	broad.mit.edu	37	2	47178628	47178628	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47178628delA	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_Intron	NM_020458	NP_065191			tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
TTC7A	57217	broad.mit.edu	37	2	47223484	47223484	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47223484delA	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_Intron|TTC7A_uc002rvq.2_Intron|TTC7A_uc002rvr.2_Intron	NM_020458	NP_065191			tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
CALM2	805	broad.mit.edu	37	2	47390955	47390955	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47390955delT	uc002rvt.2	-						C2orf61_uc010fbd.2_Intron|CALM2_uc010fbe.2_Intron	NM_001743	NP_001734			calmodulin 2						activation of phospholipase C activity|G-protein coupled receptor protein signaling pathway|glucose metabolic process|glycogen catabolic process|muscle contraction|negative regulation of ryanodine-sensitive calcium-release channel activity|nerve growth factor receptor signaling pathway|nitric oxide metabolic process|platelet activation|platelet degranulation|positive regulation of ryanodine-sensitive calcium-release channel activity|regulation of cytokinesis|regulation of nitric-oxide synthase activity|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to calcium ion|synaptic transmission	centrosome|cytosol|extracellular region|nucleoplasm|plasma membrane|spindle microtubule|spindle pole	calcium ion binding|N-terminal myristoylation domain binding|phospholipase binding|protein domain specific binding|thioesterase binding|titin binding	p.0?(2)			0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)		Aprindine(DB01429)|Bepridil(DB01244)|Dibucaine(DB00527)|Felodipine(DB01023)|Flunarizine(DB04841)|Fluphenazine(DB00623)|Isoflurane(DB00753)|Loperamide(DB00836)|Miconazole(DB01110)|Perphenazine(DB00850)|Phenoxybenzamine(DB00925)|Pimozide(DB01100)|Promethazine(DB01069)													---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47635524	47635525	+	Intron	DEL	TT	-	-	rs76376509		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47635524_47635525delTT	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_5'Flank|MSH2_uc010fbf.1_Intron	NM_000251	NP_000242			mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47694582	47694583	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47694582_47694583delTT	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron|MSH2_uc010fbi.1_Intron	NM_000251	NP_000242			mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding	p.?(2)		large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47750081	47750081	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47750081delA	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				---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47819568	47819568	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47819568delA	uc002rvz.2	+							NM_000251	NP_000242			mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
FBXO11	80204	broad.mit.edu	37	2	48041563	48041564	+	Intron	INS	-	TGGAGT	TGGAGT	rs144830956	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48041563_48041564insTGGAGT	uc010fbl.2	-						FBXO11_uc002rwe.2_Intron|FBXO11_uc002rwf.2_Intron|FBXO11_uc010fbk.2_Intron	NM_025133	NP_079409			F-box only protein 11 isoform 1						ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	48148032	48148032	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48148032delT								FBXO11 (15218 upstream) : FOXN2 (393763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48260004	48260004	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48260004delT								FBXO11 (127190 upstream) : FOXN2 (281791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48331721	48331721	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48331721delT								FBXO11 (198907 upstream) : FOXN2 (210074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48361875	48361875	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48361875delA								FBXO11 (229061 upstream) : FOXN2 (179920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48501577	48501577	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48501577delT								FBXO11 (368763 upstream) : FOXN2 (40218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48513440	48513440	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48513440delT								FBXO11 (380626 upstream) : FOXN2 (28355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48636386	48636387	+	IGR	INS	-	AG	AG	rs140826070	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48636386_48636387insAG								FOXN2 (29952 upstream) : KLRAQ1 (31521 downstream)																																			---	---	---	---
LHCGR	3973	broad.mit.edu	37	2	48952906	48952906	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48952906delA	uc002rwu.3	-						GTF2A1L_uc002rwt.2_Intron|LHCGR_uc002rwv.2_Intron	NM_000233	NP_000224			luteinizing hormone/choriogonadotropin receptor						male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|lung(2)|breast(2)|skin(1)	8		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)									Familial_Male-Limited_Precocious_Puberty				---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50774702	50774702	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50774702delA	uc010fbq.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxc.1_Intron	NM_001135659	NP_001129131			neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	51231208	51231210	+	Intron	DEL	AAA	-	-	rs113774881		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51231208_51231210delAAA	uc010fbq.2	-						NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxd.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	51641525	51641526	+	IGR	INS	-	GT	GT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51641525_51641526insGT								NRXN1 (381851 upstream) : None (None downstream)																																			---	---	---	---
ASB3	51130	broad.mit.edu	37	2	53954604	53954604	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53954604delA	uc002rxg.1	-						ASB3_uc002rxh.1_Intron|ASB3_uc002rxi.3_Intron|ASB3_uc010yoo.1_Intron	NM_016115	NP_057199			ankyrin repeat and SOCS box-containing protein 3						intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
ASB3	51130	broad.mit.edu	37	2	53958801	53958802	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53958801_53958802insT	uc002rxg.1	-						ASB3_uc002rxh.1_Intron|ASB3_uc002rxi.3_Intron|ASB3_uc010yoo.1_Intron	NM_016115	NP_057199			ankyrin repeat and SOCS box-containing protein 3						intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
ASB3	51130	broad.mit.edu	37	2	54022951	54022952	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54022951_54022952insT	uc002rxi.3	-						ERLEC1_uc002rxl.2_Intron|ERLEC1_uc002rxm.2_Intron|ERLEC1_uc002rxn.2_Intron	NM_001164165	NP_001157637			hypothetical protein LOC100302652						intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54107568	54107568	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54107568delA	uc002rxp.2	-						PSME4_uc010yop.1_Intron|PSME4_uc010yoq.1_Intron|PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron|PSME4_uc010fbt.1_Intron	NM_014614	NP_055429			proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54163035	54163037	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54163035_54163037delTTT	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)															---	---	---	---
ACYP2	98	broad.mit.edu	37	2	54372751	54372751	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54372751delT	uc002rxq.3	+							NM_138448	NP_612457			acylphosphatase 2						phosphate metabolic process		acylphosphatase activity				0																		---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54728434	54728434	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54728434delT	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)															---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54748661	54748661	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54748661delT	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)															---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54838959	54838959	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54838959delA	uc002rxu.2	+						SPTBN1_uc002rxv.1_Intron|SPTBN1_uc002rxx.2_Intron	NM_003128	NP_003119			spectrin, beta, non-erythrocytic 1 isoform 1						actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)															---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54895818	54895820	+	3'UTR	DEL	TTT	-	-	rs78796985		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54895818_54895820delTTT	uc002rxu.2	+	36					SPTBN1_uc010you.1_3'UTR	NM_003128	NP_003119			spectrin, beta, non-erythrocytic 1 isoform 1						actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)															---	---	---	---
EML6	400954	broad.mit.edu	37	2	55119193	55119196	+	Intron	DEL	TTGC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55119193_55119196delTTGC	uc002ryb.3	+							NM_001039753	NP_001034842			echinoderm microtubule associated protein like							cytoplasm|microtubule					0																		---	---	---	---
C2orf63	130162	broad.mit.edu	37	2	55417188	55417188	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55417188delT	uc002ryi.2	-						C2orf63_uc002ryh.2_Intron|C2orf63_uc002ryj.2_Intron	NM_152385	NP_689598			hypothetical protein LOC130162 isoform 1								binding			ovary(2)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(58;0.179)|Lung(47;0.189)															---	---	---	---
MTIF2	4528	broad.mit.edu	37	2	55479363	55479363	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55479363delA	uc002ryn.2	-						MTIF2_uc010yox.1_Intron|MTIF2_uc002ryo.2_Intron	NM_001005369	NP_001005369			mitochondrial translational initiation factor 2						regulation of translational initiation	mitochondrion	GTP binding|GTPase activity|ribosomal small subunit binding|translation initiation factor activity			ovary(1)	1																		---	---	---	---
CCDC88A	55704	broad.mit.edu	37	2	55596754	55596754	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55596754delT	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron|CCDC88A_uc010ypb.1_Intron	NM_001135597	NP_001129069			coiled-coil domain containing 88A isoform 1						activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4																		---	---	---	---
CCDC88A	55704	broad.mit.edu	37	2	55632517	55632518	+	Intron	INS	-	CT	CT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55632517_55632518insCT	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron|CCDC88A_uc010fbz.2_RNA	NM_001135597	NP_001129069			coiled-coil domain containing 88A isoform 1						activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4																		---	---	---	---
SMEK2	57223	broad.mit.edu	37	2	55809040	55809040	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55809040delA	uc002rzc.2	-						SMEK2_uc002rzb.2_Intron|SMEK2_uc002rzd.2_Intron|SMEK2_uc002rza.2_Intron	NM_001122964	NP_001116436			SMEK homolog 2, suppressor of mek1 isoform 1							microtubule organizing center|nucleus	protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
PNPT1	87178	broad.mit.edu	37	2	55910980	55910980	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55910980delA	uc002rzf.2	-						PNPT1_uc002rzg.2_Intron	NM_033109	NP_149100			polyribonucleotide nucleotidyltransferase 1						mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
PNPT1	87178	broad.mit.edu	37	2	55914574	55914574	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55914574delA	uc002rzf.2	-						PNPT1_uc002rzg.2_Intron	NM_033109	NP_149100			polyribonucleotide nucleotidyltransferase 1						mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	56204177	56204177	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56204177delA	uc002rzk.2	+											Homo sapiens, clone IMAGE:3873411, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	56386062	56386063	+	Intron	DEL	AA	-	-	rs111318970		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56386062_56386063delAA	uc002rzk.2	+											Homo sapiens, clone IMAGE:3873411, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	56963272	56963273	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56963272_56963273insA								CCDC85A (349964 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	58119042	58119042	+	IGR	DEL	T	-	-	rs71837020		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58119042delT								None (None upstream) : VRK2 (15744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59185581	59185582	+	Intron	DEL	AC	-	-	rs113407515		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59185581_59185582delAC	uc002rzy.2	+						uc002rzz.2_Intron					Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	59259932	59259932	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59259932delT	uc002rzy.2	+						uc002rzz.2_Intron					Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																														---	---	---	---
BCL11A	53335	broad.mit.edu	37	2	60718076	60718076	+	Intron	DEL	A	-	-	rs71400256		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60718076delA	uc002sae.1	-						BCL11A_uc002sab.2_Intron|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Intron|BCL11A_uc002sad.1_Intron|BCL11A_uc002saf.1_Intron	NM_022893	NP_075044			B-cell CLL/lymphoma 11A isoform 1						negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleus|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding			central_nervous_system(6)|breast(3)|ovary(2)|skin(2)	13			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)					T	IGH@	B-CLL								---	---	---	---
PAPOLG	64895	broad.mit.edu	37	2	60986842	60986842	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60986842delA	uc002sai.2	+						PAPOLG_uc002saj.2_Intron|PAPOLG_uc002sak.2_5'Flank	NM_022894	NP_075045			poly(A) polymerase gamma						mRNA processing|RNA polyadenylation|transcription, DNA-dependent	nucleus	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity|RNA binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61546218	61546218	+	Intron	DEL	A	-	-	rs35281857		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61546218delA	uc002sbe.2	-							NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
XPO1	7514	broad.mit.edu	37	2	61730401	61730401	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61730401delT	uc002sbj.2	-						XPO1_uc010fcl.2_Intron|XPO1_uc010ypn.1_Intron|XPO1_uc002sbk.2_Intron	NM_003400	NP_003391			exportin 1						intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)															---	---	---	---
TMEM17	200728	broad.mit.edu	37	2	62728113	62728113	+	3'UTR	DEL	A	-	-	rs75662659		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62728113delA	uc002sbt.2	-	4					TMEM17_uc002sbu.2_3'UTR|TMEM17_uc002sbv.1_3'UTR	NM_198276	NP_938017			transmembrane protein 17							integral to membrane					0	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)															---	---	---	---
TMEM17	200728	broad.mit.edu	37	2	62760376	62760376	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62760376delT	uc002sbv.1	-											Homo sapiens cDNA FLJ34583 fis, clone KIDNE2008666.							integral to membrane					0	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)															---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	62957760	62957761	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62957760_62957761delAG	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc010fcq.1_Intron|EHBP1_uc002sbx.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron|EHBP1_uc002sca.2_Intron	NM_015252	NP_056067			EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	63220993	63220993	+	Intron	DEL	T	-	-	rs78094292		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63220993delT	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				---	---	---	---
Unknown	0	broad.mit.edu	37	2	64526479	64526479	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64526479delA								PELI1 (154874 upstream) : HSPC159 (154848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	64577492	64577492	+	IGR	DEL	G	-	-	rs35938933		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64577492delG								PELI1 (205887 upstream) : HSPC159 (103835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	65398146	65398146	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65398146delT								RAB1A (40711 upstream) : ACTR2 (56683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	65668217	65668218	+	Intron	INS	-	T	T	rs143403201	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65668217_65668218insT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	65727695	65727695	+	Intron	DEL	T	-	-	rs113792144		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65727695delT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	65813210	65813211	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65813210_65813211delTG	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	65993269	65993269	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65993269delT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	66515535	66515535	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66515535delT								SPRED2 (855879 upstream) : MEIS1 (146997 downstream)																																			---	---	---	---
MEIS1	4211	broad.mit.edu	37	2	66696655	66696655	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66696655delT	uc002sdu.2	+						MEIS1_uc002sdt.2_Intron|MEIS1_uc002sdv.2_Intron|MEIS1_uc010yqh.1_Intron|MEIS1_uc010yqi.1_Intron|MEIS1_uc002sdw.1_Intron	NM_002398	NP_002389			Meis homeobox 1								sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
MEIS1	4211	broad.mit.edu	37	2	66704034	66704034	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66704034delA	uc002sdu.2	+						MEIS1_uc002sdt.2_Intron|MEIS1_uc002sdv.2_Intron|MEIS1_uc010yqh.1_Intron|MEIS1_uc010yqi.1_Intron|MEIS1_uc002sdw.1_Intron	NM_002398	NP_002389			Meis homeobox 1								sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	67282823	67282823	+	IGR	DEL	T	-	-	rs75403654		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67282823delT								MEIS1 (482933 upstream) : ETAA1 (341619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67551651	67551651	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67551651delT								MEIS1 (751761 upstream) : ETAA1 (72791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67819218	67819218	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67819218delA								ETAA1 (181685 upstream) : C1D (450115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	68075500	68075500	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68075500delA								ETAA1 (437967 upstream) : C1D (193833 downstream)																																			---	---	---	---
APLF	200558	broad.mit.edu	37	2	68716108	68716108	+	Intron	DEL	A	-	-	rs112908692	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68716108delA	uc002sep.2	+						APLF_uc010fdf.2_Intron	NM_173545	NP_775816			aprataxin and PNKP like factor						double-strand break repair|single strand break repair	cytosol|nucleus	3'-5' exonuclease activity|DNA-(apurinic or apyrimidinic site) lyase activity|endodeoxyribonuclease activity|metal ion binding|nucleotide binding|protein binding			ovary(2)	2																		---	---	---	---
NFU1	27247	broad.mit.edu	37	2	69626530	69626530	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69626530delA	uc002sfk.2	-						NFU1_uc002sfj.2_Intron|NFU1_uc002sfl.2_Intron|NFU1_uc002sfm.2_Intron|NFU1_uc010fdi.2_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	69657350	69657350	+	Intron	DEL	T	-	-	rs113587680		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69657350delT	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																		---	---	---	---
ADD2	119	broad.mit.edu	37	2	70917812	70917812	+	Intron	DEL	C	-	-	rs10084293	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70917812delC	uc002sgz.2	-						ADD2_uc010fds.1_Intron|ADD2_uc002sgy.2_Intron|ADD2_uc002sha.2_Intron|ADD2_uc002sgx.2_Intron|ADD2_uc010fdt.1_Intron|ADD2_uc002shc.1_Intron|ADD2_uc002shd.1_Intron|ADD2_uc010fdu.1_Intron	NM_001617	NP_001608			adducin 2 isoform a						actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding			ovary(2)|pancreas(1)	3																		---	---	---	---
VAX2	25806	broad.mit.edu	37	2	71126039	71126042	+	5'Flank	DEL	CCTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71126039_71126042delCCTT	uc002shh.2	+							NM_012476	NP_036608			ventral anterior homeobox 2						ectoderm development|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
ATP6V1B1	525	broad.mit.edu	37	2	71170318	71170319	+	Intron	DEL	AC	-	-	rs66707483		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71170318_71170319delAC	uc002shj.2	+						ATP6V1B1_uc002shi.1_Intron|ATP6V1B1_uc010fdv.2_Intron|ATP6V1B1_uc010fdw.2_Intron|ATP6V1B1_uc010fdx.2_Intron	NM_001692	NP_001683			ATPase, H+ transporting, lysosomal 56/58kDa, V1						ATP hydrolysis coupled proton transport|calcium ion homeostasis|cellular iron ion homeostasis|excretion|inner ear morphogenesis|insulin receptor signaling pathway|ossification|pH reduction|sensory perception of sound|transferrin transport	apical plasma membrane|basolateral plasma membrane|cytosol|endomembrane system|lateral plasma membrane|microvillus|proton-transporting V-type ATPase, V1 domain|vacuolar proton-transporting V-type ATPase complex	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			skin(1)	1																		---	---	---	---
TEX261	113419	broad.mit.edu	37	2	71219277	71219281	+	Intron	DEL	TTTTT	-	-	rs112462352		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71219277_71219281delTTTTT	uc002shn.2	-						TEX261_uc010fdy.2_Intron	NM_144582	NP_653183			testis expressed sequence 261							integral to membrane					0																		---	---	---	---
ZNF638	27332	broad.mit.edu	37	2	71658576	71658576	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71658576delT	uc002shx.2	+						ZNF638_uc002shy.2_Intron|ZNF638_uc002shz.2_Intron|ZNF638_uc002sia.2_Intron|ZNF638_uc010fed.2_Intron|ZNF638_uc002sic.2_Intron|ZNF638_uc002sid.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	71841978	71841979	+	Intron	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71841978_71841979insG	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron|DYSF_uc010yqy.1_Intron|DYSF_uc010yqz.1_Intron	NM_003494	NP_003485			dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7																		---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71845911	71845911	+	Intron	DEL	G	-	-	rs77367656	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71845911delG	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron|DYSF_uc010yqy.1_Intron|DYSF_uc010yqz.1_Intron	NM_003494	NP_003485			dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	72190889	72190889	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72190889delT								DYSF (276997 upstream) : CYP26B1 (165478 downstream)																																			---	---	---	---
CCT7	10574	broad.mit.edu	37	2	73476418	73476418	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73476418delT	uc002siz.2	+						CCT7_uc002sja.2_Intron|CCT7_uc010yrf.1_Intron|CCT7_uc010feu.2_Intron|CCT7_uc010yrg.1_Intron|CCT7_uc010yrh.1_Intron|CCT7_uc010yri.1_Intron	NM_006429	NP_006420			chaperonin containing TCP1, subunit 7 isoform a						'de novo' posttranslational protein folding		ATP binding|unfolded protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	73549423	73549423	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73549423delT								EGR4 (28594 upstream) : ALMS1 (63463 downstream)																																			---	---	---	---
LOXL3	84695	broad.mit.edu	37	2	74778062	74778063	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74778062_74778063delTT	uc002smp.1	-						LOXL3_uc002smo.1_5'Flank|LOXL3_uc010ffm.1_Intron|LOXL3_uc002smq.1_Intron|LOXL3_uc010ffn.1_Intron|DOK1_uc002smr.2_Intron	NM_032603	NP_115992			lysyl oxidase-like 3 precursor							extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity				0																		---	---	---	---
SEMA4F	10505	broad.mit.edu	37	2	74893030	74893031	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74893030_74893031delTT	uc002sna.1	+						SEMA4F_uc010ysb.1_Intron|SEMA4F_uc010ffq.1_Intron|SEMA4F_uc010ffr.1_Intron|SEMA4F_uc002snb.1_Intron|SEMA4F_uc002snc.1_Intron	NM_004263	NP_004254			semaphorin W precursor						cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
HK2	3099	broad.mit.edu	37	2	75094527	75094527	+	Intron	DEL	A	-	-	rs151230031		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75094527delA	uc002snd.2	+							NM_000189	NP_000180			hexokinase 2						apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	76475106	76475106	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76475106delA								C2orf3 (536995 upstream) : LRRTM4 (499752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76515406	76515407	+	IGR	DEL	CA	-	-	rs112612710		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76515406_76515407delCA								C2orf3 (577295 upstream) : LRRTM4 (459451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76610424	76610424	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76610424delT								C2orf3 (672313 upstream) : LRRTM4 (364434 downstream)																																			---	---	---	---
LRRTM4	80059	broad.mit.edu	37	2	77313425	77313425	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77313425delA	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	78330725	78330725	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78330725delT	uc002snu.3	-											Homo sapiens cDNA clone IMAGE:4816654.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	78439922	78439922	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78439922delA	uc002snu.3	-											Homo sapiens cDNA clone IMAGE:4816654.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	78695824	78695825	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78695824_78695825delAA	uc002snv.3	-											Homo sapiens cytochrome c, somatic pseudogene 6, mRNA (cDNA clone IMAGE:4815768).																														---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	79647702	79647702	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79647702delT	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	80344029	80344032	+	Intron	DEL	GTGT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80344029_80344032delGTGT	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80436728	80436729	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80436728_80436729delAC	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80478281	80478281	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80478281delT	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	81164996	81164996	+	IGR	DEL	T	-	-	rs66565229		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81164996delT								CTNNA2 (289092 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	81699733	81699734	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81699733_81699734delAG								CTNNA2 (823829 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	81755224	81755225	+	IGR	INS	-	T	T	rs139524869	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81755224_81755225insT								CTNNA2 (879320 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82413106	82413109	+	IGR	DEL	GGAA	-	-	rs35040802		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82413106_82413109delGGAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82662364	82662365	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82662364_82662365delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83106557	83106558	+	IGR	INS	-	ACA	ACA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83106557_83106558insACA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83802471	83802471	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83802471delA								None (None upstream) : FUNDC2P2 (715335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83816099	83816100	+	IGR	INS	-	AC	AC	rs145426751	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83816099_83816100insAC								None (None upstream) : FUNDC2P2 (701706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83916724	83916724	+	IGR	DEL	A	-	-	rs77065267		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83916724delA								None (None upstream) : FUNDC2P2 (601082 downstream)																																			---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	85044731	85044731	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85044731delA	uc010fgb.2	+							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																		---	---	---	---
TCF7L1	83439	broad.mit.edu	37	2	85489798	85489798	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85489798delG	uc002soy.2	+							NM_031283	NP_112573			HMG-box transcription factor TCF-3						chromatin organization|regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|breast(1)|central_nervous_system(1)	3																		---	---	---	---
ELMOD3	84173	broad.mit.edu	37	2	85587802	85587802	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85587802delT	uc002spf.3	+						ELMOD3_uc010fgg.2_Intron|ELMOD3_uc002spg.3_Intron|ELMOD3_uc002sph.3_Intron|ELMOD3_uc010ysn.1_Intron|ELMOD3_uc010yso.1_Intron|ELMOD3_uc010ysp.1_Intron	NM_001135021	NP_001128493			ELMO/CED-12 domain containing 3 isoform b						phagocytosis	cytoskeleton				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	86046789	86046789	+	IGR	DEL	T	-	-	rs111713637		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86046789delT								ATOH8 (28284 upstream) : ST3GAL5 (19482 downstream)																																			---	---	---	---
REEP1	65055	broad.mit.edu	37	2	86469622	86469641	+	Intron	DEL	GGCATTAACCTGGAGGAGAT	-	-	rs71377065		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86469622_86469641delGGCATTAACCTGGAGGAGAT	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																		---	---	---	---
REEP1	65055	broad.mit.edu	37	2	86532152	86532152	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86532152delT	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	86697175	86697175	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86697175delG	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	86760633	86760633	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86801404	86801404	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86801404delA	uc010ytl.1	-							NM_001005753	NP_001005753			vacuolar protein sorting 24 isoform 2						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87028788	87028788	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87028788delA	uc002srs.3	+						CD8A_uc002srv.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	87114861	87114861	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87114861delT	uc002srs.3	+						uc010fgu.1_Intron					SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
RGPD1	400966	broad.mit.edu	37	2	88091357	88091357	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88091357delA	uc010fhc.1	-						RGPD1_uc002ssm.1_Intron	NM_001024457	NP_001019628			RANBP2-like and GRIP domain containing 1						intracellular transport		binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	88785113	88785113	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88785113delA								FOXI3 (33060 upstream) : C2orf51 (39056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88799498	88799498	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88799498delA								FOXI3 (47445 upstream) : C2orf51 (24671 downstream)																																			---	---	---	---
RPIA	22934	broad.mit.edu	37	2	89013430	89013431	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89013430_89013431delTT	uc002ste.2	+							NM_144563	NP_653164			ribose 5-phosphate isomerase A						pentose-phosphate shunt, non-oxidative branch	cytosol	ribose-5-phosphate isomerase activity			ovary(1)	1		Acute lymphoblastic leukemia(2;0.000456)|all_hematologic(2;0.00287)																---	---	---	---
FLJ40330	645784	broad.mit.edu	37	2	89104503	89104504	+	Intron	INS	-	C	C	rs149625899	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89104503_89104504insC	uc010fhg.2	+						FLJ40330_uc010fhh.2_Intron|FLJ40330_uc010fhi.1_Intron	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	89301139	89301139	+	Intron	DEL	C	-	-	rs111913624		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89301139delC	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	89336662	89336662	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89336662delT	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	89859747	89859756	+	IGR	DEL	TCCATTCCAT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89859747_89859756delTCCATTCCAT								FLJ40330 (753622 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	90475232	90475233	+	IGR	INS	-	TTCT	TTCT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90475232_90475233insTTCT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91660173	91660174	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91660173_91660174insC								None (None upstream) : LOC654342 (145018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91691066	91691066	+	IGR	DEL	A	-	-	rs78171192	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91691066delA								None (None upstream) : LOC654342 (114126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91738225	91738229	+	IGR	DEL	TCATC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91738225_91738229delTCATC								None (None upstream) : LOC654342 (66963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91765424	91765424	+	IGR	DEL	T	-	-	rs148923379		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91765424delT								None (None upstream) : LOC654342 (39768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91798087	91798087	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91798087delA								None (None upstream) : LOC654342 (7105 downstream)																																			---	---	---	---
LOC654342	654342	broad.mit.edu	37	2	91847514	91847515	+	Intron	INS	-	C	C	rs60502943		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91847514_91847515insC	uc002sts.3	-						LOC654342_uc002stt.2_Intron|LOC654342_uc010yub.1_Intron					Homo sapiens cDNA clone IMAGE:4801360.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	91857931	91857931	+	IGR	DEL	T	-	-	rs1818340		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91857931delT								LOC654342 (9956 upstream) : GGT8P (105437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92071842	92071842	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92071842delT								GGT8P (101689 upstream) : FKSG73 (57317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92076875	92076875	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92076875delT								GGT8P (106722 upstream) : FKSG73 (52284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	95391333	95391333	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95391333delA								None (None upstream) : ANKRD20B (35342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	96183238	96183238	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96183238delT								FAHD2A (104360 upstream) : TRIM43 (74528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	96524948	96524948	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96524948delT	uc002sva.1	-						uc002suz.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	96820358	96820358	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96820358delC								DUSP2 (9179 upstream) : STARD7 (30247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	96828370	96828372	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96828370_96828372delTTT								DUSP2 (17191 upstream) : STARD7 (22233 downstream)																																			---	---	---	---
SNRNP200	23020	broad.mit.edu	37	2	96942485	96942485	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96942485delA	uc002svu.2	-						SNRNP200_uc002svt.2_Intron|SNRNP200_uc010yuj.1_Intron	NM_014014	NP_054733			activating signal cointegrator 1 complex subunit							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10																		---	---	---	---
SNRNP200	23020	broad.mit.edu	37	2	96955213	96955213	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96955213delT	uc002svu.2	-						SNRNP200_uc002svw.1_Intron	NM_014014	NP_054733			activating signal cointegrator 1 complex subunit							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10																		---	---	---	---
ANKRD39	51239	broad.mit.edu	37	2	97525052	97525052	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97525052delT	uc002sxd.3	-							NM_016466	NP_057550			ankyrin repeat domain 39												0																		---	---	---	---
ANKRD36	375248	broad.mit.edu	37	2	97809410	97809410	+	Intron	DEL	A	-	-	rs146553468		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97809410delA	uc010yva.1	+						ANKRD36_uc010yuz.1_Intron|ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron	NM_001164315	NP_001157787			ankyrin repeat domain 36												0																		---	---	---	---
ANKRD36	375248	broad.mit.edu	37	2	97835482	97835484	+	Intron	DEL	GGG	-	-	rs75624212		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97835482_97835484delGGG	uc010yva.1	+						ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron|ANKRD36_uc002sxq.1_Intron	NM_001164315	NP_001157787			ankyrin repeat domain 36												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	99015600	99015604	+	IGR	DEL	AAAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99015600_99015604delAAAAA								CNGA3 (543 upstream) : INPP4A (45717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	99377835	99377835	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99377835delT								MGAT4A (30246 upstream) : C2orf55 (32474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	99402234	99402234	+	IGR	DEL	T	-	-	rs74868220		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99402234delT								MGAT4A (54645 upstream) : C2orf55 (8075 downstream)																																			---	---	---	---
C2orf55	343990	broad.mit.edu	37	2	99453919	99453920	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99453919_99453920delAA	uc002szf.1	-							NM_207362	NP_997245			hypothetical protein LOC343990												0																		---	---	---	---
TSGA10	80705	broad.mit.edu	37	2	99655772	99655774	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99655772_99655774delAAA	uc002szg.3	-						TSGA10_uc002szh.3_Intron|TSGA10_uc002szi.3_Intron|TSGA10_uc010fin.1_Intron	NM_182911	NP_878915			testis specific, 10						spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
EIF5B	9669	broad.mit.edu	37	2	99977965	99977965	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99977965delA	uc002tab.2	+	4	785	c.601delA	c.(601-603)AAAfs	p.K201fs		NM_015904	NP_056988	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	201					regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
REV1	51455	broad.mit.edu	37	2	100051004	100051004	+	Intron	DEL	T	-	-	rs67016484		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100051004delT	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					---	---	---	---
REV1	51455	broad.mit.edu	37	2	100051316	100051317	+	Intron	INS	-	A	A	rs145320463	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100051316_100051317insA	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	100126637	100126637	+	IGR	DEL	T	-	-	rs79664989		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100126637delT								REV1 (20157 upstream) : AFF3 (37081 downstream)																																			---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100456080	100456080	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100456080delT	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100663429	100663429	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100663429delA	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																		---	---	---	---
LONRF2	164832	broad.mit.edu	37	2	100898348	100898348	+	3'UTR	DEL	T	-	-	rs71890189		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100898348delT	uc002tal.3	-	12					LONRF2_uc010yvs.1_RNA	NM_198461	NP_940863			LON peptidase N-terminal domain and ring finger						proteolysis		ATP-dependent peptidase activity|zinc ion binding			large_intestine(1)|skin(1)	2																		---	---	---	---
CHST10	9486	broad.mit.edu	37	2	101018332	101018332	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101018332delT	uc002tam.2	-							NM_004854	NP_004845			HNK-1 sulfotransferase						carbohydrate biosynthetic process|cell adhesion	Golgi membrane|integral to membrane|membrane fraction				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	101069951	101069951	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101069951delT								CHST10 (35860 upstream) : NMS (16993 downstream)																																			---	---	---	---
TBC1D8	11138	broad.mit.edu	37	2	101628160	101628163	+	Intron	DEL	CTGT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101628160_101628163delCTGT	uc010fiv.2	-						RPL31_uc010yvu.1_Intron|RPL31_uc010yvv.1_Intron|RPL31_uc010fiu.1_Intron|TBC1D8_uc002tau.3_Intron	NM_001102426	NP_001095896			TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	102225015	102225016	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102225015_102225016insC								RFX8 (133850 upstream) : MAP4K4 (89472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	102248945	102248945	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102248945delA								RFX8 (157780 upstream) : MAP4K4 (65543 downstream)																																			---	---	---	---
MAP4K4	9448	broad.mit.edu	37	2	102423503	102423504	+	Intron	INS	-	T	T	rs113890224		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102423503_102423504insT	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Intron|MAP4K4_uc010fiw.1_Intron	NM_145687	NP_663720			mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
IL1R1	3554	broad.mit.edu	37	2	102748107	102748108	+	Intron	INS	-	A	A	rs150959607	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102748107_102748108insA	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)													---	---	---	---
TMEM182	130827	broad.mit.edu	37	2	103355145	103355145	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103355145delA	uc002tcc.3	+						TMEM182_uc002tcd.3_Intron|MFSD9_uc002tcb.2_5'Flank|MFSD9_uc010fja.2_5'Flank	NM_144632	NP_653233			transmembrane protein 182 precursor							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	103653423	103653423	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103653423delT								TMEM182 (219287 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	105388666	105388666	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105388666delA								LOC150568 (259452 upstream) : POU3F3 (83303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	106225190	106225190	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106225190delT	uc002tdf.2	-											Homo sapiens hypothetical protein LOC285000, mRNA (cDNA clone IMAGE:3925223), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	106552823	106552824	+	IGR	INS	-	AC	AC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106552823_106552824insAC								NCK2 (42097 upstream) : C2orf40 (129289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107175441	107175441	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107175441delT								RGPD3 (90640 upstream) : ST6GAL2 (242617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107315190	107315190	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107315190delA								RGPD3 (230389 upstream) : ST6GAL2 (102868 downstream)																																			---	---	---	---
ST6GAL2	84620	broad.mit.edu	37	2	107483057	107483057	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107483057delC	uc002tdq.2	-						ST6GAL2_uc002tdr.2_Intron|ST6GAL2_uc002tds.3_Intron	NM_001142351	NP_001135823			ST6 beta-galactosamide						growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(4)|skin(1)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	107790828	107790828	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107790828delT								ST6GAL2 (287265 upstream) : LOC729121 (648692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108387641	108387641	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108387641delA								ST6GAL2 (884078 upstream) : LOC729121 (51879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108387710	108387710	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108387710delA								ST6GAL2 (884147 upstream) : LOC729121 (51810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108637977	108637977	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108637977delT								SLC5A7 (7538 upstream) : SULT1C3 (225674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108751251	108751251	+	IGR	DEL	T	-	-	rs67917782		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108751251delT								SLC5A7 (120812 upstream) : SULT1C3 (112400 downstream)																																			---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109102254	109102254	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109102254delA	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																		---	---	---	---
SH3RF3	344558	broad.mit.edu	37	2	109794006	109794006	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109794006delG	uc010ywt.1	+							NM_001099289	NP_001092759			SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1																		---	---	---	---
SEPT10	151011	broad.mit.edu	37	2	110346428	110346432	+	Intron	DEL	AAAAA	-	-	rs147171145		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110346428_110346432delAAAAA	uc002tew.2	-						SEPT10_uc010ywu.1_Intron|SEPT10_uc002tex.2_Intron|SEPT10_uc002tey.2_Intron|SEPT10_uc010ywv.1_Intron	NM_144710	NP_653311			septin 10 isoform 1						cell cycle|cell division	septin complex	GTP binding				0																		---	---	---	---
ACOXL	55289	broad.mit.edu	37	2	111604766	111604766	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111604766delT	uc002tgr.3	+						ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986			acyl-Coenzyme A oxidase-like 2						fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	111947816	111947817	+	IGR	INS	-	AA	AA	rs113012716		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111947816_111947817insAA								BCL2L11 (21794 upstream) : LOC541471 (17542 downstream)																																			---	---	---	---
LOC541471	541471	broad.mit.edu	37	2	112170955	112170956	+	Intron	INS	-	AC	AC	rs62160678		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112170955_112170956insAC	uc002the.2	-						LOC541471_uc010yxl.1_Intron					Homo sapiens hypothetical LOC541471, mRNA (cDNA clone IMAGE:3459303).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	112392288	112392288	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112392288delA								LOC541471 (139596 upstream) : ANAPC1 (134353 downstream)																																			---	---	---	---
TMEM87B	84910	broad.mit.edu	37	2	112875240	112875240	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112875240delA	uc002thm.2	+	19						NM_032824	NP_116213			transmembrane protein 87B precursor							integral to membrane					0																		---	---	---	---
FBLN7	129804	broad.mit.edu	37	2	112945285	112945285	+	3'UTR	DEL	T	-	-	rs76063207		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112945285delT	uc002tho.1	+	8					FBLN7_uc002thn.2_3'UTR|FBLN7_uc010fki.1_3'UTR|FBLN7_uc010fkj.1_3'UTR	NM_153214	NP_694946			fibulin 7 isoform 1						cell adhesion	proteinaceous extracellular matrix	calcium ion binding|heparin binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TTL	150465	broad.mit.edu	37	2	113278192	113278193	+	Intron	INS	-	TA	TA	rs138859384	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113278192_113278193insTA	uc002thu.2	+						TTL_uc010fkm.1_Intron	NM_153712	NP_714923			tubulin tyrosine ligase						protein modification process		ATP binding|tubulin-tyrosine ligase activity				0		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)				T	ETV6	ALL								---	---	---	---
PSD4	23550	broad.mit.edu	37	2	113928595	113928595	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113928595delA	uc002tjc.2	+						PSD4_uc002tjd.2_5'Flank|PSD4_uc002tje.2_5'Flank	NM_012455	NP_036587			pleckstrin and Sec7 domain containing 4						regulation of ARF protein signal transduction	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
PAX8	7849	broad.mit.edu	37	2	114007470	114007470	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114007470delT	uc010yxt.1	-						PAX8_uc010yxu.1_Intron|PAX8_uc010yxv.1_Intron|PAX8_uc002tjm.2_Intron|PAX8_uc002tjn.2_Intron|PAX8_uc010fku.1_Intron|LOC654433_uc002tjq.3_Intron|LOC654433_uc010fks.2_Intron|LOC654433_uc010fkt.2_Intron|LOC654433_uc002tjr.3_Intron|LOC654433_uc002tjs.3_5'Flank	NM_003466	NP_003457			paired box 8 isoform PAX8A						branching involved in ureteric bud morphogenesis|cellular response to gonadotropin stimulus|central nervous system development|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric comma-shaped body morphogenesis|metanephric distal convoluted tubule development|metanephric nephron tubule formation|metanephric S-shaped body morphogenesis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|otic vesicle development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of thyroid-stimulating hormone secretion|thyroid gland development|transcription, DNA-dependent	nucleoplasm	protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity			ovary(1)|lung(1)	2								T	PPARG	follicular thyroid		Thyroid dysgenesis 				OREG0014907	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CBWD2	150472	broad.mit.edu	37	2	114217481	114217481	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114217481delA	uc002tju.2	+						CBWD2_uc010yxw.1_Intron|CBWD2_uc002tjv.2_Intron|CBWD2_uc010fkv.2_Intron	NM_172003	NP_742000			COBW domain-containing protein 2								ATP binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	114739955	114739955	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114739955delT	uc002tky.1	+						uc002tkz.1_Intron					full-length cDNA clone CS0DI083YD04 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	114820512	114820512	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114820512delA								ACTR3 (104345 upstream) : DPP10 (379387 downstream)																																			---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115366282	115366283	+	Intron	DEL	AA	-	-	rs75634061		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115366282_115366283delAA	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115376959	115376960	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115376959_115376960delTG	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115559395	115559395	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115559395delT	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115742797	115742797	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115742797delT	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115755713	115755714	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115755713_115755714insA	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115837604	115837604	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115837604delT	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																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	116264634	116264635	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116264634_116264635delAC	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	116572705	116572705	+	Intron	DEL	T	-	-	rs79224686		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116572705delT	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	116898560	116898560	+	IGR	DEL	A	-	-	rs138153822		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116898560delA								DPP10 (296624 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117542057	117542057	+	IGR	DEL	T	-	-	rs34051687		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117542057delT								DPP10 (940121 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117567784	117567785	+	IGR	DEL	TG	-	-	rs10541597		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117567784_117567785delTG								DPP10 (965848 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117609308	117609308	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117609308delA								None (None upstream) : DDX18 (962947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118160119	118160120	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118160119_118160120delTT								None (None upstream) : DDX18 (412135 downstream)																																			---	---	---	---
C2orf76	130355	broad.mit.edu	37	2	120109540	120109540	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120109540delA	uc002tls.2	-						C2orf76_uc010flf.1_Intron|C2orf76_uc010yyg.1_Intron|C2orf76_uc002tlt.2_Intron|C2orf76_uc002tlu.2_Intron	NM_001017927	NP_001017927			hypothetical protein LOC130355												0																		---	---	---	---
PTPN4	5775	broad.mit.edu	37	2	120521719	120521720	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120521719_120521720insT	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	120587566	120587566	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120587566delT	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)													---	---	---	---
EPB41L5	57669	broad.mit.edu	37	2	120918261	120918261	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120918261delA	uc002tmg.2	+						EPB41L5_uc010fll.2_Intron|EPB41L5_uc010flm.2_Intron	NM_020909	NP_065960			erythrocyte membrane protein band 4.1 like 5							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	121296397	121296397	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121296397delC								LOC84931 (72472 upstream) : GLI2 (196802 downstream)																																			---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121527455	121527456	+	Intron	DEL	TG	-	-	rs112913541		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121527455_121527456delTG	uc010yyu.1	+						GLI2_uc002tmp.1_Intron					SubName: Full=cDNA FLJ60878, highly similar to Homo sapiens GLI-Kruppel family member GLI2, mRNA;						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)																---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121655754	121655755	+	Intron	DEL	AC	-	-	rs71974395		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121655754_121655755delAC	uc010flp.2	+						GLI2_uc010yyu.1_Intron|GLI2_uc002tmp.1_Intron|GLI2_uc010fln.1_Intron|GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Intron|GLI2_uc010flo.1_Intron|GLI2_uc002tmw.1_Intron	NM_005270	NP_005261			GLI-Kruppel family member GLI2						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)																---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121656982	121656983	+	Intron	INS	-	AC	AC	rs148463486	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121656982_121656983insAC	uc010flp.2	+						GLI2_uc010yyu.1_Intron|GLI2_uc002tmp.1_Intron|GLI2_uc010fln.1_Intron|GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Intron|GLI2_uc010flo.1_Intron|GLI2_uc002tmw.1_Intron	NM_005270	NP_005261			GLI-Kruppel family member GLI2						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)																---	---	---	---
CLASP1	23332	broad.mit.edu	37	2	122220294	122220294	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122220294delT	uc002tnc.2	-						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	122466740	122466740	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122466740delT	uc002tnj.1	+											Homo sapiens cDNA FLJ40945 fis, clone UTERU2008747.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	122699889	122699891	+	IGR	DEL	CTT	-	-	rs1400828	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122699889_122699891delCTT								TSN (174463 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123375152	123375152	+	IGR	DEL	T	-	-	rs34366781		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123375152delT								TSN (849726 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123621710	123621710	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123621710delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124628767	124628767	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124628767delT								None (None upstream) : CNTNAP5 (154097 downstream)																																			---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125314906	125314906	+	Intron	DEL	A	-	-	rs72298715		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125314906delA	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	125689499	125689499	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125689499delA								CNTNAP5 (16638 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126148348	126148349	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126148348_126148349insG								CNTNAP5 (475487 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126288710	126288712	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126288710_126288712delTTT								CNTNAP5 (615849 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126498657	126498657	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126498657delA								CNTNAP5 (825796 upstream) : GYPC (915027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127802034	127802035	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127802034_127802035delCA								GYPC (347789 upstream) : BIN1 (3572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	128215854	128215854	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128215854delA								PROC (29038 upstream) : IWS1 (22529 downstream)																																			---	---	---	---
POLR2D	5433	broad.mit.edu	37	2	128605982	128605982	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128605982delT	uc002tpj.2	-						uc010fmc.2_5'Flank|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	128825103	128825104	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128825103_128825104delAA								SAP130 (39470 upstream) : UGGT1 (23650 downstream)																																			---	---	---	---
UGGT1	56886	broad.mit.edu	37	2	128888377	128888377	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128888377delT	uc002tps.2	+						UGGT1_uc010fme.1_Intron|UGGT1_uc002tpr.2_Intron	NM_020120	NP_064505			UDP-glucose ceramide glucosyltransferase-like 1						'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	129097969	129097970	+	IGR	INS	-	TGG	TGG	rs146005050	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129097969_129097970insTGG								HS6ST1 (21798 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130152630	130152631	+	IGR	INS	-	A	A	rs7604373	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130152630_130152631insA								None (None upstream) : LOC389033 (527804 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130193868	130193868	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130193868delT								None (None upstream) : LOC389033 (486567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	131108658	131108658	+	IGR	DEL	T	-	-	rs11325164		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131108658delT								IMP4 (4461 upstream) : PTPN18 (4922 downstream)																																			---	---	---	---
PLEKHB2	55041	broad.mit.edu	37	2	131874692	131874692	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131874692delA	uc002tsg.3	+						PLEKHB2_uc002tsh.2_Intron|PLEKHB2_uc002tsj.3_Intron|PLEKHB2_uc002tsf.3_Intron|PLEKHB2_uc010zao.1_Intron|PLEKHB2_uc010zap.1_Intron|PLEKHB2_uc010zaq.1_Intron	NM_001100623	NP_001094093			pleckstrin homology domain containing, family B							membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0828)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	132158953	132158953	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132158953delA	uc002tss.2	+						uc010fmz.1_5'Flank					Homo sapiens cDNA FLJ43994 fis, clone TESTI4020806.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	132207979	132207979	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132207979delT								LOC401010 (5512 upstream) : TUBA3D (25687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	132770579	132770582	+	IGR	DEL	CTAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132770579_132770582delCTAA								C2orf27B (211345 upstream) : NCRNA00164 (134582 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	132796584	132796584	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132796584delT								C2orf27B (237350 upstream) : NCRNA00164 (108580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133030268	133030269	+	IGR	INS	-	A	A	rs62167504	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133030268_133030269insA								NCRNA00164 (14726 upstream) : GPR39 (143878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133043512	133043512	+	IGR	DEL	A	-	-	rs71001182		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133043512delA								NCRNA00164 (27970 upstream) : GPR39 (130635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133062601	133062604	+	Intron	DEL	CTCA	-	-	rs4063334	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133062601_133062604delCTCA	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	133072392	133072393	+	Intron	INS	-	AA	AA	rs141663990		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133072392_133072393insAA	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	133110394	133110394	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133110394delG								NCRNA00164 (94852 upstream) : GPR39 (63753 downstream)																																			---	---	---	---
GPR39	2863	broad.mit.edu	37	2	133241402	133241402	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133241402delA	uc002ttl.2	+							NM_001508	NP_001499			G protein-coupled receptor 39							integral to plasma membrane	G-protein coupled receptor activity|metal ion binding				0																		---	---	---	---
GPR39	2863	broad.mit.edu	37	2	133308857	133308857	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133308857delA	uc002ttl.2	+							NM_001508	NP_001499			G protein-coupled receptor 39							integral to plasma membrane	G-protein coupled receptor activity|metal ion binding				0																		---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133694272	133694273	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133694272_133694273insA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|NCKAP5_uc002tts.1_Intron	NM_207363	NP_997246			Nck-associated protein 5 isoform 1								protein binding				0																		---	---	---	---
RAB3GAP1	22930	broad.mit.edu	37	2	135887668	135887668	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135887668delT	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	135997553	135997554	+	Intron	DEL	AA	-	-	rs148300644		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135997553_135997554delAA	uc002tum.2	-						ZRANB3_uc002tuk.2_Intron|ZRANB3_uc002tul.2_Intron	NM_032143	NP_115519			zinc finger, RAN-binding domain containing 3							intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	136490550	136490551	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136490550_136490551insC								R3HDM1 (7714 upstream) : UBXN4 (8638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	136641168	136641168	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136641168delA								MCM6 (7157 upstream) : DARS (23086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	136884095	136884095	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136884095delT								CXCR4 (8370 upstream) : THSD7B (639020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	136956493	136956493	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136956493delT								CXCR4 (80768 upstream) : THSD7B (566622 downstream)																																			---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	138417162	138417162	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138417162delA	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	139027651	139027651	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139027651delA								HNMT (253718 upstream) : SPOPL (231699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	139045444	139045447	+	3'UTR	DEL	TTAA	-	-	rs11900034	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139045444_139045447delTTAA	uc010zbk.1	-	1										SubName: Full=cDNA, FLJ79100, highly similar to 14-3-3 protein epsilon (14-3-3E);																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	140263625	140263625	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140263625delA								NXPH2 (725814 upstream) : LRP1B (725371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140333271	140333272	+	IGR	DEL	TT	-	-	rs71780757		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140333271_140333272delTT								NXPH2 (795460 upstream) : LRP1B (655724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140746155	140746155	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140746155delT								None (None upstream) : LRP1B (242841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140963857	140963857	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140963857delT								None (None upstream) : LRP1B (25139 downstream)																																			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141084269	141084269	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141084269delA	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	141719572	141719572	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141719572delT	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	141909690	141909690	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141909690delT	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	142030361	142030361	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142030361delA	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	142278043	142278043	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142278043delT	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	142348109	142348109	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142348109delT	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-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)													---	---	---	---
KYNU	8942	broad.mit.edu	37	2	143787161	143787161	+	Intron	DEL	C	-	-	rs6429999	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143787161delC	uc002tvl.2	+						KYNU_uc010fnm.2_Intron	NM_003937	NP_003928			kynureninase (L-kynurenine hydrolase) isoform a						anthranilate metabolic process|NAD biosynthetic process|quinolinate biosynthetic process|response to interferon-gamma|response to vitamin B6	cytosol|mitochondrion|soluble fraction	kynureninase activity|protein homodimerization activity			skin(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.072)	L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)													---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144075578	144075578	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144075578delT	uc002tvm.3	+						ARHGAP15_uc010zbl.1_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	144742869	144742869	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144742869delC	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	NM_001006636	NP_001006637			glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)														---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	144986524	144986525	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144986524_144986525delAA	uc002tvp.2	-						GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.2_Intron|GTDC1_uc010fnn.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637			glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	148294249	148294252	+	IGR	DEL	ATAG	-	-	rs71999093		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148294249_148294252delATAG								PABPC1P2 (945692 upstream) : ACVR2A (307834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	148450024	148450025	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148450024_148450025delAC								None (None upstream) : ACVR2A (152061 downstream)																																			---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148683686	148683686	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148683686delA	uc002twg.2	+	11	1572	c.1303delA	c.(1303-1305)AAAfs	p.K435fs	ACVR2A_uc010zbn.1_Frame_Shift_Del_p.K327fs|ACVR2A_uc002twh.2_Frame_Shift_Del_p.K435fs	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	435	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)														---	---	---	---
MBD5	55777	broad.mit.edu	37	2	148789969	148789969	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148789969delT	uc002twm.3	+							NM_018328	NP_060798			methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)														---	---	---	---
KIF5C	3800	broad.mit.edu	37	2	149841049	149841049	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149841049delA	uc010zbu.1	+						KIF5C_uc002tws.1_Intron|KIF5C_uc002twt.2_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)														---	---	---	---
KIF5C	3800	broad.mit.edu	37	2	149864394	149864394	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149864394delT	uc010zbu.1	+						KIF5C_uc002tws.1_Intron|KIF5C_uc002twu.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)														---	---	---	---
LYPD6B	130576	broad.mit.edu	37	2	150009996	150009998	+	Intron	DEL	AAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150009996_150009998delAAG	uc002twv.1	+						LYPD6B_uc002tww.1_Intron|LYPD6B_uc002twx.1_Intron	NM_177964	NP_808879			LY6/PLAUR domain containing 6B							anchored to membrane|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	150717251	150717252	+	IGR	INS	-	A	A	rs150664420	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150717251_150717252insA								MMADHC (272921 upstream) : RND3 (607460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151294191	151294198	+	IGR	DEL	GTGTGTGT	-	-	rs72529653		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151294191_151294198delGTGTGTGT								MMADHC (849861 upstream) : RND3 (30514 downstream)																																			---	---	---	---
RND3	390	broad.mit.edu	37	2	151334916	151334916	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151334916delA	uc002txe.2	-						RND3_uc002txf.2_Intron|RND3_uc002txg.2_Intron|RND3_uc010zbv.1_Intron|RND3_uc010zbw.1_Intron	NM_005168	NP_005159			ras homolog gene family, member E precursor						actin cytoskeleton organization|cell adhesion|small GTPase mediated signal transduction	Golgi membrane	GTP binding|GTPase activity			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.106)														---	---	---	---
RND3	390	broad.mit.edu	37	2	151343675	151343675	+	Intron	DEL	T	-	-	rs73967183		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151343675delT	uc002txe.2	-						RND3_uc002txf.2_Intron|RND3_uc002txg.2_Intron|RND3_uc010zbv.1_Intron|RND3_uc010zbw.1_5'Flank	NM_005168	NP_005159			ras homolog gene family, member E precursor						actin cytoskeleton organization|cell adhesion|small GTPase mediated signal transduction	Golgi membrane	GTP binding|GTPase activity			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.106)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	151449769	151449770	+	IGR	DEL	AC	-	-	rs66882966		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151449769_151449770delAC								RND3 (105589 upstream) : RBM43 (654959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151982957	151982957	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151982957delA								RND3 (638777 upstream) : RBM43 (121772 downstream)																																			---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152695482	152695483	+	3'UTR	DEL	TT	-	-	rs111950042		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152695482_152695483delTT	uc002tya.2	-	14					CACNB4_uc002txy.2_3'UTR|CACNB4_uc002txz.2_3'UTR|CACNB4_uc010fnz.2_3'UTR	NM_000726	NP_000717			calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)													---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152727578	152727578	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152727578delC	uc002tya.2	-						CACNB4_uc002txy.2_Intron|CACNB4_uc002txz.2_Intron|CACNB4_uc010fnz.2_Intron|CACNB4_uc002tyb.2_Intron	NM_000726	NP_000717			calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)													---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152858233	152858234	+	Intron	DEL	AA	-	-	rs71410452		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152858233_152858234delAA	uc002tya.2	-						CACNB4_uc002txz.2_Intron|CACNB4_uc010fnz.2_Intron	NM_000726	NP_000717			calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)													---	---	---	---
FMNL2	114793	broad.mit.edu	37	2	153471358	153471358	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153471358delT	uc002tye.2	+							NM_052905	NP_443137			formin-like 2						actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
FMNL2	114793	broad.mit.edu	37	2	153481699	153481699	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153481699delA	uc002tye.2	+						FMNL2_uc010fob.2_Intron|FMNL2_uc002tyf.2_Intron	NM_052905	NP_443137			formin-like 2						actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
GALNT13	114805	broad.mit.edu	37	2	154943815	154943815	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154943815delT	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	155069347	155069347	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155069347delT	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron|GALNT13_uc010foc.1_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	156011663	156011663	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156011663delA								KCNJ3 (298649 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156605045	156605045	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156605045delT								KCNJ3 (892031 upstream) : NR4A2 (575901 downstream)																																			---	---	---	---
ACVR1C	130399	broad.mit.edu	37	2	158430055	158430056	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158430055_158430056delTT	uc002tzk.3	-						ACVR1C_uc002tzl.3_Intron|ACVR1C_uc010fof.2_Intron|ACVR1C_uc010foe.2_Intron	NM_145259	NP_660302			activin A receptor, type IC isoform 1						apoptosis|cell differentiation|regulation of apoptosis	activin receptor complex	activin receptor activity, type I|ATP binding|transforming growth factor beta receptor activity			lung(3)|ovary(2)|skin(2)	7																		---	---	---	---
ACVR1	90	broad.mit.edu	37	2	158620489	158620490	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158620489_158620490insC	uc002tzm.3	-						ACVR1_uc002tzn.3_Intron|ACVR1_uc010fog.2_Intron	NM_001111067	NP_001104537			activin A receptor, type I precursor						BMP signaling pathway|G1/S transition of mitotic cell cycle|negative regulation of activin receptor signaling pathway|negative regulation of apoptosis|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	activin receptor complex	activin binding|ATP binding|follistatin binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta binding			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)													---	---	---	---
ACVR1	90	broad.mit.edu	37	2	158735273	158735274	+	5'Flank	DEL	GT	-	-	rs112534857		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158735273_158735274delGT	uc010fog.2	-							NM_001111067	NP_001104537			activin A receptor, type I precursor						BMP signaling pathway|G1/S transition of mitotic cell cycle|negative regulation of activin receptor signaling pathway|negative regulation of apoptosis|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	activin receptor complex	activin binding|ATP binding|follistatin binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta binding			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)													---	---	---	---
UPP2	151531	broad.mit.edu	37	2	158973481	158973481	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158973481delA	uc002tzp.2	+						UPP2_uc002tzo.2_Intron	NM_173355	NP_775491			uridine phosphorylase 2 isoform a						nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|uridine metabolic process	cytosol|type III intermediate filament	uridine phosphorylase activity				0																		---	---	---	---
LY75	4065	broad.mit.edu	37	2	160666554	160666554	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160666554delT	uc002ubc.3	-						LY75_uc002ubb.3_Intron|LY75_uc010fos.2_Intron	NM_002349	NP_002340			lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)														---	---	---	---
RBMS1	5937	broad.mit.edu	37	2	161322399	161322400	+	Intron	INS	-	CACACT	CACACT	rs72016205		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161322399_161322400insCACACT	uc002ubo.2	-						RBMS1_uc002ubn.2_Intron|RBMS1_uc002ubi.3_Intron|RBMS1_uc002ubm.2_Intron|RBMS1_uc002ubp.2_Intron|RBMS1_uc010fox.2_Intron	NM_016836	NP_058520			RNA binding motif, single stranded interacting						DNA replication|RNA processing	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding|single-stranded DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	161951096	161951096	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161951096delC								RBMS1 (600778 upstream) : TANK (42370 downstream)																																			---	---	---	---
TANK	10010	broad.mit.edu	37	2	162085047	162085047	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162085047delA	uc002ubr.1	+						TANK_uc002ubs.2_Intron	NM_004180	NP_004171			TRAF interacting protein TANK isoform a							cytosol	metal ion binding|protein binding			ovary(1)	1																		---	---	---	---
SLC4A10	57282	broad.mit.edu	37	2	162738845	162738845	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162738845delT	uc002ubx.3	+						SLC4A10_uc010fpa.1_Intron|SLC4A10_uc010zcr.1_Intron|SLC4A10_uc002uby.3_Intron|SLC4A10_uc010zcs.1_Intron	NM_022058	NP_071341			solute carrier family 4, sodium bicarbonate						bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5																		---	---	---	---
GCA	25801	broad.mit.edu	37	2	163216300	163216300	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163216300delA	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																		---	---	---	---
KCNH7	90134	broad.mit.edu	37	2	163436324	163436324	+	Intron	DEL	T	-	-	rs113283141		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163436324delT	uc002uch.1	-						KCNH7_uc002uci.2_Intron	NM_033272	NP_150375			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	164113525	164113525	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	164606328	164606331	+	IGR	DEL	TCCT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164606328_164606331delTCCT								FIGN (13815 upstream) : GRB14 (743002 downstream)																																			---	---	---	---
SCN3A	6328	broad.mit.edu	37	2	165971884	165971884	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165971884delT	uc002ucx.2	-						SCN3A_uc002ucy.2_Intron|SCN3A_uc002ucz.2_Intron|SCN3A_uc002uda.1_Intron|SCN3A_uc002udb.1_Intron	NM_006922	NP_008853			sodium channel, voltage-gated, type III, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)													---	---	---	---
SCN3A	6328	broad.mit.edu	37	2	166023413	166023413	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166023413delT	uc002ucx.2	-						SCN3A_uc002ucy.2_Intron|SCN3A_uc002ucz.2_Intron|SCN3A_uc002uda.1_Intron|SCN3A_uc002udb.1_Intron	NM_006922	NP_008853			sodium channel, voltage-gated, type III, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)													---	---	---	---
SCN3A	6328	broad.mit.edu	37	2	166042814	166042814	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166042814delA	uc002ucx.2	-						SCN3A_uc002ucy.2_Intron|SCN3A_uc002ucz.2_Intron	NM_006922	NP_008853			sodium channel, voltage-gated, type III, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)													---	---	---	---
SCN2A	6326	broad.mit.edu	37	2	166150884	166150884	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166150884delA	uc002udc.2	+						SCN2A_uc002udd.2_Intron|SCN2A_uc002ude.2_5'Flank	NM_001040142	NP_001035232			sodium channel, voltage-gated, type II, alpha						myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)													---	---	---	---
SCN9A	6335	broad.mit.edu	37	2	167186077	167186078	+	Intron	DEL	GG	-	-	rs71822149		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167186077_167186078delGG	uc010fpl.2	-							NM_002977	NP_002968			sodium channel, voltage-gated, type IX, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)													---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	167877083	167877084	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167877083_167877084delTG	uc002udx.2	+						XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron	NM_152381	NP_689594			xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	167906020	167906020	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167906020delA	uc002udx.2	+						XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron	NM_152381	NP_689594			xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168024882	168024882	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168024882delT	uc002udx.2	+						XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Intron	NM_152381	NP_689594			xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
NOSTRIN	115677	broad.mit.edu	37	2	169644386	169644387	+	5'UTR	DEL	AG	-	-	rs140770843		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169644386_169644387delAG	uc002uef.2	+	2					uc002ued.2_5'Flank	NM_001039724	NP_001034813			nitric oxide synthase trafficker isoform 2						endocytosis|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	protein binding				0																		---	---	---	---
NOSTRIN	115677	broad.mit.edu	37	2	169699335	169699335	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169699335delT	uc002ueg.2	+						NOSTRIN_uc002uef.2_Intron|NOSTRIN_uc002uei.2_Intron|NOSTRIN_uc010fpu.2_Intron|NOSTRIN_uc002ueh.2_Intron|NOSTRIN_uc002uej.2_Intron	NM_001039724	NP_001034813			nitric oxide synthase trafficker isoform 2						endocytosis|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	protein binding				0																		---	---	---	---
NOSTRIN	115677	broad.mit.edu	37	2	169705071	169705071	+	Intron	DEL	A	-	-	rs11354593		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169705071delA	uc002ueg.2	+						NOSTRIN_uc002uef.2_Intron|NOSTRIN_uc002uei.2_Intron|NOSTRIN_uc010fpu.2_Intron|NOSTRIN_uc002ueh.2_Intron|NOSTRIN_uc002uej.2_Intron	NM_001039724	NP_001034813			nitric oxide synthase trafficker isoform 2						endocytosis|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	169776074	169776074	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169776074delT								G6PC2 (9565 upstream) : ABCB11 (3375 downstream)																																			---	---	---	---
LRP2	4036	broad.mit.edu	37	2	169994160	169994163	+	Intron	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169994160_169994163delAAAA	uc002ues.2	-							NM_004525	NP_004516			low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170093598	170093598	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170093598delA	uc002ues.2	-							NM_004525	NP_004516			low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
KBTBD10	10324	broad.mit.edu	37	2	170378426	170378426	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170378426delA	uc002ueu.1	+						KBTBD10_uc010zdh.1_Intron	NM_006063	NP_006054			kelch repeat and BTB (POZ) domain containing 10						striated muscle contraction	centrosome|nucleolus|plasma membrane|pseudopodium|ruffle					0																		---	---	---	---
FASTKD1	79675	broad.mit.edu	37	2	170394710	170394710	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170394710delT	uc002uev.3	-						FASTKD1_uc002uew.3_Intron|FASTKD1_uc002uex.3_Intron	NM_024622	NP_078898			FAST kinase domains 1						apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(4)	4																		---	---	---	---
UBR3	130507	broad.mit.edu	37	2	170897261	170897261	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170897261delT	uc010zdi.1	+						UBR3_uc002ufr.3_Intron|UBR3_uc010fqa.2_Intron|UBR3_uc002uft.3_Intron|UBR3_uc010zdj.1_Intron|UBR3_uc002ufu.3_Intron	NM_172070	NP_742067			E3 ubiquitin-protein ligase UBR3						sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	171604558	171604558	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171604558delA	uc002ugf.1	-											Homo sapiens cDNA FLJ13453 fis, clone PLACE1003205.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	172161778	172161779	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172161778_172161779delTT								TLK1 (73954 upstream) : METTL8 (12136 downstream)																																			---	---	---	---
METTL8	79828	broad.mit.edu	37	2	172174951	172174951	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172174951delT	uc010zdo.1	-	11					METTL8_uc002ugu.3_3'UTR|METTL8_uc002ugv.3_3'UTR|METTL8_uc002ugt.3_3'UTR|METTL8_uc002ugs.3_3'UTR|METTL8_uc010zdp.1_3'UTR	NM_024770	NP_079046			methyltransferase like 8								methyltransferase activity			ovary(1)	1																		---	---	---	---
METTL8	79828	broad.mit.edu	37	2	172217029	172217029	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172217029delA	uc010zdo.1	-						METTL8_uc002ugu.3_Intron|METTL8_uc002ugv.3_Intron|METTL8_uc002ugt.3_Intron|METTL8_uc002ugs.3_Intron|METTL8_uc010zdp.1_Intron	NM_024770	NP_079046			methyltransferase like 8								methyltransferase activity			ovary(1)	1																		---	---	---	---
DCAF17	80067	broad.mit.edu	37	2	172339179	172339179	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172339179delT	uc002ugx.2	+	14					DCAF17_uc010zdq.1_RNA|DCAF17_uc010zdr.1_RNA|DCAF17_uc010fqg.2_3'UTR	NM_025000	NP_079276			DDB1 and CUL4 associated factor 17 isoform 1							CUL4 RING ubiquitin ligase complex|integral to membrane|nucleolus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	172457444	172457445	+	IGR	INS	-	A	A	rs151036455		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172457444_172457445insA								CYBRD1 (42801 upstream) : DYNC1I2 (86537 downstream)																																			---	---	---	---
DYNC1I2	1781	broad.mit.edu	37	2	172584624	172584624	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172584624delT	uc002uha.1	+						DYNC1I2_uc002uhc.2_Intron|DYNC1I2_uc002uhb.1_Intron|DYNC1I2_uc010zds.1_Intron|DYNC1I2_uc002uhe.1_Intron|DYNC1I2_uc002uhf.1_Intron|DYNC1I2_uc010zdt.1_Intron|DYNC1I2_uc002uhg.1_Intron|DYNC1I2_uc010zdu.1_Intron	NM_001378	NP_001369			dynein, cytoplasmic 1, intermediate chain 2						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|microtubule-based movement|transport	centrosome|cytosol|dynein complex|microtubule|vesicle	microtubule motor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.198)															---	---	---	---
ITGA6	3655	broad.mit.edu	37	2	173368990	173368990	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173368990delA	uc002uhp.1	+	25					ITGA6_uc010zdy.1_3'UTR|ITGA6_uc002uho.1_3'UTR|ITGA6_uc010fqm.1_3'UTR	NM_001079818	NP_001073286			integrin alpha chain, alpha 6 isoform a						blood coagulation|cell adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|positive regulation of apoptosis|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter	integrin complex	protein binding|receptor activity			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0979)															---	---	---	---
RAPGEF4	11069	broad.mit.edu	37	2	173662239	173662239	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173662239delT	uc002uhv.3	+						RAPGEF4_uc002uhu.2_Intron|RAPGEF4_uc010fqn.2_Intron	NM_007023	NP_008954			Rap guanine nucleotide exchange factor (GEF) 4						blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	174414005	174414005	+	IGR	DEL	T	-	-	rs112517738		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174414005delT								CDCA7 (180287 upstream) : SP3 (359254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174752221	174752221	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174752221delT								CDCA7 (518503 upstream) : SP3 (21038 downstream)																																			---	---	---	---
OLA1	29789	broad.mit.edu	37	2	174938353	174938353	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174938353delT	uc002uih.2	-	11					OLA1_uc002uii.2_3'UTR|OLA1_uc010fqq.2_3'UTR|OLA1_uc002uij.2_3'UTR|OLA1_uc002uik.2_3'UTR|OLA1_uc010fqr.2_3'UTR	NM_013341	NP_037473			Obg-like ATPase 1 isoform 1						ATP catabolic process	cytoplasm	ATP binding|GTP binding|hydrolase activity|protein binding			ovary(1)|breast(1)	2																		---	---	---	---
WIPF1	7456	broad.mit.edu	37	2	175442646	175442646	+	Intron	DEL	A	-	-	rs113650894		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175442646delA	uc002uiy.2	-						uc002uiw.2_Intron|uc002uix.1_Intron|WIPF1_uc002uja.2_Intron|WIPF1_uc010fqt.1_Intron|WIPF1_uc002ujc.1_Intron|WIPF1_uc002uiz.2_Intron|WIPF1_uc002ujb.1_Intron|WIPF1_uc010zep.1_Intron	NM_003387	NP_003378			WAS/WASL interacting protein family, member 1						actin polymerization or depolymerization|protein complex assembly	cytoplasmic membrane-bounded vesicle	actin binding|profilin binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	177221023	177221026	+	IGR	DEL	CTTT	-	-	rs140826392		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177221023_177221026delCTTT								MTX2 (18272 upstream) : MIR1246 (244682 downstream)																																			---	---	---	---
TTC30A	92104	broad.mit.edu	37	2	178481375	178481375	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178481375delA	uc002ulo.2	-	1						NM_152275	NP_689488			tetratricopeptide repeat domain 30A						cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)															---	---	---	---
RBM45	129831	broad.mit.edu	37	2	178989549	178989550	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178989549_178989550insT	uc002ulv.2	+							NM_152945	NP_694453			RNA binding motif protein 45						cell differentiation|nervous system development	cytoplasm|nucleus	nucleotide binding|RNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)															---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179255915	179255915	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179255915delC	uc002ulx.2	+	22	2795	c.2417delC	c.(2416-2418)GCCfs	p.A806fs	OSBPL6_uc002uly.2_Frame_Shift_Del_p.A831fs|OSBPL6_uc010zfe.1_Frame_Shift_Del_p.A775fs|OSBPL6_uc002ulz.2_Frame_Shift_Del_p.A770fs|OSBPL6_uc002uma.2_Frame_Shift_Del_p.A810fs	NM_032523	NP_115912	Q9BZF3	OSBL6_HUMAN	oxysterol-binding protein-like protein 6 isoform	806					lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)															---	---	---	---
SESTD1	91404	broad.mit.edu	37	2	180032362	180032362	+	Intron	DEL	G	-	-	rs112114818		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180032362delG	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	180542745	180542745	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180542745delT	uc002unn.3	-						ZNF385B_uc002unm.2_Intron	NM_152520	NP_689733			zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)															---	---	---	---
ZNF385B	151126	broad.mit.edu	37	2	180554511	180554524	+	Intron	DEL	TGTGTGTGTGTGTG	-	-	rs112957152		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180554511_180554524delTGTGTGTGTGTGTG	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	180894680	180894680	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180894680delT								CWC22 (22840 upstream) : UBE2E3 (950432 downstream)																																			---	---	---	---
UBE2E3	10477	broad.mit.edu	37	2	181864329	181864329	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181864329delT	uc002unq.1	+						UBE2E3_uc002unr.1_Intron|UBE2E3_uc010fri.1_Intron	NM_182678	NP_872619			ubiquitin-conjugating enzyme E2E 3						protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|regulation of growth	cytoplasm|nucleolus	ATP binding|protein binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
UBE2E3	10477	broad.mit.edu	37	2	181887467	181887467	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181887467delA	uc002unq.1	+						UBE2E3_uc002unr.1_Intron|UBE2E3_uc010fri.1_Intron	NM_182678	NP_872619			ubiquitin-conjugating enzyme E2E 3						protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|regulation of growth	cytoplasm|nucleolus	ATP binding|protein binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
UBE2E3	10477	broad.mit.edu	37	2	181925322	181925322	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181925322delT	uc002unq.1	+						UBE2E3_uc002unr.1_Intron|UBE2E3_uc010fri.1_Intron	NM_182678	NP_872619			ubiquitin-conjugating enzyme E2E 3						protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|regulation of growth	cytoplasm|nucleolus	ATP binding|protein binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	182216993	182216993	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182216993delT	uc002uns.1	+											Homo sapiens cDNA FLJ43011 fis, clone BRTHA2015853.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	182646811	182646812	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182646811_182646812delTT								CERKL (101430 upstream) : SSFA2 (109660 downstream)																																			---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183139407	183139408	+	Intron	INS	-	TC	TC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183139407_183139408insTC	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	183359415	183359415	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183359415delT	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	183500402	183500403	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183500402_183500403delTC								PDE1A (112895 upstream) : DNAJC10 (80596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	183696648	183696649	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183696648_183696649delAA								DNAJC10 (53393 upstream) : FRZB (2088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	183743109	183743109	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183743109delA								FRZB (11611 upstream) : NCKAP1 (46497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	184434675	184434675	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184434675delT								NUP35 (408268 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	184931939	184931939	+	IGR	DEL	T	-	-	rs71401966		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184931939delT								NUP35 (905532 upstream) : ZNF804A (531154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	185085390	185085391	+	IGR	DEL	TT	-	-	rs77661063		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185085390_185085391delTT								None (None upstream) : ZNF804A (377702 downstream)																																			---	---	---	---
ZNF804A	91752	broad.mit.edu	37	2	185505082	185505082	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185505082delT	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	186254420	186254420	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186254420delA								ZNF804A (450208 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	186466986	186466986	+	IGR	DEL	A	-	-	rs67941020		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186466986delA								ZNF804A (662774 upstream) : ZC3H15 (883899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	186821297	186821298	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186821297_186821298insT								None (None upstream) : ZC3H15 (529587 downstream)																																			---	---	---	---
ITGAV	3685	broad.mit.edu	37	2	187505703	187505703	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187505703delA	uc002upq.2	+						ITGAV_uc010frs.2_Intron|ITGAV_uc010zfv.1_Intron	NM_002210	NP_002201			integrin alpha-V isoform 1 precursor						angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)														---	---	---	---
FAM171B	165215	broad.mit.edu	37	2	187582924	187582927	+	Intron	DEL	CTGT	-	-	rs150718172		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187582924_187582927delCTGT	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	187647628	187647628	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187647628delA								FAM171B (16944 upstream) : ZSWIM2 (44579 downstream)																																			---	---	---	---
GULP1	51454	broad.mit.edu	37	2	189239486	189239487	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189239486_189239487delAA	uc010fru.2	+						GULP1_uc002uqc.3_Intron|GULP1_uc002uqd.2_Intron|GULP1_uc010zfw.1_Intron|GULP1_uc002uqe.2_Intron|GULP1_uc002uqf.2_Intron|GULP1_uc002uqg.2_Intron	NM_016315	NP_057399			GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	189809538	189809538	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189809538delC								DIRC1 (154707 upstream) : COL3A1 (29561 downstream)																																			---	---	---	---
COL3A1	1281	broad.mit.edu	37	2	189857695	189857695	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189857695delA	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)													---	---	---	---
COL5A2	1290	broad.mit.edu	37	2	189936954	189936954	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189936954delA	uc002uqk.2	-						COL5A2_uc010frx.2_Intron	NM_000393	NP_000384			alpha 2 type V collagen preproprotein						axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	190077365	190077366	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190077365_190077366delAA								COL5A2 (32760 upstream) : WDR75 (228793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	190177598	190177599	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190177598_190177599delAA								COL5A2 (132993 upstream) : WDR75 (128560 downstream)																																			---	---	---	---
ANKAR	150709	broad.mit.edu	37	2	190569693	190569693	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190569693delT	uc002uqw.1	+						ANKAR_uc002uqu.2_Intron	NM_144708	NP_653309			ankyrin and armadillo repeat containing							integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	190933863	190933870	+	IGR	DEL	TGTGTGTG	-	-	rs68160708		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190933863_190933870delTGTGTGTG								MSTN (6408 upstream) : C2orf88 (68616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	190954717	190954717	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190954717delC								MSTN (27262 upstream) : C2orf88 (47769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	191265865	191265865	+	IGR	DEL	T	-	-	rs75628863		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191265865delT								INPP1 (29475 upstream) : MFSD6 (7216 downstream)																																			---	---	---	---
MFSD6	54842	broad.mit.edu	37	2	191286452	191286453	+	Intron	DEL	AA	-	-	rs72507936		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191286452_191286453delAA	uc002urz.2	+							NM_017694	NP_060164			major facilitator superfamily domain containing						transmembrane transport	integral to membrane				ovary(2)	2																		---	---	---	---
TMEM194B	100131211	broad.mit.edu	37	2	191377636	191377637	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191377636_191377637delCA	uc010zgf.1	-						TMEM194B_uc010zgg.1_Intron	NM_001142645	NP_001136117			transmembrane protein 194B							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	191674215	191674216	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191674215_191674216insT								NAB1 (116724 upstream) : GLS (71331 downstream)																																			---	---	---	---
STAT4	6775	broad.mit.edu	37	2	191904037	191904037	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191904037delA	uc002usm.1	-						STAT4_uc002usn.1_Intron|STAT4_uc010zgk.1_Intron|STAT4_uc002uso.2_Intron	NM_003151	NP_003142			signal transducer and activator of transcription						JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(3)|skin(2)|lung(1)|ovary(1)|prostate(1)|pancreas(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)															---	---	---	---
STAT4	6775	broad.mit.edu	37	2	191971089	191971089	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191971089delA	uc002usm.1	-						STAT4_uc002usn.1_Intron|STAT4_uc002uso.2_Intron|STAT4_uc002usp.3_Intron	NM_003151	NP_003142			signal transducer and activator of transcription						JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(3)|skin(2)|lung(1)|ovary(1)|prostate(1)|pancreas(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)															---	---	---	---
OBFC2A	64859	broad.mit.edu	37	2	192543874	192543874	+	Intron	DEL	G	-	-	rs10171106	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192543874delG	uc002usx.2	+						OBFC2A_uc002usw.2_Intron|OBFC2A_uc002usy.2_Intron|OBFC2A_uc002usz.2_Intron|OBFC2A_uc002uta.2_Intron	NM_001031716	NP_001026886			oligonucleotide/oligosaccharide-binding fold						double-strand break repair via homologous recombination|G2/M transition checkpoint|response to ionizing radiation	SOSS complex	single-stranded DNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.061)|Epithelial(96;0.244)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	192665643	192665643	+	IGR	DEL	A	-	-	rs77945136		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192665643delA								OBFC2A (112396 upstream) : SDPR (33398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	192788682	192788683	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192788682_192788683delGT								SDPR (76701 upstream) : TMEFF2 (26066 downstream)																																			---	---	---	---
TMEFF2	23671	broad.mit.edu	37	2	192952005	192952006	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192952005_192952006insA	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	193405022	193405022	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193405022delT								TMEFF2 (345378 upstream) : PCGEM1 (209549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194520705	194520705	+	IGR	DEL	C	-	-	rs6718964	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194520705delC								PCGEM1 (879084 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194622287	194622287	+	IGR	DEL	T	-	-	rs71406756		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194622287delT								PCGEM1 (980666 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194798445	194798446	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194798445_194798446delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195048598	195048598	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195048598delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195087794	195087794	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195087794delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195456588	195456589	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195456588_195456589delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196602560	196602560	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196602560delA	uc002utj.3	-	65					DNAH7_uc002uti.3_3'UTR	NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196642421	196642421	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196642421delA	uc002utj.3	-						DNAH7_uc002uti.3_Intron	NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196807112	196807112	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196807112delG	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
HECW2	57520	broad.mit.edu	37	2	197147547	197147547	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197147547delC	uc002utm.1	-						HECW2_uc002utl.1_Intron	NM_020760	NP_065811			HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18																		---	---	---	---
CCDC150	284992	broad.mit.edu	37	2	197541991	197541991	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197541991delT	uc002utp.1	+						CCDC150_uc010zgq.1_Intron|CCDC150_uc010zgr.1_Intron|CCDC150_uc010zgs.1_Intron	NM_001080539	NP_001074008			coiled-coil domain containing 150												0																		---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	197871003	197871003	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197871003delA	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)															---	---	---	---
MOBKL3	25843	broad.mit.edu	37	2	198404920	198404920	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198404920delT	uc002uun.3	+						MOBKL3_uc002uum.3_Intron|MOBKL3_uc010fsn.2_Intron|MOBKL3_uc010fso.2_Intron|MOBKL3_uc010zgz.1_Intron	NM_015387	NP_056202			Mps One Binder kinase activator-like 3 isoform						transport	Golgi cisterna membrane|perinuclear region of cytoplasm	metal ion binding|protein binding				0			Epithelial(96;0.225)															---	---	---	---
RFTN2	130132	broad.mit.edu	37	2	198540351	198540354	+	5'UTR	DEL	AAAC	-	-	rs148812496		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198540351_198540354delAAAC	uc002uuo.3	-	1						NM_144629	NP_653230			raftlin family member 2							plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	200749891	200749891	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200749891delA								FLJ32063 (408233 upstream) : C2orf69 (26088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	200986572	200986572	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200986572delA								C2orf47 (157727 upstream) : SPATS2L (184032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	201052608	201052608	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201052608delT								C2orf47 (223763 upstream) : SPATS2L (117996 downstream)																																			---	---	---	---
SPATS2L	26010	broad.mit.edu	37	2	201219340	201219340	+	Intron	DEL	G	-	-	rs295143	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201219340delG	uc002uvn.3	+						SPATS2L_uc010fst.2_Intron|SPATS2L_uc002uvo.3_Intron|SPATS2L_uc002uvp.3_Intron|SPATS2L_uc002uvq.3_Intron|SPATS2L_uc002uvr.3_Intron|SPATS2L_uc010zhc.1_Intron	NM_015535	NP_056350			SPATS2-like protein isoform a							cytoplasm|nucleolus				ovary(2)|pancreas(1)	3																		---	---	---	---
AOX1	316	broad.mit.edu	37	2	201495240	201495241	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201495240_201495241delAA	uc002uvx.2	+						AOX1_uc010zhf.1_Intron|AOX1_uc010fsu.2_Intron	NM_001159	NP_001150			aldehyde oxidase 1						inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)													---	---	---	---
ORC2L	4999	broad.mit.edu	37	2	201791818	201791818	+	Intron	DEL	T	-	-	rs77724287		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201791818delT	uc002uwr.2	-						ORC2L_uc010zhj.1_Intron	NM_006190	NP_006181			origin recognition complex, subunit 2						cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0																		---	---	---	---
ORC2L	4999	broad.mit.edu	37	2	201829138	201829140	+	5'Flank	DEL	AGA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201829138_201829140delAGA	uc002uwr.2	-						ORC2L_uc010zhj.1_5'Flank	NM_006190	NP_006181			origin recognition complex, subunit 2						cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0																		---	---	---	---
FAM126B	285172	broad.mit.edu	37	2	201933644	201933644	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201933644delA	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																		---	---	---	---
TRAK2	66008	broad.mit.edu	37	2	202315412	202315413	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202315412_202315413delTT	uc002uyb.3	-						TRAK2_uc002uyc.2_Intron|STRADB_uc002uyd.3_5'Flank	NM_015049	NP_055864			trafficking protein, kinesin binding 2							early endosome|plasma membrane	GABA receptor binding				0																		---	---	---	---
ALS2CR11	151254	broad.mit.edu	37	2	202473540	202473540	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202473540delA	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	202587740	202587740	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202587740delA	uc002uyo.2	-						ALS2_uc002uyp.3_3'UTR|ALS2_uc010ftl.2_Intron	NM_020919	NP_065970			alsin isoform 1						cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7																		---	---	---	---
ALS2	57679	broad.mit.edu	37	2	202615315	202615315	+	Intron	DEL	G	-	-	rs35449399		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202615315delG	uc002uyo.2	-						ALS2_uc002uyp.3_Intron|ALS2_uc002uyq.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	202778568	202778568	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202778568delT								CDK15 (20305 upstream) : FZD7 (120742 downstream)																																			---	---	---	---
BMPR2	659	broad.mit.edu	37	2	203420130	203420130	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203420130delA	uc002uzf.3	+	12	2890	c.1742delA	c.(1741-1743)GAAfs	p.E581fs	BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor type II	581	Cytoplasmic (Potential).				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																		---	---	---	---
NBEAL1	65065	broad.mit.edu	37	2	203969591	203969591	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203969591delT	uc002uzt.3	+							NM_001114132	NP_001107604			neurobeachin-like 1 isoform 3								binding			ovary(1)|skin(1)	2																		---	---	---	---
ABI2	10152	broad.mit.edu	37	2	204291747	204291747	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204291747delA	uc002vaa.2	+						ABI2_uc002uzz.2_Intron|ABI2_uc010zih.1_Intron|ABI2_uc010zii.1_Intron|ABI2_uc010zij.1_Intron|ABI2_uc002vab.2_Intron|ABI2_uc010zik.1_Intron|ABI2_uc010zil.1_Intron|ABI2_uc010zim.1_Intron|ABI2_uc002vac.2_Intron|ABI2_uc010zin.1_Intron	NM_005759	NP_005750			abl interactor 2						actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0																		---	---	---	---
CD28	940	broad.mit.edu	37	2	204571164	204571164	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204571164delA	uc002vah.3	+						CD28_uc002vag.1_5'Flank|CD28_uc010zio.1_5'Flank|CD28_uc010ftx.2_5'Flank|CD28_uc002vaj.3_5'Flank	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	205121067	205121070	+	IGR	DEL	TGTG	-	-	rs35109508		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205121067_205121070delTGTG								ICOS (294771 upstream) : PARD3B (289446 downstream)																																			---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205571090	205571091	+	Intron	DEL	AA	-	-	rs77087085		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205571090_205571091delAA	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	206117705	206117705	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206117705delT	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	206494328	206494328	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206494328delT								PARD3B (13791 upstream) : NRP2 (52896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	206529898	206529899	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206529898_206529899delTT								PARD3B (49361 upstream) : NRP2 (17325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	206734517	206734528	+	IGR	DEL	GGATGGATGGAT	-	-	rs10554726		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206734517_206734528delGGATGGATGGAT								NRP2 (71661 upstream) : INO80D (123918 downstream)																																			---	---	---	---
NDUFS1	4719	broad.mit.edu	37	2	206994674	206994674	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206994674delA	uc002vbe.2	-						NDUFS1_uc010ziq.1_Intron|NDUFS1_uc010zir.1_Intron|NDUFS1_uc010zis.1_Intron|NDUFS1_uc010zit.1_Intron|NDUFS1_uc010ziu.1_Intron	NM_005006	NP_004997			NADH dehydrogenase (ubiquinone) Fe-S protein 1,						apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
GPR1	2825	broad.mit.edu	37	2	207074064	207074064	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207074064delA	uc002vbl.3	-						GPR1_uc010fue.2_Intron|GPR1_uc010fuf.2_Intron	NM_005279	NP_005270			G protein-coupled receptor 1							integral to plasma membrane	G-protein coupled receptor activity				0		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)														---	---	---	---
ZDBF2	57683	broad.mit.edu	37	2	207175826	207175826	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207175826delA	uc002vbp.2	+	5	6824	c.6574delA	c.(6574-6576)AAAfs	p.K2192fs		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	2192							nucleic acid binding|zinc ion binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	207496684	207496685	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207496684_207496685delTG								ADAM23 (14007 upstream) : LOC200726 (10457 downstream)																																			---	---	---	---
KLF7	8609	broad.mit.edu	37	2	207992567	207992567	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207992567delA	uc002vbz.1	-						KLF7_uc002vca.1_Intron|KLF7_uc010zix.1_Intron	NM_003709	NP_003700			Kruppel-like factor 7 (ubiquitous)						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			central_nervous_system(1)|skin(1)	2				LUSC - Lung squamous cell carcinoma(261;0.0856)|Lung(261;0.166)|Epithelial(149;0.173)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	208288244	208288255	+	IGR	DEL	TGTGTGTGTGTG	-	-	rs72513047		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208288244_208288255delTGTGTGTGTGTG								MIR1302-4 (154096 upstream) : CREB1 (106361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208339424	208339424	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208339424delA								MIR1302-4 (205276 upstream) : CREB1 (55192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208500802	208500802	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208500802delA								FAM119A (10737 upstream) : CCNYL1 (75462 downstream)																																			---	---	---	---
PLEKHM3	389072	broad.mit.edu	37	2	208801571	208801572	+	Intron	DEL	GT	-	-	rs149366341		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208801571_208801572delGT	uc002vcl.2	-						PLEKHM3_uc002vcm.2_Intron	NM_001080475	NP_001073944			pleckstrin homology domain containing, family M,						intracellular signal transduction		metal ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	208956513	208956513	+	IGR	DEL	T	-	-	rs76479194		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208956513delT								PLEKHM3 (66229 upstream) : CRYGD (29819 downstream)																																			---	---	---	---
CRYGA	1418	broad.mit.edu	37	2	209028422	209028422	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209028422delT	uc002vcq.3	-							NM_014617	NP_055432			crystallin, gamma A						visual perception		structural constituent of eye lens				0				Epithelial(149;0.067)|LUSC - Lung squamous cell carcinoma(261;0.0708)|Lung(261;0.135)														---	---	---	---
C2orf80	389073	broad.mit.edu	37	2	209036457	209036458	+	Intron	INS	-	CCACTCCAT	CCACTCCAT	rs149518601	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209036457_209036458insCCACTCCAT	uc002vcr.2	-							NM_001099334	NP_001092804			hypothetical protein LOC389073											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	209093690	209093691	+	IGR	INS	-	T	T	rs140151132		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209093690_209093691insT								C2orf80 (38917 upstream) : IDH1 (7263 downstream)																																			---	---	---	---
PTH2R	5746	broad.mit.edu	37	2	209363797	209363797	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209363797delA	uc010fuo.1	+											Homo sapiens cDNA FLJ60238 complete cds, highly similar to Parathyroid hormone receptor precursor.							integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)														---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210422143	210422143	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210422143delT	uc002vdc.1	+						MAP2_uc002vdd.1_Intron	NM_002374	NP_002365			microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
UNC80	285175	broad.mit.edu	37	2	210709812	210709812	+	Intron	DEL	A	-	-	rs111733831		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210709812delA	uc010zjc.1	+						UNC80_uc002vdk.2_Intron	NM_032504	NP_115893			chromosome 2 open reading frame 21 isoform 1							integral to membrane					0																		---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212804116	212804116	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212804116delT	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	212967210	212967210	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212967210delA	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_Intron	NM_005235	NP_005226			v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)											TSP Lung(8;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	2	213508574	213508574	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213508574delT								ERBB4 (105222 upstream) : IKZF2 (355839 downstream)																																			---	---	---	---
IKZF2	22807	broad.mit.edu	37	2	213869994	213869994	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213869994delA	uc002vem.2	-	8					IKZF2_uc010fuu.2_3'UTR|IKZF2_uc002vej.2_3'UTR|IKZF2_uc002vek.2_RNA|IKZF2_uc010fuv.2_3'UTR|IKZF2_uc002vel.2_3'UTR|IKZF2_uc010fuw.2_3'UTR|IKZF2_uc010fux.2_3'UTR|IKZF2_uc010fuy.2_3'UTR|IKZF2_uc002ven.2_3'UTR|IKZF2_uc002vei.2_3'UTR	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)														---	---	---	---
IKZF2	22807	broad.mit.edu	37	2	214015629	214015629	+	5'Flank	DEL	T	-	-	rs114287184	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214015629delT	uc002vem.2	-						IKZF2_uc010fuu.2_5'Flank|IKZF2_uc002vej.2_5'Flank|IKZF2_uc002vek.2_5'Flank|IKZF2_uc010fuv.2_5'Flank|IKZF2_uc002vel.2_5'Flank|IKZF2_uc010fuw.2_5'Flank|IKZF2_uc010fux.2_5'Flank|IKZF2_uc010fuy.2_5'Flank|IKZF2_uc002ven.2_Intron	NM_016260	NP_057344			helios isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)														---	---	---	---
VWC2L	402117	broad.mit.edu	37	2	215308116	215308116	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215308116delA	uc002vet.2	+						VWC2L_uc010zjl.1_Intron	NM_001080500	NP_001073969			von Willebrand factor C domain-containing							extracellular region					0																		---	---	---	---
BARD1	580	broad.mit.edu	37	2	215665947	215665948	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215665947_215665948delAA	uc002veu.2	-						BARD1_uc010zjm.1_Intron	NM_000465	NP_000456			BRCA1 associated RING domain 1						cell cycle arrest|DNA repair|negative regulation of apoptosis|negative regulation of mRNA 3'-end processing|negative regulation of protein export from nucleus|positive regulation of apoptosis|positive regulation of protein catabolic process|protein K6-linked ubiquitination|regulation of phosphorylation|tissue homeostasis	BRCA1-A complex|BRCA1-BARD1 complex|cytoplasm	kinase binding|protein heterodimerization activity|protein homodimerization activity|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)										Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
ATIC	471	broad.mit.edu	37	2	216184275	216184275	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216184275delT	uc002vex.3	+						ATIC_uc010zjo.1_Intron|ATIC_uc002vey.3_Intron	NM_004044	NP_004035			5-aminoimidazole-4-carboxamide ribonucleotide						IMP biosynthetic process|purine base metabolic process	cytosol	IMP cyclohydrolase activity|phosphoribosylaminoimidazolecarboxamide formyltransferase activity|protein homodimerization activity		ATIC/ALK(24)	haematopoietic_and_lymphoid_tissue(22)|ovary(2)|lung(2)|soft_tissue(2)|skin(1)	29		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Tetrahydrofolic acid(DB00116)			T	ALK	ALCL								---	---	---	---
MARCH4	57574	broad.mit.edu	37	2	217136522	217136522	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217136522delT	uc002vgb.2	-							NM_020814	NP_065865			membrane-associated ring finger (C3HC4) 4							Golgi membrane|Golgi stack|integral to membrane|trans-Golgi network	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	217650443	217650443	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217650443delT								IGFBP5 (90171 upstream) : TNP1 (73741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217989633	217989633	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217989633delT								TNP1 (264851 upstream) : DIRC3 (159115 downstream)																																			---	---	---	---
RUFY4	285180	broad.mit.edu	37	2	218941466	218941467	+	Intron	DEL	CC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218941466_218941467delCC	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)														---	---	---	---
VIL1	7429	broad.mit.edu	37	2	219299999	219299999	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219299999delT	uc002via.2	+						VIL1_uc010zke.1_Intron|VIL1_uc002vib.2_Intron	NM_007127	NP_009058			villin 1						actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
VIL1	7429	broad.mit.edu	37	2	219313779	219313781	+	Intron	DEL	CTC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219313779_219313781delCTC	uc002via.2	+						VIL1_uc010zke.1_Intron|VIL1_uc002vib.2_Intron	NM_007127	NP_009058			villin 1						actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
USP37	57695	broad.mit.edu	37	2	219412053	219412053	+	Intron	DEL	A	-	-	rs34759621		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219412053delA	uc002vie.2	-						USP37_uc010fvs.1_Intron|USP37_uc010zkf.1_Intron|USP37_uc002vif.2_Intron|USP37_uc002vig.2_Intron|USP37_uc010zkg.1_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)														---	---	---	---
CYP27A1	1593	broad.mit.edu	37	2	219651518	219651518	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219651518delT	uc002viz.3	+							NM_000784	NP_000775			cytochrome P450, family 27, subfamily A,						bile acid biosynthetic process|xenobiotic metabolic process	mitochondrial matrix	cholestanetriol 26-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Cholecalciferol(DB00169)													---	---	---	---
NHEJ1	79840	broad.mit.edu	37	2	220013611	220013611	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220013611delT	uc002vjp.3	-						NHEJ1_uc002vjq.3_Intron	NM_024782	NP_079058			nonhomologous end-joining factor 1						B cell differentiation|central nervous system development|DNA recombination|double-strand break repair via nonhomologous end joining|positive regulation of ligase activity|response to ionizing radiation|T cell differentiation	nonhomologous end joining complex|nucleus	DNA binding|identical protein binding			lung(1)	1		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)									Direct_reversal_of_damage|NHEJ					---	---	---	---
DES	1674	broad.mit.edu	37	2	220286392	220286392	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220286392delT	uc002vll.2	+							NM_001927	NP_001918			desmin						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	220836436	220836436	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220836436delT								SLC4A3 (329735 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221129414	221129415	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221129414_221129415insT								SLC4A3 (622713 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222032201	222032201	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222032201delA								None (None upstream) : EPHA4 (250548 downstream)																																			---	---	---	---
EPHA4	2043	broad.mit.edu	37	2	222429297	222429298	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222429297_222429298delTT	uc002vmq.2	-						EPHA4_uc002vmr.2_Intron|EPHA4_uc010zlm.1_Intron|EPHA4_uc010zln.1_Intron	NM_004438	NP_004429			ephrin receptor EphA4 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(6)|large_intestine(2)|central_nervous_system(2)|urinary_tract(1)|skin(1)	12		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	222823807	222823807	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222823807delT								EPHA4 (384885 upstream) : PAX3 (240800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222964244	222964245	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222964244_222964245insT								EPHA4 (525322 upstream) : PAX3 (100362 downstream)																																			---	---	---	---
SGPP2	130367	broad.mit.edu	37	2	223355862	223355862	+	Intron	DEL	A	-	-	rs62992564		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223355862delA	uc010zlo.1	+						SGPP2_uc010zlp.1_Intron	NM_152386	NP_689599			sphingosine-1-phosphate phosphotase 2						sphingosine metabolic process	endoplasmic reticulum membrane|integral to membrane	dihydrosphingosine-1-phosphate phosphatase activity|sphingosine-1-phosphate phosphatase activity			central_nervous_system(1)|skin(1)	2		Renal(207;0.0376)		Epithelial(121;2.08e-09)|all cancers(144;9.25e-07)|LUSC - Lung squamous cell carcinoma(224;0.011)|Lung(261;0.0143)														---	---	---	---
FARSB	10056	broad.mit.edu	37	2	223505480	223505480	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223505480delA	uc002vne.1	-						FARSB_uc010zlq.1_Intron|FARSB_uc002vnf.1_Intron	NM_005687	NP_005678			phenylalanyl-tRNA synthetase, beta subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)													---	---	---	---
ACSL3	2181	broad.mit.edu	37	2	223725212	223725212	+	5'Flank	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223725212delC	uc002vni.2	+						ACSL3_uc002vnj.2_5'Flank	NM_004457	NP_004448			acyl-CoA synthetase long-chain family member 3						long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|fatty-acyl-CoA synthase activity|long-chain fatty acid-CoA ligase activity|protein binding			ovary(2)	2		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)			T	ETV1	prostate								---	---	---	---
Unknown	0	broad.mit.edu	37	2	224368408	224368408	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224368408delA								KCNE4 (448055 upstream) : SCG2 (93252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	225504197	225504197	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225504197delT								CUL3 (54087 upstream) : DOCK10 (125610 downstream)																																			---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225656186	225656186	+	Intron	DEL	T	-	-	rs35936903		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225656186delT	uc010fwz.1	-						DOCK10_uc002vob.2_Intron|DOCK10_uc002voa.2_Intron|DOCK10_uc002voc.2_Intron	NM_014689	NP_055504			dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)														---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225731793	225731796	+	Intron	DEL	ACAC	-	-	rs10606480		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225731793_225731796delACAC	uc010fwz.1	-						DOCK10_uc002vob.2_Intron|DOCK10_uc002vod.1_Intron	NM_014689	NP_055504			dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)														---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225863968	225863968	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225863968delT	uc010fwz.1	-						DOCK10_uc002vod.1_Intron	NM_014689	NP_055504			dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)														---	---	---	---
KIAA1486	57624	broad.mit.edu	37	2	226375495	226375496	+	Intron	INS	-	TGTG	TGTG	rs146231874	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226375495_226375496insTGTG	uc002voe.2	+						KIAA1486_uc010fxa.1_Intron	NM_020864	NP_065915			hypothetical protein LOC57624											ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	226660491	226660491	+	IGR	DEL	A	-	-	rs78519290		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226660491delA								KIAA1486 (65020 upstream) : IRS1 (935543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	226792732	226792732	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226792732delT								KIAA1486 (197261 upstream) : IRS1 (803302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	226827144	226827144	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226827144delA								KIAA1486 (231673 upstream) : IRS1 (768890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	227519110	227519111	+	IGR	INS	-	ACAC	ACAC	rs148321261	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227519110_227519111insACAC								KIAA1486 (923639 upstream) : IRS1 (76923 downstream)																																			---	---	---	---
MFF	56947	broad.mit.edu	37	2	228203744	228203744	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228203744delC	uc002vos.2	+						MFF_uc002vot.2_Intron|MFF_uc002vou.2_Intron|MFF_uc002vov.2_Intron|MFF_uc002vow.2_Intron|MFF_uc002vox.2_Intron|MFF_uc002voy.2_Intron|MFF_uc002voz.2_Intron	NM_020194	NP_064579			mitochondrial fission factor							integral to membrane|mitochondrial outer membrane				large_intestine(1)	1																		---	---	---	---
WDR69	164781	broad.mit.edu	37	2	228788462	228788462	+	Intron	DEL	A	-	-	rs78456977		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228788462delA	uc002vpn.1	+						WDR69_uc010zlw.1_Intron|WDR69_uc002vpo.1_Intron	NM_178821	NP_849143			WD repeat domain 69											breast(1)	1		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;1.22e-10)|all cancers(144;8.11e-08)|Lung(261;0.011)|LUSC - Lung squamous cell carcinoma(224;0.0148)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	228811038	228811039	+	IGR	INS	-	TT	TT	rs146897473	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228811038_228811039insTT								WDR69 (22012 upstream) : SPHKAP (33631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229080624	229080624	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229080624delT								SPHKAP (34263 upstream) : PID1 (808066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229380205	229380206	+	IGR	DEL	TG	-	-	rs10524395	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229380205_229380206delTG								SPHKAP (333844 upstream) : PID1 (508484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229822677	229822677	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229822677delT								SPHKAP (776316 upstream) : PID1 (66013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	230189097	230189097	+	IGR	DEL	A	-	-	rs79323469	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230189097delA								PID1 (53040 upstream) : DNER (33249 downstream)																																			---	---	---	---
DNER	92737	broad.mit.edu	37	2	230407872	230407872	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230407872delA	uc002vpv.2	-						DNER_uc010zly.1_Intron	NM_139072	NP_620711			delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)														---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230652431	230652431	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230652431delA	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.1_Intron	NM_004238	NP_004229			thyroid hormone receptor interactor 12						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	231442553	231442553	+	IGR	DEL	T	-	-	rs72480706		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231442553delT								SP100 (32236 upstream) : CAB39 (135004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	231480526	231480526	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231480526delT								SP100 (70209 upstream) : CAB39 (97031 downstream)																																			---	---	---	---
GPR55	9290	broad.mit.edu	37	2	231774722	231774722	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231774722delC	uc002vrg.2	-	2	1149	c.956delG	c.(955-957)GGCfs	p.G319fs	GPR55_uc002vrf.2_RNA|GPR55_uc010fxs.1_Frame_Shift_Del_p.G319fs	NM_005683	NP_005674	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	319	Cytoplasmic (Potential).				activation of phospholipase C activity|bone resorption|negative regulation of osteoclast differentiation|positive regulation of ERK1 and ERK2 cascade|positive regulation of Rho protein signal transduction	integral to plasma membrane	cannabinoid receptor activity			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	231832994	231832994	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231832994delA								GPR55 (7303 upstream) : SPATA3 (27845 downstream)																																			---	---	---	---
NCL	4691	broad.mit.edu	37	2	232327984	232327986	+	In_Frame_Del	DEL	GGA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232327984_232327986delGGA	uc002vru.2	-	2	201_203	c.60_62delTCC	c.(58-63)CCTCCA>CCA	p.20_21PP>P	SNORD82_uc010fxw.1_5'Flank	NM_005381	NP_005372	P19338	NUCL_HUMAN	nucleolin	20_21					angiogenesis	cell cortex|nucleolus|ribonucleoprotein complex	nucleotide binding|protein C-terminus binding|RNA binding|telomeric DNA binding			ovary(2)|pancreas(1)	3		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	232716834	232716834	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232716834delT								COPS7B (43400 upstream) : MIR1471 (40118 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	232718996	232718997	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232718996_232718997delTT								COPS7B (45562 upstream) : MIR1471 (37955 downstream)																																			---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	232876068	232876069	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232876068_232876069delTT	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron	NM_152383	NP_689596			DIS3 mitotic control homolog (S.								exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)														---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	232995570	232995570	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232995570delA	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron|DIS3L2_uc002vsn.1_3'UTR|DIS3L2_uc002vso.2_Intron	NM_152383	NP_689596			DIS3 mitotic control homolog (S.								exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)														---	---	---	---
EFHD1	80303	broad.mit.edu	37	2	233524004	233524004	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233524004delA	uc002vtc.2	+						EFHD1_uc010fyf.2_Intron	NM_025202	NP_079478			EF-hand domain family, member D1								calcium ion binding|protein binding				0		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)														---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233765204	233765205	+	Intron	DEL	AT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233765204_233765205delAT	uc002vts.2	-						NGEF_uc010zmm.1_Intron|NGEF_uc010fyg.1_Intron|NGEF_uc002vtt.2_Intron	NM_019850	NP_062824			neuronal guanine nucleotide exchange factor						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)														---	---	---	---
HJURP	55355	broad.mit.edu	37	2	234746304	234746304	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234746304delA	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)														---	---	---	---
TRPM8	79054	broad.mit.edu	37	2	234873229	234873229	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234873229delA	uc002vvh.2	+						TRPM8_uc010fyj.2_Intron	NM_024080	NP_076985			transient receptor potential cation channel,							integral to membrane				skin(4)	4		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	235128392	235128392	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235128392delG								SPP2 (142616 upstream) : ARL4C (273296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235431703	235431703	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235431703delC								ARL4C (26010 upstream) : SH3BP4 (428925 downstream)																																			---	---	---	---
SH3BP4	23677	broad.mit.edu	37	2	235931166	235931166	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235931166delA	uc002vvp.2	+						SH3BP4_uc010fym.2_Intron|SH3BP4_uc002vvq.2_Intron	NM_014521	NP_055336			SH3-domain binding protein 4						endocytosis	clathrin-coated vesicle|coated pit|nucleus	protein binding			skin(3)|ovary(1)	4		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	236104930	236104930	+	IGR	DEL	A	-	-	rs6738868	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236104930delA								SH3BP4 (140574 upstream) : AGAP1 (297806 downstream)																																			---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236550079	236550079	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236550079delT	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	236685993	236685994	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236685993_236685994insA	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	236865157	236865158	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236865157_236865158delAA	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	237045651	237045651	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237045651delA								AGAP1 (11537 upstream) : GBX2 (28656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	237561595	237561595	+	IGR	DEL	T	-	-	rs113508776		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237561595delT								CXCR7 (70603 upstream) : COPS8 (432489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	237720346	237720352	+	IGR	DEL	GCCTCAA	-	-	rs149035909		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237720346_237720352delGCCTCAA								CXCR7 (229354 upstream) : COPS8 (273732 downstream)																																			---	---	---	---
MLPH	79083	broad.mit.edu	37	2	238398971	238398971	+	Intron	DEL	A	-	-	rs114792326	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238398971delA	uc002vwt.2	+						MLPH_uc002vws.2_Intron|MLPH_uc010fyt.1_Intron|MLPH_uc002vwu.2_Intron|MLPH_uc002vwv.2_Intron	NM_024101	NP_077006			melanophilin isoform 1								metal ion binding			ovary(1)	1		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)														---	---	---	---
MLPH	79083	broad.mit.edu	37	2	238444136	238444137	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238444136_238444137delTG	uc002vwt.2	+						MLPH_uc002vws.2_Intron|MLPH_uc010fyt.1_Intron|MLPH_uc002vwu.2_Intron|MLPH_uc002vwv.2_Intron|MLPH_uc002vww.2_Intron|MLPH_uc002vwx.2_Intron|MLPH_uc010fyu.2_Intron	NM_024101	NP_077006			melanophilin isoform 1								metal ion binding			ovary(1)	1		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)														---	---	---	---
RAMP1	10267	broad.mit.edu	37	2	238770494	238770495	+	Intron	INS	-	A	A	rs77751617		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238770494_238770495insA	uc002vxj.2	+							NM_005855	NP_005846			receptor activity-modifying protein 1 precursor						intracellular protein transport|regulation of G-protein coupled receptor protein signaling pathway	integral to plasma membrane	protein transporter activity				0		Breast(86;0.000596)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;9.56e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.49e-11)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.49e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00013)|Lung(119;0.0119)|LUSC - Lung squamous cell carcinoma(224;0.0288)	Pramlintide(DB01278)													---	---	---	---
SCLY	51540	broad.mit.edu	37	2	238925156	238925156	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238925156delT	uc002vxm.3	+						UBE2F_uc010znn.1_Intron|UBE2F_uc002vxk.2_Intron|UBE2F_uc002vxl.2_Intron|UBE2F_uc010zno.1_Intron|UBE2F_uc010znp.1_Intron	NM_016510	NP_057594			selenocysteine lyase						cellular amino acid metabolic process	cytosol	pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity			ovary(2)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)														---	---	---	---
ILKAP	80895	broad.mit.edu	37	2	239088809	239088809	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239088809delA	uc002vxv.2	-						ILKAP_uc010zns.1_Intron|ILKAP_uc002vxw.2_Intron	NM_030768	NP_110395			integrin-linked kinase-associated protein							cytoplasm|protein serine/threonine phosphatase complex	metal ion binding|protein binding			ovary(3)	3		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)														---	---	---	---
TRAF3IP1	26146	broad.mit.edu	37	2	239232718	239232718	+	Intron	DEL	T	-	-	rs72172620		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239232718delT	uc002vye.2	+						TRAF3IP1_uc002vyf.2_Intron	NM_015650	NP_056465			TNF receptor-associated factor 3 interacting							cytoplasm|cytoskeleton	protein binding			ovary(1)	1		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)														---	---	---	---
TRAF3IP1	26146	broad.mit.edu	37	2	239258710	239258710	+	Intron	DEL	A	-	-	rs75329415		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239258710delA	uc002vye.2	+						TRAF3IP1_uc002vyf.2_Intron	NM_015650	NP_056465			TNF receptor-associated factor 3 interacting							cytoplasm|cytoskeleton	protein binding			ovary(1)	1		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	239323047	239323047	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239323047delA								TRAF3IP1 (13508 upstream) : ASB1 (12579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	239741880	239741880	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239741880delT								ASB1 (380990 upstream) : TWIST2 (14793 downstream)																																			---	---	---	---
TWIST2	117581	broad.mit.edu	37	2	239758754	239758754	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239758754delT	uc010znx.1	+						TWIST2_uc010zny.1_Intron	NM_057179	NP_476527			twist homolog 2						negative regulation of osteoblast differentiation	cytoplasm	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	239833307	239833308	+	IGR	INS	-	GAGGGGTCTT	GAGGGGTCTT	rs146219588	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239833307_239833308insGAGGGGTCTT								TWIST2 (1070 upstream) : HDAC4 (136557 downstream)																																			---	---	---	---
HDAC4	9759	broad.mit.edu	37	2	239972878	239972878	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239972878delA	uc002vyk.3	-	27					HDAC4_uc010fyy.2_3'UTR	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	240394517	240394518	+	IGR	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240394517_240394518delGA								HDAC4 (71171 upstream) : NDUFA10 (505640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	241089267	241089267	+	IGR	DEL	G	-	-	rs10460443	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241089267delG								OTOS (9194 upstream) : GPC1 (285848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	241415390	241415390	+	IGR	DEL	T	-	-	rs111610906		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241415390delT								GPC1 (7896 upstream) : ANKMY1 (3449 downstream)																																			---	---	---	---
GPR35	2859	broad.mit.edu	37	2	241557488	241557488	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241557488delT	uc010fzh.1	+						GPR35_uc010fzi.1_Intron	NM_005301	NP_005292			G protein-coupled receptor 35							integral to plasma membrane	G-protein coupled receptor activity			skin(2)|pancreas(1)	3		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;5.29e-32)|all cancers(36;1.38e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.02e-06)|Lung(119;0.00163)|Colorectal(34;0.00463)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.031)														---	---	---	---
D2HGDH	728294	broad.mit.edu	37	2	242680356	242680356	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242680356delA	uc002wce.1	+						D2HGDH_uc010zpc.1_Intron|D2HGDH_uc010fzq.1_Intron|D2HGDH_uc002wcg.1_Intron	NM_152783	NP_689996			D-2-hydroxyglutarate dehydrogenase precursor						2-oxoglutarate metabolic process|cellular protein metabolic process|response to cobalt ion|response to manganese ion|response to zinc ion	mitochondrial matrix	(R)-2-hydroxyglutarate dehydrogenase activity|flavin adenine dinucleotide binding|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)														---	---	---	---
D2HGDH	728294	broad.mit.edu	37	2	242682821	242682821	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242682821delT	uc002wce.1	+						D2HGDH_uc010zpc.1_Intron|D2HGDH_uc010fzq.1_Intron|D2HGDH_uc002wcg.1_Intron	NM_152783	NP_689996			D-2-hydroxyglutarate dehydrogenase precursor						2-oxoglutarate metabolic process|cellular protein metabolic process|response to cobalt ion|response to manganese ion|response to zinc ion	mitochondrial matrix	(R)-2-hydroxyglutarate dehydrogenase activity|flavin adenine dinucleotide binding|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)														---	---	---	---
CHL1	10752	broad.mit.edu	37	3	247325	247326	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:247325_247326delTG	uc003bou.2	+						CHL1_uc003bot.2_Intron|CHL1_uc003bov.1_Intron|CHL1_uc003bow.1_Intron	NM_006614	NP_006605			cell adhesion molecule with homology to L1CAM						axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1)	12		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)														---	---	---	---
CHL1	10752	broad.mit.edu	37	3	367893	367893	+	Intron	DEL	A	-	-	rs34362207		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:367893delA	uc003bou.2	+						CHL1_uc003bot.2_Intron|CHL1_uc003bow.1_Intron|CHL1_uc011asi.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	834763	834764	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:834763_834764insA	uc003boy.1	+											Homo sapiens cDNA FLJ44328 fis, clone TRACH3002871.																														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2152423	2152424	+	Intron	INS	-	GTT	GTT	rs150577505	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2152423_2152424insGTT	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron	NM_175607	NP_783200			contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2744779	2744781	+	Intron	DEL	TTA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2744779_2744781delTTA	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron|CNTN4_uc003bpd.1_Intron	NM_175607	NP_783200			contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)														---	---	---	---
IL5RA	3568	broad.mit.edu	37	3	3131331	3131331	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3131331delT	uc011ask.1	-						IL5RA_uc010hbq.2_Intron|IL5RA_uc010hbr.2_Intron|IL5RA_uc010hbs.2_Intron|IL5RA_uc011asl.1_Intron|IL5RA_uc010hbp.2_Intron	NM_000564	NP_000555			interleukin 5 receptor, alpha isoform 1						cell proliferation	extracellular space|integral to membrane|plasma membrane	interleukin-5 receptor activity			ovary(1)	1				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)														---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	4070807	4070807	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4070807delT	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	4669376	4669376	+	Intron	DEL	T	-	-	rs72259044		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4669376delT	uc003bqa.2	+						ITPR1_uc010hbz.2_Intron|ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc010hcb.1_Intron	NM_001099952	NP_001093422			inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)														---	---	---	---
ITPR1	3708	broad.mit.edu	37	3	4669682	4669682	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4669682delT	uc003bqa.2	+						ITPR1_uc010hbz.2_Intron|ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc010hcb.1_Intron	NM_001099952	NP_001093422			inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)														---	---	---	---
ITPR1	3708	broad.mit.edu	37	3	4844509	4844510	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4844509_4844510insA	uc003bqa.2	+						ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc003bqc.2_Intron|ITPR1_uc010hcc.1_Intron|ITPR1_uc011asv.1_Intron	NM_001099952	NP_001093422			inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	4954140	4954140	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4954140delA	uc003bqe.1	-						uc010hce.1_Intron					Homo sapiens cDNA FLJ32330 fis, clone PROST2004742.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	5280960	5280961	+	IGR	INS	-	AC	AC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5280960_5280961insAC								EDEM1 (19311 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5662578	5662578	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5662578delT								EDEM1 (400929 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6191374	6191374	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6191374delT								EDEM1 (929725 upstream) : GRM7 (711428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6230664	6230665	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6230664_6230665delTC								EDEM1 (969015 upstream) : GRM7 (672137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6875740	6875741	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6875740_6875741insA								None (None upstream) : GRM7 (27061 downstream)																																			---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7378000	7378000	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7378000delA	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7633946	7633946	+	Intron	DEL	A	-	-	rs79227010	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7633946delA	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron|GRM7_uc010hch.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	7990060	7990060	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7990060delC								GRM7 (206842 upstream) : LMCD1 (553451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	8920049	8920049	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8920049delA								OXTR (108749 upstream) : RAD18 (1512 downstream)																																			---	---	---	---
THUMPD3	25917	broad.mit.edu	37	3	9425697	9425697	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9425697delA	uc003bro.3	+						LOC440944_uc003brm.2_Intron|THUMPD3_uc003brn.3_Intron	NM_001114092	NP_001107564			THUMP domain containing 3								methyltransferase activity|protein binding|RNA binding			ovary(1)	1	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	9524851	9524851	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9524851delA								SETD5 (5015 upstream) : LHFPL4 (15195 downstream)																																			---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10081677	10081677	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10081677delA	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc003buv.2_3'UTR	NM_033084	NP_149075			Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)				D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
C3orf24	115795	broad.mit.edu	37	3	10143828	10143829	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10143828_10143829delTT	uc003buz.2	-							NM_173472	NP_775743			hypothetical protein LOC115795												0				OV - Ovarian serous cystadenocarcinoma(96;0.196)														---	---	---	---
C3orf10	55845	broad.mit.edu	37	3	10167887	10167887	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10167887delT	uc003bvb.2	+							NM_018462	NP_060932			chromosome 3 open reading frame 10							cytoplasm|cytoskeleton					0																		---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10427117	10427117	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10427117delA	uc003bvt.2	-						ATP2B2_uc003bvv.2_Intron|ATP2B2_uc003bvw.2_Intron|ATP2B2_uc010hdo.2_Intron	NM_001001331	NP_001001331			plasma membrane calcium ATPase 2 isoform 1						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10512540	10512540	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10512540delC	uc003bvt.2	-						ATP2B2_uc003bvv.2_Intron|ATP2B2_uc003bvw.2_Intron|ATP2B2_uc010hdp.2_Intron	NM_001001331	NP_001001331			plasma membrane calcium ATPase 2 isoform 1						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
HRH1	3269	broad.mit.edu	37	3	11198593	11198593	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11198593delC	uc010hdr.2	+						HRH1_uc010hds.2_Intron	NM_001098213	NP_001091683			histamine receptor H1						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|inflammatory response	cytoplasm|integral to plasma membrane|nucleus	histamine receptor activity			large_intestine(1)|ovary(1)	2					Aceprometazine(DB01615)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzquinamide(DB00767)|Bepotastine(DB04890)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlophedianol(DB04837)|Chlorpheniramine(DB01114)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clemastine(DB00283)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Maprotiline(DB00934)|Meclizine(DB00737)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nedocromil(DB00716)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Pemirolast(DB00885)|Phenindamine(DB01619)|Pheniramine(DB01620)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Terfenadine(DB00342)|Thiethylperazine(DB00372)|Trazodone(DB00656)|Trimeprazine(DB01246)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)													---	---	---	---
HRH1	3269	broad.mit.edu	37	3	11212796	11212796	+	Intron	DEL	T	-	-	rs138516344	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11212796delT	uc010hdr.2	+						HRH1_uc010hds.2_Intron	NM_001098213	NP_001091683			histamine receptor H1						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|inflammatory response	cytoplasm|integral to plasma membrane|nucleus	histamine receptor activity			large_intestine(1)|ovary(1)	2					Aceprometazine(DB01615)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzquinamide(DB00767)|Bepotastine(DB04890)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlophedianol(DB04837)|Chlorpheniramine(DB01114)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clemastine(DB00283)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Maprotiline(DB00934)|Meclizine(DB00737)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nedocromil(DB00716)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Pemirolast(DB00885)|Phenindamine(DB01619)|Pheniramine(DB01620)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Terfenadine(DB00342)|Thiethylperazine(DB00372)|Trazodone(DB00656)|Trimeprazine(DB01246)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)													---	---	---	---
HRH1	3269	broad.mit.edu	37	3	11212810	11212810	+	Intron	DEL	T	-	-	rs72251330		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11212810delT	uc010hdr.2	+						HRH1_uc010hds.2_Intron	NM_001098213	NP_001091683			histamine receptor H1						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|inflammatory response	cytoplasm|integral to plasma membrane|nucleus	histamine receptor activity			large_intestine(1)|ovary(1)	2					Aceprometazine(DB01615)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzquinamide(DB00767)|Bepotastine(DB04890)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlophedianol(DB04837)|Chlorpheniramine(DB01114)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clemastine(DB00283)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Maprotiline(DB00934)|Meclizine(DB00737)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nedocromil(DB00716)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Pemirolast(DB00885)|Phenindamine(DB01619)|Pheniramine(DB01620)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Terfenadine(DB00342)|Thiethylperazine(DB00372)|Trazodone(DB00656)|Trimeprazine(DB01246)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)													---	---	---	---
ATG7	10533	broad.mit.edu	37	3	11335330	11335330	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11335330delA	uc003bwc.2	+						ATG7_uc003bwd.2_Intron|ATG7_uc011aum.1_Intron	NM_006395	NP_006386			APG7 autophagy 7-like isoform a						autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1																		---	---	---	---
VGLL4	9686	broad.mit.edu	37	3	11762675	11762675	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11762675delA	uc003bwf.2	-						VGLL4_uc003bwg.2_5'Flank	NM_014667	NP_055482			vestigial like 4 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)														---	---	---	---
C3orf31	132001	broad.mit.edu	37	3	11884182	11884182	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11884182delA	uc003bwh.2	-						C3orf31_uc003bwj.2_Intron|C3orf31_uc003bwi.2_Intron|C3orf31_uc011auo.1_Intron|C3orf31_uc011aup.1_Intron|C3orf31_uc010hdy.1_Intron	NM_138807	NP_620162			MMP37-like protein, mitochondrial precursor						protein import into mitochondrial matrix	extrinsic to mitochondrial inner membrane					0																		---	---	---	---
PPARG	5468	broad.mit.edu	37	3	12360358	12360358	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12360358delT	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						---	---	---	---
PPARG	5468	broad.mit.edu	37	3	12377335	12377335	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12377335delA	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						---	---	---	---
TSEN2	80746	broad.mit.edu	37	3	12574141	12574141	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12574141delT	uc003bxc.2	+						TSEN2_uc003bwz.2_Intron|TSEN2_uc003bxa.2_Intron|TSEN2_uc003bxb.2_Intron|TSEN2_uc011aur.1_Intron	NM_025265	NP_079541			tRNA-intron nuclease 2 isoform 1						mRNA processing|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|nucleolus|tRNA-intron endonuclease complex	nucleic acid binding|tRNA-intron endonuclease activity			central_nervous_system(1)	1																		---	---	---	---
RAF1	5894	broad.mit.edu	37	3	12707585	12707585	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12707585delA	uc003bxf.3	-						RAF1_uc011auu.1_5'Flank	NM_002880	NP_002871			v-raf-1 murine leukemia viral oncogene homolog						activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity		ESRP1/RAF1(4)|SRGAP3/RAF1(4)	central_nervous_system(4)|prostate(4)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|liver(1)|ovary(1)	14					Sorafenib(DB00398)			T	SRGAP3	pilocytic astrocytoma				Noonan_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	3	12907367	12907368	+	5'Flank	INS	-	G	G	rs57676256	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12907367_12907368insG	uc003bxr.1	-											DQ587889																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	13154738	13154738	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13154738delA								IQSEC1 (40121 upstream) : NUP210 (202999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	13487028	13487028	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13487028delA								NUP210 (25219 upstream) : HDAC11 (34196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	14338256	14338256	+	IGR	DEL	G	-	-	rs77875200		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14338256delG								LSM3 (98420 upstream) : SLC6A6 (105850 downstream)																																			---	---	---	---
NR2C2	7182	broad.mit.edu	37	3	15059515	15059515	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15059515delT	uc003bzj.3	+						NR2C2_uc003bzi.2_Intron	NM_003298	NP_003289			nuclear receptor subfamily 2, group C, member 2						cell differentiation|nervous system development|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding				0																		---	---	---	---
CAPN7	23473	broad.mit.edu	37	3	15282164	15282164	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15282164delA	uc003bzn.2	+							NM_014296	NP_055111			calpain 7						proteolysis	nucleus	calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
SH3BP5	9467	broad.mit.edu	37	3	15297083	15297084	+	3'UTR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15297083_15297084delTT	uc003bzp.1	-	9					SH3BP5_uc010hem.1_RNA|SH3BP5_uc003bzq.1_3'UTR|SH3BP5_uc003bzr.1_3'UTR|uc003bzo.1_RNA	NM_004844	NP_004835			SH3-domain binding protein 5 (BTK-associated)						intracellular signal transduction	mitochondrion	protein kinase inhibitor activity|SH3 domain binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	15418940	15418940	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15418940delT								SH3BP5 (36039 upstream) : METTL6 (3844 downstream)																																			---	---	---	---
HACL1	26061	broad.mit.edu	37	3	15612654	15612655	+	Intron	INS	-	TT	TT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15612654_15612655insTT	uc003caf.2	-						HACL1_uc011avr.1_Intron|HACL1_uc011avs.1_Intron|HACL1_uc011avt.1_Intron|HACL1_uc003cag.2_Intron|HACL1_uc011avu.1_Intron|HACL1_uc010hep.2_Intron	NM_012260	NP_036392			2-hydroxyphytanoyl-CoA lyase						fatty acid alpha-oxidation	peroxisomal matrix	carbon-carbon lyase activity|identical protein binding|magnesium ion binding|thiamine pyrophosphate binding				0																		---	---	---	---
ANKRD28	23243	broad.mit.edu	37	3	15826009	15826009	+	Intron	DEL	A	-	-	rs150384619		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15826009delA	uc003caj.1	-						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																		---	---	---	---
OXNAD1	92106	broad.mit.edu	37	3	16355341	16355341	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16355341delC	uc011awb.1	+						OXNAD1_uc003cax.2_Intron	NM_138381	NP_612390			oxidoreductase NAD-binding domain containing 1								oxidoreductase activity			skin(1)	1																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16549330	16549331	+	Intron	DEL	AT	-	-	rs34533718		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16549330_16549331delAT	uc003cay.2	-							NM_015150	NP_055965			raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
PLCL2	23228	broad.mit.edu	37	3	16990697	16990700	+	Intron	DEL	AGAT	-	-	rs147514564		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16990697_16990700delAGAT	uc011awc.1	+						PLCL2_uc010het.1_Intron|PLCL2_uc011awd.1_Intron	NM_001144382	NP_001137854			phospholipase C-like 2 isoform 1						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17260580	17260581	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17260580_17260581delTT	uc003cbf.2	-						TBC1D5_uc010heu.2_Intron|TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron|TBC1D5_uc010hew.1_Intron	NM_014744	NP_055559			TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17300086	17300086	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17300086delA	uc003cbf.2	-						TBC1D5_uc010heu.2_Intron|TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron|TBC1D5_uc010hew.1_Intron	NM_014744	NP_055559			TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	17943341	17943342	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17943341_17943342insT								TBC1D5 (159101 upstream) : SATB1 (445924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	17951448	17951448	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17951448delT								TBC1D5 (167208 upstream) : SATB1 (437818 downstream)																																			---	---	---	---
SATB1	6304	broad.mit.edu	37	3	18458183	18458183	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18458183delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	18495927	18495928	+	IGR	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18495927_18495928delGA								SATB1 (15675 upstream) : KCNH8 (694089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	19082293	19082294	+	IGR	INS	-	TG	TG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19082293_19082294insTG								SATB1 (602041 upstream) : KCNH8 (107723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	19777368	19777368	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19777368delA								KCNH8 (200233 upstream) : EFHB (143600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	19885192	19885192	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19885192delT								KCNH8 (308057 upstream) : EFHB (35776 downstream)																																			---	---	---	---
KAT2B	8850	broad.mit.edu	37	3	20105027	20105041	+	Intron	DEL	TTTTTTTTTTTTTTT	-	-	rs13089721		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20105027_20105041delTTTTTTTTTTTTTTT	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																		---	---	---	---
KAT2B	8850	broad.mit.edu	37	3	20120032	20120032	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20120032delT	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	20300526	20300526	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20300526delT								SGOL1 (72843 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	21315099	21315100	+	IGR	INS	-	T	T	rs142884875	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21315099_21315100insT								None (None upstream) : VENTXP7 (132118 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	22521563	22521564	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22521563_22521564delGT								ZNF385D (107440 upstream) : UBE2E2 (723089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	23035775	23035776	+	IGR	DEL	AA	-	-	rs77899591		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23035775_23035776delAA								ZNF385D (621652 upstream) : UBE2E2 (208877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	23769862	23769862	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23769862delA								UBE2E2 (137566 upstream) : UBE2E1 (77577 downstream)																																			---	---	---	---
UBE2E1	7324	broad.mit.edu	37	3	23868558	23868558	+	Intron	DEL	T	-	-	rs76178104		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23868558delT	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																		---	---	---	---
NR1D2	9975	broad.mit.edu	37	3	23997335	23997336	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23997335_23997336delAA	uc003ccs.2	+						NR1D2_uc010hfd.2_Intron|NR1D2_uc011awk.1_Intron	NM_005126	NP_005117			nuclear receptor subfamily 1, group D, member 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding			urinary_tract(1)|kidney(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	24754813	24754813	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24754813delA								THRB (218360 upstream) : RARB (461010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	24768249	24768249	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24768249delA								THRB (231796 upstream) : RARB (447574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	25110505	25110505	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25110505delA								THRB (574052 upstream) : RARB (105318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	26308494	26308494	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26308494delT								OXSM (472470 upstream) : LRRC3B (355806 downstream)																																			---	---	---	---
LRRC3B	116135	broad.mit.edu	37	3	26727578	26727578	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26727578delT	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																		---	---	---	---
SLC4A7	9497	broad.mit.edu	37	3	27438891	27438892	+	Intron	DEL	TT	-	-	rs35700630		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27438891_27438892delTT	uc003cdv.2	-						SLC4A7_uc011awu.1_Intron|SLC4A7_uc011awv.1_Intron|SLC4A7_uc003cdu.3_Intron|SLC4A7_uc011aww.1_Intron|SLC4A7_uc011awx.1_Intron|SLC4A7_uc011awy.1_Intron|SLC4A7_uc011awz.1_Intron|SLC4A7_uc011axa.1_Intron|SLC4A7_uc011axb.1_Intron|SLC4A7_uc010hfl.2_Intron|SLC4A7_uc003cdw.2_Intron	NM_003615	NP_003606			solute carrier family 4, sodium bicarbonate							apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	27563574	27563574	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27563574delT								SLC4A7 (37736 upstream) : EOMES (194314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27947134	27947135	+	IGR	DEL	AA	-	-	rs76458681		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27947134_27947135delAA								EOMES (182928 upstream) : CMC1 (335989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	28225741	28225741	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28225741delA								EOMES (461535 upstream) : CMC1 (57383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	29294934	29294934	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29294934delT								ZCWPW2 (728304 upstream) : RBMS3 (28009 downstream)																																			---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29533485	29533485	+	Intron	DEL	A	-	-	rs67042130		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29533485delA	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	29712751	29712751	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29712751delA	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	30140882	30140884	+	IGR	DEL	TAA	-	-	rs10570526		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30140882_30140884delTAA								RBMS3 (94263 upstream) : TGFBR2 (507110 downstream)																																			---	---	---	---
GADL1	339896	broad.mit.edu	37	3	30806807	30806808	+	Intron	INS	-	TCAA	TCAA	rs79312497		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30806807_30806808insTCAA	uc003cep.2	-							NM_207359	NP_997242			glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	30979548	30979548	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30979548delT								GADL1 (43395 upstream) : STT3B (594943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	32051633	32051633	+	IGR	DEL	T	-	-	rs11303839		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32051633delT								ZNF860 (18513 upstream) : GPD1L (96511 downstream)																																			---	---	---	---
CMTM8	152189	broad.mit.edu	37	3	32357891	32357891	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32357891delA	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																		---	---	---	---
CMTM8	152189	broad.mit.edu	37	3	32370571	32370571	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32370571delT	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																		---	---	---	---
SUSD5	26032	broad.mit.edu	37	3	33209736	33209736	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33209736delT	uc003cfo.1	-							NM_015551	NP_056366			sushi domain containing 5 precursor						cell adhesion	integral to membrane	hyaluronic acid binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	33298551	33298552	+	IGR	DEL	AG	-	-	rs71899271		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33298551_33298552delAG								SUSD5 (37844 upstream) : FBXL2 (20382 downstream)																																			---	---	---	---
UBP1	7342	broad.mit.edu	37	3	33454074	33454075	+	Intron	DEL	AA	-	-	rs35702863		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33454074_33454075delAA	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	33509980	33509980	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33509980delA								UBP1 (28083 upstream) : CLASP2 (27761 downstream)																																			---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33613127	33613127	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33613127delA	uc003cfu.2	-						CLASP2_uc003cfs.2_Intron|CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron|CLASP2_uc011axt.1_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33650237	33650241	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33650237_33650241delTTTTT	uc003cfu.2	-						CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron|CLASP2_uc003cfv.2_Intron|CLASP2_uc011axu.1_Intron|CLASP2_uc003cfw.2_Intron|CLASP2_uc011axt.1_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33695525	33695525	+	Intron	DEL	A	-	-	rs138918494		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33695525delA	uc003cfu.2	-						CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	34106312	34106312	+	IGR	DEL	T	-	-	rs5847803		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34106312delT								PDCD6IP (195118 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34115223	34115223	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34115223delT								PDCD6IP (204029 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34557009	34557010	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34557009_34557010delAA								PDCD6IP (645815 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34635791	34635791	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34635791delT								PDCD6IP (724597 upstream) : None (None downstream)																																			---	---	---	---
ARPP21	10777	broad.mit.edu	37	3	35756914	35756914	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35756914delT	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc011axy.1_Intron|ARPP21_uc003cgf.2_Intron	NM_016300	NP_057384			cyclic AMP-regulated phosphoprotein, 21 kD							cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3																		---	---	---	---
ARPP21	10777	broad.mit.edu	37	3	35824912	35824912	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35824912delT	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc011axy.1_Intron|ARPP21_uc003cgf.2_Intron|ARPP21_uc003cgg.2_Intron	NM_016300	NP_057384			cyclic AMP-regulated phosphoprotein, 21 kD							cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	36138340	36138340	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36138340delT								ARPP21 (302353 upstream) : STAC (283757 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	37238346	37238346	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37238346delA								LRRFIP2 (20495 upstream) : GOLGA4 (46392 downstream)																																			---	---	---	---
C3orf35	339883	broad.mit.edu	37	3	37438059	37438059	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37438059delT	uc003cha.3	+						C3orf35_uc003cgy.1_Intron|C3orf35_uc003cgz.1_Intron|C3orf35_uc003chb.2_5'Flank	NM_178339	NP_848029			AP20 region protein isoform B							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37503490	37503490	+	Intron	DEL	A	-	-	rs36016395		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37503490delA	uc003chd.2	+						ITGA9_uc003chc.2_Intron	NM_002207	NP_002198			integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37560578	37560580	+	Intron	DEL	TTT	-	-	rs67132108		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37560578_37560580delTTT	uc003chd.2	+						ITGA9_uc003chc.2_Intron	NM_002207	NP_002198			integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37851915	37851915	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37851915delT	uc003chd.2	+						uc003che.2_Intron	NM_002207	NP_002198			integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
SCN5A	6331	broad.mit.edu	37	3	38665700	38665701	+	Intron	DEL	AC	-	-	rs68123790		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38665700_38665701delAC	uc003cio.2	-						SCN5A_uc003cin.2_Intron|SCN5A_uc003cil.3_Intron|SCN5A_uc010hhi.2_Intron|SCN5A_uc010hhk.2_Intron|SCN5A_uc011ayr.1_Intron|SCN5A_uc010hhl.1_5'Flank	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)													---	---	---	---
SCN5A	6331	broad.mit.edu	37	3	38675033	38675033	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38675033delC	uc003cio.2	-						SCN5A_uc003cin.2_Intron|SCN5A_uc003cil.3_Intron|SCN5A_uc010hhi.2_Intron|SCN5A_uc010hhk.2_Intron|SCN5A_uc011ayr.1_Intron	NM_198056	NP_932173			voltage-gated sodium channel type V alpha						blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	39201889	39201889	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39201889delT								CSRNP1 (5836 upstream) : XIRP1 (22818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39497161	39497161	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39497161delC								RPSA (43131 upstream) : MOBP (11909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39610429	39610430	+	IGR	INS	-	CT	CT	rs149298976	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39610429_39610430insCT								MOBP (42574 upstream) : MYRIP (240873 downstream)																																			---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	40036573	40036574	+	Intron	INS	-	G	G	rs140012902	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40036573_40036574insG	uc003cka.2	+						MYRIP_uc010hhu.2_Intron|MYRIP_uc010hhv.2_Intron|MYRIP_uc010hhw.2_Intron|MYRIP_uc010hhx.1_Intron	NM_015460	NP_056275			myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)														---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	40251104	40251104	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40251104delA	uc003cka.2	+						MYRIP_uc010hhu.2_Intron|MYRIP_uc010hhv.2_Intron|MYRIP_uc010hhw.2_Intron|MYRIP_uc011ayz.1_Intron|uc003ckb.2_Intron	NM_015460	NP_056275			myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	41196804	41196804	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41196804delA								ZNF621 (615761 upstream) : CTNNB1 (39597 downstream)																																			---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41859144	41859144	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41859144delA	uc003ckv.3	-						ULK4_uc003ckw.2_Intron	NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41961098	41961099	+	Intron	INS	-	A	A	rs77111787	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41961098_41961099insA	uc003ckv.3	-						ULK4_uc003ckw.2_Intron|ULK4_uc003ckx.1_Intron	NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	42050018	42050018	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42050018delT								ULK4 (46358 upstream) : TRAK1 (82728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	42121282	42121282	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42121282delT								ULK4 (117622 upstream) : TRAK1 (11464 downstream)																																			---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42202060	42202061	+	Intron	DEL	TG	-	-	rs59260540		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42202060_42202061delTG	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron|TRAK1_uc003ckz.3_Intron|TRAK1_uc011azj.1_Intron|TRAK1_uc003cla.2_Intron	NM_001042646	NP_001036111			OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	42426275	42426276	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42426275_42426276delGT								CCK (118613 upstream) : LYZL4 (12301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	42491184	42491184	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42491184delT								LYZL4 (39119 upstream) : VIPR1 (52920 downstream)																																			---	---	---	---
ANO10	55129	broad.mit.edu	37	3	43438426	43438426	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43438426delT	uc003cmv.2	-						ANO10_uc011azs.1_Intron|ANO10_uc003cmw.2_Intron|ANO10_uc010hil.2_Intron|ANO10_uc011azt.1_Intron	NM_018075	NP_060545			transmembrane protein 16K						cell death	chloride channel complex	chloride channel activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	43727786	43727786	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43727786delT								ANO10 (64226 upstream) : ABHD5 (4589 downstream)																																			---	---	---	---
ZNF445	353274	broad.mit.edu	37	3	44561469	44561469	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44561469delA	uc011azw.1	-							NM_181489	NP_852466			zinc finger protein 445						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)														---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44882740	44882740	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44882740delT	uc003cnx.3	+						KIF15_uc010hiq.2_Intron|KIF15_uc010hir.2_Intron	NM_020242	NP_064627			kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
ZDHHC3	51304	broad.mit.edu	37	3	44968020	44968020	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44968020delT	uc003cod.2	-	8					ZDHHC3_uc003cog.2_3'UTR|ZDHHC3_uc011bad.1_Intron	NM_016598	NP_057682			zinc finger, DHHC-type containing 3 isoform 2							Golgi membrane|integral to membrane	zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00943)|KIRC - Kidney renal clear cell carcinoma(197;0.053)|Kidney(197;0.0665)														---	---	---	---
ZDHHC3	51304	broad.mit.edu	37	3	45004993	45004993	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45004993delA	uc003cod.2	-						ZDHHC3_uc003cog.2_Intron|ZDHHC3_uc011bad.1_Intron	NM_016598	NP_057682			zinc finger, DHHC-type containing 3 isoform 2							Golgi membrane|integral to membrane	zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00943)|KIRC - Kidney renal clear cell carcinoma(197;0.053)|Kidney(197;0.0665)														---	---	---	---
EXOSC7	23016	broad.mit.edu	37	3	45037267	45037267	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45037267delA	uc003coi.2	+						EXOSC7_uc003coh.1_Intron|EXOSC7_uc011bae.1_Intron|EXOSC7_uc010his.1_Intron|EXOSC7_uc003coj.2_Intron	NM_015004	NP_055819			exosome component 7						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|protein binding|RNA binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)														---	---	---	---
EXOSC7	23016	broad.mit.edu	37	3	45045755	45045755	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45045755delT	uc003coi.2	+						EXOSC7_uc003coh.1_Intron|EXOSC7_uc010his.1_Intron|EXOSC7_uc003coj.2_Intron	NM_015004	NP_055819			exosome component 7						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|protein binding|RNA binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	45305118	45305118	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45305118delT								TMEM158 (37304 upstream) : LARS2 (124957 downstream)																																			---	---	---	---
LIMD1	8994	broad.mit.edu	37	3	45707271	45707271	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45707271delG	uc003coq.2	+							NM_014240	NP_055055			LIM domains containing 1						cytoplasmic mRNA processing body assembly|gene silencing by miRNA|multicellular organismal development|negative regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasmic mRNA processing body|nucleus|RNA-induced silencing complex	protein binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	46428090	46428090	+	IGR	DEL	A	-	-	rs11298823		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46428090delA								CCR5 (10400 upstream) : CCRL2 (20631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	46635386	46635387	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46635386_46635387delAA								TDGF1 (11436 upstream) : ALS2CL (75292 downstream)																																			---	---	---	---
C3orf75	54859	broad.mit.edu	37	3	47553872	47553872	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47553872delA	uc003crk.2	-						C3orf75_uc003crj.2_Intron|C3orf75_uc011bba.1_Intron|C3orf75_uc003crl.1_Intron	NM_001031703	NP_001026873			transmembrane protein 103												0																		---	---	---	---
SMARCC1	6599	broad.mit.edu	37	3	47770731	47770731	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47770731delA	uc003crq.2	-						SMARCC1_uc011bbd.1_Intron	NM_003074	NP_003065			SWI/SNF-related matrix-associated						chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity			skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)														---	---	---	---
FBXW12	285231	broad.mit.edu	37	3	48423615	48423615	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48423615delT	uc003csr.2	+						FBXW12_uc010hjv.2_Intron|FBXW12_uc003css.2_Intron|FBXW12_uc010hjw.2_Intron	NM_207102	NP_996985			F-box and WD repeat domain containing 12 isoform												0				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
SHISA5	51246	broad.mit.edu	37	3	48524059	48524059	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48524059delT	uc003ctp.1	-						SHISA5_uc003cto.1_Intron|SHISA5_uc003ctq.1_Intron|SHISA5_uc003ctr.1_Intron|SHISA5_uc003cts.1_Intron	NM_016479	NP_057563			scotin precursor						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade	endoplasmic reticulum membrane|integral to membrane|nuclear membrane	signal transducer activity|WW domain binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	48941153	48941153	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48941153delA								SLC25A20 (4751 upstream) : C3orf71 (14068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	48950906	48950906	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48950906delA								SLC25A20 (14504 upstream) : C3orf71 (4315 downstream)																																			---	---	---	---
QRICH1	54870	broad.mit.edu	37	3	49095768	49095768	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49095768delT	uc010hkq.2	-						QRICH1_uc003cvu.2_Intron|QRICH1_uc003cvv.2_Intron	NM_198880	NP_942581			glutamine-rich 1											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)														---	---	---	---
USP19	10869	broad.mit.edu	37	3	49155556	49155556	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49155556delA	uc003cwd.1	-						USP19_uc003cwa.2_5'Flank|USP19_uc003cvz.3_Intron|USP19_uc011bcg.1_Intron|USP19_uc003cwb.2_Intron|USP19_uc003cwc.1_5'Flank|USP19_uc011bch.1_Intron|USP19_uc011bci.1_Intron	NM_006677	NP_006668			ubiquitin thioesterase 19						ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(4)|breast(2)|lung(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
CCDC36	339834	broad.mit.edu	37	3	49233370	49233370	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49233370delA	uc003cwk.2	+							NM_178173	NP_835467			coiled-coil domain containing 36											ovary(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)														---	---	---	---
CCDC36	339834	broad.mit.edu	37	3	49234734	49234734	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49234734delA	uc003cwk.2	+						CCDC36_uc003cwl.3_5'Flank|CCDC36_uc011bck.1_5'Flank|CCDC36_uc010hkt.2_5'Flank	NM_178173	NP_835467			coiled-coil domain containing 36											ovary(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)														---	---	---	---
USP4	7375	broad.mit.edu	37	3	49330918	49330919	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49330918_49330919insA	uc003cwq.2	-						USP4_uc003cwo.2_Intron|USP4_uc003cwp.2_Intron|USP4_uc003cwr.2_Intron	NM_003363	NP_003354			ubiquitin specific protease 4 isoform a						negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process	lysosome|nucleus	adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|urinary_tract(1)|lung(1)	4		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)														---	---	---	---
USP4	7375	broad.mit.edu	37	3	49335477	49335477	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49335477delA	uc003cwq.2	-						USP4_uc003cwo.2_Intron|USP4_uc003cwp.2_Intron|USP4_uc003cwr.2_Intron	NM_003363	NP_003354			ubiquitin specific protease 4 isoform a						negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process	lysosome|nucleus	adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|urinary_tract(1)|lung(1)	4		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)														---	---	---	---
USP4	7375	broad.mit.edu	37	3	49354915	49354915	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49354915delT	uc003cwq.2	-						USP4_uc003cwr.2_Intron	NM_003363	NP_003354			ubiquitin specific protease 4 isoform a						negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process	lysosome|nucleus	adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|urinary_tract(1)|lung(1)	4		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)														---	---	---	---
AMT	275	broad.mit.edu	37	3	49454234	49454234	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49454234delT	uc003cww.2	-	9					AMT_uc011bcn.1_3'UTR|AMT_uc003cwx.2_3'UTR|AMT_uc011bco.1_3'UTR|AMT_uc003cwy.2_3'UTR|AMT_uc011bcp.1_3'UTR|AMT_uc011bcq.1_3'UTR	NM_000481	NP_000472			aminomethyltransferase isoform 1 precursor						glycine catabolic process	mitochondrion	aminomethyltransferase activity|transaminase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	NADH(DB00157)|Tetrahydrofolic acid(DB00116)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	49486985	49486985	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49486985delT								NICN1 (20228 upstream) : DAG1 (20580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	49574928	49574928	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49574928delA								DAG1 (1882 upstream) : BSN (16994 downstream)																																			---	---	---	---
IP6K1	9807	broad.mit.edu	37	3	49765948	49765949	+	Intron	INS	-	ATTT	ATTT	rs144785405	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49765948_49765949insATTT	uc003cxm.1	-						IP6K1_uc003cxn.1_Intron|IP6K1_uc011bcv.1_Intron|IP6K1_uc003cxo.2_Intron	NM_153273	NP_695005			inositol hexakisphosphate kinase 1 isoform 1						phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol hexakisphosphate 5-kinase activity|inositol trisphosphate 3-kinase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	49920795	49920795	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49920795delA								CAMKV (13426 upstream) : MST1R (3643 downstream)																																			---	---	---	---
MST1R	4486	broad.mit.edu	37	3	49928163	49928164	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49928163_49928164delTT	uc003cxy.3	-						MST1R_uc011bdc.1_Intron	NM_002447	NP_002438			macrophage stimulating 1 receptor precursor						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)														---	---	---	---
RBM6	10180	broad.mit.edu	37	3	49993434	49993434	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49993434delT	uc003cyc.2	+						RBM6_uc011bdh.1_Intron|RBM6_uc010hlc.1_Intron|RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768			RNA binding motif protein 6						RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)														---	---	---	---
RBM6	10180	broad.mit.edu	37	3	50004794	50004794	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50004794delA	uc003cyc.2	+						RBM6_uc011bdh.1_Intron|RBM6_uc010hlc.1_Intron|RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768			RNA binding motif protein 6						RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)														---	---	---	---
RBM6	10180	broad.mit.edu	37	3	50020449	50020449	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50020449delT	uc003cyc.2	+						RBM6_uc011bdh.1_Intron|RBM6_uc010hlc.1_Intron|RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768			RNA binding motif protein 6						RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)														---	---	---	---
SEMA3F	6405	broad.mit.edu	37	3	50218500	50218501	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50218500_50218501delAA	uc003cyj.2	+						SEMA3F_uc003cyk.2_Intron	NM_004186	NP_004177			semaphorin 3F precursor						axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)														---	---	---	---
SLC38A3	10991	broad.mit.edu	37	3	50245695	50245699	+	Intron	DEL	TTTTT	-	-	rs35306902		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50245695_50245699delTTTTT	uc003cyn.3	+						SLC38A3_uc011bdl.1_Intron	NM_006841	NP_006832			solute carrier family 38, member 3						cellular nitrogen compound metabolic process|sodium ion transport	integral to plasma membrane	antiporter activity|L-alanine transmembrane transporter activity|L-asparagine transmembrane transporter activity|L-glutamine transmembrane transporter activity|L-histidine transmembrane transporter activity|symporter activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)	L-Asparagine(DB00174)|L-Glutamine(DB00130)|L-Histidine(DB00117)													---	---	---	---
HYAL1	3373	broad.mit.edu	37	3	50347215	50347215	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50347215delA	uc003czs.2	-							NM_153281	NP_695013			hyaluronoglucosaminidase 1 isoform 1							extracellular space|lysosome	hyalurononglucosaminidase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)	Hyaluronidase(DB00070)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	50689379	50689379	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50689379delA								MAPKAPK3 (2660 upstream) : DOCK3 (23293 downstream)																																			---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	50905510	50905510	+	Intron	DEL	T	-	-	rs149170025		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50905510delT	uc011bds.1	+							NM_004947	NP_004938			dedicator of cytokinesis 3							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51413261	51413261	+	Frame_Shift_Del	DEL	A	-	-	rs34788750		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51413261delA	uc011bds.1	+	51	5518	c.5495delA	c.(5494-5496)GAAfs	p.E1832fs		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1832						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
RAD54L2	23132	broad.mit.edu	37	3	51696359	51696360	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51696359_51696360insT	uc011bdt.1	+						RAD54L2_uc003dbh.2_Intron|RAD54L2_uc011bdu.1_Intron|RAD54L2_uc003dbj.2_Intron	NM_015106	NP_055921			RAD54-like 2							nucleus	ATP binding|DNA binding|helicase activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)														---	---	---	---
TLR9	54106	broad.mit.edu	37	3	52257017	52257017	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52257017delC	uc003dda.1	-	2	1949	c.1315delG	c.(1315-1317)GAGfs	p.E439fs	TLR9_uc003ddb.2_Frame_Shift_Del_p.E536fs	NM_017442	NP_059138	Q9NR96	TLR9_HUMAN	toll-like receptor 9 isoform A precursor	439	LRR 14.|Extracellular (Potential).				defense response to bacterium|fibroblast growth factor receptor signaling pathway|I-kappaB phosphorylation|inflammatory response|innate immune response|insulin receptor signaling pathway|maintenance of gastrointestinal epithelium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-beta production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|response to molecule of bacterial origin	apical plasma membrane|basolateral plasma membrane|early phagosome|endoplasmic reticulum membrane|endosome membrane|extracellular region|integral to membrane|lysosome	interleukin-1 receptor binding|siRNA binding|transmembrane receptor activity			large_intestine(2)|skin(2)	4				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)													---	---	---	---
WDR82	80335	broad.mit.edu	37	3	52294706	52294707	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52294706_52294707insA	uc003ddl.2	-						WDR82_uc003ddk.2_Intron	NM_025222	NP_079498			WD repeat domain 82						histone H3-K4 methylation	chromatin|PTW/PP1 phosphatase complex|Set1C/COMPASS complex	protein binding				0				BRCA - Breast invasive adenocarcinoma(193;2.67e-05)|Kidney(197;0.00198)|KIRC - Kidney renal clear cell carcinoma(197;0.00223)|OV - Ovarian serous cystadenocarcinoma(275;0.246)														---	---	---	---
TNNC1	7134	broad.mit.edu	37	3	52486500	52486501	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52486500_52486501insT	uc003deb.2	-	2	79_80	c.53_54insA	c.(52-54)AATfs	p.N18fs	NISCH_uc011beg.1_5'Flank	NM_003280	NP_003271	P63316	TNNC1_HUMAN	troponin C, slow	18	EF-hand 1.				cardiac muscle contraction|muscle filament sliding|regulation of ATPase activity|regulation of muscle filament sliding speed|ventricular cardiac muscle tissue morphogenesis	cytosol|troponin complex	actin filament binding|calcium ion binding|calcium-dependent protein binding|protein homodimerization activity|troponin I binding|troponin T binding				0				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00175)|KIRC - Kidney renal clear cell carcinoma(197;0.00198)|OV - Ovarian serous cystadenocarcinoma(275;0.0525)	Bepridil(DB01244)|Dihydroxyaluminium(DB01375)|Levosimendan(DB00922)													---	---	---	---
GLT8D1	55830	broad.mit.edu	37	3	52734193	52734195	+	Intron	DEL	GAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52734193_52734195delGAA	uc003dfi.3	-						GLT8D1_uc003dfj.2_Intron|GLT8D1_uc003dfk.2_Intron|GLT8D1_uc003dfl.2_Intron|GLT8D1_uc003dfm.2_Intron|GLT8D1_uc003dfn.2_Intron|GLT8D1_uc003dfo.1_Intron	NM_152932	NP_690909			glycosyltransferase 8 domain containing 1							integral to membrane|mitochondrion	transferase activity, transferring glycosyl groups				0				BRCA - Breast invasive adenocarcinoma(193;6.78e-05)|Kidney(197;0.000618)|KIRC - Kidney renal clear cell carcinoma(197;0.000779)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
NEK4	6787	broad.mit.edu	37	3	52793417	52793418	+	Intron	DEL	AA	-	-	rs76023136		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52793417_52793418delAA	uc003dfq.3	-						NEK4_uc011bej.1_Intron|NEK4_uc003dfr.2_Intron	NM_003157	NP_003148			NIMA-related kinase 4						cell division|mitosis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)														---	---	---	---
TMEM110	375346	broad.mit.edu	37	3	52908356	52908356	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52908356delA	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	52941394	52941394	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52941394delA	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	53165154	53165154	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53165154delA	uc003dgj.2	-						RFT1_uc003dgk.2_5'Flank	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)														---	---	---	---
TKT	7086	broad.mit.edu	37	3	53261284	53261309	+	Intron	DEL	CAGAGGCCCACGTGCGGCCCCAGCAG	-	-	rs66691362		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53261284_53261309delCAGAGGCCCACGTGCGGCCCCAGCAG	uc003dgo.2	-						TKT_uc003dgp.2_Intron|TKT_uc011beo.1_Intron|TKT_uc003dgq.2_Intron|TKT_uc011beq.1_Intron|TKT_uc011ber.1_Intron|TKT_uc011bep.1_Intron	NM_001135055	NP_001128527			transketolase isoform 1						energy reserve metabolic process|xylulose biosynthetic process	cytosol	protein binding|transketolase activity			ovary(2)	2		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)	Thiamine(DB00152)													---	---	---	---
DCP1A	55802	broad.mit.edu	37	3	53368940	53368940	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53368940delT	uc003dgs.3	-						DCP1A_uc003dgt.3_Intron	NM_018403	NP_060873			DCP1 decapping enzyme homolog A						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus	hydrolase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)														---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53656072	53656073	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53656072_53656073delTT	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)													---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53770916	53770918	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53770916_53770918delAAA	uc003dgv.3	+						CACNA1D_uc003dgu.3_Intron|CACNA1D_uc003dgy.3_Intron|CACNA1D_uc003dgw.3_Intron|CACNA1D_uc003dgx.1_Intron	NM_001128840	NP_001122312			calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	53849348	53849348	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53849348delG								CACNA1D (2857 upstream) : CHDH (1040 downstream)																																			---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54499082	54499083	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54499082_54499083insT	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	54615772	54615774	+	Intron	DEL	AAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54615772_54615774delAAG	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	54875437	54875437	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54875437delA	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868			calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	55211685	55211686	+	IGR	DEL	TG	-	-	rs35015435		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55211685_55211686delTG								CACNA2D3 (103103 upstream) : WNT5A (288058 downstream)																																			---	---	---	---
WNT5A	7474	broad.mit.edu	37	3	55500925	55500925	+	3'UTR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55500925delG	uc003dhn.2	-	5					WNT5A_uc003dhm.2_3'UTR|WNT5A_uc010hmw.2_3'UTR|WNT5A_uc010hmx.2_3'UTR	NM_003392	NP_003383			wingless-type MMTV integration site family,						activation of JUN kinase activity|activation of protein kinase B activity|axon guidance|cartilage development|cellular protein localization|cellular response to calcium ion|cellular response to interferon-gamma|cellular response to lipopolysaccharide|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|cervix development|cochlea morphogenesis|convergent extension involved in organogenesis|dopaminergic neuron differentiation|dorsal/ventral axis specification|embryonic digit morphogenesis|embryonic skeletal system development|epithelial cell proliferation involved in mammary gland duct elongation|epithelial to mesenchymal transition|face development|genitalia development|heart looping|hemopoietic stem cell proliferation|keratinocyte differentiation|lateral sprouting involved in mammary gland duct morphogenesis|lens development in camera-type eye|male gonad development|mammary gland branching involved in thelarche|negative regulation of apoptosis|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of mesenchymal cell proliferation|negative regulation of transcription, DNA-dependent|neural tube closure|olfactory bulb interneuron development|optic cup formation involved in camera-type eye development|palate development|positive regulation of angiogenesis|positive regulation of cartilage development|positive regulation of cGMP metabolic process|positive regulation of chemokine biosynthetic process|positive regulation of cytokine secretion involved in immune response|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of macrophage activation|positive regulation of macrophage cytokine production|positive regulation of mesenchymal cell proliferation|positive regulation of neuron projection development|positive regulation of NF-kappaB transcription factor activity|positive regulation of ossification|positive regulation of protein catabolic process|positive regulation of protein kinase C signaling cascade|positive regulation of T cell chemotaxis|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|primitive streak formation|regulation of branching involved in mammary gland duct morphogenesis|somitogenesis|tail morphogenesis|type B pancreatic cell development|urinary bladder development|uterus development|vagina development|Wnt receptor signaling pathway, calcium modulating pathway|wound healing	extracellular space|membrane fraction|plasma membrane|proteinaceous extracellular matrix	frizzled binding|frizzled-2 binding|receptor tyrosine kinase-like orphan receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.00377)|Kidney(284;0.00408)|OV - Ovarian serous cystadenocarcinoma(275;0.204)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	55595703	55595703	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55595703delT	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)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56168594	56168594	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56168594delT	uc003dhr.1	-							NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56427973	56427974	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56427973_56427974delAA	uc003dhr.1	-							NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
ARHGEF3	50650	broad.mit.edu	37	3	56775213	56775213	+	Intron	DEL	T	-	-	rs66498238		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56775213delT	uc003dig.2	-						ARHGEF3_uc011bew.1_Intron|ARHGEF3_uc003dih.2_Intron|ARHGEF3_uc011bev.1_Intron|ARHGEF3_uc003dif.2_Intron|ARHGEF3_uc010hmy.1_Intron|ARHGEF3_uc003dii.2_Intron	NM_019555	NP_062455			Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)														---	---	---	---
APPL1	26060	broad.mit.edu	37	3	57276921	57276921	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57276921delA	uc003dio.2	+	7	600	c.453delA	c.(451-453)TCAfs	p.S151fs	APPL1_uc010hnb.2_Frame_Shift_Del_p.S151fs|APPL1_uc011bey.1_Frame_Shift_Del_p.S134fs	NM_012096	NP_036228	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH	151	Required for RAB5A binding.				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)														---	---	---	---
APPL1	26060	broad.mit.edu	37	3	57294067	57294067	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57294067delA	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)														---	---	---	---
FAM116A	201627	broad.mit.edu	37	3	57672759	57672759	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57672759delT	uc003dja.2	-							NM_152678	NP_689891			hypothetical protein LOC201627											pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(55;0.000621)|KIRC - Kidney renal clear cell carcinoma(284;0.0485)|Kidney(284;0.0607)														---	---	---	---
SLMAP	7871	broad.mit.edu	37	3	57841778	57841778	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57841778delA	uc003dje.1	+						SLMAP_uc003djc.1_Intron|SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron	NM_007159	NP_009090			sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)														---	---	---	---
SLMAP	7871	broad.mit.edu	37	3	57898511	57898511	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57898511delT	uc003dje.1	+						SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron|SLMAP_uc003djg.1_Intron|SLMAP_uc011bez.1_Intron|SLMAP_uc011bfa.1_Intron|SLMAP_uc003djh.2_Intron|SLMAP_uc003dji.1_Intron|SLMAP_uc011bfb.1_Intron|SLMAP_uc011bfc.1_Intron	NM_007159	NP_009090			sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	57931211	57931211	+	IGR	DEL	T	-	-	rs142063250	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57931211delT								SLMAP (16317 upstream) : FLNB (62916 downstream)																																			---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58071753	58071754	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58071753_58071754delCT	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron|FLNB_uc003djl.2_Intron|FLNB_uc003djm.2_Intron	NM_001457	NP_001448			filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	59358180	59358180	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59358180delA								C3orf67 (322422 upstream) : FHIT (376858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59544411	59544411	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59544411delG								C3orf67 (508653 upstream) : FHIT (190627 downstream)																																			---	---	---	---
FHIT	2272	broad.mit.edu	37	3	59910749	59910749	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59910749delT	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	60176085	60176086	+	Intron	DEL	AA	-	-	rs75459473		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60176085_60176086delAA	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	61112174	61112174	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61112174delA	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	61526845	61526845	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61526845delA								FHIT (289712 upstream) : PTPRG (20398 downstream)																																			---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	61597107	61597108	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61597107_61597108insA	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron|PTPRG_uc003dla.3_Intron	NM_002841	NP_002832			protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)														---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	62278688	62278688	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)														---	---	---	---
CADPS	8618	broad.mit.edu	37	3	62542763	62542763	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62542763delT	uc003dll.2	-						CADPS_uc003dlk.1_Intron|CADPS_uc003dlm.2_Intron|CADPS_uc003dln.2_Intron	NM_003716	NP_003707			Ca2+-dependent secretion activator isoform 1						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)														---	---	---	---
ATXN7	6314	broad.mit.edu	37	3	63974140	63974141	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63974140_63974141delAA	uc003dlw.3	+						ATXN7_uc003dlv.2_Intron|ATXN7_uc010hnv.2_Intron|ATXN7_uc011bfn.1_Intron	NM_000333	NP_000324			ataxin 7 isoform a						cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)														---	---	---	---
ATXN7	6314	broad.mit.edu	37	3	63985557	63985557	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63985557delT	uc003dlw.3	+	13					ATXN7_uc010hnv.2_3'UTR|ATXN7_uc011bfn.1_3'UTR	NM_000333	NP_000324			ataxin 7 isoform a						cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)														---	---	---	---
PRICKLE2	166336	broad.mit.edu	37	3	64188321	64188322	+	Intron	INS	-	GT	GT	rs138497838	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64188321_64188322insGT	uc003dmf.2	-							NM_198859	NP_942559			prickle-like 2							cytoplasm|nuclear membrane	zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	64358169	64358169	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64358169delT								PRICKLE2 (147038 upstream) : ADAMTS9 (143164 downstream)																																			---	---	---	---
ADAMTS9	56999	broad.mit.edu	37	3	64523103	64523103	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64523103delA	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc011bfp.1_Intron	NM_182920	NP_891550			ADAM metallopeptidase with thrombospondin type 1						glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)														---	---	---	---
ADAMTS9	56999	broad.mit.edu	37	3	64599332	64599332	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64599332delT	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc003dmh.1_Intron|ADAMTS9_uc011bfp.1_Intron	NM_182920	NP_891550			ADAM metallopeptidase with thrombospondin type 1						glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	65038171	65038171	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65038171delT								ADAMTS9 (364806 upstream) : MAGI1 (301736 downstream)																																			---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65342221	65342221	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65342221delG	uc003dmn.2	-	23	4747	c.4221delC	c.(4219-4221)CCCfs	p.P1407fs	MAGI1_uc003dmm.2_3'UTR	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ	1436					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	65355943	65355943	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65355943delA	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.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	65544736	65544736	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65544736delA	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	65782688	65782688	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65782688delT	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	65825824	65825824	+	Intron	DEL	T	-	-	rs34338889		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65825824delT	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)														---	---	---	---
SLC25A26	115286	broad.mit.edu	37	3	66378310	66378310	+	Intron	DEL	T	-	-	rs71823698		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66378310delT	uc011bfq.1	+						SLC25A26_uc011bfs.1_Intron|SLC25A26_uc011bft.1_Intron|SLC25A26_uc011bfr.1_Intron|SLC25A26_uc003dmt.2_Intron	NM_173471	NP_775742			solute carrier family 25, member 26 isoform a							integral to membrane|mitochondrial inner membrane|nucleus	S-adenosylmethionine transmembrane transporter activity			pancreas(1)	1		Lung NSC(201;0.00774)		BRCA - Breast invasive adenocarcinoma(55;0.00046)|KIRC - Kidney renal clear cell carcinoma(15;0.0515)|Kidney(15;0.0648)														---	---	---	---
LRIG1	26018	broad.mit.edu	37	3	66529164	66529164	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66529164delT	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	67006990	67006993	+	IGR	DEL	GTGT	-	-	rs10545785	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67006990_67006993delGTGT								LRIG1 (456145 upstream) : KBTBD8 (41734 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	67159411	67159412	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67159411_67159412delTT								KBTBD8 (97781 upstream) : SUCLG2 (265733 downstream)																																			---	---	---	---
FAM19A1	407738	broad.mit.edu	37	3	68555624	68555625	+	Intron	DEL	AC	-	-	rs71112658		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68555624_68555625delAC	uc003dnd.2	+						FAM19A1_uc003dne.2_Intron|FAM19A1_uc003dng.2_Intron	NM_213609	NP_998774			family with sequence similarity 19 (chemokine							endoplasmic reticulum|extracellular region				ovary(1)	1		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	68997009	68997011	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68997009_68997011delAAA								FAM19A4 (15298 upstream) : C3orf64 (27358 downstream)																																			---	---	---	---
ARL6IP5	10550	broad.mit.edu	37	3	69153415	69153415	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69153415delA	uc003dnr.2	+							NM_006407	NP_006398			ADP-ribosylation-like factor 6 interacting						L-glutamate transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.78e-05)|Epithelial(33;0.000818)|LUSC - Lung squamous cell carcinoma(21;0.0118)|Lung(16;0.0189)|KIRC - Kidney renal clear cell carcinoma(39;0.203)|Kidney(39;0.238)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69319721	69319721	+	Intron	DEL	T	-	-	rs71955416		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69319721delT	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnx.1_Intron	NM_015123	NP_055938			FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69336796	69336796	+	Intron	DEL	T	-	-	rs78688753		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69336796delT	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnx.1_Intron	NM_015123	NP_055938			FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71105973	71105973	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71105973delA	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003doi.2_Intron|FOXP1_uc003doj.2_Intron|FOXP1_uc003dok.2_Intron	NM_032682	NP_116071			forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)				T	PAX5	ALL								---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71409500	71409500	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71409500delT	uc003dop.2	-						FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003doq.1_5'Flank|FOXP1_uc003dos.2_Intron	NM_032682	NP_116071			forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)				T	PAX5	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	3	71839473	71839473	+	IGR	DEL	T	-	-	rs145336002	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71839473delT								PROK2 (5116 upstream) : RYBP (584278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72291862	72291863	+	IGR	DEL	AC	-	-	rs4677118	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72291862_72291863delAC								PROK2 (457505 upstream) : RYBP (131888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72404257	72404257	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72404257delT								PROK2 (569900 upstream) : RYBP (19494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72533315	72533316	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72533315_72533316delTT								RYBP (37541 upstream) : SHQ1 (265114 downstream)																																			---	---	---	---
PDZRN3	23024	broad.mit.edu	37	3	73501991	73501992	+	Intron	DEL	TG	-	-	rs35308043		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73501991_73501992delTG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	73753324	73753324	+	IGR	DEL	A	-	-	rs35902440		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73753324delA								PDZRN3 (79252 upstream) : CNTN3 (558398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	73893812	73893812	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73893812delA								PDZRN3 (219740 upstream) : CNTN3 (417910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	74012794	74012794	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74012794delA								PDZRN3 (338722 upstream) : CNTN3 (298928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	74225989	74225989	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74225989delT								PDZRN3 (551917 upstream) : CNTN3 (85733 downstream)																																			---	---	---	---
CNTN3	5067	broad.mit.edu	37	3	74548737	74548737	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74548737delA	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)														---	---	---	---
CNTN3	5067	broad.mit.edu	37	3	74555801	74555801	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74555801delA	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	75124366	75124366	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75124366delT								CNTN3 (554023 upstream) : FAM86D (346339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75739615	75739615	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75739615delG								MIR1324 (59606 upstream) : ZNF717 (19179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76291211	76291211	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76291211delT								ZNF717 (456541 upstream) : ROBO2 (798083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76337634	76337635	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76337634_76337635delTT								ZNF717 (502964 upstream) : ROBO2 (751659 downstream)																																			---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77656758	77656758	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77656758delA	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron|ROBO2_uc003dqa.2_Intron	NM_002942	NP_002933			roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	78080576	78080576	+	IGR	DEL	A	-	-	rs67974587		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78080576delA								ROBO2 (383915 upstream) : ROBO1 (565812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	78345865	78345865	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78345865delA								ROBO2 (649204 upstream) : ROBO1 (300523 downstream)																																			---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79643492	79643492	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79643492delT	uc003dqe.2	-							NM_002941	NP_002932			roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	80051927	80051927	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80051927delA								ROBO1 (234868 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80905344	80905345	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80905344_80905345delTG								None (None upstream) : GBE1 (633505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81423377	81423378	+	IGR	DEL	TT	-	-	rs112076087		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81423377_81423378delTT								None (None upstream) : GBE1 (115472 downstream)																																			---	---	---	---
GBE1	2632	broad.mit.edu	37	3	81720107	81720107	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81720107delA	uc003dqg.2	-						GBE1_uc011bgm.1_Intron	NM_000158	NP_000149			glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)										Glycogen_Storage_Disease_type_IV				---	---	---	---
Unknown	0	broad.mit.edu	37	3	82489097	82489097	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82489097delG	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	82538801	82538801	+	IGR	DEL	A	-	-	rs147372505		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82538801delA								GBE1 (727851 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	82628362	82628362	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82628362delT								GBE1 (817412 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83080470	83080471	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83080470_83080471delCT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83537466	83537466	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83537466delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84686953	84686954	+	IGR	INS	-	TT	TT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84686953_84686954insTT								None (None upstream) : CADM2 (321179 downstream)																																			---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85158536	85158537	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85158536_85158537delGA	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85376188	85376188	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85376188delT	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85821159	85821161	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85821159_85821161delTTT	uc003dqj.2	+						CADM2_uc003dqk.2_Intron|CADM2_uc003dql.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	86246264	86246264	+	IGR	DEL	A	-	-	rs66464834		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86246264delA								CADM2 (128316 upstream) : VGLL3 (740861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	86587161	86587161	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86587161delT								CADM2 (469213 upstream) : VGLL3 (399964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	86905514	86905514	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86905514delA								CADM2 (787566 upstream) : VGLL3 (81611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	86972714	86972714	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86972714delA								CADM2 (854766 upstream) : VGLL3 (14411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87185606	87185606	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87185606delC								VGLL3 (145349 upstream) : CHMP2B (90807 downstream)																																			---	---	---	---
POU1F1	5449	broad.mit.edu	37	3	87309260	87309260	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87309260delG	uc003dqq.1	-						POU1F1_uc010hoj.1_Intron	NM_000306	NP_000297			pituitary specific transcription factor 1						negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)|skin(1)	2	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)														---	---	---	---
POU1F1	5449	broad.mit.edu	37	3	87311118	87311118	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87311118delA	uc003dqq.1	-						POU1F1_uc010hoj.1_Intron	NM_000306	NP_000297			pituitary specific transcription factor 1						negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)|skin(1)	2	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	89856182	89856182	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89856182delA								EPHA3 (324900 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	90164040	90164040	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90164040delA								EPHA3 (632758 upstream) : None (None downstream)																																			---	---	---	---
ARL13B	200894	broad.mit.edu	37	3	93717770	93717770	+	Intron	DEL	T	-	-	rs76734068		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93717770delT	uc003drc.2	+						ARL13B_uc010hop.2_Intron|ARL13B_uc003drd.2_Intron|ARL13B_uc003dre.2_Intron|ARL13B_uc003drf.2_Intron|ARL13B_uc003drg.2_Intron	NM_182896	NP_878899			ADP-ribosylation factor-like 2-like 1 isoform 1								GTP binding				0																		---	---	---	---
ARL13B	200894	broad.mit.edu	37	3	93768421	93768421	+	Intron	DEL	A	-	-	rs79420917		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93768421delA	uc003drc.2	+						ARL13B_uc010hop.2_Intron|ARL13B_uc003drd.2_Intron|ARL13B_uc003dre.2_Intron|ARL13B_uc003drf.2_Intron|ARL13B_uc003drg.2_Intron	NM_182896	NP_878899			ADP-ribosylation factor-like 2-like 1 isoform 1								GTP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	93918730	93918730	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93918730delT								NSUN3 (73100 upstream) : LOC255025 (738377 downstream)																																			---	---	---	---
LOC255025	255025	broad.mit.edu	37	3	94786193	94786193	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94786193delA	uc003drn.2	+											Homo sapiens hypothetical protein LOC255025, mRNA (cDNA clone IMAGE:5267157).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	95551773	95551773	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95551773delA								LOC255025 (656694 upstream) : EPHA6 (981652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95644882	95644882	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95644882delT								LOC255025 (749803 upstream) : EPHA6 (888543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95661771	95661771	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95661771delT								LOC255025 (766692 upstream) : EPHA6 (871654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95680349	95680349	+	IGR	DEL	A	-	-	rs67367925		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95680349delA								LOC255025 (785270 upstream) : EPHA6 (853076 downstream)																																			---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	97212098	97212099	+	Intron	INS	-	TG	TG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97212098_97212099insTG	uc010how.1	+						EPHA6_uc011bgo.1_Intron|EPHA6_uc011bgp.1_Intron|EPHA6_uc003drs.3_Intron|EPHA6_uc003drr.3_Intron|EPHA6_uc003drt.2_Intron|EPHA6_uc010hox.1_Intron	NM_001080448	NP_001073917			EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16																		---	---	---	---
CLDND1	56650	broad.mit.edu	37	3	98239732	98239732	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98239732delA	uc003dsp.2	-						CLDND1_uc003dso.2_Intron|CLDND1_uc003dsq.2_Intron|CLDND1_uc003dss.2_Intron|CLDND1_uc003dsr.2_Intron|CLDND1_uc003dst.2_Intron|CLDND1_uc003dsu.2_Intron|CLDND1_uc003dsv.2_Intron	NM_019895	NP_063948			claudin domain containing 1 protein isoform a							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	98421742	98421745	+	IGR	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98421742_98421745delAAAA								CPOX (109301 upstream) : ST3GAL6 (29407 downstream)																																			---	---	---	---
DCBLD2	131566	broad.mit.edu	37	3	98529907	98529907	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98529907delT	uc003dtd.2	-						DCBLD2_uc003dte.2_Intron	NM_080927	NP_563615			discoidin, CUB and LCCL domain containing 2						cell adhesion|intracellular receptor mediated signaling pathway|negative regulation of cell growth|wound healing	cell surface|integral to plasma membrane				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
DCBLD2	131566	broad.mit.edu	37	3	98619320	98619320	+	Intron	DEL	A	-	-	rs55650073	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98619320delA	uc003dtd.2	-						DCBLD2_uc003dte.2_Intron|DCBLD2_uc003dtf.1_Intron	NM_080927	NP_563615			discoidin, CUB and LCCL domain containing 2						cell adhesion|intracellular receptor mediated signaling pathway|negative regulation of cell growth|wound healing	cell surface|integral to plasma membrane				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
COL8A1	1295	broad.mit.edu	37	3	99509436	99509436	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99509436delT	uc003dtg.1	+						COL8A1_uc003dth.1_Intron|COL8A1_uc003dti.1_Intron	NM_001850	NP_001841			alpha 1 type VIII collagen precursor						angiogenesis|cell adhesion	basement membrane|collagen type VIII					0																		---	---	---	---
TMEM30C	644444	broad.mit.edu	37	3	99908163	99908163	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99908163delT	uc003dtr.1	+											Homo sapiens mRNA, putative transmembrane protein 30C sequence.												0																		---	---	---	---
TOMM70A	9868	broad.mit.edu	37	3	100090456	100090456	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100090456delA	uc003dtw.2	-							NM_014820	NP_055635			translocase of outer mitochondrial membrane 70						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	protein binding|protein transmembrane transporter activity			ovary(1)	1																		---	---	---	---
TFG	10342	broad.mit.edu	37	3	100466187	100466187	+	Intron	DEL	T	-	-	rs3832236		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100466187delT	uc003due.2	+						TFG_uc003duf.2_Intron|TFG_uc003dug.2_Intron|TFG_uc003duh.2_Intron|TFG_uc003dui.2_Intron	NM_006070	NP_006061			TRK-fused						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm	signal transducer activity		TFG/ALK(7)	haematopoietic_and_lymphoid_tissue(7)|lung(2)|large_intestine(1)|prostate(1)	11								T	NTRK1|ALK	papillary thyroid|ALCL|NSCLC								---	---	---	---
IMPG2	50939	broad.mit.edu	37	3	101018340	101018340	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101018340delT	uc003duq.1	-						IMPG2_uc011bhe.1_Intron	NM_016247	NP_057331			interphotoreceptor matrix proteoglycan 2						visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3																		---	---	---	---
NFKBIZ	64332	broad.mit.edu	37	3	101550754	101550754	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101550754delT	uc003dvo.2	+						NFKBIZ_uc010hpo.2_Intron	NM_001005474	NP_001005474			nuclear factor of kappa light polypeptide gene						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(2)	2																		---	---	---	---
NFKBIZ	64332	broad.mit.edu	37	3	101573901	101573902	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101573901_101573902delCA	uc003dvp.2	+						NFKBIZ_uc003dvo.2_Intron|NFKBIZ_uc010hpo.2_Intron|NFKBIZ_uc003dvq.2_Intron	NM_031419	NP_113607			nuclear factor of kappa light polypeptide gene						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(2)	2																		---	---	---	---
ZPLD1	131368	broad.mit.edu	37	3	101819893	101819893	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101819893delA	uc003dvs.1	+							NM_175056	NP_778226			zona pellucida-like domain containing 1							integral to membrane				ovary(2)|skin(2)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	102295191	102295191	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102295191delT								ZPLD1 (96506 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	102656520	102656520	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102656520delT								ZPLD1 (457835 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	102797038	102797038	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102797038delT								ZPLD1 (598353 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103768921	103768921	+	IGR	DEL	A	-	-	rs113307531		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103768921delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104536124	104536124	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104536124delT								None (None upstream) : ALCAM (549589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104961512	104961513	+	IGR	DEL	TT	-	-	rs112189125		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104961512_104961513delTT								None (None upstream) : ALCAM (124200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	106094807	106094809	+	IGR	DEL	AAA	-	-	rs112857814	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106094807_106094809delAAA								CBLB (506541 upstream) : LOC100302640 (460851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	106114210	106114211	+	IGR	INS	-	TAGTGTT	TAGTGTT	rs148226136	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106114210_106114211insTAGTGTT								CBLB (525944 upstream) : LOC100302640 (441449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	106358818	106358818	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106358818delA								CBLB (770552 upstream) : LOC100302640 (196842 downstream)																																			---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106636525	106636526	+	Intron	DEL	AA	-	-	rs140177716		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106636525_106636526delAA	uc003dwf.3	-											Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106742745	106742745	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106742745delA	uc003dwf.3	-											Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	107128104	107128104	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107128104delA								CCDC54 (30623 upstream) : BBX (113679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	107184172	107184173	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107184172_107184173insA								CCDC54 (86691 upstream) : BBX (57610 downstream)																																			---	---	---	---
BBX	56987	broad.mit.edu	37	3	107251041	107251042	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107251041_107251042delAA	uc010hpr.2	+						BBX_uc003dwk.3_Intron|BBX_uc003dwl.3_Intron	NM_001142568	NP_001136040			HMG-BOX transcription factor BBX isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(3;0.112)															---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108115541	108115541	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108115541delA	uc003dxa.1	-							NM_014981	NP_055796			myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7																		---	---	---	---
RETNLB	84666	broad.mit.edu	37	3	108475579	108475579	+	Intron	DEL	T	-	-	rs76269450		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108475579delT	uc003dxh.2	-							NM_032579	NP_115968			resistin like beta precursor						cell proliferation	extracellular region	hormone activity			skin(1)	1																		---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108690160	108690160	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108690160delA	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244			MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8																		---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108715123	108715124	+	Intron	DEL	GC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108715123_108715124delGC	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244			MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8																		---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108773613	108773613	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108773613delC	uc003dxl.2	-	14	1379	c.1292delG	c.(1291-1293)GGAfs	p.G431fs	MORC1_uc011bhn.1_Frame_Shift_Del_p.G431fs	NM_014429	NP_055244	Q86VD1	MORC1_HUMAN	MORC family CW-type zinc finger 1	431					cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8																		---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108813922	108813922	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108813922delA	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244			MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8																		---	---	---	---
DPPA2	151871	broad.mit.edu	37	3	109028542	109028542	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109028542delA	uc003dxo.2	-							NM_138815	NP_620170			developmental pluripotency associated 2							nucleus	nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
DPPA2	151871	broad.mit.edu	37	3	109037888	109037888	+	5'Flank	DEL	A	-	-	rs11429890		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109037888delA	uc003dxo.2	-							NM_138815	NP_620170			developmental pluripotency associated 2							nucleus	nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
PVRL3	25945	broad.mit.edu	37	3	110879854	110879854	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110879854delA	uc003dxu.1	+							NM_015480	NP_056295			poliovirus receptor-related 3 precursor						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane	cell adhesion molecule binding|protein homodimerization activity			upper_aerodigestive_tract(2)	2																		---	---	---	---
PVRL3	25945	broad.mit.edu	37	3	110898738	110898738	+	Intron	DEL	A	-	-	rs63419362		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110898738delA	uc003dxu.1	+							NM_015480	NP_056295			poliovirus receptor-related 3 precursor						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane	cell adhesion molecule binding|protein homodimerization activity			upper_aerodigestive_tract(2)	2																		---	---	---	---
CD96	10225	broad.mit.edu	37	3	111337270	111337270	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111337270delA	uc003dxw.2	+						CD96_uc003dxx.2_Intron|CD96_uc010hpy.1_Intron	NM_198196	NP_937839			CD96 antigen isoform 1 precursor						cell adhesion|immune response|regulation of immune response	integral to plasma membrane				skin(2)|central_nervous_system(1)	3														Opitz_Trigonocephaly_syndrome				---	---	---	---
SLC9A10	285335	broad.mit.edu	37	3	111865053	111865053	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111865053delT	uc003dyu.2	-						SLC9A10_uc011bhu.1_Intron|SLC9A10_uc010hqc.2_Intron	NM_183061	NP_898884			sperm-specific sodium proton exchanger						cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	112222454	112222454	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112222454delT								BTLA (4046 upstream) : ATG3 (28906 downstream)																																			---	---	---	---
ATG3	64422	broad.mit.edu	37	3	112277374	112277374	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112277374delA	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																		---	---	---	---
CCDC80	151887	broad.mit.edu	37	3	112337382	112337382	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112337382delA	uc003dzf.2	-						CCDC80_uc011bhv.1_Intron|CCDC80_uc003dzg.2_Intron|CCDC80_uc003dzh.1_Intron	NM_199512	NP_955806			steroid-sensitive protein 1 precursor											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	112610197	112610197	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112610197delA								CD200R1L (45400 upstream) : CD200R1 (31335 downstream)																																			---	---	---	---
BOC	91653	broad.mit.edu	37	3	113005754	113005755	+	3'UTR	DEL	AA	-	-	rs5022662	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113005754_113005755delAA	uc003dzx.2	+	20					BOC_uc003dzy.2_3'UTR|BOC_uc003dzz.2_3'UTR|BOC_uc003eab.2_3'UTR|BOC_uc003eac.2_Intron	NM_033254	NP_150279			brother of CDO precursor						cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)															---	---	---	---
WDR52	55779	broad.mit.edu	37	3	113079774	113079774	+	Intron	DEL	A	-	-	rs111698499		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113079774delA	uc003ead.1	-											RecName: Full=WD repeat protein 52.; Flags: Fragment;											central_nervous_system(1)	1																		---	---	---	---
CCDC52	152185	broad.mit.edu	37	3	113222100	113222100	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113222100delA	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	113541902	113541903	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113541902_113541903insT								ATP6V1A (11001 upstream) : GRAMD1C (5126 downstream)																																			---	---	---	---
GRAMD1C	54762	broad.mit.edu	37	3	113630566	113630567	+	Intron	INS	-	T	T	rs79130601		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113630566_113630567insT	uc003eaq.3	+						GRAMD1C_uc011bil.1_Intron|GRAMD1C_uc011bim.1_Intron|GRAMD1C_uc003ear.2_Intron|GRAMD1C_uc003eas.2_Intron|GRAMD1C_uc003eat.2_5'Flank	NM_017577	NP_060047			GRAM domain containing 1C							integral to membrane				ovary(2)|skin(1)	3																		---	---	---	---
DRD3	1814	broad.mit.edu	37	3	113873173	113873174	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113873173_113873174delTG	uc003ebd.2	-						DRD3_uc010hqn.1_Intron|DRD3_uc003ebb.1_Intron|DRD3_uc003ebc.1_Intron	NM_000796	NP_000787			dopamine receptor D3 isoform a						activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)													---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114058003	114058003	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114058003delG	uc003ebi.2	-	5	2255	c.2075delC	c.(2074-2076)CCTfs	p.P692fs	ZBTB20_uc003ebj.2_Frame_Shift_Del_p.P619fs|ZBTB20_uc010hqp.2_Frame_Shift_Del_p.P619fs|ZBTB20_uc003ebk.2_Frame_Shift_Del_p.P619fs|ZBTB20_uc003ebl.2_Frame_Shift_Del_p.P619fs|ZBTB20_uc003ebm.2_Frame_Shift_Del_p.P619fs|ZBTB20_uc003ebn.2_Frame_Shift_Del_p.P619fs	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform	692					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114421842	114421843	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114421842_114421843delTG	uc003ebk.2	-						ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron|ZBTB20_uc003ebp.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114585563	114585563	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114585563delT	uc003ebm.2	-						ZBTB20_uc003ebn.2_Intron|ZBTB20_uc003ebp.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	115296253	115296254	+	IGR	INS	-	TG	TG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115296253_115296254insTG								ZBTB20 (430126 upstream) : GAP43 (45897 downstream)																																			---	---	---	---
GAP43	2596	broad.mit.edu	37	3	115408644	115408644	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115408644delA	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036			growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)														---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	116013790	116013791	+	Intron	INS	-	TTC	TTC	rs140134640	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116013790_116013791insTTC	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	116176589	116176589	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116176589delC								LSAMP (652571 upstream) : LOC285194 (252046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	116365150	116365150	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116365150delT								LSAMP (841132 upstream) : LOC285194 (63485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	116513908	116513910	+	IGR	DEL	AAA	-	-	rs76322187		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116513908_116513910delAAA								LOC285194 (78023 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	116627059	116627059	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116627059delA								LOC285194 (191174 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	116941237	116941237	+	IGR	DEL	T	-	-	rs112127464		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116941237delT								LOC285194 (505352 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117110932	117110932	+	IGR	DEL	A	-	-	rs140966667		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117110932delA								LOC285194 (675047 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117347376	117347376	+	IGR	DEL	A	-	-	rs63744660		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117347376delA								LOC285194 (911491 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117898524	117898524	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117898524delT								None (None upstream) : IGSF11 (720957 downstream)																																			---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118798207	118798208	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118798207_118798208insA	uc003eby.2	-						IGSF11_uc003ebz.2_Intron|IGSF11_uc010hqs.2_Intron	NM_152538	NP_689751			immunoglobulin superfamily, member 11 isoform a						cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0																		---	---	---	---
ARHGAP31	57514	broad.mit.edu	37	3	119083111	119083111	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119083111delA	uc003ecj.3	+							NM_020754	NP_065805			Cdc42 GTPase-activating protein						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2																		---	---	---	---
CD80	941	broad.mit.edu	37	3	119279425	119279427	+	5'Flank	DEL	CTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119279425_119279427delCTT	uc003ecq.2	-						CD80_uc010hqt.1_5'Flank|CD80_uc010hqu.1_5'Flank|CD80_uc003ecr.1_5'Flank	NM_005191	NP_005182			CD80 antigen precursor						interspecies interaction between organisms|intracellular signal transduction|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process|positive regulation of interleukin-2 biosynthetic process|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of signal transduction|positive regulation of T-helper 1 cell differentiation|positive regulation of transcription, DNA-dependent|T cell costimulation	intracellular	coreceptor activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2					Abatacept(DB01281)													---	---	---	---
POPDC2	64091	broad.mit.edu	37	3	119372844	119372845	+	Intron	INS	-	G	G	rs138591919	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119372844_119372845insG	uc003ecx.1	-						POPDC2_uc010hqw.1_Intron|POPDC2_uc003ecy.1_Intron	NM_022135	NP_071418			popeye protein 2							integral to membrane				central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.242)														---	---	---	---
GSK3B	2932	broad.mit.edu	37	3	119592180	119592180	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119592180delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	120242899	120242899	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120242899delA								FSTL1 (72981 upstream) : NDUFB4 (72229 downstream)																																			---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	120663772	120663772	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120663772delA	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)														---	---	---	---
CD86	942	broad.mit.edu	37	3	121825017	121825017	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121825017delT	uc003eet.2	+						CD86_uc011bjo.1_Intron|CD86_uc011bjp.1_Intron|CD86_uc003eeu.2_Intron	NM_175862	NP_787058			CD86 antigen isoform 1						interspecies interaction between organisms|positive regulation of cell proliferation|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of lymphotoxin A biosynthetic process|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription, DNA-dependent|T cell costimulation		coreceptor activity|protein binding			pancreas(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)													---	---	---	---
CASR	846	broad.mit.edu	37	3	122000728	122000729	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122000728_122000729delTG	uc003eev.3	+						CASR_uc003eew.3_Intron	NM_000388	NP_000379			calcium-sensing receptor precursor						anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)													---	---	---	---
KPNA1	3836	broad.mit.edu	37	3	122149363	122149364	+	Intron	DEL	GT	-	-	rs66494869		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122149363_122149364delGT	uc003efd.1	-						KPNA1_uc003efb.1_Intron|KPNA1_uc003efc.1_Intron|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)														---	---	---	---
DIRC2	84925	broad.mit.edu	37	3	122554412	122554412	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122554412delA	uc003efw.3	+						DIRC2_uc010hrl.2_Intron|DIRC2_uc010hrm.2_Intron	NM_032839	NP_116228			disrupted in renal carcinoma 2						transport	integral to membrane					0				GBM - Glioblastoma multiforme(114;0.0614)														---	---	---	---
SEMA5B	54437	broad.mit.edu	37	3	122704735	122704736	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122704735_122704736delAG	uc003efz.1	-						SEMA5B_uc011bju.1_Intron|SEMA5B_uc003ega.1_Intron|SEMA5B_uc003egb.1_Intron|SEMA5B_uc010hro.1_Intron|SEMA5B_uc010hrp.1_Intron	NM_001031702	NP_001026872			semaphorin 5B isoform 1						cell differentiation|nervous system development	integral to membrane	receptor activity			ovary(2)|breast(2)|pancreas(2)|central_nervous_system(1)	7				GBM - Glioblastoma multiforme(114;0.0367)														---	---	---	---
ADCY5	111	broad.mit.edu	37	3	123022313	123022313	+	Intron	DEL	A	-	-	rs139309270		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123022313delA	uc003egh.1	-						ADCY5_uc003egg.1_Intron|ADCY5_uc003egi.1_Intron	NM_183357	NP_899200			adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)														---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123360288	123360288	+	Intron	DEL	T	-	-	rs79522909		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123360288delT	uc003ego.2	-						MYLK_uc010hrr.2_Intron|MYLK_uc011bjv.1_Intron|MYLK_uc011bjw.1_Intron|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	124175366	124175366	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124175366delT	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron|KALRN_uc003ehh.1_Intron	NM_001024660	NP_001019831			kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124229802	124229802	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124229802delT	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron|KALRN_uc003ehi.2_Intron	NM_001024660	NP_001019831			kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124359134	124359136	+	Intron	DEL	TTT	-	-	rs71777187		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124359134_124359136delTTT	uc003ehg.2	+						KALRN_uc003ehi.2_Intron|KALRN_uc003ehk.2_Intron|KALRN_uc011bjz.1_Intron|KALRN_uc003ehj.2_Intron	NM_001024660	NP_001019831			kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
SLC12A8	84561	broad.mit.edu	37	3	124803232	124803232	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124803232delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	125125012	125125013	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125125012_125125013delTG								ZNF148 (30814 upstream) : SNX4 (40482 downstream)																																			---	---	---	---
OSBPL11	114885	broad.mit.edu	37	3	125295526	125295527	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125295526_125295527delTT	uc003eic.2	-							NM_022776	NP_073613			oxysterol binding protein-like 11						lipid transport		lipid binding			ovary(3)|breast(1)|kidney(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	125504059	125504059	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125504059delA								OSBPL11 (189678 upstream) : MIR548I1 (5188 downstream)																																			---	---	---	---
MIR548I1	100302204	broad.mit.edu	37	3	125512075	125512075	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125512075delA	hsa-mir-548i-1|MI0006421	-																							0																		---	---	---	---
ALDH1L1	10840	broad.mit.edu	37	3	125897590	125897591	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125897590_125897591delTG	uc003eim.1	-						ALDH1L1_uc010hse.1_Intron|ALDH1L1_uc011bki.1_Intron|ALDH1L1_uc010hsf.1_Intron|ALDH1L1_uc011bkj.1_Intron|uc003eiq.2_5'Flank	NM_012190	NP_036322			aldehyde dehydrogenase 1 family, member L1						10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	125949577	125949577	+	IGR	DEL	T	-	-	rs35848329		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125949577delT								ALDH1L1 (50092 upstream) : KLF15 (111901 downstream)																																			---	---	---	---
TXNRD3IT1	645840	broad.mit.edu	37	3	126342696	126342697	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126342696_126342697delAA	uc003ejd.1	-						TXNRD3IT1_uc011bkl.1_Intron					RecName: Full=Thioredoxin reductase 3;          EC=1.8.1.9; AltName: Full=Thioredoxin reductase TR2; AltName: Full=Thioredoxin and glutathione reductase;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	126894488	126894488	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126894488delA								PLXNA1 (138260 upstream) : TPRA1 (397420 downstream)																																			---	---	---	---
MCM2	4171	broad.mit.edu	37	3	127315957	127315957	+	5'Flank	DEL	A	-	-	rs111589837		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127315957delA	uc003ejp.2	+						MCM2_uc011bkm.1_5'Flank|MCM2_uc010hsl.2_5'Flank	NM_004526	NP_004517			minichromosome maintenance complex component 2						cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|helicase activity|metal ion binding			ovary(3)|skin(1)	4																		---	---	---	---
PODXL2	50512	broad.mit.edu	37	3	127353269	127353269	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127353269delA	uc003ejq.2	+							NM_015720	NP_056535			podocalyxin-like 2 precursor						leukocyte tethering or rolling	integral to plasma membrane	glycosaminoglycan binding|protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	127760978	127760978	+	IGR	DEL	A	-	-	rs72015715		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127760978delA								KBTBD12 (54465 upstream) : SEC61A1 (10234 downstream)																																			---	---	---	---
RUVBL1	8607	broad.mit.edu	37	3	127866965	127866966	+	Intron	DEL	TT	-	-	rs113586064		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127866965_127866966delTT	uc003ekf.2	-							NM_003707	NP_003698			RuvB-like 1						cell division|CenH3-containing nucleosome assembly at centromere|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|mitosis|regulation of growth|regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription, DNA-dependent	Golgi apparatus|Ino80 complex|membrane|microtubule organizing center|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|DNA helicase activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.181)														---	---	---	---
RPN1	6184	broad.mit.edu	37	3	128342834	128342835	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128342834_128342835delAC	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	128483138	128483138	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128483138delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	128537370	128537371	+	IGR	DEL	TT	-	-	rs11326986		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128537370_128537371delTT								RAB7A (3729 upstream) : ACAD9 (60962 downstream)																																			---	---	---	---
ACAD9	28976	broad.mit.edu	37	3	128614030	128614030	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128614030delT	uc003ela.3	+						ACAD9_uc010hsw.1_Intron|ACAD9_uc011bks.1_Intron|ACAD9_uc003elb.2_Intron|ACAD9_uc003elc.1_5'Flank	NM_014049	NP_054768			acyl-Coenzyme A dehydrogenase family, member 9							mitochondrion	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
C3orf37	56941	broad.mit.edu	37	3	129002178	129002179	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129002178_129002179delTT	uc003elt.2	+						C3orf37_uc003elu.2_Intron|C3orf37_uc003elv.2_Intron|C3orf37_uc003elw.2_Intron	NM_020187	NP_064572			hypothetical protein LOC56941											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	129124892	129124894	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129124892_129124894delAAA	uc003emg.2	-							NM_207307	NP_997190			hypothetical protein LOC90288																														---	---	---	---
IFT122	55764	broad.mit.edu	37	3	129220330	129220330	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129220330delT	uc003emm.2	+						IFT122_uc003eml.2_Intron|IFT122_uc003emn.2_Intron|IFT122_uc003emo.2_Intron|IFT122_uc003emp.2_Intron|IFT122_uc010htc.2_Intron|IFT122_uc011bky.1_Intron|IFT122_uc003emq.2_Intron|IFT122_uc003emr.2_Intron|IFT122_uc011bla.1_Intron|IFT122_uc010hte.2_Intron|IFT122_uc003ems.2_Intron|IFT122_uc011bkx.1_Intron|IFT122_uc010htd.1_Intron	NM_052989	NP_443715			WD repeat domain 10 isoform 2						camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	129258746	129258746	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129258746delG								RHO (4560 upstream) : H1FOO (3311 downstream)																																			---	---	---	---
TMCC1	23023	broad.mit.edu	37	3	129380932	129380932	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129380932delT	uc003emz.3	-						TMCC1_uc003emy.3_Intron|TMCC1_uc011blc.1_Intron|TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395			transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1																		---	---	---	---
TMCC1	23023	broad.mit.edu	37	3	129608765	129608766	+	Intron	DEL	AA	-	-	rs145308190		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129608765_129608766delAA	uc003emz.3	-						TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395			transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1																		---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130338964	130338964	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130338964delT	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	130494575	130494576	+	IGR	DEL	AA	-	-	rs75398311		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130494575_130494576delAA								PIK3R4 (28879 upstream) : ATP2C1 (74869 downstream)																																			---	---	---	---
ATP2C1	27032	broad.mit.edu	37	3	130614349	130614349	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130614349delT	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	130659456	130659456	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130659456delT	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				---	---	---	---
Unknown	0	broad.mit.edu	37	3	131145292	131145292	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131145292delT								NUDT16 (40363 upstream) : MRPL3 (35754 downstream)																																			---	---	---	---
CPNE4	131034	broad.mit.edu	37	3	131728815	131728815	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131728815delG	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																		---	---	---	---
UBA5	79876	broad.mit.edu	37	3	132393369	132393369	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132393369delA	uc003epa.3	+						NPHP3_uc003eoz.1_Intron|UBA5_uc010htr.2_Intron|UBA5_uc010htt.2_Intron|UBA5_uc003epb.3_Intron|UBA5_uc003epc.2_5'Flank	NM_024818	NP_079094			ubiquitin-activating enzyme 5 isoform 1						protein ufmylation	aggresome|cytoplasm|cytoplasm|nucleus	ATP binding|cofactor binding|metal ion binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding|UFM1 activating enzyme activity			kidney(1)	1																		---	---	---	---
NCRNA00119	348808	broad.mit.edu	37	3	132509854	132509854	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132509854delT	uc003epg.1	+							NR_002811				Homo sapiens cDNA clone IMAGE:4826885.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	132614549	132614551	+	IGR	DEL	GAG	-	-	rs143164037		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132614549_132614551delGAG								NCRNA00119 (21499 upstream) : TMEM108 (142620 downstream)																																			---	---	---	---
SLCO2A1	6578	broad.mit.edu	37	3	133683973	133683973	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133683973delA	uc003eqa.3	-						SLCO2A1_uc003eqb.3_Intron|SLCO2A1_uc011blv.1_Intron|SLCO2A1_uc010htw.1_Intron	NM_005630	NP_005621			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to plasma membrane|membrane fraction	prostaglandin transmembrane transporter activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134695580	134695580	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134695580delA	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134790919	134790919	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134790919delA	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron|EPHB1_uc003equ.2_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134936319	134936320	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134936319_134936320delGA	uc003eqt.2	+						EPHB1_uc003equ.2_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
PPP2R3A	5523	broad.mit.edu	37	3	135721164	135721164	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135721164delA	uc003eqv.1	+	2	1389	c.824delA	c.(823-825)GAAfs	p.E275fs	PPP2R3A_uc011blz.1_Intron	NM_002718	NP_002709	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'',	275					protein dephosphorylation	protein phosphatase type 2A complex	calcium ion binding|protein binding|protein phosphatase type 2A regulator activity			ovary(3)|pancreas(1)|lung(1)|breast(1)|skin(1)	7																		---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136170610	136170611	+	Intron	DEL	AA	-	-	rs75378142		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136170610_136170611delAA	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_Intron	NM_005862	NP_005853			stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136341884	136341884	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136341884delT	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	136525297	136525297	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136525297delA								STAG1 (54052 upstream) : TMEM22 (12564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	136672516	136672516	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136672516delT								NCK1 (4549 upstream) : IL20RB (4191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137048732	137048733	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137048732_137048733delAA								IL20RB (318812 upstream) : SOX14 (434846 downstream)																																	OREG0002750	type=REGULATORY REGION|Gene=MGC34923-SOX14|Dataset=Vista Enhancers|EvidenceSubtype=In-vivo LacZ Expression Assay	---	---	---	---
Unknown	0	broad.mit.edu	37	3	137049795	137049795	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137049795delT								IL20RB (319875 upstream) : SOX14 (433784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137147144	137147144	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137147144delA								IL20RB (417224 upstream) : SOX14 (336435 downstream)																																			---	---	---	---
DZIP1L	199221	broad.mit.edu	37	3	137787113	137787113	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137787113delG	uc003erq.2	-	13	2075	c.1712delC	c.(1711-1713)CCAfs	p.P571fs		NM_173543	NP_775814	Q8IYY4	DZI1L_HUMAN	DAZ interacting protein 1-like	571						intracellular	zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
TXNDC6	347736	broad.mit.edu	37	3	138025724	138025724	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138025724delG	uc003esg.2	-						TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron	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																		---	---	---	---
CEP70	80321	broad.mit.edu	37	3	138250541	138250541	+	Intron	DEL	T	-	-	rs72301948		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138250541delT	uc003esl.2	-						CEP70_uc011bmk.1_Intron|CEP70_uc011bml.1_Intron|CEP70_uc011bmm.1_Intron|CEP70_uc003esm.2_Intron	NM_024491	NP_077817			centrosomal protein 70 kDa						G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding			skin(1)	1																		---	---	---	---
PIK3CB	5291	broad.mit.edu	37	3	138461382	138461382	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138461382delA	uc011bmq.1	-							NM_006219	NP_006210			catalytic phosphatidylinositol 3-kinase beta						activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
C3orf72	401089	broad.mit.edu	37	3	138671292	138671293	+	3'UTR	INS	-	GT	GT	rs142418585	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138671292_138671293insGT	uc003esx.1	+	3						NM_001040061	NP_001035150			chromosome 3 open reading frame 72												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	138955921	138955921	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138955921delA								PISRT1 (3557 upstream) : MRPS22 (106877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	139009084	139009084	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139009084delG								PISRT1 (56720 upstream) : MRPS22 (53714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	139585618	139585618	+	IGR	DEL	A	-	-	rs74611819		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139585618delA								NMNAT3 (188778 upstream) : CLSTN2 (68409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	140421751	140421752	+	IGR	INS	-	GTGTGTGT	GTGTGTGT	rs144911559	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140421751_140421752insGTGTGTGT								TRIM42 (1760 upstream) : SLC25A36 (238910 downstream)																																			---	---	---	---
SPSB4	92369	broad.mit.edu	37	3	140775293	140775293	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140775293delA	uc003ett.2	+							NM_080862	NP_543138			splA/ryanodine receptor domain and SOCS box						intracellular signal transduction	cytoplasm	protein binding				0																		---	---	---	---
ATP1B3	483	broad.mit.edu	37	3	141626484	141626484	+	Intron	DEL	A	-	-	rs146369392		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141626484delA	uc003eug.1	+						ATP1B3_uc011bne.1_Intron|ATP1B3_uc003euh.1_Intron	NM_001679	NP_001670			Na+/K+ -ATPase beta 3 subunit						ATP biosynthetic process|blood coagulation|leukocyte migration	melanosome|sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity				0																		---	---	---	---
TFDP2	7029	broad.mit.edu	37	3	141713820	141713820	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141713820delT	uc003eun.3	-						TFDP2_uc003euk.3_Intron|TFDP2_uc010hur.2_Intron|TFDP2_uc003eul.3_Intron|TFDP2_uc011bnf.1_Intron|TFDP2_uc011bng.1_Intron|TFDP2_uc003eum.3_Intron	NM_006286	NP_006277			transcription factor Dp-2 (E2F dimerization						cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1																		---	---	---	---
TFDP2	7029	broad.mit.edu	37	3	141786846	141786848	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141786846_141786848delAAA	uc003eun.3	-						TFDP2_uc003eum.3_Intron|TFDP2_uc003euo.2_Intron	NM_006286	NP_006277			transcription factor Dp-2 (E2F dimerization						cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1																		---	---	---	---
GK5	256356	broad.mit.edu	37	3	141892042	141892043	+	Intron	DEL	AA	-	-	rs76226034		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141892042_141892043delAA	uc003euq.1	-						GK5_uc003eup.1_Intron|GK5_uc010hus.1_Intron	NM_001039547	NP_001034636			glycerol kinase 5 (putative)						glycerol metabolic process		ATP binding|glycerol kinase activity				0																		---	---	---	---
ATR	545	broad.mit.edu	37	3	142266538	142266538	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142266538delA	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					---	---	---	---
PLS1	5357	broad.mit.edu	37	3	142368480	142368480	+	Intron	DEL	A	-	-	rs79287934		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142368480delA	uc010huv.2	+						PLS1_uc003euz.2_Intron	NM_001145319	NP_001138791			plastin 1							cytoplasm	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(1)	1																		---	---	---	---
SLC9A9	285195	broad.mit.edu	37	3	142984734	142984734	+	3'UTR	DEL	G	-	-	rs113375950		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142984734delG	uc003evn.2	-	16						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	145000160	145000160	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145000160delT								None (None upstream) : PLOD2 (787068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	145244598	145244598	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145244598delG								None (None upstream) : PLOD2 (542630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146089170	146089170	+	IGR	DEL	T	-	-	rs80346648	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146089170delT								PLSCR4 (120204 upstream) : PLSCR2 (61912 downstream)																																			---	---	---	---
CPB1	1360	broad.mit.edu	37	3	148562685	148562685	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148562685delA	uc003ewl.2	+							NM_001871	NP_001862			pancreatic carboxypeptidase B1 preproprotein						proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	148622502	148622503	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148622502_148622503insA								CPA3 (7632 upstream) : GYG1 (86872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	149005292	149005292	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149005292delA								CP (65460 upstream) : TM4SF18 (33564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	149167381	149167382	+	IGR	INS	-	A	A	rs139494912	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149167381_149167382insA								TM4SF1 (71813 upstream) : TM4SF4 (25052 downstream)																																			---	---	---	---
WWTR1	25937	broad.mit.edu	37	3	149290080	149290080	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149290080delA	uc003exe.2	-						WWTR1_uc003exf.2_Intron|WWTR1_uc011bns.1_Intron|WWTR1_uc003exh.2_Intron	NM_015472	NP_056287			WW domain containing transcription regulator 1						hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent	cytoplasm	transcription coactivator activity			breast(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)															---	---	---	---
WWTR1	25937	broad.mit.edu	37	3	149379214	149379214	+	Intron	DEL	T	-	-	rs66869057		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149379214delT	uc003exh.2	-							NM_015472	NP_056287			WW domain containing transcription regulator 1						hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent	cytoplasm	transcription coactivator activity			breast(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)															---	---	---	---
C3orf16	389161	broad.mit.edu	37	3	149489737	149489737	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149489737delT	uc003exl.2	-						C3orf16_uc011bnt.1_Intron	NM_001144960	NP_001138432			hypothetical protein LOC389161												0																		---	---	---	---
RNF13	11342	broad.mit.edu	37	3	149614873	149614873	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149614873delA	uc003exn.3	+						RNF13_uc003exp.3_Intron|RNF13_uc010hvh.2_Intron	NM_007282	NP_009213			ring finger protein 13						protein autoubiquitination	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane|nuclear inner membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)															---	---	---	---
RNF13	11342	broad.mit.edu	37	3	149670902	149670902	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149670902delT	uc003exn.3	+						RNF13_uc003exp.3_Intron|RNF13_uc010hvh.2_Intron	NM_007282	NP_009213			ring finger protein 13						protein autoubiquitination	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane|nuclear inner membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	149779708	149779708	+	IGR	DEL	T	-	-	rs76755763		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149779708delT								PFN2 (90967 upstream) : TSC22D2 (347080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	150034217	150034217	+	IGR	DEL	A	-	-	rs78253351	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150034217delA								PFN2 (345476 upstream) : TSC22D2 (92571 downstream)																																			---	---	---	---
SELT	51714	broad.mit.edu	37	3	150331736	150331751	+	Intron	DEL	ACAGGAGAAAGCACAT	-	-	rs148351494	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150331736_150331751delACAGGAGAAAGCACAT	uc011bnx.1	+							NM_016275	NP_057359			selenoprotein T precursor						cell redox homeostasis|selenocysteine incorporation		selenium binding				0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)															---	---	---	---
SIAH2	6478	broad.mit.edu	37	3	150465396	150465397	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150465396_150465397delAC	uc003eyi.2	-							NM_005067	NP_005058			seven in absentia homolog 2						apoptosis|axon guidance|cell cycle|negative regulation of canonical Wnt receptor signaling pathway|small GTPase mediated signal transduction|ubiquitin-dependent protein catabolic process	cytosol|nucleus	transcription corepressor activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150828548	150828549	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150828548_150828549delTG	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|MED12L_uc003eym.1_Intron|MED12L_uc003eyn.2_Intron|MED12L_uc003eyo.2_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150837100	150837100	+	Intron	DEL	G	-	-	rs60818439		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150837100delG	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|MED12L_uc003eym.1_Intron|MED12L_uc003eyn.2_Intron|MED12L_uc003eyo.2_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
IGSF10	285313	broad.mit.edu	37	3	151164080	151164081	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151164080_151164081insT	uc011bod.1	-	4	3688_3689	c.3688_3689insA	c.(3688-3690)AGCfs	p.S1230fs		NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	1230					cell differentiation|multicellular organismal development|ossification	extracellular region				skin(7)|ovary(5)|central_nervous_system(1)	13			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	151612404	151612404	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151612404delC								SUCNR1 (12754 upstream) : LOC401093 (368009 downstream)																																			---	---	---	---
MBNL1	4154	broad.mit.edu	37	3	152062876	152062876	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152062876delT	uc003ezm.2	+						MBNL1_uc003ezh.2_Intron|MBNL1_uc003ezi.2_Intron|MBNL1_uc003ezj.2_Intron|MBNL1_uc003ezl.2_Intron|MBNL1_uc003ezp.2_Intron|MBNL1_uc003ezn.2_Intron|MBNL1_uc003ezo.2_Intron	NM_207293	NP_997176			muscleblind-like 1 isoform c						embryonic limb morphogenesis|in utero embryonic development|myoblast differentiation|nervous system development	nucleus|stress granule	double-stranded RNA binding|protein binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)															---	---	---	---
MBNL1	4154	broad.mit.edu	37	3	152146515	152146516	+	Intron	INS	-	G	G	rs143446323	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152146515_152146516insG	uc003ezm.2	+						MBNL1_uc003ezh.2_Intron|MBNL1_uc003ezi.2_Intron|MBNL1_uc003ezj.2_Intron|MBNL1_uc003ezl.2_Intron|MBNL1_uc003ezp.2_Intron|MBNL1_uc003ezn.2_Intron|MBNL1_uc003ezo.2_Intron|MBNL1_uc010hvp.2_Intron	NM_207293	NP_997176			muscleblind-like 1 isoform c						embryonic limb morphogenesis|in utero embryonic development|myoblast differentiation|nervous system development	nucleus|stress granule	double-stranded RNA binding|protein binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	152238201	152238201	+	IGR	DEL	A	-	-	rs11342379		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152238201delA								MBNL1 (54633 upstream) : P2RY1 (314535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	153277207	153277209	+	IGR	DEL	ACA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153277207_153277209delACA								C3orf79 (56724 upstream) : SGEF (561940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	153527135	153527138	+	IGR	DEL	ACTT	-	-	rs71962850		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153527135_153527138delACTT								C3orf79 (306652 upstream) : SGEF (312011 downstream)																																			---	---	---	---
SGEF	26084	broad.mit.edu	37	3	153842162	153842163	+	Intron	DEL	TT	-	-	rs66618151		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153842162_153842163delTT	uc011bog.1	+						SGEF_uc011boh.1_Intron	NM_015595	NP_056410			Src homology 3 domain-containing guanine						regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
SGEF	26084	broad.mit.edu	37	3	153890990	153890991	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153890990_153890991insC	uc011bog.1	+						SGEF_uc011boh.1_Intron	NM_015595	NP_056410			Src homology 3 domain-containing guanine						regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	154321984	154321984	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154321984delA								GPR149 (174480 upstream) : MME (419929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154396531	154396532	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154396531_154396532insT								GPR149 (249027 upstream) : MME (345381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	155463297	155463297	+	IGR	DEL	A	-	-	rs63655261		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155463297delA								PLCH1 (41300 upstream) : C3orf33 (17104 downstream)																																			---	---	---	---
GMPS	8833	broad.mit.edu	37	3	155611240	155611240	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155611240delT	uc003faq.2	+						GMPS_uc011bom.1_Intron	NM_003875	NP_003866			guanine monophosphate synthetase						glutamine metabolic process|purine base biosynthetic process	cytosol	ATP binding|GMP synthase (glutamine-hydrolyzing) activity|GMP synthase activity			ovary(2)|lung(1)	3			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)			T	MLL	AML								---	---	---	---
GMPS	8833	broad.mit.edu	37	3	155648978	155648978	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155648978delT	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	156198459	156198459	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156198459delT	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Intron|KCNAB1_uc010hvt.1_Intron|KCNAB1_uc011boo.1_Intron	NM_172160	NP_751892			potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	157342017	157342017	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157342017delT								C3orf55 (22998 upstream) : SHOX2 (471784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	157413914	157413914	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157413914delA								C3orf55 (94895 upstream) : SHOX2 (399887 downstream)																																			---	---	---	---
RSRC1	51319	broad.mit.edu	37	3	158226293	158226293	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158226293delT	uc003fbt.2	+						RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709			arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	158338641	158338641	+	IGR	DEL	T	-	-	rs12636691	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158338641delT								MLF1 (14389 upstream) : GFM1 (23676 downstream)																																			---	---	---	---
GFM1	85476	broad.mit.edu	37	3	158386654	158386655	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158386654_158386655insC	uc003fce.2	+						GFM1_uc003fcd.2_Intron|GFM1_uc003fcf.2_Intron|GFM1_uc003fcg.2_Intron|LXN_uc003fch.2_Intron	NM_024996	NP_079272			G elongation factor, mitochondrial 1 precursor						mitochondrial translational elongation	mitochondrion	GTP binding|GTPase activity|translation elongation factor activity			ovary(3)|central_nervous_system(1)	4			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	158553250	158553251	+	IGR	INS	-	AAACAAAA	AAACAAAA	rs138416234	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158553250_158553251insAAACAAAA								MFSD1 (5746 upstream) : SCHIP1 (233866 downstream)																																			---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	158898074	158898075	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158898074_158898075delTC	uc003fcq.1	+						IQCJ_uc003fco.2_Intron|IQCJ_uc010hvy.1_Intron|IQCJ_uc003fcp.1_Intron	NM_014575	NP_055390			schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)															---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159218502	159218502	+	Intron	DEL	A	-	-	rs79405720		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159218502delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	159687019	159687019	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159687019delT	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																														---	---	---	---
IFT80	57560	broad.mit.edu	37	3	159980114	159980114	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159980114delA	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)															---	---	---	---
SMC4	10051	broad.mit.edu	37	3	160129696	160129696	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160129696delT	uc003fdh.2	+						IFT80_uc003fda.2_Intron|SMC4_uc003fdf.1_Intron|SMC4_uc003fdg.1_Intron|SMC4_uc010hwc.1_Intron|SMC4_uc003fdi.2_Intron|SMC4_uc003fdj.2_Intron|SMC4_uc010hwd.2_Intron|SMC4_uc003fdl.2_5'Flank	NM_001002800	NP_001002800			SMC4 structural maintenance of chromosomes						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity			ovary(1)|breast(1)	2			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
TRIM59	286827	broad.mit.edu	37	3	160156368	160156368	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160156368delT	uc003fdm.2	-	3	799	c.604delA	c.(604-606)AGTfs	p.S202fs	IFT80_uc003fda.2_RNA	NM_173084	NP_775107	Q8IWR1	TRI59_HUMAN	tripartite motif-containing 59	202	Potential.					integral to membrane|intracellular	zinc ion binding				0			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	160335459	160335459	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160335459delA								KPNA4 (52083 upstream) : ARL14 (59489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	160431773	160431773	+	IGR	DEL	A	-	-	rs149702638	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160431773delA								ARL14 (35540 upstream) : PPM1L (42223 downstream)																																			---	---	---	---
PPM1L	151742	broad.mit.edu	37	3	160497705	160497705	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160497705delT	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	160835966	160835966	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160835966delA								B3GALNT1 (12806 upstream) : NMD3 (103133 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161048117	161048120	+	IGR	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161048117_161048120delTTTT								NMD3 (76798 upstream) : C3orf57 (14461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161356481	161356482	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161356481_161356482delAG								OTOL1 (134753 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161374811	161374811	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161374811delT								OTOL1 (153083 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162136369	162136372	+	IGR	DEL	TAAT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162136369_162136372delTAAT								OTOL1 (914641 upstream) : None (None downstream)																																			---	---	---	---
SI	6476	broad.mit.edu	37	3	164758862	164758862	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164758862delA	uc003fei.2	-	18	2087	c.2025delT	c.(2023-2025)TTTfs	p.F675fs		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	675	Lumenal.|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	164882475	164882475	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164882475delT								SI (86193 upstream) : SLITRK3 (22043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	164984198	164984198	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164984198delT								SLITRK3 (69729 upstream) : BCHE (506496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165443277	165443286	+	IGR	DEL	ACACAGAGAG	-	-	rs71147126		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165443277_165443286delACACAGAGAG								SLITRK3 (528808 upstream) : BCHE (47408 downstream)																																			---	---	---	---
BCHE	590	broad.mit.edu	37	3	165491219	165491219	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165491219delT	uc003fem.3	-	4	1920	c.1760delA	c.(1759-1761)AATfs	p.N587fs	BCHE_uc003fen.3_RNA	NM_000055	NP_000046	P06276	CHLE_HUMAN	butyrylcholinesterase precursor	587					choline metabolic process|cocaine metabolic process|synaptic transmission, cholinergic	endoplasmic reticulum lumen|extracellular space|membrane	acetylcholinesterase activity|beta-amyloid binding|carboxylesterase activity|cholinesterase activity|enzyme binding			ovary(3)|pancreas(1)	4					Ambenonium(DB01122)|Atropine(DB00572)|Bambuterol(DB01408)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinnarizine(DB00568)|Demecarium bromide(DB00944)|Dibucaine(DB00527)|Donepezil(DB00843)|Echothiophate Iodide(DB01057)|Edrophonium(DB01010)|Ethopropazine(DB00392)|Etomidate(DB00292)|Galantamine(DB00674)|Hexafluronium bromide(DB00941)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Mivacurium(DB01226)|Neostigmine(DB01400)|Pancuronium(DB01337)|Pralidoxime(DB00733)|Procainamide(DB01035)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Terbutaline(DB00871)|Trimethaphan(DB01116)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	165828827	165828827	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165828827delA								BCHE (273574 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166564294	166564294	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166564294delT								None (None upstream) : ZBBX (393787 downstream)																																			---	---	---	---
SERPINI2	5276	broad.mit.edu	37	3	167188863	167188863	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167188863delT	uc003fer.1	-						SERPINI2_uc003fes.1_Intron|SERPINI2_uc003fet.1_Intron	NM_006217	NP_006208			serpin peptidase inhibitor, clade I (pancpin),						cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(2)|urinary_tract(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	167385571	167385571	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167385571delA								WDR49 (13843 upstream) : PDCD10 (16126 downstream)																																			---	---	---	---
PDCD10	11235	broad.mit.edu	37	3	167402273	167402273	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167402273delA	uc003fex.2	-						PDCD10_uc003fez.2_Intron|PDCD10_uc003fey.2_Intron	NM_007217	NP_009148			programmed cell death 10						angiogenesis|apoptosis|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of MAP kinase activity	cytosol|Golgi membrane|plasma membrane	protein homodimerization activity|protein N-terminus binding			lung(1)|central_nervous_system(1)	2														Familial_Cerebral_Cavernous_Angioma				---	---	---	---
Unknown	0	broad.mit.edu	37	3	167606634	167606634	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167606634delT								SERPINI1 (63278 upstream) : GOLIM4 (121020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	167820444	167820444	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167820444delT								GOLIM4 (7027 upstream) : MIR551B (449198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168064022	168064022	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168064022delT								GOLIM4 (250605 upstream) : MIR551B (205620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168508569	168508570	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168508569_168508570delTT								MIR551B (238832 upstream) : C3orf50 (19014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168615317	168615318	+	IGR	INS	-	A	A	rs141344370	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168615317_168615318insA								C3orf50 (66945 upstream) : MECOM (185969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168693517	168693517	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168693517delT								C3orf50 (145145 upstream) : MECOM (107770 downstream)																																			---	---	---	---
CLDN11	5010	broad.mit.edu	37	3	170355518	170355519	+	Intron	DEL	AC	-	-	rs72385303		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170355518_170355519delAC	uc011bpt.1	+						uc003fha.1_Intron	NM_005602	NP_005593			claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
CLDN11	5010	broad.mit.edu	37	3	170414201	170414201	+	Intron	DEL	T	-	-	rs71847330		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170414201delT	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)															---	---	---	---
PLD1	5337	broad.mit.edu	37	3	171389693	171389693	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171389693delA	uc003fhs.2	-						PLD1_uc003fht.2_Intron|PLD1_uc003fhu.3_Intron|PLD1_uc003fhv.1_Intron	NM_002662	NP_002653			phospholipase D1 isoform a						cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)													---	---	---	---
PLD1	5337	broad.mit.edu	37	3	171488519	171488519	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171488519delA	uc003fhs.2	-						PLD1_uc003fht.2_Intron	NM_002662	NP_002653			phospholipase D1 isoform a						cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	172932194	172932194	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172932194delT								SPATA16 (73162 upstream) : NLGN1 (184050 downstream)																																			---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173130101	173130102	+	Intron	INS	-	AC	AC	rs141636643	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173130101_173130102insAC	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	174037164	174037164	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174037164delA								NLGN1 (36048 upstream) : NAALADL2 (539947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	174237425	174237425	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174237425delT	uc003fiq.1	+						uc003fir.2_Intron|uc003fis.2_Intron|uc010hwx.1_Intron					Homo sapiens NAALADL2 gene, partial 5'UTR, variant 1.																														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	174635005	174635005	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174635005delA	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron	NM_207015	NP_996898			N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	176598850	176598851	+	IGR	INS	-	AG	AG	rs143023860	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176598850_176598851insAG								None (None upstream) : TBL1XR1 (139692 downstream)																																			---	---	---	---
TBL1XR1	79718	broad.mit.edu	37	3	176860703	176860703	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176860703delA	uc003fiw.3	-						TBL1XR1_uc003fix.3_Intron|TBL1XR1_uc011bpz.1_Intron|TBL1XR1_uc003fiy.2_Intron	NM_024665	NP_078941			transducin (beta)-like 1 X-linked receptor 1						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	177005990	177005990	+	IGR	DEL	A	-	-	rs144866851		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177005990delA								TBL1XR1 (90942 upstream) : None (None downstream)																																			---	---	---	---
USP13	8975	broad.mit.edu	37	3	179479203	179479203	+	Intron	DEL	T	-	-	rs74695249		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179479203delT	uc003fkh.2	+							NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	180297639	180297639	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180297639delA								PEX5L (543122 upstream) : TTC14 (22279 downstream)																																			---	---	---	---
CCDC39	339829	broad.mit.edu	37	3	180402382	180402382	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180402382delT	uc003fkn.2	-											Homo sapiens cDNA FLJ58733 complete cds, moderately similar to Coiled-coil domain-containing protein 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)															---	---	---	---
SOX2OT	347689	broad.mit.edu	37	3	181450230	181450230	+	Intron	DEL	T	-	-	rs71959268		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181450230delT	uc003fkv.2	+						SOX2OT_uc003fkw.3_Intron					Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	181467644	181467644	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181467644delT								SOX2OT (8641 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181544473	181544473	+	IGR	DEL	T	-	-	rs66901345		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181544473delT								SOX2OT (85470 upstream) : ATP11B (966818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182219013	182219014	+	IGR	INS	-	TG	TG	rs143883440	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182219013_182219014insTG								SOX2OT (760010 upstream) : ATP11B (292277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182649203	182649203	+	IGR	DEL	T	-	-	rs7611381	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182649203delT								ATP11B (9784 upstream) : DCUN1D1 (11356 downstream)																																			---	---	---	---
MCCC1	56922	broad.mit.edu	37	3	182740084	182740084	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182740084delA	uc003fle.2	-						MCCC1_uc010hxi.2_Intron|MCCC1_uc011bqo.1_Intron|MCCC1_uc003flf.2_Intron|MCCC1_uc003flg.2_Intron|MCCC1_uc011bqp.1_Intron	NM_020166	NP_064551			methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)						biotin metabolic process|leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)													---	---	---	---
MCF2L2	23101	broad.mit.edu	37	3	182996146	182996147	+	Intron	INS	-	TG	TG	rs146133276	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182996146_182996147insTG	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc011bqr.1_Intron	NM_015078	NP_055893			Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)															---	---	---	---
KLHL6	89857	broad.mit.edu	37	3	183217134	183217134	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183217134delA	uc003flr.2	-						KLHL6_uc003fls.1_Intron|KLHL6_uc003flt.1_Intron	NM_130446	NP_569713			kelch-like 6											haematopoietic_and_lymphoid_tissue(2)|ovary(1)	3	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)															---	---	---	---
KLHL6	89857	broad.mit.edu	37	3	183261089	183261089	+	Intron	DEL	G	-	-	rs72409384		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183261089delG	uc003flr.2	-						KLHL6_uc003fls.1_Intron|KLHL6_uc003flt.1_Intron	NM_130446	NP_569713			kelch-like 6											haematopoietic_and_lymphoid_tissue(2)|ovary(1)	3	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183436187	183436187	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183436187delT	uc003fly.2	+							NM_018023	NP_060493			YEATS domain containing 2						histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
ABCC5	10057	broad.mit.edu	37	3	183662527	183662527	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183662527delT	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)															---	---	---	---
ABCC5	10057	broad.mit.edu	37	3	183695546	183695546	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183695546delT	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)															---	---	---	---
HTR3D	200909	broad.mit.edu	37	3	183748959	183748959	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183748959delA	uc011bqv.1	+						HTR3D_uc003fmj.2_5'Flank|HTR3D_uc011bqu.1_5'Flank	NM_001163646	NP_001157118			5-hydroxytryptamine receptor 3 subunit D isoform							integral to membrane|plasma membrane	extracellular ligand-gated ion channel activity|receptor activity				0	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
HTR3E	285242	broad.mit.edu	37	3	183812687	183812687	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183812687delA	uc010hxq.2	+						HTR3E_uc003fml.3_5'Flank	NM_182589	NP_872395			5-hydroxytryptamine receptor 3 subunit E							integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.46e-10)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	184314352	184314353	+	IGR	DEL	TT	-	-	rs11288168		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184314352_184314353delTT								EPHB3 (14157 upstream) : MAGEF1 (113803 downstream)																																			---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184533606	184533607	+	Intron	DEL	AA	-	-	rs67561609		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184533606_184533607delAA	uc003fpb.1	+						VPS8_uc010hyd.1_Intron	NM_015303	NP_056118			vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)															---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184642305	184642305	+	Intron	DEL	A	-	-	rs71701922		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184642305delA	uc003fpb.1	+						VPS8_uc010hyd.1_Intron|VPS8_uc010hye.1_Intron	NM_015303	NP_056118			vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)															---	---	---	---
DGKG	1608	broad.mit.edu	37	3	185973605	185973606	+	Intron	INS	-	A	A	rs1468946	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185973605_185973606insA	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337			diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)													---	---	---	---
DGKG	1608	broad.mit.edu	37	3	186038536	186038536	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186038536delA	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337			diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	186245874	186245874	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186245874delA								DGKG (165851 upstream) : CRYGS (10359 downstream)																																			---	---	---	---
AHSG	197	broad.mit.edu	37	3	186330746	186330746	+	5'Flank	DEL	T	-	-	rs66939339		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186330746delT	uc003fqk.3	+						AHSG_uc003fqj.2_5'Flank|AHSG_uc003fql.3_5'Flank|AHSG_uc003fqm.3_5'Flank|AHSG_uc010hyp.2_5'Flank	NM_001622	NP_001613			alpha-2-HS-glycoprotein						acute-phase response|negative regulation of bone mineralization|negative regulation of insulin receptor signaling pathway|pinocytosis|positive regulation of phagocytosis|regulation of inflammatory response|skeletal system development	extracellular space	cysteine-type endopeptidase inhibitor activity|protein binding				0	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)														---	---	---	---
MASP1	5648	broad.mit.edu	37	3	186967887	186967887	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186967887delT	uc003frh.1	-						MASP1_uc003fri.2_Intron|MASP1_uc003frj.2_Intron|MASP1_uc003frk.1_Intron|MASP1_uc011bse.1_Intron	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)														---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	188804143	188804144	+	Intron	DEL	TT	-	-	rs72164759		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188804143_188804144delTT	uc003frv.1	+							NM_198485	NP_940887			tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)														---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	188975987	188975987	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188975987delT	uc003frv.1	+						TPRG1_uc003frw.1_Intron	NM_198485	NP_940887			tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	189062648	189062648	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189062648delG								TPRG1 (21378 upstream) : TP63 (286568 downstream)																																			---	---	---	---
TP63	8626	broad.mit.edu	37	3	189361244	189361247	+	Intron	DEL	TAAA	-	-	rs71747870		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189361244_189361247delTAAA	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	189892430	189892431	+	IGR	INS	-	CCTTCCTT	CCTTCCTT	rs143607563	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189892430_189892431insCCTTCCTT								LEPREL1 (52204 upstream) : CLDN1 (131072 downstream)																																			---	---	---	---
TMEM207	131920	broad.mit.edu	37	3	190147648	190147648	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190147648delA	uc003fsj.2	-							NM_207316	NP_997199			transmembrane protein 207 precursor							integral to membrane					0	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)														---	---	---	---
TMEM207	131920	broad.mit.edu	37	3	190166003	190166003	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190166003delA	uc003fsj.2	-							NM_207316	NP_997199			transmembrane protein 207 precursor							integral to membrane					0	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	191563661	191563661	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191563661delT								PYDC2 (384418 upstream) : FGF12 (296023 downstream)																																			---	---	---	---
HRASLS	57110	broad.mit.edu	37	3	192978475	192978476	+	Intron	DEL	AA	-	-	rs113221506		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192978475_192978476delAA	uc003fta.2	+							NM_020386	NP_065119			HRAS-like suppressor												0	all_cancers(143;9.1e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000159)														---	---	---	---
ATP13A5	344905	broad.mit.edu	37	3	193092091	193092096	+	Intron	DEL	AGAGAG	-	-	rs71177401	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193092091_193092096delAGAGAG	uc011bsq.1	-							NM_198505	NP_940907			ATPase type 13A5						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|skin(4)|large_intestine(2)	11	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)														---	---	---	---
ATP13A4	84239	broad.mit.edu	37	3	193140234	193140234	+	Intron	DEL	G	-	-	rs111533558		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193140234delG	uc003ftd.2	-						ATP13A4_uc010hzi.2_Intron	NM_032279	NP_115655			ATPase type 13A4						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)														---	---	---	---
OPA1	4976	broad.mit.edu	37	3	193400776	193400776	+	Intron	DEL	G	-	-	rs2088335	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193400776delG	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	193892857	193892857	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193892857delT								HES1 (36461 upstream) : LOC100131551 (124567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	194440292	194440295	+	IGR	DEL	TAGA	-	-	rs141725243		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194440292_194440295delTAGA								FAM43A (30528 upstream) : C3orf21 (348720 downstream)																																			---	---	---	---
C3orf21	152002	broad.mit.edu	37	3	194824469	194824469	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194824469delA	uc003fum.3	-						C3orf21_uc003ful.2_Intron|C3orf21_uc003fuk.2_Intron	NM_152531	NP_689744			hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)														---	---	---	---
C3orf21	152002	broad.mit.edu	37	3	194968151	194968151	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194968151delG	uc003fum.3	-						C3orf21_uc011bsw.1_Intron	NM_152531	NP_689744			hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	195289653	195289653	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195289653delT								PPP1R2 (19429 upstream) : APOD (5920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	195426649	195426650	+	5'Flank	DEL	TC	-	-	rs63642461		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195426649_195426650delTC	uc011btd.1	+						uc003fux.1_5'Flank					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																														---	---	---	---
TCTEX1D2	255758	broad.mit.edu	37	3	196044138	196044139	+	Intron	INS	-	GTGT	GTGT	rs112515550		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196044138_196044139insGTGT	uc003fwi.2	-						TM4SF19_uc003fwj.2_Intron|uc003fwk.1_5'Flank	NM_152773	NP_689986			Tctex1 domain containing 2								protein binding			ovary(1)|breast(1)	2	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)														---	---	---	---
UBXN7	26043	broad.mit.edu	37	3	196118944	196118944	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196118944delA	uc003fwm.3	-						UBXN7_uc003fwn.3_Intron|UBXN7_uc010iae.2_Intron	NM_015562	NP_056377			UBX domain containing 7								protein binding			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	196281024	196281024	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196281024delT								C3orf43 (38787 upstream) : WDR53 (37 downstream)																																			---	---	---	---
SENP5	205564	broad.mit.edu	37	3	196626757	196626757	+	Intron	DEL	T	-	-	rs76178058		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196626757delT	uc003fwz.3	+						SENP5_uc011bty.1_Intron	NM_152699	NP_689912			SUMO1/sentrin specific peptidase 5						cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196786890	196786890	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196786890delA	uc003fxo.3	-						DLG1_uc011bub.1_Intron|DLG1_uc011buc.1_Intron|DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron	NM_001098424	NP_001091894			discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)														---	---	---	---
IQCG	84223	broad.mit.edu	37	3	197671050	197671050	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197671050delA	uc003fyo.2	-						IQCG_uc003fyp.2_Intron|IQCG_uc003fyq.3_Intron	NM_001134435	NP_001127907			IQ motif containing G												0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	29239	29239	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29239delT								None (None upstream) : ZNF595 (23988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43797	43797	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43797delA								None (None upstream) : ZNF595 (9430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	48513	48513	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48513delT								None (None upstream) : ZNF595 (4714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	254806	254807	+	IGR	INS	-	A	A	rs74482758		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:254806_254807insA								ZNF876P (5035 upstream) : ZNF732 (4675 downstream)																																			---	---	---	---
PDE6B	5158	broad.mit.edu	37	4	630508	630508	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:630508delC	uc003gap.2	+						PDE6B_uc003gao.3_Intron	NM_000283	NP_000274			phosphodiesterase 6B isoform 1						cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0																		---	---	---	---
PDE6B	5158	broad.mit.edu	37	4	646670	646670	+	Intron	DEL	A	-	-	rs71640339		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:646670delA	uc003gap.2	+						PDE6B_uc003gao.3_Intron|PDE6B_uc011buy.1_5'Flank|PDE6B_uc010ibg.2_5'Flank	NM_000283	NP_000274			phosphodiesterase 6B isoform 1						cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0																		---	---	---	---
FGFRL1	53834	broad.mit.edu	37	4	1019287	1019288	+	3'UTR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1019287_1019288delAC	uc003gce.2	+	7					FGFRL1_uc003gcf.2_3'UTR|FGFRL1_uc003gcg.2_3'UTR|FGFRL1_uc010ibo.2_3'UTR	NM_021923	NP_068742			fibroblast growth factor receptor-like 1						regulation of cell growth	integral to membrane|plasma membrane	fibroblast growth factor receptor activity|heparin binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)															---	---	---	---
KIAA1530	57654	broad.mit.edu	37	4	1356904	1356905	+	Intron	INS	-	C	C	rs146797277	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1356904_1356905insC	uc003gde.3	+						KIAA1530_uc010ibv.2_5'Flank	NM_020894	NP_065945			hypothetical protein LOC57654												0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)															---	---	---	---
KIAA1530	57654	broad.mit.edu	37	4	1366721	1366722	+	Intron	INS	-	C	C	rs144700445	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1366721_1366722insC	uc003gde.3	+						KIAA1530_uc010ibv.2_Intron	NM_020894	NP_065945			hypothetical protein LOC57654												0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	1532108	1532109	+	IGR	INS	-	A	A	rs113172680		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1532108_1532109insA								CRIPAK (142326 upstream) : FAM53A (109500 downstream)																																			---	---	---	---
FGFR3	2261	broad.mit.edu	37	4	1800827	1800827	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1800827delT	uc003gdr.3	+						FGFR3_uc003gdu.2_Intron|FGFR3_uc003gds.3_Intron|FGFR3_uc003gdq.3_Intron|FGFR3_uc010icb.1_5'Flank|FGFR3_uc003gdt.1_5'Flank	NM_000142	NP_000133			fibroblast growth factor receptor 3 isoform 1						bone maturation|cell growth|insulin receptor signaling pathway|JAK-STAT cascade|MAPKKK cascade|negative regulation of developmental growth|positive regulation of cell proliferation	integral to plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|identical protein binding			urinary_tract(2177)|skin(314)|upper_aerodigestive_tract(57)|haematopoietic_and_lymphoid_tissue(24)|prostate(9)|cervix(6)|central_nervous_system(4)|large_intestine(3)|lung(3)|testis(2)|pancreas(1)	2600		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)		1	Mis|T	IGH@|ETV6	bladder|MM|T-cell lymphoma		Hypochondroplasia|Thanatophoric dysplasia		Muenke_syndrome|Saethre-Chotzen_syndrome				---	---	---	---
LETM1	3954	broad.mit.edu	37	4	1834801	1834801	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1834801delT	uc003gdv.2	-							NM_012318	NP_036450			leucine zipper-EF-hand containing transmembrane						cristae formation	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			central_nervous_system(1)	1			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)															---	---	---	---
FAM193A	8603	broad.mit.edu	37	4	2613566	2613568	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2613566_2613568delTTT	uc010ick.2	+							NM_003704	NP_003695			hypothetical protein LOC8603											ovary(3)	3																		---	---	---	---
SH3BP2	6452	broad.mit.edu	37	4	2834285	2834285	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2834285delC	uc003gfi.3	+						SH3BP2_uc011bvp.1_Intron|SH3BP2_uc003gfj.3_Intron|SH3BP2_uc003gfk.3_Intron|SH3BP2_uc003gfl.3_Intron|SH3BP2_uc003gfm.3_Intron	NM_001122681	NP_001116153			SH3-domain binding protein 2 isoform a						signal transduction		SH3 domain binding|SH3/SH2 adaptor activity			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)										Cherubism				---	---	---	---
NOP14	8602	broad.mit.edu	37	4	2956407	2956407	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2956407delA	uc003ggj.1	-						C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_5'Flank|NOP14_uc003ggk.3_Intron|NOP14_uc003ggl.2_Intron|NOP14_uc010icq.1_Intron	NM_003703	NP_003694			probable nucleolar complex protein 14						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1																		---	---	---	---
GRK4	2868	broad.mit.edu	37	4	2978126	2978126	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2978126delT	uc003ggn.1	+						GRK4_uc003ggo.1_Intron|GRK4_uc003ggp.1_Intron|GRK4_uc003ggq.1_Intron	NM_182982	NP_892027			G protein-coupled receptor kinase 4 isoform							cell cortex	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
GRK4	2868	broad.mit.edu	37	4	3032148	3032148	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3032148delT	uc003ggn.1	+						GRK4_uc003ggo.1_Intron|GRK4_uc003ggp.1_Intron|GRK4_uc003ggq.1_Intron	NM_182982	NP_892027			G protein-coupled receptor kinase 4 isoform							cell cortex	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3364206	3364209	+	Intron	DEL	TGTA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3364206_3364209delTGTA	uc003ggw.2	+						RGS12_uc003ggu.2_Intron|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_Intron|RGS12_uc003ggv.2_Intron|RGS12_uc003ggy.1_Intron	NM_198229	NP_937872			regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3604862	3604863	+	IGR	INS	-	CT	CT	rs140129696	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3604862_3604863insCT								LRPAP1 (70638 upstream) : ADRA2C (163212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3621168	3621168	+	IGR	DEL	G	-	-	rs11339032		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3621168delG								LRPAP1 (86944 upstream) : ADRA2C (146907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3815251	3815251	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3815251delT								ADRA2C (45000 upstream) : LOC348926 (128419 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3995417	3995417	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3995417delA								LOC348926 (38269 upstream) : OTOP1 (195113 downstream)																																			---	---	---	---
ZBTB49	166793	broad.mit.edu	37	4	4300157	4300157	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	4548486	4548486	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4548486delA	uc003gid.2	+											Homo sapiens, clone IMAGE:5204729, mRNA.																														---	---	---	---
EVC	2121	broad.mit.edu	37	4	5806798	5806798	+	Intron	DEL	C	-	-	rs3214939		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5806798delC	uc003gil.1	+						EVC_uc003gim.1_Intron|CRMP1_uc003gin.1_Intron	NM_153717	NP_714928			Ellis van Creveld syndrome protein						muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)																---	---	---	---
CRMP1	1400	broad.mit.edu	37	4	5817867	5817867	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5817867delT	uc003gin.1	-						EVC_uc003gim.1_Intron					SubName: Full=cDNA FLJ37406 fis, clone BRAMY2028282, highly similar to Dihydropyrimidinase-related protein 1; SubName: Full=Collapsin response mediator protein 1, isoform CRA_d;						axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)														---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7620565	7620566	+	Intron	DEL	AC	-	-	rs71872025		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	8163095	8163095	+	5'Flank	DEL	A	-	-	rs72211097		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8163095delA	uc003gko.2	-						ABLIM2_uc003gkj.3_5'Flank|ABLIM2_uc003gkm.3_5'Flank|ABLIM2_uc003gkp.2_5'Flank|ABLIM2_uc003gkq.2_5'Flank|ABLIM2_uc003gkr.2_5'Flank|ABLIM2_uc003gks.3_5'Flank	NM_001130084	NP_001123556			actin binding LIM protein family, member 2						axon guidance|cytoskeleton organization	actin cytoskeleton|cytoplasm|intermediate filament cytoskeleton|nucleus	actin binding|zinc ion binding			pancreas(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	9436832	9436832	+	IGR	DEL	T	-	-	rs111428752		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9436832delT								USP17L6P (66038 upstream) : DEFB131 (9428 downstream)																																			---	---	---	---
CLNK	116449	broad.mit.edu	37	4	10606857	10606858	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10606857_10606858delTC	uc003gmo.3	-						CLNK_uc003gmp.2_Intron	NM_052964	NP_443196			mast cell immunoreceptor signal transducer						immune response|intracellular signal transduction	intracellular	SH3/SH2 adaptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	10813717	10813717	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10813717delA								CLNK (127331 upstream) : MIR572 (556734 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11492185	11492185	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11492185delT								HS3ST1 (61648 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11671183	11671183	+	IGR	DEL	C	-	-	rs112079809		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11671183delC								HS3ST1 (240646 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12020478	12020479	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12020478_12020479delAG								HS3ST1 (589941 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12305259	12305260	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12305259_12305260insA								HS3ST1 (874722 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12457776	12457776	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12457776delA								None (None upstream) : HSP90AB2P (877261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	13234449	13234450	+	IGR	DEL	AG	-	-	rs113530075		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13234449_13234450delAG								None (None upstream) : HSP90AB2P (100587 downstream)																																			---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13582681	13582681	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13582681delA	uc003gmz.1	-							NM_148894	NP_683692			biorientation of chromosomes in cell division								DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13590439	13590439	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13590439delA	uc003gmz.1	-							NM_148894	NP_683692			biorientation of chromosomes in cell division								DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	13637770	13637771	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13637770_13637771insA								BOD1L (8442 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	14635338	14635338	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14635338delA	uc003gne.2	-						uc003gnf.2_Intron					Homo sapiens cDNA clone IMAGE:3604199, **** WARNING: chimeric clone ****.																														---	---	---	---
CC2D2A	57545	broad.mit.edu	37	4	15471030	15471030	+	5'Flank	DEL	T	-	-	rs113272246		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15471030delT	uc010idv.2	+						CC2D2A_uc003gns.3_5'Flank|CC2D2A_uc003gnt.3_5'Flank|CC2D2A_uc003gnq.3_5'Flank|CC2D2A_uc003gnr.3_5'Flank|CC2D2A_uc003gnu.2_5'Flank|CC2D2A_uc003gnv.2_5'Flank	NM_001080522	NP_001073991			coiled-coil and C2 domain containing 2A isoform						cell projection organization	cilium|microtubule basal body				pancreas(2)|ovary(1)	3																		---	---	---	---
FBXL5	26234	broad.mit.edu	37	4	15632545	15632545	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15632545delT	uc003goc.1	-						FBXL5_uc010idw.1_Intron|FBXL5_uc003gob.1_Intron|FBXL5_uc010idx.1_Intron|FBXL5_uc003god.1_Intron|FBXL5_uc010idy.1_Intron	NM_012161	NP_036293			F-box and leucine-rich repeat protein 5 isoform						iron ion homeostasis|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|SCF ubiquitin ligase complex	iron ion binding|protein binding|ubiquitin-protein ligase activity				0																		---	---	---	---
FBXL5	26234	broad.mit.edu	37	4	15642249	15642249	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15642249delT	uc003goc.1	-						FBXL5_uc010idw.1_Intron|FBXL5_uc003gob.1_Intron|FBXL5_uc010idx.1_Intron|FBXL5_uc003god.1_Intron|FBXL5_uc010idy.1_Intron	NM_012161	NP_036293			F-box and leucine-rich repeat protein 5 isoform						iron ion homeostasis|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|SCF ubiquitin ligase complex	iron ion binding|protein binding|ubiquitin-protein ligase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	15944968	15944968	+	IGR	DEL	A	-	-	rs74735230		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15944968delA								FGFBP1 (4997 upstream) : FGFBP2 (16896 downstream)																																			---	---	---	---
TAPT1	202018	broad.mit.edu	37	4	16204227	16204227	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16204227delA	uc010ied.1	-						TAPT1_uc011bxe.1_Intron|TAPT1_uc003gow.3_Intron	NM_153365	NP_699196			transmembrane anterior posterior transformation							integral to membrane	growth hormone-releasing hormone receptor activity				0																		---	---	---	---
TAPT1	202018	broad.mit.edu	37	4	16215322	16215322	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16215322delT	uc010ied.1	-						TAPT1_uc011bxe.1_Intron|TAPT1_uc003gow.3_Intron	NM_153365	NP_699196			transmembrane anterior posterior transformation							integral to membrane	growth hormone-releasing hormone receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	16448476	16448476	+	IGR	DEL	T	-	-	rs77278974		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16448476delT								FLJ39653 (188666 upstream) : LDB2 (54691 downstream)																																			---	---	---	---
LDB2	9079	broad.mit.edu	37	4	16677771	16677772	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16677771_16677772delTG	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_Intron|LDB2_uc011bxi.1_5'Flank	NM_001290	NP_001281			LIM domain binding 2 isoform a								LIM domain binding|transcription cofactor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	16939291	16939292	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16939291_16939292delAA								LDB2 (38867 upstream) : QDPR (548728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	17083812	17083812	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17083812delT								LDB2 (183388 upstream) : QDPR (404208 downstream)																																			---	---	---	---
FAM184B	27146	broad.mit.edu	37	4	17666304	17666305	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17666304_17666305delAA	uc003gpm.3	-							NM_015688	NP_056503			hypothetical protein LOC27146											central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	18260215	18260215	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18260215delT								LCORL (236830 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18385641	18385641	+	IGR	DEL	A	-	-	rs112822498		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18385641delA								LCORL (362256 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18699294	18699295	+	IGR	INS	-	TA	TA	rs145024087	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18699294_18699295insTA								LCORL (675909 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	19493427	19493427	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19493427delG								None (None upstream) : SLIT2 (761808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	19645458	19645458	+	IGR	DEL	T	-	-	rs60670447		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19645458delT								None (None upstream) : SLIT2 (609777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	20048276	20048277	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20048276_20048277delAA								None (None upstream) : SLIT2 (206958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	20101310	20101310	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20101310delA								None (None upstream) : SLIT2 (153925 downstream)																																			---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	20778552	20778552	+	Intron	DEL	A	-	-	rs66714040		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20778552delA	uc003gqe.2	-						KCNIP4_uc003gqf.1_Intron|KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron|KCNIP4_uc010iel.2_Intron|KCNIP4_uc003gqd.3_Intron	NM_147182	NP_671711			Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)																---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21223226	21223226	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21223226delG	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	21272017	21272018	+	Intron	INS	-	A	A	rs145889756	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21272017_21272018insA	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)																---	---	---	---
GPR125	166647	broad.mit.edu	37	4	22422868	22422868	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22422868delA	uc003gqm.1	-						GPR125_uc010ieo.1_Intron|GPR125_uc003gqn.1_Intron|GPR125_uc003gqo.2_Intron	NM_145290	NP_660333			G protein-coupled receptor 125 precursor						neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)																---	---	---	---
GBA3	57733	broad.mit.edu	37	4	22750449	22750449	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22750449delT	uc003gqp.3	+						GBA3_uc010iep.2_Intron|GBA3_uc011bxo.1_Intron	NM_020973	NP_066024			cytosolic beta-glucosidase isoform a						glycoside catabolic process|glycosylceramide catabolic process	cytosol	beta-galactosidase activity|beta-glucosidase activity|cation binding|glycosylceramidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	23085445	23085452	+	IGR	DEL	TTTTTTTT	-	-	rs72451944		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23085445_23085452delTTTTTTTT								GBA3 (264254 upstream) : PPARGC1A (708193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23335781	23335782	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23335781_23335782delTT								GBA3 (514590 upstream) : PPARGC1A (457863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23366130	23366130	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23366130delT								GBA3 (544939 upstream) : PPARGC1A (427515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24738373	24738374	+	IGR	DEL	AA	-	-	rs74932168		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24738373_24738374delAA								DHX15 (152189 upstream) : SOD3 (58711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	25000275	25000275	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25000275delT								CCDC149 (18505 upstream) : LGI2 (196 downstream)																																			---	---	---	---
ANAPC4	29945	broad.mit.edu	37	4	25382231	25382231	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25382231delA	uc003gro.2	+						ANAPC4_uc003grp.2_5'Flank	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	25659563	25659563	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25659563delA	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)																---	---	---	---
SLC34A2	10568	broad.mit.edu	37	4	25664605	25664605	+	Intron	DEL	T	-	-	rs34583336		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	26041004	26041005	+	IGR	INS	-	T	T	rs11426965		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26041004_26041005insT								C4orf52 (109504 upstream) : RBPJ (280327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	26270285	26270285	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26270285delT								C4orf52 (338785 upstream) : RBPJ (51047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	26296867	26296868	+	IGR	INS	-	GT	GT	rs143325601	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26296867_26296868insGT								C4orf52 (365367 upstream) : RBPJ (24464 downstream)																																			---	---	---	---
RBPJ	3516	broad.mit.edu	37	4	26390399	26390399	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26390399delA	uc003grx.1	+						RBPJ_uc003gry.1_Intron|RBPJ_uc003grz.1_Intron|RBPJ_uc011bxt.1_Intron|RBPJ_uc003gsa.1_Intron|RBPJ_uc003gsb.1_Intron|RBPJ_uc003gsc.1_Intron	NM_005349	NP_005340			recombining binding protein suppressor of						DNA recombination|negative regulation of transcription, DNA-dependent|positive regulation of transcription of Notch receptor target	cytoplasm|nucleolus|nucleoplasm	DNA binding|protein binding|recombinase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|central_nervous_system(1)	3		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	26473243	26473244	+	IGR	DEL	TC	-	-	rs112435507		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26473243_26473244delTC								RBPJ (39965 upstream) : CCKAR (9774 downstream)																																			---	---	---	---
STIM2	57620	broad.mit.edu	37	4	26961335	26961336	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26961335_26961336delTT	uc003gsh.3	+						STIM2_uc003gsg.3_Intron|STIM2_uc010iex.2_Intron	NM_020860	NP_065911			stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
STIM2	57620	broad.mit.edu	37	4	27009063	27009064	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27009063_27009064delTT	uc003gsh.3	+						STIM2_uc003gsg.3_Intron|STIM2_uc010iex.2_Intron|STIM2_uc010iey.2_Intron	NM_020860	NP_065911			stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
STIM2	57620	broad.mit.edu	37	4	27022680	27022681	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27022680_27022681delAA	uc003gsh.3	+						STIM2_uc003gsg.3_Intron|STIM2_uc010iex.2_3'UTR|STIM2_uc010iey.2_Intron	NM_020860	NP_065911			stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	28550285	28550285	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28550285delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29711701	29711701	+	IGR	DEL	A	-	-	rs35264236		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29711701delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29849268	29849268	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29849268delA								None (None upstream) : PCDH7 (872769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29903022	29903023	+	IGR	INS	-	A	A	rs147155060	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29903022_29903023insA								None (None upstream) : PCDH7 (819014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	30284363	30284363	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30284363delT								None (None upstream) : PCDH7 (437674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	30577176	30577176	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30577176delT								None (None upstream) : PCDH7 (144861 downstream)																																			---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	30845322	30845322	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30845322delT	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	31278877	31278878	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31278877_31278878delTG								PCDH7 (130456 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	31410323	31410324	+	IGR	DEL	CA	-	-	rs11733399	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31410323_31410324delCA								PCDH7 (261902 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	31925621	31925621	+	IGR	DEL	T	-	-	rs75710850		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31925621delT								PCDH7 (777200 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32321061	32321061	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32321061delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32645151	32645152	+	IGR	INS	-	GGAGAGGA	GGAGAGGA	rs140869139	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32645151_32645152insGGAGAGGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32995636	32995636	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32995636delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33646684	33646684	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33646684delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33648200	33648200	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33648200delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	34482372	34482372	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34482372delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35194143	35194144	+	IGR	INS	-	TGTG	TGTG	rs138340370	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35194143_35194144insTGTG								None (None upstream) : ARAP2 (755700 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35492441	35492442	+	IGR	DEL	AC	-	-	rs71945257		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35492441_35492442delAC								None (None upstream) : ARAP2 (457402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35574187	35574187	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35574187delA								None (None upstream) : ARAP2 (375657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	36403572	36403572	+	IGR	DEL	T	-	-	rs34598840		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36403572delT								DTHD1 (57614 upstream) : MIR1255B-1 (24416 downstream)																																			---	---	---	---
KIAA1239	57495	broad.mit.edu	37	4	37264910	37264910	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37264910delT	uc011bxz.1	+							NM_001144990	NP_001138462			hypothetical protein LOC57495												0																		---	---	---	---
C4orf19	55286	broad.mit.edu	37	4	37590393	37590393	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37590393delA	uc003gsw.3	+						C4orf19_uc003gsy.3_Intron	NM_001104629	NP_001098099			hypothetical protein LOC55286												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	37803029	37803029	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37803029delA								RELL1 (115030 upstream) : PGM2 (25253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	38245885	38245885	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38245885delT								TBC1D1 (105092 upstream) : FLJ13197 (368437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	38574103	38574103	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38574103delA								TBC1D1 (433310 upstream) : FLJ13197 (40219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	38745665	38745666	+	IGR	DEL	AG	-	-	rs141415987	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38745665_38745666delAG								KLF3 (42537 upstream) : TLR10 (28597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	38962852	38962852	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38962852delA								FAM114A1 (17428 upstream) : TMEM156 (5591 downstream)																																			---	---	---	---
KLHL5	51088	broad.mit.edu	37	4	39120377	39120377	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39120377delA	uc003gts.2	+						KLHL5_uc003gtp.2_Intron|KLHL5_uc003gtq.2_Intron|KLHL5_uc003gtt.2_Intron	NM_015990	NP_057074			kelch-like 5 isoform 1							cytoplasm|cytoskeleton	actin binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	39125748	39125748	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39125748delA								KLHL5 (1920 upstream) : WDR19 (58276 downstream)																																			---	---	---	---
WDR19	57728	broad.mit.edu	37	4	39216394	39216394	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39216394delT	uc003gtv.2	+						WDR19_uc010ifl.1_Intron|WDR19_uc003gtu.1_Intron|WDR19_uc011byi.1_Intron|WDR19_uc003gtw.1_5'Flank	NM_025132	NP_079408			WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1																		---	---	---	---
WDR19	57728	broad.mit.edu	37	4	39279672	39279674	+	Intron	DEL	AAA	-	-	rs76348575		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39279672_39279674delAAA	uc003gtv.2	+						WDR19_uc011byi.1_Intron	NM_025132	NP_079408			WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1																		---	---	---	---
RFC1	5981	broad.mit.edu	37	4	39367767	39367767	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39367767delC	uc003gty.1	-						RFC1_uc003gtx.1_Intron|RFC1_uc003gtz.1_Intron	NM_002913	NP_002904			replication factor C large subunit						DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|telomere maintenance via telomerase|transcription, DNA-dependent|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|enzyme activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
LIAS	11019	broad.mit.edu	37	4	39478849	39478849	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39478849delA	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)													---	---	---	---
C4orf34	201895	broad.mit.edu	37	4	39626671	39626671	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39626671delA	uc003guo.2	-							NM_174921	NP_777581			hypothetical protein LOC201895							integral to membrane	protein binding				0																		---	---	---	---
C4orf34	201895	broad.mit.edu	37	4	39642608	39642609	+	5'Flank	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39642608_39642609delTT	uc003guo.2	-						uc003gup.1_Intron	NM_174921	NP_777581			hypothetical protein LOC201895							integral to membrane	protein binding				0																		---	---	---	---
UBE2K	3093	broad.mit.edu	37	4	39724831	39724831	+	Intron	DEL	T	-	-	rs74955480		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39724831delT	uc003guu.3	+						UBE2K_uc003gus.3_Intron|UBE2K_uc003gut.3_Intron|UBE2K_uc010ifn.2_Intron|UBE2K_uc011byq.1_Intron|UBE2K_uc003guq.3_Intron	NM_005339	NP_005330			ubiquitin-conjugating enzyme E2K isoform 1						protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|ubiquitin protein ligase binding|ubiquitin-ubiquitin ligase activity			ovary(1)	1																		---	---	---	---
PDS5A	23244	broad.mit.edu	37	4	39929854	39929854	+	Intron	DEL	A	-	-	rs149442914		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39929854delA	uc003guv.3	-						PDS5A_uc010ifo.2_Intron|PDS5A_uc003guw.3_Intron	NM_001100399	NP_001093869			PDS5, regulator of cohesion maintenance, homolog						cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0																		---	---	---	---
RBM47	54502	broad.mit.edu	37	4	40586884	40586885	+	Intron	INS	-	TGTT	TGTT	rs144934471	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40586884_40586885insTGTT	uc003gvc.2	-						RBM47_uc003gve.2_Intron|RBM47_uc011bys.1_Intron	NM_001098634	NP_001092104			RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3																		---	---	---	---
NSUN7	79730	broad.mit.edu	37	4	40751193	40751193	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40751193delT	uc003gvj.3	+						NSUN7_uc003gvh.2_5'Flank|NSUN7_uc003gvi.3_5'Flank	NM_024677	NP_078953			NOL1/NOP2/Sun domain family, member 7												0																		---	---	---	---
LIMCH1	22998	broad.mit.edu	37	4	41496472	41496473	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41496472_41496473delAC	uc003gvu.3	+						LIMCH1_uc003gvt.1_Intron|LIMCH1_uc003gvv.3_Intron|LIMCH1_uc003gvw.3_Intron|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Intron|LIMCH1_uc003gvy.3_Intron	NM_014988	NP_055803			LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
LIMCH1	22998	broad.mit.edu	37	4	41663418	41663418	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41663418delA	uc003gvu.3	+						LIMCH1_uc003gvv.3_Intron|LIMCH1_uc003gvw.3_Intron|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Intron|LIMCH1_uc003gvy.3_Intron|LIMCH1_uc003gwa.3_Intron|LIMCH1_uc003gvz.3_Intron|LIMCH1_uc011byu.1_Intron|LIMCH1_uc003gwc.3_Intron|LIMCH1_uc003gwd.3_Intron|LIMCH1_uc011byv.1_Intron|LIMCH1_uc011byw.1_5'Flank	NM_014988	NP_055803			LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																OREG0016170	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	4	41874582	41874584	+	IGR	DEL	TGT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41874582_41874584delTGT								PHOX2B (123595 upstream) : TMEM33 (62553 downstream)																																			---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42037517	42037518	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42037517_42037518delTT	uc003gwl.2	+						SLC30A9_uc011byx.1_Intron	NM_006345	NP_006336			solute carrier family 30 (zinc transporter),						nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
BEND4	389206	broad.mit.edu	37	4	42127763	42127763	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42127763delT	uc003gwn.2	-						BEND4_uc003gwm.2_Intron|BEND4_uc011byy.1_Intron	NM_207406	NP_997289			BEN domain containing 4 isoform a												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	42364561	42364562	+	IGR	DEL	TG	-	-	rs10562622		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42364561_42364562delTG								BEND4 (209666 upstream) : SHISA3 (35294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	42396702	42396702	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42396702delA								BEND4 (241807 upstream) : SHISA3 (3154 downstream)																																			---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42445527	42445527	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42445527delA	uc003gwr.2	-						ATP8A1_uc003gwq.2_Intron|ATP8A1_uc003gws.2_Intron	NM_006095	NP_006086			ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	43121475	43121475	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43121475delA								GRXCR1 (88802 upstream) : None (None downstream)																																			---	---	---	---
GUF1	60558	broad.mit.edu	37	4	44682662	44682662	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44682662delT	uc003gww.3	+						GUF1_uc010ifz.1_Intron	NM_021927	NP_068746			GUF1 GTPase homolog						translation	mitochondrial inner membrane	GTP binding|GTPase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	45419977	45419977	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45419977delT								GNPDA2 (691365 upstream) : GABRG1 (617812 downstream)																																			---	---	---	---
COX7B2	170712	broad.mit.edu	37	4	46791009	46791011	+	Intron	DEL	CTG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46791009_46791011delCTG	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																		---	---	---	---
COX7B2	170712	broad.mit.edu	37	4	46824398	46824398	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46824398delA	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																		---	---	---	---
GABRB1	2560	broad.mit.edu	37	4	47143100	47143101	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47143100_47143101insT	uc003gxh.2	+						GABRB1_uc011bze.1_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)													---	---	---	---
ATP10D	57205	broad.mit.edu	37	4	47559698	47559698	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47559698delG	uc003gxk.1	+	12	2006	c.1842delG	c.(1840-1842)CTGfs	p.L614fs	ATP10D_uc003gxl.1_Intron	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	614	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3																		---	---	---	---
NFXL1	152518	broad.mit.edu	37	4	47899965	47899965	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
TEC	7006	broad.mit.edu	37	4	48233773	48233774	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48233773_48233774insA	uc003gxz.2	-							NM_003215	NP_003206			tec protein tyrosine kinase						intracellular protein kinase cascade	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)	9																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48625213	48625213	+	Intron	DEL	C	-	-	rs776579	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48625213delC	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																		---	---	---	---
CWH43	80157	broad.mit.edu	37	4	49017280	49017280	+	Intron	DEL	T	-	-	rs145285553		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49017280delT	uc003gyv.2	+						CWH43_uc011bzl.1_Intron	NM_025087	NP_079363			cell wall biogenesis 43 C-terminal homolog						GPI anchor biosynthetic process	integral to membrane				skin(2)|ovary(1)	3																		---	---	---	---
CWH43	80157	broad.mit.edu	37	4	49019229	49019229	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49019229delT	uc003gyv.2	+						CWH43_uc011bzl.1_Intron	NM_025087	NP_079363			cell wall biogenesis 43 C-terminal homolog						GPI anchor biosynthetic process	integral to membrane				skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	49090257	49090257	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49090257delT								CWH43 (26164 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49137281	49137282	+	IGR	INS	-	TTTAC	TTTAC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49137281_49137282insTTTAC								CWH43 (73188 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49153840	49153844	+	IGR	DEL	GTTCT	-	-	rs139457139	by1000genomes;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49153840_49153844delGTTCT								CWH43 (89747 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49217676	49217677	+	IGR	INS	-	C	C	rs146012723	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49217676_49217677insC								CWH43 (153583 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49226029	49226029	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49226029delG								CWH43 (161936 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49263143	49263143	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49263143delA								CWH43 (199050 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49533117	49533118	+	IGR	INS	-	TT	TT	rs76401321		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49533117_49533118insTT								CWH43 (469024 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49642428	49642429	+	IGR	INS	-	T	T	rs141114608		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49642428_49642429insT								CWH43 (578335 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49655511	49655512	+	IGR	INS	-	G	G	rs144104492		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49655511_49655512insG								CWH43 (591418 upstream) : None (None downstream)																																			---	---	---	---
SPATA18	132671	broad.mit.edu	37	4	52926826	52926826	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52926826delT	uc003gzl.2	+						SPATA18_uc010igl.1_Intron|SPATA18_uc011bzq.1_Intron|SPATA18_uc003gzk.1_Intron	NM_145263	NP_660306			spermatogenesis associated 18 homolog						mitochondrial protein catabolic process|mitochondrion degradation by induced vacuole formation|response to DNA damage stimulus	mitochondrial outer membrane	protein binding			ovary(2)|skin(2)	4			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)															---	---	---	---
SPATA18	132671	broad.mit.edu	37	4	52938570	52938571	+	Intron	INS	-	T	T	rs76413467		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52938570_52938571insT	uc003gzl.2	+						SPATA18_uc010igl.1_Intron|SPATA18_uc011bzq.1_Intron|SPATA18_uc003gzk.1_Intron	NM_145263	NP_660306			spermatogenesis associated 18 homolog						mitochondrial protein catabolic process|mitochondrion degradation by induced vacuole formation|response to DNA damage stimulus	mitochondrial outer membrane	protein binding			ovary(2)|skin(2)	4			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	53012362	53012363	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53012362_53012363insT								SPATA18 (48905 upstream) : USP46 (444766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53064723	53064724	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53064723_53064724delTG								SPATA18 (101266 upstream) : USP46 (392405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53250267	53250268	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53250267_53250268insA								SPATA18 (286810 upstream) : USP46 (206861 downstream)																																			---	---	---	---
USP46	64854	broad.mit.edu	37	4	53461200	53461200	+	3'UTR	DEL	T	-	-	rs11351768		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53461200delT	uc003gzn.2	-	9					USP46_uc003gzm.3_3'UTR|USP46_uc011bzr.1_3'UTR|USP46_uc011bzs.1_3'UTR	NM_022832	NP_073743			ubiquitin specific peptidase 46 isoform 1						behavior|protein deubiquitination|regulation of synaptic transmission, GABAergic|ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1			LUSC - Lung squamous cell carcinoma(32;0.0295)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	53586490	53586490	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53586490delT								KIAA0114 (6185 upstream) : RASL11B (142005 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53717758	53717759	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53717758_53717759insA								KIAA0114 (137453 upstream) : RASL11B (10736 downstream)																																			---	---	---	---
SCFD2	152579	broad.mit.edu	37	4	53918072	53918072	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53918072delA	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	54183274	54183276	+	Intron	DEL	AAA	-	-	rs111865937		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54183274_54183276delAAA	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	54205944	54205945	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54205944_54205945delAA	uc003gzu.2	-						SCFD2_uc010igm.2_Intron	NM_152540	NP_689753			sec1 family domain containing 2						protein transport|vesicle docking involved in exocytosis					ovary(2)|pancreas(1)	3			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)															---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54308915	54308915	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54308915delT	uc003haa.2	+						FIP1L1_uc003gzy.2_Intron|FIP1L1_uc011bzu.1_Intron|FIP1L1_uc003gzz.2_Intron|FIP1L1_uc003hab.2_Intron|FIP1L1_uc003hac.2_Intron|FIP1L1_uc010ign.2_Intron|FIP1L1_uc003had.2_Intron|FIP1L1_uc003hae.2_Intron	NM_006206	NP_006197			platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	55227500	55227501	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55227500_55227501delAA								PDGFRA (63089 upstream) : KIT (296594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	55869091	55869092	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55869091_55869092delCT								KIT (262212 upstream) : KDR (75335 downstream)																																			---	---	---	---
KDR	3791	broad.mit.edu	37	4	55990386	55990386	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55990386delT	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)			---	---	---	---
NMU	10874	broad.mit.edu	37	4	56475552	56475554	+	Intron	DEL	AAA	-	-	rs67858032		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56475552_56475554delAAA	uc003hbc.2	-						NMU_uc003hbd.1_Intron|NMU_uc010igv.1_Intron|NMU_uc010igw.1_Intron|NMU_uc010igx.1_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	56547644	56547645	+	IGR	INS	-	G	G	rs138057344	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56547644_56547645insG								NMU (45179 upstream) : LOC644145 (138592 downstream)																																			---	---	---	---
KIAA1211	57482	broad.mit.edu	37	4	57181941	57181941	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57181941delC	uc003hbk.2	+	8	2664	c.2273delC	c.(2272-2274)GCCfs	p.A758fs	KIAA1211_uc010iha.2_Frame_Shift_Del_p.A751fs|KIAA1211_uc011bzz.1_Frame_Shift_Del_p.A668fs|KIAA1211_uc003hbm.1_Frame_Shift_Del_p.A644fs	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	758										ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
SRP72	6731	broad.mit.edu	37	4	57336042	57336042	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57336042delT	uc003hbv.2	+						SRP72_uc010ihe.2_Intron	NM_006947	NP_008878			signal recognition particle 72kDa						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|nucleolus|plasma membrane|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding			ovary(1)	1	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	57605173	57605175	+	IGR	DEL	GAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57605173_57605175delGAG								HOPX (57301 upstream) : SPINK2 (70859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	57741817	57741817	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57741817delA								SPINK2 (53924 upstream) : REST (32225 downstream)																																			---	---	---	---
POLR2B	5431	broad.mit.edu	37	4	57871705	57871705	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57871705delA	uc003hcl.1	+						POLR2B_uc011cae.1_Intron|POLR2B_uc011caf.1_Intron	NM_000938	NP_000929			DNA directed RNA polymerase II polypeptide B						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(2)	2	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
POLR2B	5431	broad.mit.edu	37	4	57889965	57889965	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57889965delT	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	58023655	58023655	+	Intron	DEL	T	-	-	rs35656325		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58023655delT	uc003hco.2	+											Homo sapiens, clone IMAGE:5722917, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	58798994	58798994	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58798994delA								IGFBP7 (822455 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	59998007	59998008	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59998007_59998008delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60749024	60749024	+	IGR	DEL	T	-	-	rs116222557	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60749024delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61159439	61159439	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61159439delG								None (None upstream) : LPHN3 (907535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61231219	61231219	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61231219delA								None (None upstream) : LPHN3 (835755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61277010	61277010	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61277010delT								None (None upstream) : LPHN3 (789964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61303401	61303401	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61303401delA								None (None upstream) : LPHN3 (763573 downstream)																																			---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62496278	62496278	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62496278delT	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc010ihg.1_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62782190	62782190	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62782190delA	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hct.2_Intron|LPHN3_uc003hcs.1_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	62971330	62971330	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62971330delT								LPHN3 (33163 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63223760	63223760	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63223760delA								LPHN3 (285593 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63321675	63321675	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63321675delT								LPHN3 (383508 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63468851	63468852	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63468851_63468852insA								LPHN3 (530684 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	65402578	65402578	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65402578delT								TECRL (127400 upstream) : EPHA5 (782704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	65470468	65470468	+	IGR	DEL	G	-	-	rs7695225		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65470468delG								TECRL (195290 upstream) : EPHA5 (714814 downstream)																																			---	---	---	---
EPHA5	2044	broad.mit.edu	37	4	66462304	66462304	+	Intron	DEL	A	-	-	rs34012574		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66462304delA	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	66878088	66878088	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66878088delT								EPHA5 (342435 upstream) : MIR1269 (264454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67853569	67853569	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67853569delT								MIR1269 (710923 upstream) : CENPC1 (484420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	68072577	68072577	+	IGR	DEL	A	-	-	rs35181687		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68072577delA								MIR1269 (929931 upstream) : CENPC1 (265412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	68258804	68258804	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68258804delT								None (None upstream) : CENPC1 (79185 downstream)																																			---	---	---	---
LOC550112	550112	broad.mit.edu	37	4	68597965	68597965	+	RNA	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68597965delC	uc003hdl.3	+	5		c.1823delC								Homo sapiens chromosome 4 cDNA.												0																		---	---	---	---
LOC550112	550112	broad.mit.edu	37	4	68669961	68669962	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68669961_68669962delTG	uc003hdl.3	+											Homo sapiens chromosome 4 cDNA.												0																		---	---	---	---
TMPRSS11D	9407	broad.mit.edu	37	4	68692479	68692481	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68692479_68692481delAAA	uc003hdq.2	-						LOC550112_uc003hdl.3_Intron|TMPRSS11D_uc003hdp.2_Intron|TMPRSS11D_uc011caj.1_Intron	NM_004262	NP_004253			transmembrane protease, serine 11D						proteolysis|respiratory gaseous exchange	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
TMPRSS11D	9407	broad.mit.edu	37	4	68749629	68749629	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68749629delA	uc003hdq.2	-						LOC550112_uc003hdl.3_Intron|TMPRSS11D_uc011caj.1_Intron	NM_004262	NP_004253			transmembrane protease, serine 11D						proteolysis|respiratory gaseous exchange	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
YTHDC1	91746	broad.mit.edu	37	4	69182317	69182317	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69182317delT	uc003hdx.2	-						YTHDC1_uc003hdy.2_Intron	NM_001031732	NP_001026902			splicing factor YT521-B isoform 1											upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
YTHDC1	91746	broad.mit.edu	37	4	69198815	69198815	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69198815delA	uc003hdx.2	-						YTHDC1_uc003hdy.2_Intron	NM_001031732	NP_001026902			splicing factor YT521-B isoform 1											upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	69447408	69447408	+	IGR	DEL	T	-	-	rs76217088		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69447408delT								YTHDC1 (231584 upstream) : UGT2B15 (64908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	69574859	69574859	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69574859delA								UGT2B15 (38485 upstream) : UGT2B10 (106854 downstream)																																			---	---	---	---
CSN2	1447	broad.mit.edu	37	4	70826811	70826811	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70826811delA	uc003hes.3	-						CSN2_uc003het.3_5'Flank	NM_001891	NP_001882			casein beta precursor						calcium ion transport	extracellular region	calcium ion binding|enzyme inhibitor activity|transporter activity				0																		---	---	---	---
HTN1	3346	broad.mit.edu	37	4	70916035	70916036	+	5'Flank	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70916035_70916036delAG	uc003hex.2	+							NM_002159	NP_002150			histatin 1 precursor						biomineral tissue development|defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular region	protein binding			skin(1)	1																		---	---	---	---
HTN1	3346	broad.mit.edu	37	4	70921372	70921372	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70921372delA	uc003hex.2	+							NM_002159	NP_002150			histatin 1 precursor						biomineral tissue development|defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular region	protein binding			skin(1)	1																		---	---	---	---
MUC7	4589	broad.mit.edu	37	4	71327782	71327783	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71327782_71327783insT	uc011cat.1	+							NM_001145006	NP_001138478			mucin 7, secreted precursor							extracellular region	protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4			Lung(101;0.211)															---	---	---	---
AMBN	258	broad.mit.edu	37	4	71464057	71464057	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71464057delT	uc003hfl.2	+							NM_016519	NP_057603			ameloblastin precursor						bone mineralization|cell adhesion|cell proliferation|odontogenesis of dentine-containing tooth	proteinaceous extracellular matrix	growth factor activity|structural constituent of tooth enamel			ovary(3)|skin(1)	4			Lung(101;0.235)															---	---	---	---
IGJ	3512	broad.mit.edu	37	4	71527706	71527706	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71527706delA	uc003hfn.3	-						IGJ_uc010ihz.2_Intron	NM_144646	NP_653247			immunoglobulin J chain						immune response	extracellular region	antigen binding				0			Lung(101;0.235)															---	---	---	---
MOBKL1A	92597	broad.mit.edu	37	4	71801377	71801377	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71801377delT	uc003hfw.2	+						MOBKL1A_uc003hfv.1_Intron|MOBKL1A_uc011cba.1_Intron	NM_173468	NP_775739			MOB1, Mps One Binder kinase activator-like 1A						hippo signaling cascade|protein autophosphorylation	cytoplasm|nucleus	kinase activator activity|kinase binding|metal ion binding				0		all_hematologic(202;0.21)	Lung(101;0.235)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	73113842	73113842	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73113842delA								NPFFR2 (95094 upstream) : ADAMTS3 (32845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	74292060	74292060	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74292060delT								ALB (4933 upstream) : AFP (4795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	74575612	74575612	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74575612delT								RASSF6 (89272 upstream) : IL8 (30663 downstream)																																			---	---	---	---
IL8	3576	broad.mit.edu	37	4	74687015	74687015	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74687015delT	uc011cbh.1	+							NM_000584	NP_000575			interleukin 8 precursor						angiogenesis|calcium-mediated signaling|cell cycle arrest|cellular response to lipopolysaccharide|embryonic digestive tract development|G-protein coupled receptor protein signaling pathway|immune response|induction of positive chemotaxis|inflammatory response|negative regulation of cell proliferation|neutrophil activation|neutrophil chemotaxis|positive regulation of neutrophil chemotaxis|regulation of cell adhesion|regulation of retroviral genome replication	extracellular space|intracellular	chemokine activity|interleukin-8 receptor binding			ovary(2)	2	Breast(15;0.00102)		all cancers(17;0.00169)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)	LUSC - Lung squamous cell carcinoma(721;0.008)	Ketoprofen(DB01009)|Salbutamol(DB01001)|Simvastatin(DB00641)|Zileuton(DB00744)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	75551216	75551216	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75551216delG								AREG (70585 upstream) : BTC (120232 downstream)																																			---	---	---	---
G3BP2	9908	broad.mit.edu	37	4	76583912	76583912	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76583912delA	uc003hir.2	-						G3BP2_uc003his.2_Intron|G3BP2_uc003hit.2_Intron	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	76721734	76721734	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76721734delT	uc003hiu.2	+						USO1_uc003hiv.2_Intron|USO1_uc003hiw.2_Intron	NM_003715	NP_003706			USO1 homolog, vesicle docking protein						intracellular protein transport|vesicle fusion with Golgi apparatus	cytosol|Golgi membrane	protein binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
SEPT11	55752	broad.mit.edu	37	4	77933163	77933163	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77933163delT	uc003hkj.2	+						SEPT11_uc010ijh.1_Intron|SEPT11_uc011cca.1_Intron|SEPT11_uc003hkk.1_5'Flank	NM_018243	NP_060713			septin 11						cell cycle|cell division|protein heterooligomerization	axon|cell junction|dendritic spine|septin complex|stress fiber|synapse	GTP binding|protein binding				0																		---	---	---	---
SEPT11	55752	broad.mit.edu	37	4	77950489	77950490	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77950489_77950490delGT	uc003hkj.2	+						SEPT11_uc010ijh.1_Intron|SEPT11_uc011cca.1_Intron	NM_018243	NP_060713			septin 11						cell cycle|cell division|protein heterooligomerization	axon|cell junction|dendritic spine|septin complex|stress fiber|synapse	GTP binding|protein binding				0																		---	---	---	---
CCNG2	901	broad.mit.edu	37	4	78080669	78080669	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78080669delT	uc003hkq.3	+						CCNG2_uc003hkn.3_Intron|CCNG2_uc011ccc.1_Intron|CCNG2_uc003hkp.3_Intron	NM_004354	NP_004345			cyclin G2						cell cycle checkpoint|cell division|mitosis	cytoplasm				ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	78286943	78286943	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78286943delT								CCNG2 (195733 upstream) : CXCL13 (145964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	78413817	78413817	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78413817delA								CCNG2 (322607 upstream) : CXCL13 (19090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	78879131	78879131	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78879131delA								MRPL1 (5187 upstream) : FRAS1 (99593 downstream)																																			---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79101922	79101923	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79101922_79101923delTT	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron	NM_025074	NP_079350			Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5																		---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79206514	79206514	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79206514delA	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron|FRAS1_uc003hky.1_Intron|FRAS1_uc003hkz.2_Intron|FRAS1_uc003hla.1_5'Flank	NM_025074	NP_079350			Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	79618018	79618018	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79618018delA								ANXA3 (86416 upstream) : BMP2K (79514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	79952385	79952385	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79952385delT	uc003hlr.1	+											Homo sapiens full length insert cDNA clone YY75G10.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	80055272	80055272	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80055272delT	uc003hlr.1	+											Homo sapiens full length insert cDNA clone YY75G10.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	80212452	80212453	+	Intron	INS	-	A	A	rs57861971	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80212452_80212453insA	uc003hlr.1	+						uc003hls.2_Intron					Homo sapiens full length insert cDNA clone YY75G10.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	80808779	80808780	+	IGR	DEL	TC	-	-	rs72020269		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80808779_80808780delTC								GDEP (24380 upstream) : ANTXR2 (13993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	81002524	81002524	+	IGR	DEL	A	-	-	rs113749920		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81002524delA								ANTXR2 (8047 upstream) : PRDM8 (102915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	81240390	81240391	+	IGR	INS	-	TGTG	TGTG	rs113164367		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81240390_81240391insTGTG								FGF5 (28220 upstream) : C4orf22 (16483 downstream)																																			---	---	---	---
PRKG2	5593	broad.mit.edu	37	4	82057830	82057831	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82057830_82057831delTC	uc003hmh.2	-						PRKG2_uc011ccf.1_Intron|PRKG2_uc011ccg.1_Intron|PRKG2_uc011cch.1_Intron	NM_006259	NP_006250			protein kinase, cGMP-dependent, type II						platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7																		---	---	---	---
RASGEF1B	153020	broad.mit.edu	37	4	82353260	82353260	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82353260delA	uc003hmi.1	-						RASGEF1B_uc003hmj.1_Intron|RASGEF1B_uc010ijq.1_Intron	NM_152545	NP_689758			RasGEF domain family, member 1B						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	82907912	82907912	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82907912delT								RASGEF1B (514851 upstream) : HNRNPD (366555 downstream)																																			---	---	---	---
SCD5	79966	broad.mit.edu	37	4	83636390	83636392	+	Intron	DEL	AAA	-	-	rs66483115		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83636390_83636392delAAA	uc003hna.2	-						SCD5_uc003hnb.3_Intron|SCD5_uc003hnc.2_Intron	NM_001037582	NP_001032671			stearoyl-CoA desaturase 5 isoform a						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity			ovary(1)	1		Colorectal(4;0.0323)|Hepatocellular(203;0.115)																---	---	---	---
COPS4	51138	broad.mit.edu	37	4	83996434	83996434	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83996434delT	uc003hoa.2	+						COPS4_uc003hob.2_Intron|COPS4_uc010ijw.2_Intron|COPS4_uc010ijx.2_Intron	NM_016129	NP_057213			COP9 signalosome subunit 4						cullin deneddylation	cytoplasm|signalosome	protein binding			kidney(1)	1		Hepatocellular(203;0.114)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	84584647	84584647	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84584647delA								AGPAT9 (57622 upstream) : NKX6-1 (829789 downstream)																																			---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85711202	85711202	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85711202delA	uc003hpd.2	-							NM_014991	NP_055806			WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85716121	85716121	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85716121delA	uc003hpd.2	-	20	3587	c.3179delT	c.(3178-3180)TTGfs	p.L1060fs		NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	1060						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85729434	85729434	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85729434delA	uc003hpd.2	-							NM_014991	NP_055806			WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85748160	85748160	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85748160delT	uc003hpd.2	-						WDFY3_uc003hpf.2_Intron	NM_014991	NP_055806			WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	86308401	86308402	+	IGR	INS	-	AC	AC	rs146652881	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86308401_86308402insAC								C4orf12 (380233 upstream) : ARHGAP24 (87882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	86375744	86375744	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86375744delT								C4orf12 (447576 upstream) : ARHGAP24 (20540 downstream)																																			---	---	---	---
ARHGAP24	83478	broad.mit.edu	37	4	86679217	86679217	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86679217delA	uc003hpk.2	+						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	87004596	87004596	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87004596delA	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)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87572610	87572610	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87572610delT	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-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	87956717	87956717	+	Intron	DEL	A	-	-	rs71712552		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87956717delA	uc003hqj.3	+						AFF1_uc011ccx.1_Intron|AFF1_uc003hqh.1_Intron|AFF1_uc011ccy.1_Intron|AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926			myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88066403	88066404	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88066403_88066404delAA								AFF1 (4213 upstream) : KLHL8 (15810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	88180873	88180874	+	IGR	DEL	TT	-	-	rs72317013		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88180873_88180874delTT								KLHL8 (39199 upstream) : HSD17B13 (44067 downstream)																																			---	---	---	---
DMP1	1758	broad.mit.edu	37	4	88584031	88584031	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88584031delC	uc003hqv.2	+	6	1205	c.1101delC	c.(1099-1101)AACfs	p.N367fs	DMP1_uc003hqw.2_Frame_Shift_Del_p.N351fs	NM_004407	NP_004398	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1 isoform 1	367					biomineral tissue development|ossification	cytoplasm|nucleus|proteinaceous extracellular matrix	calcium ion binding|integrin binding			pancreas(1)|skin(1)	2		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88787616	88787616	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88787616delC								MEPE (19674 upstream) : SPP1 (109186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	89255486	89255487	+	IGR	DEL	TT	-	-	rs111763581		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89255486_89255487delTT								PPM1K (49598 upstream) : HERC6 (44404 downstream)																																			---	---	---	---
HERC3	8916	broad.mit.edu	37	4	89527947	89527947	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89527947delC	uc003hrw.1	+						HERC3_uc003hrv.2_Intron|HERC3_uc011cdn.1_Intron	NM_014606	NP_055421			hect domain and RLD 3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasmic membrane-bounded vesicle	ubiquitin-protein ligase activity			lung(2)|prostate(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000319)														---	---	---	---
HERC3	8916	broad.mit.edu	37	4	89627723	89627723	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89627723delT	uc003hrw.1	+						HERC3_uc011cdn.1_Intron|HERC3_uc011cdo.1_Intron	NM_014606	NP_055421			hect domain and RLD 3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasmic membrane-bounded vesicle	ubiquitin-protein ligase activity			lung(2)|prostate(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000319)												OREG0016265	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM13A	10144	broad.mit.edu	37	4	89926258	89926261	+	Intron	DEL	TTCT	-	-	rs72453221		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89926258_89926261delTTCT	uc003hse.1	-						FAM13A_uc003hsf.1_Intron|FAM13A_uc003hsh.1_Intron|FAM13A_uc003hsi.2_Intron|FAM13A_uc003hsj.2_Intron	NM_014883	NP_055698			family with sequence similarity 13, member A1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2																		---	---	---	---
FAM13A	10144	broad.mit.edu	37	4	90013198	90013198	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90013198delA	uc003hsh.1	-											Homo sapiens mRNA for KIAA0914 protein, partial cds.						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	90938249	90938250	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90938249_90938250insC								MMRN1 (62471 upstream) : FAM190A (110434 downstream)																																			---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91854644	91854644	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91854644delT	uc003hsv.3	+						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	91941029	91941029	+	Intron	DEL	C	-	-	rs2054331	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91941029delC	uc003hsv.3	+						FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	92967270	92967270	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92967270delT								FAM190A (443901 upstream) : GRID2 (258280 downstream)																																			---	---	---	---
GRID2	2895	broad.mit.edu	37	4	93451197	93451197	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93451197delG	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	93965522	93965522	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93965522delT	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	94536791	94536792	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94536791_94536792delAA	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)													---	---	---	---
ATOH1	474	broad.mit.edu	37	4	94750382	94750382	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94750382delG	uc003hta.1	+	1	305	c.305delG	c.(304-306)CGGfs	p.R102fs		NM_005172	NP_005163	Q92858	ATOH1_HUMAN	atonal homolog 1	102					transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.57e-07)														---	---	---	---
SMARCAD1	56916	broad.mit.edu	37	4	95164765	95164765	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95164765delT	uc003htc.3	+						SMARCAD1_uc003htb.3_Intron|SMARCAD1_uc003htd.3_Intron|SMARCAD1_uc010ila.2_Intron	NM_020159	NP_064544			SWI/SNF-related, matrix-associated						chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)														---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96370217	96370217	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96370217delA	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	96664236	96664237	+	IGR	INS	-	C	C	rs145903900	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96664236_96664237insC								UNC5C (194074 upstream) : PDHA2 (97002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97088451	97088452	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97088451_97088452delAC								PDHA2 (325827 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97313099	97313100	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97313099_97313100delCT								PDHA2 (550475 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97765638	97765638	+	IGR	DEL	A	-	-	rs77600830		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97765638delA								None (None upstream) : C4orf37 (714396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97797331	97797332	+	IGR	INS	-	T	T	rs142300748	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97797331_97797332insT								None (None upstream) : C4orf37 (682702 downstream)																																			---	---	---	---
C4orf37	285555	broad.mit.edu	37	4	98487550	98487550	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98487550delA	uc003htt.1	-							NM_174952	NP_777612			hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	99089717	99089717	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99089717delA								C4orf37 (25326 upstream) : RAP1GDS1 (92810 downstream)																																			---	---	---	---
RAP1GDS1	5910	broad.mit.edu	37	4	99342309	99342309	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99342309delT	uc003htx.3	+						RAP1GDS1_uc003htw.3_Intron|RAP1GDS1_uc003htv.3_Intron|RAP1GDS1_uc003htz.3_Intron|RAP1GDS1_uc003hty.3_Intron|RAP1GDS1_uc003hua.3_Intron	NM_001100427	NP_001093897			RAP1, GTP-GDP dissociation stimulator 1 isoform								binding|GTPase activator activity			ovary(1)|lung(1)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)				T	NUP98	T-ALL								---	---	---	---
TSPAN5	10098	broad.mit.edu	37	4	99512229	99512229	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99512229delT	uc003hub.2	-						TSPAN5_uc011cdz.1_Intron	NM_005723	NP_005714			transmembrane 4 superfamily member 9							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)														---	---	---	---
EIF4E	1977	broad.mit.edu	37	4	99823226	99823226	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99823226delT	uc003hue.2	-						EIF4E_uc011cea.1_Intron|EIF4E_uc011ceb.1_Intron|EIF4E_uc011cec.1_Intron	NM_001968	NP_001959			eukaryotic translation initiation factor 4E						G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|interspecies interaction between organisms|mRNA export from nucleus|nuclear-transcribed mRNA poly(A) tail shortening|positive regulation of mitotic cell cycle|regulation of translation	cytoplasmic mRNA processing body|cytosol|eukaryotic translation initiation factor 4F complex|mRNA cap binding complex|RNA-induced silencing complex	protein binding|RNA cap binding|translation initiation factor activity			lung(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)														---	---	---	---
ADH6	130	broad.mit.edu	37	4	100125498	100125498	+	Intron	DEL	T	-	-	rs68081403		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100125498delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	100168067	100168067	+	Intron	DEL	T	-	-	rs35526998		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100168067delT	uc003hum.1	+											Homo sapiens full length insert cDNA clone ZD94A03.																														---	---	---	---
ADH1A	124	broad.mit.edu	37	4	100205902	100205903	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100205902_100205903insT	uc003hur.1	-	4	388_389	c.317_318insA	c.(316-318)AACfs	p.N106fs	uc003hum.1_Intron|ADH1A_uc011ceg.1_Frame_Shift_Ins_p.N106fs|ADH1A_uc010ilf.1_5'Flank|ADH1A_uc010ilg.1_Frame_Shift_Ins_p.N106fs	NM_000667	NP_000658	P07327	ADH1A_HUMAN	class I alcohol dehydrogenase, alpha subunit	106					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)													---	---	---	---
MTTP	4547	broad.mit.edu	37	4	100512170	100512170	+	Intron	DEL	A	-	-	rs34244951		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100512170delA	uc003hvc.3	+						MTTP_uc011cej.1_Intron	NM_000253	NP_000244			microsomal triglyceride transfer protein large						lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	100581823	100581823	+	IGR	DEL	C	-	-	rs2718673		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100581823delC								MTTP (36670 upstream) : DAPP1 (156158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	100713813	100713813	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100713813delT								MTTP (168660 upstream) : DAPP1 (24168 downstream)																																			---	---	---	---
DAPP1	27071	broad.mit.edu	37	4	100789086	100789086	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100789086delA	uc003hvf.3	+						DAPP1_uc010ilh.2_Intron	NM_014395	NP_055210			dual adaptor of phosphotyrosine and						signal transduction	cytoplasm|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|protein tyrosine phosphatase activity				0				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)														---	---	---	---
H2AFZ	3015	broad.mit.edu	37	4	100870779	100870779	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100870779delA	uc003hvo.1	-						DNAJB14_uc003hvl.2_5'Flank|DNAJB14_uc010ili.2_5'Flank|DNAJB14_uc003hvm.2_5'Flank|H2AFZ_uc003hvn.1_Frame_Shift_Del_p.F41fs|LOC256880_uc003hvp.1_5'Flank	NM_002106	NP_002097			H2A histone family, member Z						nucleosome assembly	nucleosome|nucleus	DNA binding				0				OV - Ovarian serous cystadenocarcinoma(123;2.32e-08)												OREG0016271	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EMCN	51705	broad.mit.edu	37	4	101337124	101337124	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101337124delA	uc003hvr.2	-						EMCN_uc011cel.1_Intron|EMCN_uc011cem.1_Intron	NM_016242	NP_057326			endomucin isoform 1							extracellular region|integral to membrane|plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	101468420	101468421	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101468420_101468421delTG								EMCN (29170 upstream) : PPP3CA (476166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	101603341	101603343	+	IGR	DEL	TTC	-	-	rs11723230	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101603341_101603343delTTC								EMCN (164091 upstream) : PPP3CA (341244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	102280940	102280940	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102280940delT								PPP3CA (12312 upstream) : BANK1 (60178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	103004782	103004782	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103004782delA								BANK1 (8815 upstream) : SLC39A8 (167416 downstream)																																			---	---	---	---
NFKB1	4790	broad.mit.edu	37	4	103517339	103517339	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103517339delA	uc011ceq.1	+	14	1809	c.1342delA	c.(1342-1344)AAAfs	p.K448fs	NFKB1_uc011cep.1_Frame_Shift_Del_p.K449fs|NFKB1_uc011cer.1_Frame_Shift_Del_p.K268fs	NM_003998	NP_003989	P19838	NFKB1_HUMAN	nuclear factor kappa-B, subunit 1 isoform 1	448	Interaction with CFLAR.				anti-apoptosis|apoptosis|cellular response to mechanical stimulus|inflammatory response|innate immune response|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of calcidiol 1-monooxygenase activity|nerve growth factor receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter	cytosol|I-kappaB/NF-kappaB complex|mitochondrion|nucleoplasm	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|breast(2)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Dexamethasone(DB01234)|Pranlukast(DB01411)|Thalidomide(DB01041)													---	---	---	---
MANBA	4126	broad.mit.edu	37	4	103592592	103592592	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103592592delA	uc003hwg.2	-						MANBA_uc011ces.1_Intron	NM_005908	NP_005899			mannosidase, beta A, lysosomal precursor						carbohydrate metabolic process|protein modification process	lysosome	beta-mannosidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)														---	---	---	---
UBE2D3	7323	broad.mit.edu	37	4	103730907	103730907	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103730907delA	uc003hwk.2	-						UBE2D3_uc003hwi.2_Intron|UBE2D3_uc003hwj.2_Intron|UBE2D3_uc003hwl.2_Intron|UBE2D3_uc011cet.1_Intron|UBE2D3_uc011ceu.1_Intron|UBE2D3_uc003hwo.2_Intron|UBE2D3_uc003hwp.2_Intron|UBE2D3_uc003hwq.2_Intron|UBE2D3_uc003hwr.2_Intron	NM_181887	NP_871616			ubiquitin-conjugating enzyme E2D 3 isoform 1						apoptosis|BMP signaling pathway|DNA repair|negative regulation of type I interferon production|proteasomal ubiquitin-dependent protein catabolic process|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein monoubiquitination|transforming growth factor beta receptor signaling pathway	endosome membrane|plasma membrane	ATP binding|protein binding|ubiquitin-protein ligase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.13e-08)														---	---	---	---
CENPE	1062	broad.mit.edu	37	4	104053733	104053733	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104053733delT	uc003hxb.1	-						CENPE_uc003hxc.1_Intron	NM_001813	NP_001804			centromere protein E						blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	105443301	105443301	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105443301delT	uc003hxh.1	+											Homo sapiens cDNA FLJ37242 fis, clone BRAMY2004335.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	106221741	106221741	+	IGR	DEL	A	-	-	rs2454203	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106221741delA								TET2 (20783 upstream) : PPA2 (68494 downstream)																																			---	---	---	---
TBCK	93627	broad.mit.edu	37	4	106967842	106967842	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106967842delA	uc010ilv.2	-						TBCK_uc003hyb.2_Intron|TBCK_uc003hye.2_Intron|TBCK_uc003hyc.2_Intron|TBCK_uc003hyd.2_Intron|TBCK_uc003hyf.2_Intron	NM_001163435	NP_001156907			TBC domain-containing protein kinase-like							intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5																		---	---	---	---
TBCK	93627	broad.mit.edu	37	4	107037539	107037539	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107037539delA	uc010ilv.2	-						TBCK_uc003hyb.2_Intron|TBCK_uc003hye.2_Intron|TBCK_uc003hyc.2_Intron|TBCK_uc003hyd.2_Intron|TBCK_uc003hyf.2_Intron	NM_001163435	NP_001156907			TBC domain-containing protein kinase-like							intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	108900707	108900707	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108900707delA								CYP2U1 (26096 upstream) : HADH (10233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	109593125	109593125	+	IGR	DEL	G	-	-	rs33967102		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109593125delG								OSTC (4145 upstream) : AGXT2L1 (70079 downstream)																																			---	---	---	---
COL25A1	84570	broad.mit.edu	37	4	109925559	109925561	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109925559_109925561delTTT	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzd.2_Intron|COL25A1_uc003hzf.2_Intron	NM_198721	NP_942014			collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)														---	---	---	---
CCDC109B	55013	broad.mit.edu	37	4	110562208	110562208	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110562208delC	uc011cfs.1	+						CCDC109B_uc010imf.2_Intron	NM_017918	NP_060388			coiled-coil domain containing 109B							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	110629587	110629587	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110629587delT								CASP6 (4958 upstream) : PLA2G12A (1559 downstream)																																			---	---	---	---
EGF	1950	broad.mit.edu	37	4	110909148	110909149	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110909148_110909149insA	uc003hzy.3	+						EGF_uc011cfu.1_Intron|EGF_uc011cfv.1_Intron|EGF_uc010imk.2_Intron	NM_001963	NP_001954			epidermal growth factor precursor						angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	112582729	112582730	+	IGR	INS	-	TG	TG	rs147684543	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112582729_112582730insTG								MIR297 (800926 upstream) : C4orf32 (483823 downstream)																																			---	---	---	---
AP1AR	55435	broad.mit.edu	37	4	113178967	113178967	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113178967delA	uc003iaj.3	+						AP1AR_uc010imm.1_Intron|AP1AR_uc003iak.3_Intron	NM_018569	NP_061039			adaptor-related protein complex 1 associated						protein transport	early endosome|Golgi apparatus|late endosome|transport vesicle					0																		---	---	---	---
ALPK1	80216	broad.mit.edu	37	4	113303547	113303547	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113303547delT	uc003iap.3	+						ALPK1_uc003iam.2_Intron|ALPK1_uc011cfw.1_Intron|ALPK1_uc003ian.3_Intron|ALPK1_uc011cfx.1_Intron|ALPK1_uc003iao.3_Intron|ALPK1_uc003iaq.2_5'Flank|ALPK1_uc010imo.2_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	113451686	113451687	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113451686_113451687insT								NEUROG2 (14358 upstream) : C4orf21 (8803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	113453888	113453888	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113453888delT								NEUROG2 (16560 upstream) : C4orf21 (6602 downstream)																																			---	---	---	---
C4orf21	55345	broad.mit.edu	37	4	113504970	113504970	+	Intron	DEL	A	-	-	rs140732512		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113504970delA	uc003iau.2	-						C4orf21_uc003iav.2_Intron	NM_018392	NP_060862			prematurely terminated mRNA decay factor-like							integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)														---	---	---	---
C4orf21	55345	broad.mit.edu	37	4	113540916	113540916	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113540916delA	uc003iau.2	-						C4orf21_uc003iaw.2_Intron	NM_018392	NP_060862			prematurely terminated mRNA decay factor-like							integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)														---	---	---	---
LARP7	51574	broad.mit.edu	37	4	113560695	113560695	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113560695delT	uc003iay.2	+						C4orf21_uc003iau.2_5'Flank|C4orf21_uc003iaw.2_5'Flank|LARP7_uc003iaz.2_Intron|LARP7_uc003iba.2_Intron|LARP7_uc003ibb.2_Intron	NM_016648	NP_057732			La ribonucleoprotein domain family, member 7						RNA processing	nucleoplasm|ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(3)	3		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
LARP7	51574	broad.mit.edu	37	4	113574479	113574479	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113574479delT	uc003iay.2	+						LARP7_uc003iaz.2_Intron|LARP7_uc003iba.2_Intron|LARP7_uc003ibb.2_Intron	NM_016648	NP_057732			La ribonucleoprotein domain family, member 7						RNA processing	nucleoplasm|ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(3)	3		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	113858485	113858485	+	Intron	DEL	T	-	-	rs10712090		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113858485delT	uc003ibd.3	+						ANK2_uc003ibc.2_Intron	NM_001127493	NP_001120965			ankyrin 2 isoform 3						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	114034340	114034341	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114034340_114034341insT	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc003ibc.2_Intron|ANK2_uc011cgb.1_Intron	NM_001148	NP_001139			ankyrin 2 isoform 1						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114300948	114300948	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	114403434	114403434	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114403434delA	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)														---	---	---	---
CAMK2D	817	broad.mit.edu	37	4	114608018	114608019	+	Intron	DEL	AC	-	-	rs36009295		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114608018_114608019delAC	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)														---	---	---	---
NDST4	64579	broad.mit.edu	37	4	115843110	115843110	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115843110delT	uc003ibu.2	-						NDST4_uc010imw.2_Intron	NM_022569	NP_072091			heparan sulfate N-deacetylase/N-sulfotransferase							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			skin(3)|ovary(1)	4		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)														---	---	---	---
NDST4	64579	broad.mit.edu	37	4	115845613	115845613	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115845613delA	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	117092907	117092907	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117092907delT								None (None upstream) : MIR1973 (127974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117858906	117858907	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117858906_117858907delAG								MIR1973 (637982 upstream) : TRAM1L1 (145809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118024410	118024410	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118024410delA								TRAM1L1 (17674 upstream) : NDST3 (930363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118753529	118753529	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118753529delA								TRAM1L1 (746793 upstream) : NDST3 (201244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118815252	118815253	+	IGR	DEL	AA	-	-	rs34615819		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118815252_118815253delAA								TRAM1L1 (808516 upstream) : NDST3 (139520 downstream)																																			---	---	---	---
NDST3	9348	broad.mit.edu	37	4	119163441	119163441	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119163441delA	uc003ibx.2	+							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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	119308758	119308758	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119308758delT								PRSS12 (34836 upstream) : CEP170L (128737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	119428156	119428156	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119428156delT								PRSS12 (154234 upstream) : CEP170L (9339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	119802457	119802457	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119802457delA								SEC24D (42630 upstream) : SYNPO2 (7539 downstream)																																			---	---	---	---
MYOZ2	51778	broad.mit.edu	37	4	120057672	120057672	+	5'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120057672delA	uc003icp.3	+	2						NM_016599	NP_057683			myozenin 2								protein phosphatase 2B binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	122530722	122530723	+	IGR	DEL	AA	-	-	rs72231949		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122530722_122530723delAA								QRFPR (228541 upstream) : ANXA5 (58430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	122886585	122886585	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122886585delT								TRPC3 (13676 upstream) : KIAA1109 (205173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	123021935	123021936	+	IGR	DEL	AA	-	-	rs7680744	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123021935_123021936delAA								TRPC3 (149026 upstream) : KIAA1109 (69822 downstream)																																			---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123111049	123111049	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123111049delT	uc003ieh.2	+						KIAA1109_uc003iei.1_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123184541	123184541	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123184541delT	uc003ieh.2	+						KIAA1109_uc003iel.1_Intron|KIAA1109_uc003iek.2_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
SPATA5	166378	broad.mit.edu	37	4	123963490	123963491	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123963490_123963491delAG	uc003iez.3	+							NM_145207	NP_660208			spermatogenesis associated 5						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0																		---	---	---	---
LOC285419	285419	broad.mit.edu	37	4	124586901	124586902	+	RNA	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124586901_124586902delCA	uc003ifc.2	+	3		c.4176_4177delCA			LOC285419_uc011cgn.1_Intron					Homo sapiens mRNA; cDNA DKFZp686P12109 (from clone DKFZp686P12109).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	126145653	126145653	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126145653delA								ANKRD50 (511766 upstream) : FAT4 (91914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126699141	126699141	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126699141delA								MIR2054 (270679 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	127399326	127399327	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127399326_127399327insT								MIR2054 (970864 upstream) : None (None downstream)																																			---	---	---	---
C4orf29	80167	broad.mit.edu	37	4	128949558	128949558	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128949558delT	uc003ifr.2	+						C4orf29_uc003ifs.2_Intron|C4orf29_uc003ift.2_Intron|C4orf29_uc003ifu.2_Intron|C4orf29_uc010inz.2_Intron|C4orf29_uc003ifv.2_Intron	NM_001039717	NP_001034806			hypothetical protein LOC80167 precursor							extracellular region				ovary(1)	1																		---	---	---	---
LARP1B	55132	broad.mit.edu	37	4	129127627	129127627	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129127627delA	uc003iga.2	+	18	2485	c.2354delA	c.(2353-2355)GAAfs	p.E785fs	LARP1B_uc003igc.2_Frame_Shift_Del_p.E204fs|LARP1B_uc010ioa.1_RNA|LARP1B_uc003ige.2_Intron|LARP1B_uc003igd.2_RNA|LARP1B_uc003igf.2_Intron	NM_018078	NP_060548	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family member 2	785							RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	129516441	129516443	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129516441_129516443delTTT								PGRMC2 (307493 upstream) : PHF17 (214336 downstream)																																			---	---	---	---
PHF17	79960	broad.mit.edu	37	4	129796160	129796160	+	3'UTR	DEL	A	-	-	rs112076815		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129796160delA	uc003igk.2	+	11					PHF17_uc003igl.2_3'UTR|PHF17_uc011cgy.1_3'UTR	NM_199320	NP_955352			PHD finger protein 17 long isoform						apoptosis|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation|negative regulation of cell growth|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	histone acetyltransferase complex|mitochondrion	protein binding|zinc ion binding				0																		---	---	---	---
SCLT1	132320	broad.mit.edu	37	4	130014087	130014087	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130014087delT	uc003igp.2	-						C4orf33_uc010ioc.1_5'Flank|C4orf33_uc003igu.3_5'Flank|SCLT1_uc003igq.2_Intron|SCLT1_uc010iob.1_Intron|SCLT1_uc003igr.2_Intron|SCLT1_uc003igs.2_Intron|SCLT1_uc003igt.3_Intron	NM_144643	NP_653244			sodium channel associated protein 1							centrosome				ovary(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	131117144	131117145	+	IGR	DEL	AC	-	-	rs111692469		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131117144_131117145delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	132273471	132273472	+	IGR	INS	-	T	T	rs137947151	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132273471_132273472insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133374166	133374166	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133374166delC								None (None upstream) : PCDH10 (696304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133425111	133425111	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133425111delA								None (None upstream) : PCDH10 (645359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134418989	134418989	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134418989delA								PCDH10 (306258 upstream) : PABPC4L (698502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134572467	134572467	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134572467delT								PCDH10 (459736 upstream) : PABPC4L (545024 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135954267	135954267	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135954267delA								PABPC4L (831364 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136178122	136178122	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136178122delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136896659	136896659	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136896659delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	137494545	137494545	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137494545delC								None (None upstream) : PCDH18 (945531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	137816430	137816430	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137816430delT								None (None upstream) : PCDH18 (623646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138547743	138547744	+	IGR	DEL	GT	-	-	rs35581699		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138547743_138547744delGT								PCDH18 (94095 upstream) : SLC7A11 (537504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139905238	139905238	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139905238delT								SLC7A11 (741735 upstream) : CCRN4L (31705 downstream)																																			---	---	---	---
CCRN4L	25819	broad.mit.edu	37	4	139943612	139943612	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139943612delA	uc003ihl.2	+						CCRN4L_uc003ihk.1_Intron	NM_012118	NP_036250			CCR4 carbon catabolite repression 4-like						rhythmic process|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
CCRN4L	25819	broad.mit.edu	37	4	139961197	139961198	+	Intron	DEL	TT	-	-	rs151067690		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139961197_139961198delTT	uc003ihl.2	+						CCRN4L_uc003ihk.1_Intron	NM_012118	NP_036250			CCR4 carbon catabolite repression 4-like						rhythmic process|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
ELF2	1998	broad.mit.edu	37	4	139983329	139983330	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139983329_139983330delTT	uc003ihp.1	-						ELF2_uc003ihm.1_Intron|ELF2_uc003ihn.1_Intron|ELF2_uc003iho.1_Intron|ELF2_uc011chc.1_5'UTR	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	139985010	139985010	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139985010delA	uc003ihp.1	-						ELF2_uc003ihm.1_Intron|ELF2_uc003ihn.1_Intron|ELF2_uc003iho.1_Intron	NM_201999	NP_973728			E74-like factor 2 (ets domain transcription						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2	all_hematologic(180;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	142552686	142552686	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142552686delT								ZNF330 (396838 upstream) : IL15 (5068 downstream)																																			---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143439352	143439353	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143439352_143439353insA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	144232039	144232039	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144232039delA								USP38 (88899 upstream) : GAB1 (25944 downstream)																																			---	---	---	---
GAB1	2549	broad.mit.edu	37	4	144359094	144359094	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144359094delA	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)																	---	---	---	---
SMARCA5	8467	broad.mit.edu	37	4	144451491	144451491	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144451491delT	uc003ijg.2	+							NM_003601	NP_003592			SWI/SNF-related matrix-associated						CenH3-containing nucleosome assembly at centromere|nucleosome positioning|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	condensed chromosome|nucleolus|nucleoplasm|NURF complex|RSF complex	ATP binding|ATPase activity|DNA binding|helicase activity|nucleosome binding|protein binding			skin(1)	1	all_hematologic(180;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	144476723	144476723	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144476723delT								SMARCA5 (2157 upstream) : LOC441046 (3902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	144553964	144553964	+	IGR	DEL	A	-	-	rs72125581		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144553964delA								LOC441046 (64651 upstream) : GYPE (238056 downstream)																																			---	---	---	---
GYPE	2996	broad.mit.edu	37	4	144826695	144826695	+	5'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144826695delA	uc003ijj.2	-	1					GYPE_uc010ion.2_RNA|GYPE_uc003ijk.3_5'UTR	NM_198682	NP_941391			glycophorin E precursor							integral to plasma membrane					0	all_hematologic(180;0.158)																	---	---	---	---
HHIP	64399	broad.mit.edu	37	4	145581738	145581738	+	Intron	DEL	A	-	-	rs34167724		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145581738delA	uc003ijs.1	+							NM_022475	NP_071920			hedgehog-interacting protein precursor							cytoplasm|extracellular region	catalytic activity|protein binding|zinc ion binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	146257381	146257382	+	IGR	DEL	TT	-	-	rs113335939		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146257381_146257382delTT								OTUD4 (156549 upstream) : SMAD1 (145569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	146515107	146515108	+	IGR	INS	-	G	G	rs145979650	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146515107_146515108insG								SMAD1 (34784 upstream) : MMAA (25432 downstream)																																			---	---	---	---
ZNF827	152485	broad.mit.edu	37	4	146815097	146815097	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146815097delA	uc003ikn.2	-						ZNF827_uc003ikm.2_Intron|ZNF827_uc010iox.2_Intron	NM_178835	NP_849157			zinc finger protein 827						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	146868730	146868731	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146868730_146868731insT								ZNF827 (9123 upstream) : LSM6 (228104 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	147027696	147027698	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147027696_147027698delAAA								ZNF827 (168089 upstream) : LSM6 (69137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	147574884	147574884	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147574884delT								POU4F2 (11262 upstream) : TTC29 (53296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	147952592	147952592	+	IGR	DEL	A	-	-	rs71978927		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147952592delA								TTC29 (85558 upstream) : MIR548G (313189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	147962594	147962594	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147962594delA								TTC29 (95560 upstream) : MIR548G (303187 downstream)																																			---	---	---	---
ARHGAP10	79658	broad.mit.edu	37	4	148898805	148898805	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148898805delT	uc003ilf.2	+						ARHGAP10_uc003ilg.2_Intron|ARHGAP10_uc003ilh.2_Intron	NM_024605	NP_078881			Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)														---	---	---	---
NR3C2	4306	broad.mit.edu	37	4	149010806	149010806	+	Intron	DEL	T	-	-	rs36047772		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149010806delT	uc003ilj.3	-						NR3C2_uc003ilk.3_Intron|NR3C2_uc010iph.2_Intron	NM_000901	NP_000892			nuclear receptor subfamily 3, group C, member 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)													---	---	---	---
NR3C2	4306	broad.mit.edu	37	4	149135514	149135514	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149135514delT	uc003ilj.3	-						NR3C2_uc003ilk.3_Intron|NR3C2_uc010iph.2_Intron	NM_000901	NP_000892			nuclear receptor subfamily 3, group C, member 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	149542654	149542655	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149542654_149542655delAG								NR3C2 (179011 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150699083	150699083	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150699083delA	uc003ill.2	-											Homo sapiens cDNA clone IMAGE:5295442.																														---	---	---	---
DCLK2	166614	broad.mit.edu	37	4	151126044	151126044	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151126044delA	uc003ilm.3	+						DCLK2_uc003iln.3_Intron|DCLK2_uc003ilo.3_Intron|DCLK2_uc003ilp.3_Intron	NM_001040260	NP_001035350			doublecortin-like kinase 2 isoform a						intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)																	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151474221	151474221	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151474221delA	uc010ipj.2	-						LRBA_uc003ils.3_Intron|LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron	NM_006726	NP_006717			LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151677198	151677198	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151677198delA	uc010ipj.2	-						LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron	NM_006726	NP_006717			LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151789050	151789050	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151789050delA	uc010ipj.2	-						LRBA_uc003ilu.3_Intron	NM_006726	NP_006717			LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
SH3D19	152503	broad.mit.edu	37	4	152043156	152043156	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152043156delA	uc010ipl.1	-	21					SH3D19_uc003imb.2_3'UTR|SH3D19_uc003imc.2_3'UTR|SH3D19_uc003ime.2_3'UTR|SH3D19_uc010ipm.2_3'UTR	NM_001009555	NP_001009555			SH3 domain containing 19 isoform a						cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)|skin(1)	2	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)																---	---	---	---
SH3D19	152503	broad.mit.edu	37	4	152061073	152061073	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152061073delT	uc010ipl.1	-						SH3D19_uc003imb.2_Intron|SH3D19_uc003imc.2_Intron|SH3D19_uc003ime.2_Intron|SH3D19_uc010ipm.2_Intron	NM_001009555	NP_001009555			SH3 domain containing 19 isoform a						cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)|skin(1)	2	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)																---	---	---	---
FAM160A1	729830	broad.mit.edu	37	4	152512246	152512246	+	Intron	DEL	T	-	-	rs78064638		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152512246delT	uc003imj.2	+							NM_001109977	NP_001103447			hypothetical protein LOC729830												0																		---	---	---	---
PET112L	5188	broad.mit.edu	37	4	152665339	152665340	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152665339_152665340insA	uc003iml.2	-						PET112L_uc003imm.3_Intron	NM_004564	NP_004555			PET112-like precursor							mitochondrion	ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding				0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)			L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	153515040	153515040	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153515040delA								FBXW7 (58697 upstream) : TMEM154 (32231 downstream)																																			---	---	---	---
ARFIP1	27236	broad.mit.edu	37	4	153729139	153729139	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153729139delT	uc003imz.2	+						ARFIP1_uc003inb.2_Intron|ARFIP1_uc003ina.2_Intron|ARFIP1_uc003inc.2_Intron|ARFIP1_uc011cij.1_Intron	NM_001025595	NP_001020766			ADP-ribosylation factor interacting protein 1						intracellular protein transport|regulation of protein secretion	cytosol|Golgi membrane				ovary(1)	1	all_hematologic(180;0.093)																	---	---	---	---
FHDC1	85462	broad.mit.edu	37	4	153879459	153879459	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153879459delT	uc003inf.2	+							NM_033393	NP_203751			FH2 domain containing 1						actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	153971464	153971464	+	IGR	DEL	A	-	-	rs71598232		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153971464delA								FHDC1 (70616 upstream) : TRIM2 (102806 downstream)																																			---	---	---	---
KIAA0922	23240	broad.mit.edu	37	4	154542814	154542814	+	Intron	DEL	G	-	-	rs7663417	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154542814delG	uc003inm.3	+						KIAA0922_uc010ipp.2_Intron|KIAA0922_uc010ipq.2_Intron	NM_015196	NP_056011			hypothetical protein LOC23240 isoform 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
RNF175	285533	broad.mit.edu	37	4	154679927	154679927	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154679927delA	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	155180929	155180929	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155180929delA	uc003inw.2	-							NM_017639	NP_060109			dachsous 2 isoform 1						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	155455959	155455959	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155455959delT								DCHS2 (43029 upstream) : PLRG1 (1704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	155814559	155814559	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155814559delA								RBM46 (64595 upstream) : NPY2R (315222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	156417236	156417237	+	IGR	DEL	TT	-	-	rs111584751		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156417236_156417237delTT								MAP9 (119114 upstream) : GUCY1A3 (170625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	157248975	157248975	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157248975delT								CTSO (373927 upstream) : PDGFC (433789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	157435135	157435135	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157435135delT								CTSO (560087 upstream) : PDGFC (247629 downstream)																																			---	---	---	---
PDGFC	56034	broad.mit.edu	37	4	157844969	157844969	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157844969delA	uc003iph.1	-						PDGFC_uc003ipi.1_Intron|PDGFC_uc011cis.1_Intron	NM_016205	NP_057289			platelet-derived growth factor C precursor						central nervous system development|platelet-derived growth factor receptor signaling pathway|positive regulation of cell division|positive regulation of DNA replication|positive regulation of fibroblast proliferation|vascular endothelial growth factor receptor signaling pathway	endoplasmic reticulum lumen|extracellular space|Golgi membrane|nucleus	cell surface binding|growth factor activity|platelet-derived growth factor receptor binding|protein homodimerization activity			ovary(1)|lung(1)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	158110355	158110355	+	IGR	DEL	T	-	-	rs76715476		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158110355delT								GLRB (17113 upstream) : GRIA2 (30940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	158302140	158302140	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158302140delA								GRIA2 (14916 upstream) : LOC340017 (191502 downstream)																																			---	---	---	---
FNIP2	57600	broad.mit.edu	37	4	159754658	159754659	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159754658_159754659insC	uc003iqe.3	+						FNIP2_uc003iqd.2_Intron	NM_020840	NP_065891			folliculin interacting protein 2						DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)														---	---	---	---
FNIP2	57600	broad.mit.edu	37	4	159772218	159772218	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159772218delT	uc003iqe.3	+							NM_020840	NP_065891			folliculin interacting protein 2						DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	160112356	160112356	+	IGR	DEL	A	-	-	rs71993124		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160112356delA								C4orf45 (88251 upstream) : RAPGEF2 (76642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	160286111	160286111	+	IGR	DEL	A	-	-	rs11361032		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160286111delA								RAPGEF2 (4812 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	160309618	160309618	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160309618delA								RAPGEF2 (28319 upstream) : None (None downstream)																																			---	---	---	---
FSTL5	56884	broad.mit.edu	37	4	162686952	162686952	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162686952delT	uc003iqh.2	-						FSTL5_uc003iqi.2_Intron|FSTL5_uc010iqv.2_Intron	NM_020116	NP_064501			follistatin-like 5 isoform a							extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	164125743	164125743	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164125743delT								NAF1 (37670 upstream) : NPY1R (119374 downstream)																																			---	---	---	---
C4orf43	55319	broad.mit.edu	37	4	164436769	164436769	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164436769delT	uc003iqq.3	+							NM_018352	NP_060822			hypothetical protein LOC55319												0																		---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	164768665	164768665	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164768665delT	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)																---	---	---	---
KLHL2	11275	broad.mit.edu	37	4	166165210	166165210	+	Intron	DEL	T	-	-	rs35091242		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166165210delT	uc003irb.2	+						KLHL2_uc011cjm.1_Intron|KLHL2_uc003irc.2_Intron	NM_007246	NP_009177			kelch-like 2, Mayven isoform 1						intracellular protein transport	actin cytoskeleton|cytoplasm	actin binding|transporter activity				0	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	166750844	166750845	+	IGR	INS	-	A	A	rs146875922	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166750844_166750845insA								CPE (331363 upstream) : TLL1 (43565 downstream)																																			---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166794335	166794335	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166794335delT	uc003irh.1	+						TLL1_uc011cjn.1_5'Flank|TLL1_uc011cjo.1_5'Flank	NM_012464	NP_036596			tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	167235916	167235917	+	IGR	DEL	GT	-	-	rs111551355		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167235916_167235917delGT								TLL1 (210923 upstream) : SPOCK3 (418619 downstream)																																			---	---	---	---
SPOCK3	50859	broad.mit.edu	37	4	168136364	168136364	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168136364delG	uc003iri.1	-						SPOCK3_uc011cjp.1_Intron|SPOCK3_uc011cjq.1_Intron|SPOCK3_uc011cjr.1_Intron|SPOCK3_uc003irj.1_Intron|SPOCK3_uc011cjs.1_Intron|SPOCK3_uc011cjt.1_Intron|SPOCK3_uc011cju.1_Intron|SPOCK3_uc011cjv.1_Intron|SPOCK3_uc003irk.3_Intron|SPOCK3_uc011cjw.1_Intron	NM_016950	NP_058646			testican 3 isoform 2						signal transduction	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase inhibitor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	168549907	168549908	+	IGR	DEL	AG	-	-	rs61528664		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168549907_168549908delAG								SPOCK3 (394166 upstream) : ANXA10 (463799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	168649633	168649634	+	IGR	INS	-	TG	TG	rs146433088	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168649633_168649634insTG								SPOCK3 (493892 upstream) : ANXA10 (364073 downstream)																																			---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169213201	169213201	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169213201delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	169257239	169257239	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169257239delA								DDX60 (17281 upstream) : DDX60L (20648 downstream)																																			---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169572729	169572729	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169572729delT	uc011cjx.1	+						PALLD_uc003iru.2_Intron|PALLD_uc003irv.2_Intron	NM_016081	NP_057165			palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169674766	169674766	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169674766delA	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				---	---	---	---
SH3RF1	57630	broad.mit.edu	37	4	170142463	170142463	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170142463delA	uc003isa.1	-							NM_020870	NP_065921			SH3 domain containing ring finger 1							Golgi apparatus|lamellipodium|perinuclear region of cytoplasm	ligase activity|zinc ion binding			breast(2)|lung(1)	3		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)														---	---	---	---
NEK1	4750	broad.mit.edu	37	4	170381489	170381490	+	Intron	INS	-	A	A	rs113914665		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170381489_170381490insA	uc003isb.1	-						NEK1_uc003isc.1_Intron|NEK1_uc003isd.1_Intron|NEK1_uc003ise.1_Intron|NEK1_uc003isf.1_Intron	NM_012224	NP_036356			NIMA-related kinase 1						cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)														---	---	---	---
NEK1	4750	broad.mit.edu	37	4	170407266	170407266	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170407266delA	uc003isb.1	-						NEK1_uc003isc.1_Intron|NEK1_uc003isd.1_Intron|NEK1_uc003ise.1_Intron|NEK1_uc003isf.1_Intron	NM_012224	NP_036356			NIMA-related kinase 1						cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)														---	---	---	---
CLCN3	1182	broad.mit.edu	37	4	170613460	170613460	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170613460delA	uc003isi.2	+	7	1434	c.925delA	c.(925-927)AAAfs	p.K309fs	CLCN3_uc003ish.2_Frame_Shift_Del_p.K309fs|CLCN3_uc011cjz.1_Frame_Shift_Del_p.K292fs|CLCN3_uc011cka.1_Frame_Shift_Del_p.K309fs|CLCN3_uc003isj.1_Frame_Shift_Del_p.K282fs	NM_001829	NP_001820	P51790	CLCN3_HUMAN	chloride channel 3 isoform b	309					endosomal lumen acidification	cell surface|early endosome membrane|Golgi membrane|integral to membrane|late endosome membrane|transport vesicle membrane	antiporter activity|ATP binding|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity			breast(2)|ovary(1)	3		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	170800573	170800573	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170800573delT								C4orf27 (121480 upstream) : MFAP3L (107177 downstream)																																			---	---	---	---
AADAT	51166	broad.mit.edu	37	4	170994663	170994663	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170994663delT	uc003isr.2	-						AADAT_uc003iss.2_Intron|AADAT_uc003ist.2_Intron	NM_016228	NP_057312			kynurenine aminotransferase II						2-oxoglutarate metabolic process|biosynthetic process|glutamate metabolic process|lysine catabolic process	mitochondrial matrix	2-aminoadipate transaminase activity|kynurenine-oxoglutarate transaminase activity|protein homodimerization activity				0		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	171658246	171658247	+	IGR	INS	-	TA	TA	rs148595120	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171658246_171658247insTA								AADAT (646874 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	171680257	171680257	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171680257delT								AADAT (668885 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	172298864	172298867	+	IGR	DEL	ACAC	-	-	rs112676333		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172298864_172298867delACAC								None (None upstream) : GALNTL6 (435708 downstream)																																			---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173258708	173258708	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173258708delT	uc003isv.2	+							NM_001034845	NP_001030017			N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	174024010	174024010	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174024010delA								GALNTL6 (62454 upstream) : GALNT7 (65894 downstream)																																			---	---	---	---
GALNT7	51809	broad.mit.edu	37	4	174124255	174124255	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174124255delT	uc003isz.3	+							NM_017423	NP_059119			polypeptide N-acetylgalactosaminyltransferase 7						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)														---	---	---	---
GALNT7	51809	broad.mit.edu	37	4	174128103	174128103	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174128103delA	uc003isz.3	+							NM_017423	NP_059119			polypeptide N-acetylgalactosaminyltransferase 7						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	174440309	174440310	+	IGR	DEL	AC	-	-	rs3213920	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174440309_174440310delAC								SCRG1 (112781 upstream) : HAND2 (7342 downstream)																																			---	---	---	---
FBXO8	26269	broad.mit.edu	37	4	175173805	175173808	+	Intron	DEL	CACA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175173805_175173808delCACA	uc003itp.2	-						FBXO8_uc003itq.2_Intron	NM_012180	NP_036312			F-box only protein 8						regulation of ARF protein signal transduction|ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ARF guanyl-nucleotide exchange factor activity			breast(2)	2		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)														---	---	---	---
GLRA3	8001	broad.mit.edu	37	4	175568874	175568874	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175568874delA	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)													---	---	---	---
GLRA3	8001	broad.mit.edu	37	4	175666942	175666942	+	Intron	DEL	A	-	-	rs5864289		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175666942delA	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)													---	---	---	---
GLRA3	8001	broad.mit.edu	37	4	175737779	175737779	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175737779delT	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	175936681	175936682	+	IGR	INS	-	C	C	rs141226414	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175936681_175936682insC								ADAM29 (37351 upstream) : GPM6A (617407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	176510296	176510296	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176510296delT								ADAM29 (610966 upstream) : GPM6A (43793 downstream)																																			---	---	---	---
GPM6A	2823	broad.mit.edu	37	4	176556153	176556155	+	In_Frame_Del	DEL	CGG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176556153_176556155delCGG	uc003iuf.2	-	7	1542_1544	c.738_740delCCG	c.(736-741)TGCCGG>TGG	p.246_247CR>W	GPM6A_uc011ckj.1_In_Frame_Del_p.239_240CR>W|GPM6A_uc003iug.2_In_Frame_Del_p.246_247CR>W|GPM6A_uc003iuh.2_In_Frame_Del_p.235_236CR>W	NM_201591	NP_963885	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 2	246_247	Cytoplasmic (Potential).					cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)														---	---	---	---
GPM6A	2823	broad.mit.edu	37	4	176705879	176705880	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176705879_176705880delTG	uc003iuf.2	-						GPM6A_uc011ckj.1_Intron|GPM6A_uc003iug.2_Intron|GPM6A_uc003iuh.2_Intron	NM_201591	NP_963885			glycoprotein M6A isoform 2							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)														---	---	---	---
GPM6A	2823	broad.mit.edu	37	4	176838416	176838416	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176838416delT	uc003iug.2	-						GPM6A_uc003iuh.2_Intron	NM_005277	NP_005268			glycoprotein M6A isoform 1							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)														---	---	---	---
GPM6A	2823	broad.mit.edu	37	4	176914337	176914338	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176914337_176914338delTT	uc003iug.2	-						GPM6A_uc003iuh.2_Intron	NM_005277	NP_005268			glycoprotein M6A isoform 1							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)														---	---	---	---
WDR17	116966	broad.mit.edu	37	4	176991657	176991657	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176991657delT	uc003iuj.2	+						WDR17_uc003iuk.2_Intron|WDR17_uc003ium.3_Intron|WDR17_uc003iul.1_Intron	NM_170710	NP_733828			WD repeat domain 17 isoform 1											ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	178197489	178197489	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178197489delT								VEGFC (483594 upstream) : NEIL3 (33502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	178613555	178613555	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178613555delA								AGA (249964 upstream) : LOC285501 (36352 downstream)																																			---	---	---	---
LOC285501	285501	broad.mit.edu	37	4	178656363	178656363	+	Intron	DEL	G	-	-	rs11946475	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178656363delG	uc010iru.2	+							NR_028342				Homo sapiens cDNA clone IMAGE:4828874.												0		all_lung(41;6.03e-08)|Lung NSC(41;4.26e-07)|Breast(14;0.00066)|Melanoma(52;0.00168)|Prostate(90;0.0129)|all_hematologic(60;0.0202)|Renal(120;0.0246)|Colorectal(36;0.0508)|Hepatocellular(41;0.236)		all cancers(43;9.24e-25)|Epithelial(43;6.28e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.29e-10)|LUSC - Lung squamous cell carcinoma(1;2.61e-05)|Lung(1;3.22e-05)|GBM - Glioblastoma multiforme(59;0.000185)|Colorectal(24;0.000244)|STAD - Stomach adenocarcinoma(60;0.000777)|COAD - Colon adenocarcinoma(29;0.000884)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	179927026	179927026	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179927026delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180693182	180693182	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180693182delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181276458	181276458	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181276458delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181926523	181926523	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181926523delT								None (None upstream) : None (None downstream)																																			---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183300092	183300093	+	Intron	DEL	CT	-	-	rs35427117		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183300092_183300093delCT	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)														---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183594109	183594110	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183594109_183594110insT	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	184000888	184000888	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184000888delT								FAM92A3 (39617 upstream) : C4orf38 (17286 downstream)																																			---	---	---	---
WWC2	80014	broad.mit.edu	37	4	184196306	184196307	+	Intron	INS	-	TTTG	TTTG	rs150084376	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184196306_184196307insTTTG	uc010irx.2	+						WWC2_uc003ivk.3_Intron|WWC2_uc003ivl.3_Intron|WWC2_uc010iry.2_Intron|WWC2_uc003ivn.3_Intron|WWC2_uc010irz.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	184454331	184454331	+	IGR	DEL	A	-	-	rs35982917		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184454331delA								ING2 (22082 upstream) : RWDD4A (106458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184499269	184499269	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184499269delA								ING2 (67020 upstream) : RWDD4A (61520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184647423	184647423	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184647423delA								C4orf41 (12679 upstream) : STOX2 (179086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184782462	184782462	+	IGR	DEL	G	-	-	rs10709509		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184782462delG								C4orf41 (147718 upstream) : STOX2 (44047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	186040705	186040706	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186040705_186040706insT								HELT (98747 upstream) : SLC25A4 (23692 downstream)																																			---	---	---	---
KIAA1430	57587	broad.mit.edu	37	4	186097264	186097264	+	Intron	DEL	T	-	-	rs72151359		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186097264delT	uc003ixf.3	-						KIAA1430_uc003ixg.2_Intron	NM_020827	NP_065878			hypothetical protein LOC57587												0		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)														---	---	---	---
SNX25	83891	broad.mit.edu	37	4	186283364	186283364	+	Intron	DEL	A	-	-	rs78356496		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186283364delA	uc003ixh.2	+						SNX25_uc010ish.2_Intron|SNX25_uc003ixi.2_Intron	NM_031953	NP_114159			sorting nexin 25						cell communication|protein transport	endosome membrane	phosphatidylinositol binding|signal transducer activity			ovary(2)|breast(2)|pancreas(1)	5		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)														---	---	---	---
TLR3	7098	broad.mit.edu	37	4	186999946	186999946	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186999946delT	uc003iyq.2	+						TLR3_uc011ckz.1_5'Flank	NM_003265	NP_003256			toll-like receptor 3 precursor						activation of NF-kappaB-inducing kinase activity|cellular response to mechanical stimulus|defense response to bacterium|defense response to virus|detection of virus|hyperosmotic response|I-kappaB phosphorylation|inflammatory response|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of osteoclast differentiation|positive regulation of chemokine production|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-beta production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|toll-like receptor 3 signaling pathway	endoplasmic reticulum membrane|endosome membrane|integral to plasma membrane	double-stranded RNA binding|transmembrane receptor activity			ovary(2)|prostate(1)|lung(1)|breast(1)	5		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	187014089	187014101	+	IGR	DEL	GTAGGGTGCCGGG	-	-	rs35171749		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187014089_187014101delGTAGGGTGCCGGG								TLR3 (7839 upstream) : FAM149A (51114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	187247758	187247759	+	Intron	INS	-	TG	TG	rs147831490	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187247758_187247759insTG	uc003izb.1	-											Homo sapiens coagulation factor XI (plasma thromboplastin antecedent), mRNA (cDNA clone IMAGE:4831055).																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	187410965	187410965	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187410965delT	uc003izb.1	-						uc003izc.2_Intron					Homo sapiens coagulation factor XI (plasma thromboplastin antecedent), mRNA (cDNA clone IMAGE:4831055).																														---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187536345	187536346	+	Intron	INS	-	A	A	rs150156513	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187536345_187536346insA	uc003izf.2	-							NM_005245	NP_005236			FAT tumor suppressor 1 precursor						actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12															HNSCC(5;0.00058)			---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187558072	187558072	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187558072delT	uc003izf.2	-							NM_005245	NP_005236			FAT tumor suppressor 1 precursor						actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12															HNSCC(5;0.00058)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	187658459	187658459	+	IGR	DEL	A	-	-	rs35768677		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187658459delA								FAT1 (10609 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	188093452	188093452	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188093452delT								FAT1 (445602 upstream) : ZFP42 (823473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	188348319	188348320	+	IGR	INS	-	A	A	rs80257799		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188348319_188348320insA								FAT1 (700469 upstream) : ZFP42 (568605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189221140	189221140	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189221140delT								TRIML1 (152491 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189530541	189530541	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189530541delA								TRIML1 (461892 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189677233	189677234	+	IGR	DEL	TT	-	-	rs147949065		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189677233_189677234delTT								TRIML1 (608584 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189807572	189807572	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189807572delA								TRIML1 (738923 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190598155	190598156	+	IGR	DEL	CA	-	-	rs66488551		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190598155_190598156delCA								None (None upstream) : FRG1 (263818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190662128	190662129	+	IGR	INS	-	T	T	rs137993119		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190662128_190662129insT								None (None upstream) : FRG1 (199845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190832284	190832284	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190832284delG	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	190832285	190832286	+	Intron	DEL	GA	-	-	rs73876003		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190832285_190832286delGA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	190909754	190909763	+	IGR	DEL	GAGCCTGTGT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190909754_190909763delGAGCCTGTGT								TUBB4Q (3730 upstream) : LOC653545 (98803 downstream)																																			---	---	---	---
SLC9A3	6550	broad.mit.edu	37	5	517928	517931	+	Intron	DEL	CCAT	-	-	rs62641921		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:517928_517931delCCAT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	567558	567559	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:567558_567559delAG								SLC9A3 (43009 upstream) : CEP72 (44846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2115705	2115705	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2115705delA								IRX4 (232825 upstream) : IRX2 (630576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2391611	2391611	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2391611delA								IRX4 (508731 upstream) : IRX2 (354670 downstream)																																			---	---	---	---
C5orf38	153571	broad.mit.edu	37	5	2754689	2754693	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2754689_2754693delAAAAA	uc003jdc.2	+						C5orf38_uc011cmg.1_Intron|C5orf38_uc011cmh.1_Intron|C5orf38_uc011cmi.1_Intron|C5orf38_uc011cmj.1_Intron	NM_178569	NP_848664			hypothetical protein LOC153571 precursor							extracellular region					0				GBM - Glioblastoma multiforme(108;0.205)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	2855491	2855493	+	IGR	DEL	TTG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2855491_2855493delTTG								C5orf38 (99979 upstream) : IRX1 (740675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3759030	3759030	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3759030delT								IRX1 (157514 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4121841	4121841	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4121841delA								IRX1 (520325 upstream) : LOC340094 (912631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4219686	4219687	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4219686_4219687delAG								IRX1 (618170 upstream) : LOC340094 (814785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4363529	4363529	+	IGR	DEL	C	-	-	rs261117	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4363529delC								IRX1 (762013 upstream) : LOC340094 (670943 downstream)																																			---	---	---	---
KIAA0947	23379	broad.mit.edu	37	5	5456698	5456698	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5456698delT	uc003jdm.3	+							NM_015325	NP_056140			hypothetical protein LOC23379											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	5563934	5563934	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5563934delA								KIAA0947 (73597 upstream) : FLJ33360 (746620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6392962	6392963	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6392962_6392963delTC								MED10 (14323 upstream) : UBE2QL1 (55773 downstream)																																			---	---	---	---
NSUN2	54888	broad.mit.edu	37	5	6623244	6623245	+	Intron	INS	-	A	A	rs530375		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6623244_6623245insA	uc003jdu.2	-						NSUN2_uc003jdt.2_5'Flank|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	7071612	7071612	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7071612delT								PAPD7 (314451 upstream) : ADCY2 (324731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7371574	7371576	+	IGR	DEL	CAC	-	-	rs141667368		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7371574_7371576delCAC								PAPD7 (614413 upstream) : ADCY2 (24767 downstream)																																			---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7593918	7593918	+	Intron	DEL	A	-	-	rs151256440	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7593918delA	uc003jdz.1	+							NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7720130	7720131	+	Intron	INS	-	A	A	rs149175967	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7720130_7720131insA	uc003jdz.1	+						ADCY2_uc011cmo.1_Intron	NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
FASTKD3	79072	broad.mit.edu	37	5	7861239	7861239	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7861239delA	uc003jeb.2	-						FASTKD3_uc011cmp.1_Intron|FASTKD3_uc003jec.2_Intron	NM_024091	NP_076996			FAST kinase domains 3						apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(2)|breast(1)|pancreas(1)	4																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11101999	11102000	+	Intron	INS	-	TGTG	TGTG	rs10565465		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11101999_11102000insTGTG	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11728421	11728421	+	Intron	DEL	A	-	-	rs143669214		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11728421delA	uc003jfa.1	-						CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	12408501	12408501	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12408501delT								CTNND2 (504391 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13072145	13072145	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13072145delA								None (None upstream) : DNAH5 (618292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13252711	13252712	+	IGR	INS	-	AACAAC	AACAAC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13252711_13252712insAACAAC								None (None upstream) : DNAH5 (437725 downstream)																																			---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13701426	13701426	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13701426delA	uc003jfd.2	-	77	13500	c.13458delT	c.(13456-13458)TTTfs	p.F4486fs	DNAH5_uc003jfc.2_Frame_Shift_Del_p.F654fs	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4486					microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13725773	13725773	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13725773delT	uc003jfd.2	-						DNAH5_uc003jfc.2_Intron	NM_001369	NP_001360			dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13814977	13814977	+	Intron	DEL	A	-	-	rs116215381	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13814977delA	uc003jfd.2	-							NM_001369	NP_001360			dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14219956	14219956	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14219956delT	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14287249	14287249	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14287249delT	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14489275	14489275	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14508787	14508787	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14508787delA	uc003jff.2	+	57					TRIO_uc003jfg.2_RNA	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	14529710	14529710	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14529710delC								TRIO (20260 upstream) : FAM105A (52181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14949478	14949478	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14949478delC								ANKH (77591 upstream) : FBXL7 (550827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14961367	14961367	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14961367delT								ANKH (89480 upstream) : FBXL7 (538938 downstream)																																			---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15565200	15565200	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15565200delA	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15649807	15649807	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15649807delT	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15661018	15661018	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15661018delT	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15731701	15731701	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15731701delA	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																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16740995	16740995	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16740995delA	uc003jft.3	-						MYO10_uc011cnd.1_5'Flank|MYO10_uc011cne.1_Intron|MYO10_uc010itx.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16923403	16923403	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16923403delT	uc003jft.3	-						MYO10_uc003jfu.2_Intron|MYO10_uc003jfv.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	17350541	17350542	+	IGR	INS	-	T	T	rs10587019		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17350541_17350542insT								BASP1 (73606 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17415336	17415336	+	IGR	DEL	A	-	-	rs140363975	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17415336delA								BASP1 (138401 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18285031	18285031	+	IGR	DEL	A	-	-	rs2962173	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18285031delA								None (None upstream) : None (None downstream)																																			---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19633766	19633767	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19633766_19633767delTC	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19913791	19913791	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19913791delA	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	20078492	20078492	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20078492delA								CDH18 (90185 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20082244	20082244	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20082244delA								CDH18 (93937 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20444889	20444889	+	IGR	DEL	T	-	-	rs145488447		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20444889delT								CDH18 (456582 upstream) : GUSBP1 (897053 downstream)																																			---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21535549	21535549	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21535549delA	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	23441096	23441096	+	IGR	DEL	T	-	-	rs71609798		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23441096delT								CDH12 (587365 upstream) : PRDM9 (66628 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24328052	24328052	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24328052delT								PRDM9 (799348 upstream) : CDH10 (159158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24330489	24330489	+	IGR	DEL	A	-	-	rs67058611		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24330489delA								PRDM9 (801785 upstream) : CDH10 (156721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25179322	25179322	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25179322delT								CDH10 (534411 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25210744	25210744	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25210744delT								CDH10 (565833 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25409044	25409046	+	IGR	DEL	TTG	-	-	rs34061583		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25409044_25409046delTTG								CDH10 (764133 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	26344834	26344835	+	IGR	INS	-	TG	TG	rs139518347	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26344834_26344835insTG								None (None upstream) : CDH9 (535874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27650634	27650634	+	IGR	DEL	A	-	-	rs71605163		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27650634delA								CDH9 (611945 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28042638	28042639	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28042638_28042639insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29243622	29243622	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29243622delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29534986	29534986	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29534986delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30241490	30241490	+	IGR	DEL	A	-	-	rs78676042		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30241490delA								None (None upstream) : CDH6 (952306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30692687	30692687	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30692687delA								None (None upstream) : CDH6 (501109 downstream)																																			---	---	---	---
RNASEN	29102	broad.mit.edu	37	5	31429552	31429552	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31429552delA	uc003jhg.2	-						RNASEN_uc003jhh.2_Intron|RNASEN_uc003jhi.2_Intron	NM_013235	NP_037367			ribonuclease III, nuclear isoform 1						gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0																		---	---	---	---
RNASEN	29102	broad.mit.edu	37	5	31451753	31451753	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31451753delA	uc003jhg.2	-						RNASEN_uc003jhh.2_Intron|RNASEN_uc003jhi.2_Intron	NM_013235	NP_037367			ribonuclease III, nuclear isoform 1						gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0																		---	---	---	---
RNASEN	29102	broad.mit.edu	37	5	31498511	31498511	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31498511delA	uc003jhg.2	-						RNASEN_uc003jhh.2_Intron|RNASEN_uc003jhi.2_Intron|RNASEN_uc010iui.1_Intron	NM_013235	NP_037367			ribonuclease III, nuclear isoform 1						gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	31589828	31589829	+	IGR	INS	-	TGTTT	TGTTT	rs148640877	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31589828_31589829insTGTTT								C5orf22 (34664 upstream) : PDZD2 (49688 downstream)																																			---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31814768	31814768	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31814768delA	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31822566	31822566	+	Intron	DEL	C	-	-	rs16901599	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31822566delC	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31834763	31834763	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31834763delA	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31840576	31840577	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31840576_31840577delTT	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	32073714	32073714	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32073714delG	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc011cnx.1_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	32082132	32082132	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32082132delT	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	32190187	32190187	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32190187delA								GOLPH3 (15762 upstream) : MTMR12 (36925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32215928	32215928	+	IGR	DEL	A	-	-	rs111561049		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32215928delA								GOLPH3 (41503 upstream) : MTMR12 (11184 downstream)																																			---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32242341	32242341	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32242341delT	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	32816982	32816983	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32816982_32816983insA								C5orf23 (25163 upstream) : TARS (623819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	33090079	33090080	+	IGR	DEL	TT	-	-	rs112280481		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33090079_33090080delTT								C5orf23 (298260 upstream) : TARS (350722 downstream)																																			---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33641748	33641748	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33641748delT	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron	NM_030955	NP_112217			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9															HNSCC(64;0.19)			---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33668611	33668611	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33668611delT	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron	NM_030955	NP_112217			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9															HNSCC(64;0.19)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	33895193	33895193	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33895193delA								ADAMTS12 (3069 upstream) : RXFP3 (41298 downstream)																																			---	---	---	---
RAI14	26064	broad.mit.edu	37	5	34803784	34803784	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34803784delA	uc003jir.2	+						RAI14_uc010iur.2_Intron|RAI14_uc011coj.1_Intron|RAI14_uc010ius.1_Intron|RAI14_uc003jis.2_Intron|RAI14_uc003jit.2_Intron|RAI14_uc011cok.1_Intron	NM_015577	NP_056392			retinoic acid induced 14 isoform a							cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)																	---	---	---	---
TTC23L	153657	broad.mit.edu	37	5	34861084	34861084	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34861084delT	uc003jiu.2	+							NM_144725	NP_653326			tetratricopeptide repeat domain 23-like								binding			central_nervous_system(1)	1																		---	---	---	---
AGXT2	64902	broad.mit.edu	37	5	35008059	35008060	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35008059_35008060delTC	uc003jjf.2	-						AGXT2_uc003jje.1_Intron|AGXT2_uc011com.1_Intron	NM_031900	NP_114106			alanine-glyoxylate aminotransferase 2 precursor						glyoxylate metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	mitochondrial matrix	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity|alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(3)|skin(1)	4	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	35551701	35551701	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35551701delT								PRLR (320907 upstream) : SPEF2 (66288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	36469813	36469813	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36469813delA								RANBP3L (167802 upstream) : SLC1A3 (136644 downstream)																																			---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37111996	37111996	+	Intron	DEL	A	-	-	rs71761775		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37111996delA	uc011cpa.1	-						C5orf42_uc003jko.1_Intron|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	37120153	37120153	+	Intron	DEL	A	-	-	rs75040582	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37120153delA	uc011cpa.1	-						C5orf42_uc003jko.1_Intron|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	37176572	37176572	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37176572delA	uc011cpa.1	-						C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron|C5orf42_uc003jkr.1_5'Flank	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	37221411	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37221410_37221411delAA	uc011cpa.1	-							NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37223959	37223960	+	Intron	DEL	AA	-	-	rs76701099		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37223959_37223960delAA	uc011cpa.1	-							NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
NUP155	9631	broad.mit.edu	37	5	37340545	37340545	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37340545delA	uc003jku.1	-						NUP155_uc003jkt.1_Intron|NUP155_uc010iuz.1_Intron	NM_153485	NP_705618			nucleoporin 155kDa isoform 1						carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
NUP155	9631	broad.mit.edu	37	5	37351555	37351555	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37351555delT	uc003jku.1	-						NUP155_uc003jkt.1_Intron|NUP155_uc010iuz.1_Intron	NM_153485	NP_705618			nucleoporin 155kDa isoform 1						carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	37374761	37374762	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37374761_37374762delTT								NUP155 (3564 upstream) : WDR70 (4650 downstream)																																			---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37423465	37423465	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37423465delA	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37457207	37457207	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37457207delT	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	38207385	38207385	+	IGR	DEL	T	-	-	rs111369772		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38207385delT								GDNF (367603 upstream) : EGFLAM (51148 downstream)																																			---	---	---	---
EGFLAM	133584	broad.mit.edu	37	5	38451103	38451103	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38451103delA	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron|EGFLAM_uc003jle.1_Intron|EGFLAM_uc003jlf.1_Intron|EGFLAM_uc003jlg.1_Intron	NM_152403	NP_689616			EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	38631969	38631970	+	Intron	DEL	AT	-	-	rs327273		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38631969_38631970delAT	uc003jlj.2	+											Homo sapiens cDNA clone IMAGE:4829282.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	40056969	40056970	+	IGR	INS	-	CT	CT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40056969_40056970insCT								DAB2 (631634 upstream) : PTGER4 (623062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40109904	40109904	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40109904delA								DAB2 (684569 upstream) : PTGER4 (570128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40192438	40192438	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40192438delA								DAB2 (767103 upstream) : PTGER4 (487594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40426489	40426490	+	IGR	INS	-	A	A	rs71983179		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40426489_40426490insA								None (None upstream) : PTGER4 (253542 downstream)																																			---	---	---	---
PRKAA1	5562	broad.mit.edu	37	5	40800044	40800045	+	5'Flank	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40800044_40800045delAA	uc003jmc.2	-						PRKAA1_uc003jmb.2_5'Flank	NM_006251	NP_006242			protein kinase, AMP-activated, alpha 1 catalytic						activation of MAPK activity|cell cycle arrest|cholesterol biosynthetic process|fatty acid biosynthetic process|insulin receptor signaling pathway|negative regulation of glucosylceramide biosynthetic process|positive regulation of anti-apoptosis|positive regulation of cholesterol biosynthetic process|regulation of fatty acid oxidation|response to hypoxia	cytosol	ATP binding|cAMP-dependent protein kinase activity|metal ion binding|protein binding			breast(1)	1					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)													---	---	---	---
HEATR7B2	133558	broad.mit.edu	37	5	41011775	41011775	+	Intron	DEL	T	-	-	rs112390740		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41011775delT	uc003jmj.3	-						HEATR7B2_uc003jmi.3_Intron	NM_173489	NP_775760			HEAT repeat family member 7B2								binding			ovary(6)|central_nervous_system(2)	8																		---	---	---	---
HEATR7B2	133558	broad.mit.edu	37	5	41021327	41021328	+	Intron	DEL	TA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41021327_41021328delTA	uc003jmj.3	-						HEATR7B2_uc003jmi.3_Intron	NM_173489	NP_775760			HEAT repeat family member 7B2								binding			ovary(6)|central_nervous_system(2)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	41115843	41115843	+	IGR	DEL	T	-	-	rs34438179		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41115843delT								HEATR7B2 (44399 upstream) : C6 (26493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	41133673	41133673	+	IGR	DEL	A	-	-	rs76713366	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41133673delA								HEATR7B2 (62229 upstream) : C6 (8663 downstream)																																			---	---	---	---
C6	729	broad.mit.edu	37	5	41163266	41163266	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41163266delA	uc003jmk.2	-						C6_uc003jml.1_Intron	NM_000065	NP_000056			complement component 6 precursor						complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)																---	---	---	---
OXCT1	5019	broad.mit.edu	37	5	41840435	41840435	+	Intron	DEL	A	-	-	rs77659917		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41840435delA	uc003jmn.2	-							NM_000436	NP_000427			3-oxoacid CoA transferase 1 precursor						cellular lipid metabolic process|ketone body catabolic process	mitochondrial matrix	3-oxoacid CoA-transferase activity|protein homodimerization activity			ovary(2)|large_intestine(1)	3					Succinic acid(DB00139)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	42036330	42036330	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42036330delT								FBXO4 (94667 upstream) : GHR (387696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	42875977	42875977	+	IGR	DEL	T	-	-	rs113982678	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42875977delT								SEPP1 (49979 upstream) : C5orf39 (163206 downstream)																																			---	---	---	---
MGC42105	167359	broad.mit.edu	37	5	43273973	43273973	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43273973delT	uc003jno.2	+							NM_153361	NP_699192			serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9																		---	---	---	---
NNT	23530	broad.mit.edu	37	5	43607098	43607098	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43607098delT	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)													---	---	---	---
NNT	23530	broad.mit.edu	37	5	43651680	43651680	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43651680delA	uc003joe.2	+						NNT_uc003jof.2_Intron	NM_012343	NP_036475			nicotinamide nucleotide transhydrogenase						tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	43764706	43764706	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43764706delT								NNT (59039 upstream) : FGF10 (540391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	44051431	44051431	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44051431delT								NNT (345764 upstream) : FGF10 (253666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	44195047	44195048	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44195047_44195048insA								NNT (489380 upstream) : FGF10 (110049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	44228700	44228700	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44228700delA								NNT (523033 upstream) : FGF10 (76397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	44302221	44302221	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44302221delT								NNT (596554 upstream) : FGF10 (2876 downstream)																																			---	---	---	---
HCN1	348980	broad.mit.edu	37	5	45456158	45456158	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45456158delT	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	45848006	45848006	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45848006delT								HCN1 (151786 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	45893907	45893907	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45893907delG								HCN1 (197687 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	49440225	49440225	+	IGR	DEL	A	-	-	rs150430340		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49440225delA								None (None upstream) : EMB (251808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	49485338	49485338	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49485338delG								None (None upstream) : EMB (206695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51734422	51734422	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51734422delA								None (None upstream) : ITGA1 (349352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51932416	51932416	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51932416delA								None (None upstream) : ITGA1 (151358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	52490519	52490519	+	IGR	DEL	T	-	-	rs113700623		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52490519delT								MOCS2 (84921 upstream) : FST (286076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	52506998	52506998	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52506998delT								MOCS2 (101400 upstream) : FST (269597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	52507690	52507691	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52507690_52507691delTT								MOCS2 (102092 upstream) : FST (268904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	52729490	52729490	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52729490delA								MOCS2 (323892 upstream) : FST (47105 downstream)																																			---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53314037	53314038	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53314037_53314038insT	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960			ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)																---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53467775	53467775	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53467775delA	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	53866958	53866958	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53866958delT								SNX18 (24543 upstream) : ESM1 (406738 downstream)																																			---	---	---	---
GPX8	493869	broad.mit.edu	37	5	54460113	54460113	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54460113delT	uc003jpq.2	+	3					CDC20B_uc003jpn.1_Intron|CDC20B_uc010ivu.1_Intron|CDC20B_uc003jpo.1_Intron|CDC20B_uc010ivv.1_Intron|CDC20B_uc003jpp.2_Intron|GPX8_uc003jpr.2_3'UTR|GPX8_uc003jps.2_RNA|GPX8_uc003jpt.2_3'UTR	NM_001008397	NP_001008398			glutathione peroxidase 8						response to oxidative stress	integral to membrane	glutathione peroxidase activity				0					Glutathione(DB00143)													---	---	---	---
DHX29	54505	broad.mit.edu	37	5	54586202	54586202	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54586202delA	uc003jpx.2	-						DHX29_uc010ivw.2_Intron	NM_019030	NP_061903			DEAH (Asp-Glu-Ala-His) box polypeptide 29								ATP binding|ATP-dependent helicase activity|translation initiation factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	54886197	54886197	+	IGR	DEL	T	-	-	rs71600895		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54886197delT								PPAP2A (55324 upstream) : SLC38A9 (35479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	54887206	54887208	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54887206_54887208delAAA								PPAP2A (56333 upstream) : SLC38A9 (34468 downstream)																																			---	---	---	---
IL6ST	3572	broad.mit.edu	37	5	55240462	55240462	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55240462delT	uc003jqq.2	-						IL6ST_uc010iwb.2_Intron|IL6ST_uc010iwc.2_Intron|IL6ST_uc010iwd.2_Intron|IL6ST_uc011cqk.1_Intron|IL6ST_uc003jqr.2_Intron	NM_002184	NP_002175			interleukin 6 signal transducer isoform 1						interleukin-6-mediated signaling pathway|leukemia inhibitory factor signaling pathway|negative regulation of interleukin-6-mediated signaling pathway|positive regulation of anti-apoptosis|positive regulation of cardiac muscle hypertrophy|positive regulation of osteoblast differentiation|positive regulation of T cell proliferation|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation vascular endothelial growth factor production	ciliary neurotrophic factor receptor complex|extracellular region|extracellular space|interleukin-6 receptor complex|oncostatin-M receptor complex	ciliary neurotrophic factor receptor activity|ciliary neurotrophic factor receptor binding|growth factor binding|protein homodimerization activity			large_intestine(1)|ovary(1)	2		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)						O		hepatocellular ca								---	---	---	---
ANKRD55	79722	broad.mit.edu	37	5	55498145	55498145	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55498145delA	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	55835987	55835987	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55835987delT								ANKRD55 (306801 upstream) : MAP3K1 (274913 downstream)																																			---	---	---	---
MAP3K1	4214	broad.mit.edu	37	5	56114132	56114132	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56114132delA	uc003jqw.3	+							NM_005921	NP_005912			mitogen-activated protein kinase kinase kinase						cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	56695750	56695750	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56695750delT								GPBP1 (136340 upstream) : ACTBL2 (80094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57188584	57188585	+	IGR	INS	-	AAAT	AAAT	rs138503942	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57188584_57188585insAAAT								ACTBL2 (409948 upstream) : PLK2 (561227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57735669	57735670	+	IGR	INS	-	ACACACACAC	ACACACACAC	rs146960259	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57735669_57735670insACACACACAC								ACTBL2 (957033 upstream) : PLK2 (14142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	58159890	58159891	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58159890_58159891delTT								RAB3C (12485 upstream) : PDE4D (104975 downstream)																																			---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	58688161	58688162	+	Intron	INS	-	C	C	rs140929542	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58688161_58688162insC	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	59020412	59020412	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59020412delA	uc003jsa.2	-						PDE4D_uc003jry.2_Intron|PDE4D_uc003jrz.2_Intron|PDE4D_uc003jsb.2_Intron|PDE4D_uc003jsc.2_Intron	NM_001104631	NP_001098101			phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
ELOVL7	79993	broad.mit.edu	37	5	60051484	60051484	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60051484delA	uc003jsi.3	-						ELOVL7_uc011cqo.1_Intron|ELOVL7_uc010iwk.2_Intron|ELOVL7_uc003jsj.3_Intron	NM_024930	NP_079206			elongation of very long chain fatty acids-like						fatty acid elongation, polyunsaturated fatty acid|fatty acid elongation, saturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0		Lung NSC(810;2.56e-06)|Prostate(74;0.0115)|Breast(144;0.0244)|Ovarian(174;0.0481)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	60143482	60143483	+	IGR	INS	-	AG	AG	rs137956283	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60143482_60143483insAG								ELOVL7 (3381 upstream) : ERCC8 (26176 downstream)																																			---	---	---	---
ERCC8	1161	broad.mit.edu	37	5	60178797	60178798	+	Intron	INS	-	AC	AC	rs10550173		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60178797_60178798insAC	uc003jsm.3	-						ERCC8_uc003jsk.2_Intron|ERCC8_uc003jsl.3_Intron|ERCC8_uc011cqp.1_Intron	NM_000082	NP_000073			excision repair cross-complementing rodent						positive regulation of DNA repair|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein polyubiquitination|response to oxidative stress|response to UV|response to UV|transcription-coupled nucleotide-excision repair	Cul4A-RING ubiquitin ligase complex|nuclear matrix|nucleoplasm|nucleotide-excision repair complex|soluble fraction	protein binding|protein complex binding				0		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)											Direct_reversal_of_damage|NER					---	---	---	---
ZSWIM6	57688	broad.mit.edu	37	5	60676768	60676768	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60676768delA	uc003jsr.2	+							NM_020928	NP_065979			zinc finger, SWIM-type containing 6								zinc ion binding				0																		---	---	---	---
ZSWIM6	57688	broad.mit.edu	37	5	60839054	60839055	+	Intron	INS	-	T	T	rs143158409	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60839054_60839055insT	uc003jsr.2	+							NM_020928	NP_065979			zinc finger, SWIM-type containing 6								zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	61009525	61009525	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61009525delA								FLJ37543 (7163 upstream) : KIF2A (592464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61595782	61595782	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61595782delT								FLJ37543 (593420 upstream) : KIF2A (6207 downstream)																																			---	---	---	---
KIF2A	3796	broad.mit.edu	37	5	61648395	61648395	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61648395delT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron|KIF2A_uc010iwq.2_Intron	NM_004520	NP_004511			kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)														---	---	---	---
IPO11	51194	broad.mit.edu	37	5	61793846	61793847	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61793846_61793847delTT	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtb.1_Intron	NM_016338	NP_057422			Ran binding protein 11 isoform 2							cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)														---	---	---	---
IPO11	51194	broad.mit.edu	37	5	61817561	61817561	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61817561delT	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtd.1_Intron|IPO11_uc010iwr.2_Intron	NM_016338	NP_057422			Ran binding protein 11 isoform 2							cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)														---	---	---	---
IPO11	51194	broad.mit.edu	37	5	61853018	61853018	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61853018delT	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtd.1_Intron|IPO11_uc010iwr.2_Intron	NM_016338	NP_057422			Ran binding protein 11 isoform 2							cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)														---	---	---	---
SFRS12IP1	285672	broad.mit.edu	37	5	64027183	64027183	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64027183delA	uc003jtk.2	-							NM_173829	NP_776190			P18SRP protein						mRNA processing|RNA splicing		nucleic acid binding|zinc ion binding				0		Lung NSC(167;1.66e-05)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.119)														---	---	---	---
CWC27	10283	broad.mit.edu	37	5	64084762	64084763	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64084762_64084763insT	uc003jtn.1	+						CWC27_uc003jtl.2_Intron|CWC27_uc003jtm.2_Intron|CWC27_uc010iwt.1_Intron	NM_005869	NP_005860			serologically defined colon cancer antigen 10						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity				0																		---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64533913	64533914	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64533913_64533914delAA	uc003jtp.2	-						ADAMTS6_uc003jto.2_Intron|ADAMTS6_uc003jtq.2_Intron|ADAMTS6_uc003jtr.1_Intron	NM_197941	NP_922932			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	64798938	64798939	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64798938_64798939delTT								ADAMTS6 (21234 upstream) : CENPK (14655 downstream)																																			---	---	---	---
C5orf44	80006	broad.mit.edu	37	5	64954408	64954408	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64954408delT	uc003jtz.3	+						C5orf44_uc003jua.3_Intron|C5orf44_uc003juc.3_Intron|C5orf44_uc010iwv.2_Intron	NM_024941	NP_079217			hypothetical protein LOC80006 isoform 2											ovary(1)	1																		---	---	---	---
ERBB2IP	55914	broad.mit.edu	37	5	65286594	65286594	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65286594delT	uc003juk.1	+						ERBB2IP_uc003juh.1_Intron|ERBB2IP_uc003jui.1_Intron|ERBB2IP_uc003juj.1_Intron|ERBB2IP_uc011cqx.1_Intron|ERBB2IP_uc011cqy.1_Intron|ERBB2IP_uc011cqz.1_Intron|ERBB2IP_uc010iwx.1_Intron|ERBB2IP_uc003jul.1_Intron	NM_018695	NP_061165			ERBB2 interacting protein isoform 2						basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)	7		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	67463646	67463647	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67463646_67463647insA								CD180 (971029 upstream) : PIK3R1 (47957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67471374	67471375	+	IGR	DEL	AA	-	-	rs111715109		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67471374_67471375delAA								CD180 (978757 upstream) : PIK3R1 (40229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	68292057	68292058	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68292057_68292058delCA	uc003jvf.1	-											Homo sapiens cDNA FLJ46633 fis, clone TRACH2025705.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	68478977	68478978	+	Intron	DEL	TT	-	-	rs34718914		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68478977_68478978delTT	uc003jvn.1	-											Homo sapiens cDNA clone IMAGE:8327734.																														---	---	---	---
NAIP	4671	broad.mit.edu	37	5	70307058	70307058	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70307058delA	uc003kar.1	-						NAIP_uc003kat.1_Intron|NAIP_uc011crs.1_Intron|NAIP_uc003kas.1_Intron	NM_004536	NP_004527			NLR family, apoptosis inhibitory protein isoform						anti-apoptosis|apoptosis|nervous system development	basolateral plasma membrane|cytoplasm	caspase inhibitor activity|metal ion binding|nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)														---	---	---	---
NAIP	4671	broad.mit.edu	37	5	70343959	70343959	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70343959delA	uc003kat.1	-						GTF2H2_uc003kav.3_Intron|GTF2H2_uc003kau.3_Intron|GTF2H2_uc011crt.1_Intron	NM_022892	NP_075043			NLR family, apoptosis inhibitory protein isoform						anti-apoptosis|apoptosis|nervous system development	basolateral plasma membrane|cytoplasm	caspase inhibitor activity|metal ion binding|nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	71221671	71221672	+	IGR	INS	-	CA	CA	rs142857921	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71221671_71221672insCA								CARTPT (204799 upstream) : MAP1B (181446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	71249982	71249982	+	IGR	DEL	A	-	-	rs35187791		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71249982delA								CARTPT (233110 upstream) : MAP1B (153136 downstream)																																			---	---	---	---
MAP1B	4131	broad.mit.edu	37	5	71479405	71479405	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71479405delT	uc003kbw.3	+						MAP1B_uc010iyw.1_Intron|MAP1B_uc010iyx.1_Intron|MAP1B_uc010iyy.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)														---	---	---	---
FCHO2	115548	broad.mit.edu	37	5	72252724	72252724	+	Intron	DEL	T	-	-	rs74876091		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72252724delT	uc003kcl.2	+						FCHO2_uc011csl.1_Intron|FCHO2_uc011csk.1_Intron	NM_138782	NP_620137			FCH domain only 2 isoform a											ovary(1)	1		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	72637726	72637726	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72637726delA								TMEM174 (166758 upstream) : FOXD1 (104361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73265709	73265709	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73265709delA								RGNEF (28296 upstream) : ENC1 (657526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73275618	73275618	+	IGR	DEL	A	-	-	rs35732711		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73275618delA								RGNEF (38205 upstream) : ENC1 (647617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73346104	73346104	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73346104delT								RGNEF (108691 upstream) : ENC1 (577131 downstream)																																			---	---	---	---
HEXB	3074	broad.mit.edu	37	5	73965625	73965625	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73965625delA	uc003kdd.2	+							NM_000521	NP_000512			hexosaminidase B preproprotein						cell death	lysosome	cation binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	74379941	74379941	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74379941delA								GCNT4 (53217 upstream) : ANKRD31 (63121 downstream)																																			---	---	---	---
POLK	51426	broad.mit.edu	37	5	74872798	74872798	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74872798delA	uc003kdw.2	+						POLK_uc003kdx.2_Intron|POLK_uc003kdy.2_Intron|POLK_uc003kea.2_Intron|POLK_uc003keb.2_Intron|POLK_uc010izq.2_Intron|POLK_uc003kec.2_Intron|POLK_uc010izr.2_Intron|POLK_uc010izs.2_Intron|POLK_uc003ked.2_Intron|POLK_uc003kee.2_Intron|POLK_uc003kef.2_Intron	NM_016218	NP_057302			DNA-directed DNA polymerase kappa						DNA replication|nucleotide-excision repair, DNA gap filling	nucleus	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			ovary(2)|kidney(2)	4		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
Unknown	0	broad.mit.edu	37	5	75178615	75178615	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75178615delA								POC5 (165302 upstream) : SV2C (200690 downstream)																																			---	---	---	---
SV2C	22987	broad.mit.edu	37	5	75457904	75457904	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75457904delA	uc003kei.1	+							NM_014979	NP_055794			synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)														---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75876387	75876387	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75876387delT	uc003kek.2	+							NM_006633	NP_006624			IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)														---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75967514	75967519	+	Intron	DEL	GAAAAA	-	-	rs34357630		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75967514_75967519delGAAAAA	uc003kek.2	+						IQGAP2_uc010izv.2_Intron|IQGAP2_uc011csv.1_Intron|IQGAP2_uc003kel.2_Intron|IQGAP2_uc010izw.1_5'Flank	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)														---	---	---	---
LOC728723	728723	broad.mit.edu	37	5	76443008	76443008	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76443008delT	uc011csx.1	+						LOC728723_uc003key.2_Intron|LOC728723_uc003kez.2_Intron	NR_024398				Homo sapiens cDNA FLJ30582 fis, clone BRAWH2007308.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	76842129	76842129	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76842129delA								WDR41 (53797 upstream) : OTP (82409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	77178945	77178945	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77178945delT								TBCA (106760 upstream) : AP3B1 (119206 downstream)																																			---	---	---	---
AP3B1	8546	broad.mit.edu	37	5	77412439	77412439	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77412439delA	uc003kfj.2	-							NM_003664	NP_003655			adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)										Hermansky-Pudlak_syndrome				---	---	---	---
AP3B1	8546	broad.mit.edu	37	5	77458455	77458455	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77458455delA	uc003kfj.2	-							NM_003664	NP_003655			adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)										Hermansky-Pudlak_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	5	77966318	77966318	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77966318delA								LHFPL2 (21670 upstream) : ARSB (106721 downstream)																																			---	---	---	---
ARSB	411	broad.mit.edu	37	5	78155542	78155542	+	Intron	DEL	A	-	-	rs146734031		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78155542delA	uc003kfq.2	-						ARSB_uc003kfr.3_Intron	NM_000046	NP_000037			arylsulfatase B isoform 1 precursor						lysosomal transport|lysosome organization	lysosome	arylsulfatase activity|metal ion binding|N-acetylgalactosamine-4-sulfatase activity			upper_aerodigestive_tract(1)	1		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)														---	---	---	---
HOMER1	9456	broad.mit.edu	37	5	78750930	78750930	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78750930delT	uc003kfy.2	-						HOMER1_uc010jab.2_Intron|HOMER1_uc010jac.2_Intron|HOMER1_uc010jad.2_Intron	NM_004272	NP_004263			homer 1						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic density|postsynaptic membrane					0		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)														---	---	---	---
PAPD4	167153	broad.mit.edu	37	5	78936652	78936652	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78936652delT	uc010jae.1	+						PAPD4_uc003kgb.2_Intron|PAPD4_uc010jaf.1_Intron|PAPD4_uc003kga.2_Intron|PAPD4_uc003kfz.2_Intron	NM_001114393	NP_001107865			PAP associated domain containing 4						histone mRNA catabolic process|mRNA processing|RNA polyadenylation	cytoplasm	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity			ovary(1)	1		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)														---	---	---	---
CMYA5	202333	broad.mit.edu	37	5	79005412	79005413	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79005412_79005413delTT	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	79243824	79243824	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79243824delG								CMYA5 (147776 upstream) : MTX3 (28717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	79593200	79593200	+	IGR	DEL	T	-	-	rs34463055		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79593200delT								SERINC5 (41330 upstream) : LOC644936 (1719 downstream)																																			---	---	---	---
ZFYVE16	9765	broad.mit.edu	37	5	79765229	79765229	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79765229delA	uc003kgr.3	+						ZFYVE16_uc003kgq.3_Intron|ZFYVE16_uc003kgs.3_Intron|ZFYVE16_uc003kgt.3_Intron|ZFYVE16_uc003kgu.3_Intron	NM_001105251	NP_001098721			zinc finger, FYVE domain containing 16						BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|metal ion binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)														---	---	---	---
ZFYVE16	9765	broad.mit.edu	37	5	79773022	79773022	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79773022delT	uc003kgr.3	+						ZFYVE16_uc003kgq.3_Intron|ZFYVE16_uc003kgs.3_Intron|ZFYVE16_uc003kgt.3_Intron|ZFYVE16_uc003kgu.3_Intron	NM_001105251	NP_001098721			zinc finger, FYVE domain containing 16						BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|metal ion binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)														---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79837571	79837571	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79837571delA	uc003kgv.1	+	6	894	c.751delA	c.(751-753)AAAfs	p.K251fs	FAM151B_uc010jal.1_RNA	NM_205548	NP_991111	Q6UXP7	F151B_HUMAN	hypothetical protein LOC167555	251											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	80088494	80088494	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80088494delT	uc003kgz.2	+							NM_002439	NP_002430			mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)									MMR					---	---	---	---
Unknown	0	broad.mit.edu	37	5	80235217	80235218	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80235217_80235218delAA								MSH3 (62584 upstream) : RASGRF2 (21340 downstream)																																			---	---	---	---
ATG10	83734	broad.mit.edu	37	5	81460208	81460208	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81460208delT	uc003khs.2	+						ATG10_uc003khr.2_Intron|ATG10_uc010jas.2_Intron	NM_001131028	NP_001124500			APG10 autophagy 10-like						autophagy in response to ER overload|positive regulation of protein modification process|protein lipidation|protein modification by small protein conjugation|protein transport	cytoplasm	Atg12 ligase activity|protein binding				0		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)														---	---	---	---
ATG10	83734	broad.mit.edu	37	5	81516089	81516089	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81516089delT	uc003khs.2	+						ATG10_uc003khr.2_Intron|ATG10_uc010jas.2_Intron	NM_001131028	NP_001124500			APG10 autophagy 10-like						autophagy in response to ER overload|positive regulation of protein modification process|protein lipidation|protein modification by small protein conjugation|protein transport	cytoplasm	Atg12 ligase activity|protein binding				0		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	81709758	81709758	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81709758delT								ATP6AP1L (95612 upstream) : TMEM167A (638909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	81874764	81874764	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81874764delT								ATP6AP1L (260618 upstream) : TMEM167A (473903 downstream)																																			---	---	---	---
TMEM167A	153339	broad.mit.edu	37	5	82372898	82372898	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82372898delT	uc003khx.3	-						XRCC4_uc003kia.1_5'Flank|XRCC4_uc003kib.2_5'Flank|XRCC4_uc003kid.2_5'Flank|XRCC4_uc003kic.2_5'Flank|XRCC4_uc003kie.2_5'Flank	NM_174909	NP_777569			transmembrane protein 167A precursor							Golgi membrane|integral to membrane					0																		---	---	---	---
XRCC4	7518	broad.mit.edu	37	5	82549208	82549209	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82549208_82549209delTT	uc003kib.2	+						XRCC4_uc003kia.1_Intron|XRCC4_uc003kid.2_Intron|XRCC4_uc003kic.2_Intron|XRCC4_uc003kie.2_Intron|XRCC4_uc003kif.1_Intron|XRCC4_uc003kig.2_Intron	NM_022406	NP_071801			X-ray repair cross complementing protein 4						DNA ligation involved in DNA repair|double-strand break repair via nonhomologous end joining|initiation of viral infection|positive regulation of ligase activity|provirus integration|response to X-ray	cytosol|DNA ligase IV complex|DNA-dependent protein kinase-DNA ligase 4 complex|nucleoplasm	DNA binding|protein C-terminus binding			skin(3)	3		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)									NHEJ					---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82860501	82860502	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82860501_82860502delTT	uc003kii.3	+						VCAN_uc003kij.3_Intron|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Intron	NM_004385	NP_004376			versican isoform 1 precursor						cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	82888461	82888461	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82888461delT								VCAN (10339 upstream) : HAPLN1 (45557 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	83045562	83045562	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83045562delT								HAPLN1 (28666 upstream) : EDIL3 (192564 downstream)																																			---	---	---	---
EDIL3	10085	broad.mit.edu	37	5	83373673	83373673	+	Intron	DEL	T	-	-	rs143580509		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83373673delT	uc003kio.1	-						EDIL3_uc003kip.1_Intron|EDIL3_uc011ctt.1_Intron	NM_005711	NP_005702			EGF-like repeats and discoidin I-like						cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	84147708	84147709	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84147708_84147709delAC								EDIL3 (467097 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84580512	84580513	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84580512_84580513delTG								EDIL3 (899901 upstream) : NBPF22P (997749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	85363725	85363726	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85363725_85363726insA								None (None upstream) : NBPF22P (214536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	85654649	85654650	+	IGR	INS	-	TTCT	TTCT	rs140322552	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85654649_85654650insTTCT								NBPF22P (61287 upstream) : COX7C (259134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86560279	86560279	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86560279delA								COX7C (643698 upstream) : RASA1 (3872 downstream)																																			---	---	---	---
RASA1	5921	broad.mit.edu	37	5	86600723	86600723	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86600723delT	uc003kiw.2	+						RASA1_uc010jav.2_Intron|RASA1_uc003kix.2_Intron|RASA1_uc011ctv.1_Intron|RASA1_uc011ctw.1_Intron|RASA1_uc010jaw.2_Intron|RASA1_uc011ctu.1_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)														---	---	---	---
RASA1	5921	broad.mit.edu	37	5	86670198	86670198	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86670198delT	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)														---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87502325	87502328	+	Intron	DEL	GAAA	-	-	rs357515	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87502325_87502328delGAAA	uc003kjc.2	-						TMEM161B_uc011cty.1_Intron|TMEM161B_uc010jax.2_Intron|TMEM161B_uc011ctz.1_Intron|TMEM161B_uc011ctx.1_Intron	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	88860083	88860083	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88860083delA								MEF2C (660214 upstream) : CETN3 (829448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	89457959	89457959	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89457959delA								None (None upstream) : CETN3 (231572 downstream)																																			---	---	---	---
POLR3G	10622	broad.mit.edu	37	5	89791610	89791610	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89791610delT	uc003kjq.2	+						POLR3G_uc011cuc.1_Intron	NM_006467	NP_006458			polymerase (RNA) III (DNA directed) polypeptide						innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|regulation of transcription from RNA polymerase III promoter|response to virus	DNA-directed RNA polymerase III complex	DNA-directed RNA polymerase activity				0		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;2.74e-31)|Epithelial(54;8.2e-26)|all cancers(79;3.86e-22)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	89923350	89923350	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89923350delT	uc003kju.2	+	7	1091	c.995delT	c.(994-996)GTTfs	p.V332fs	GPR98_uc003kjt.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	332	Calx-beta 3.|Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	90510414	90510415	+	IGR	INS	-	G	G	rs141989852	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90510414_90510415insG								GPR98 (50382 upstream) : ARRDC3 (154126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	90573160	90573162	+	IGR	DEL	GAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90573160_90573162delGAG								GPR98 (113128 upstream) : ARRDC3 (91379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	90648756	90648756	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90648756delT								GPR98 (188724 upstream) : ARRDC3 (15785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	91235663	91235664	+	IGR	DEL	CA	-	-	rs72432484		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91235663_91235664delCA								LOC100129716 (519132 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	91886647	91886648	+	IGR	DEL	TA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91886647_91886648delTA								None (None upstream) : FLJ42709 (858417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	92662309	92662311	+	IGR	DEL	AAC	-	-	rs138884939	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92662309_92662311delAAC								None (None upstream) : FLJ42709 (82754 downstream)																																			---	---	---	---
FAM172A	83989	broad.mit.edu	37	5	93009088	93009088	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93009088delT	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron	NM_032042	NP_114431			hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0																		---	---	---	---
FAM172A	83989	broad.mit.edu	37	5	93120070	93120070	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93120070delA	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron	NM_032042	NP_114431			hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0																		---	---	---	---
FAM172A	83989	broad.mit.edu	37	5	93202694	93202694	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93202694delA	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																		---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94843635	94843635	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94843635delA	uc003klb.2	-							NM_014639	NP_055454			tetratricopeptide repeat domain 37								binding			ovary(3)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	96489821	96489821	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96489821delT								LIX1 (11301 upstream) : RIOK2 (6751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	96490931	96490931	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96490931delT								LIX1 (12411 upstream) : RIOK2 (5641 downstream)																																			---	---	---	---
RIOK2	55781	broad.mit.edu	37	5	96509055	96509055	+	Intron	DEL	G	-	-	rs316194	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96509055delG	uc003kmz.2	-						RIOK2_uc003kna.3_Intron	NM_018343	NP_060813			RIO kinase 2 isoform 1								ATP binding|protein serine/threonine kinase activity			kidney(1)	1		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)														---	---	---	---
RIOK2	55781	broad.mit.edu	37	5	96519187	96519187	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96519187delT	uc003kmz.2	-						RIOK2_uc003kna.3_5'Flank	NM_018343	NP_060813			RIO kinase 2 isoform 1								ATP binding|protein serine/threonine kinase activity			kidney(1)	1		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	96543659	96543660	+	IGR	DEL	AT	-	-	rs74986076	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96543659_96543660delAT								RIOK2 (24654 upstream) : None (None downstream)																																			---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98192527	98192527	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98192527delT	uc003knf.2	-						CHD1_uc010jbn.2_Intron	NM_001270	NP_001261			chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)													---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98199049	98199049	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98199049delA	uc003knf.2	-						CHD1_uc010jbn.2_Intron	NM_001270	NP_001261			chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)													---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98224946	98224946	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)													---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98232157	98232157	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98232157delA	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	98493894	98493894	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98493894delT								CHD1 (231656 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	98848630	98848630	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98848630delT								CHD1 (586392 upstream) : LOC100133050 (866579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	98950476	98950476	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98950476delA								CHD1 (688238 upstream) : LOC100133050 (764733 downstream)																																			---	---	---	---
FAM174A	345757	broad.mit.edu	37	5	99920582	99920582	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99920582delT	uc003knj.1	+							NM_198507	NP_940909			family with sequence similarity 174, member A							integral to membrane					0																		---	---	---	---
ST8SIA4	7903	broad.mit.edu	37	5	100172133	100172134	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100172133_100172134insT	uc003knk.2	-							NM_005668	NP_005659			ST8 alpha-N-acetyl-neuraminide						axon guidance|N-glycan processing	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			large_intestine(1)|central_nervous_system(1)	2		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	100306105	100306105	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100306105delT								ST8SIA4 (67118 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	100309161	100309161	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100309161delA								ST8SIA4 (70174 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	100420199	100420200	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100420199_100420200delTT								ST8SIA4 (181212 upstream) : None (None downstream)																																			---	---	---	---
SLCO4C1	353189	broad.mit.edu	37	5	101600665	101600665	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101600665delT	uc003knm.2	-							NM_180991	NP_851322			solute carrier organic anion transporter family,						cell differentiation|multicellular organismal development|sodium-independent organic anion transport|spermatogenesis	basolateral plasma membrane|integral to membrane	sodium-independent organic anion transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	4		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)														---	---	---	---
SLCO6A1	133482	broad.mit.edu	37	5	101748695	101748695	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101748695delT	uc003knn.2	-	9	1797	c.1625delA	c.(1624-1626)AAGfs	p.K542fs	SLCO6A1_uc003kno.2_Frame_Shift_Del_p.K289fs|SLCO6A1_uc003knp.2_Frame_Shift_Del_p.K542fs|SLCO6A1_uc003knq.2_Frame_Shift_Del_p.K480fs	NM_173488	NP_775759	Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family,	542	Extracellular (Potential).|Kazal-like.					integral to membrane|plasma membrane	transporter activity			ovary(3)|skin(3)|central_nervous_system(1)	7		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)														---	---	---	---
PPIP5K2	23262	broad.mit.edu	37	5	102495068	102495069	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102495068_102495069delAC	uc003kod.3	+						PPIP5K2_uc011cva.1_Intron|PPIP5K2_uc003koe.2_Intron	NM_015216	NP_056031			Histidine acid phosphatase domain containing 1						inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity			ovary(1)|skin(1)	2																		---	---	---	---
PPIP5K2	23262	broad.mit.edu	37	5	102537309	102537309	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102537309delA	uc003kod.3	+	31	4225	c.3706delA	c.(3706-3708)AAAfs	p.K1236fs	PPIP5K2_uc011cva.1_RNA|PPIP5K2_uc003koe.2_Frame_Shift_Del_p.K1215fs|PPIP5K2_uc003kof.2_Frame_Shift_Del_p.K418fs	NM_015216	NP_056031	O43314	VIP2_HUMAN	Histidine acid phosphatase domain containing 1	1236					inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	103047568	103047568	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103047568delT								NUDT12 (149078 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	103273066	103273066	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103273066delT								NUDT12 (374576 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	104471139	104471148	+	IGR	DEL	TTGGACTAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104471139_104471148delTTGGACTAAA								RAB9BP1 (35341 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	104650163	104650164	+	IGR	INS	-	GT	GT	rs142087413	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104650163_104650164insGT								RAB9BP1 (214365 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105287050	105287051	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105287050_105287051delTT								RAB9BP1 (851252 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105608829	105608829	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105608829delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106405765	106405765	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106405765delT								None (None upstream) : EFNA5 (306826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106649259	106649259	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106649259delA								None (None upstream) : EFNA5 (63332 downstream)																																			---	---	---	---
EFNA5	1946	broad.mit.edu	37	5	106795078	106795078	+	Intron	DEL	A	-	-	rs28707470		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106795078delA	uc003kol.2	-						EFNA5_uc010jbr.1_Intron	NM_001962	NP_001953			ephrin-A5 precursor						cell-cell signaling	anchored to plasma membrane|caveola|extracellular space	ephrin receptor binding				0		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	107023652	107023652	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107023652delA								EFNA5 (17056 upstream) : FBXL17 (171088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	107062549	107062549	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107062549delT								EFNA5 (55953 upstream) : FBXL17 (132191 downstream)																																			---	---	---	---
FER	2241	broad.mit.edu	37	5	108096639	108096639	+	Intron	DEL	T	-	-	rs142231392		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108096639delT	uc003kop.1	+						FER_uc011cve.1_Intron|FER_uc011cvf.1_Intron|FER_uc003koq.2_Intron|FER_uc011cvg.1_Intron	NM_005246	NP_005237			fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	108558487	108558487	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108558487delT								FER (35114 upstream) : PJA2 (111924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	108952553	108952553	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108952553delC								PJA2 (206878 upstream) : MAN2A1 (72603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	109377092	109377092	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109377092delT								MAN2A1 (173663 upstream) : TMEM232 (247842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	109405621	109405621	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109405621delT								MAN2A1 (202192 upstream) : TMEM232 (219313 downstream)																																			---	---	---	---
WDR36	134430	broad.mit.edu	37	5	110438541	110438542	+	Intron	DEL	TT	-	-	rs72280165		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110438541_110438542delTT	uc003kpd.2	+						WDR36_uc010jbu.2_Intron	NM_139281	NP_644810			WD repeat domain 36						response to stimulus|rRNA processing|visual perception	small-subunit processome				ovary(1)|skin(1)	2		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)														---	---	---	---
CAMK4	814	broad.mit.edu	37	5	110734783	110734783	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110734783delA	uc011cvj.1	+						CAMK4_uc003kpf.2_Intron|CAMK4_uc010jbv.2_Intron	NM_001744	NP_001735			calcium/calmodulin-dependent protein kinase IV						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission	cytosol|nucleoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(3)|lung(2)	5		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	110975299	110975299	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110975299delC								STARD4 (127066 upstream) : C5orf13 (23024 downstream)																																			---	---	---	---
SRP19	6728	broad.mit.edu	37	5	112206173	112206173	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112206173delA	uc011cvv.1	+						SRP19_uc011cvu.1_Intron					SubName: Full=Zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2;						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|mitochondrion|nucleolus|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding				0		all_cancers(142;0.00328)|all_epithelial(76;6.39e-05)|Prostate(80;0.00174)|Colorectal(10;0.00372)|Ovarian(225;0.156)		Epithelial(69;1.7e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.17e-08)|all cancers(49;3.96e-07)|Colorectal(14;0.0056)|COAD - Colon adenocarcinoma(37;0.0104)														---	---	---	---
MCC	4163	broad.mit.edu	37	5	112640707	112640707	+	Intron	DEL	A	-	-	rs146743749		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112640707delA	uc003kql.3	-						MCC_uc003kqk.3_Intron	NM_001085377	NP_001078846			mutated in colorectal cancers isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)														---	---	---	---
MCC	4163	broad.mit.edu	37	5	112753241	112753242	+	Intron	INS	-	A	A	rs145249839	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112753241_112753242insA	uc003kql.3	-							NM_001085377	NP_001078846			mutated in colorectal cancers isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	113946327	113946327	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113946327delA	uc003kqr.1	-											Homo sapiens cDNA FLJ40367 fis, clone TESTI2034785.																														---	---	---	---
COMMD10	51397	broad.mit.edu	37	5	115553612	115553612	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115553612delA	uc003krt.1	+							NM_016144	NP_057228			COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)														---	---	---	---
SEMA6A	57556	broad.mit.edu	37	5	115822384	115822384	+	Intron	DEL	C	-	-	rs2287684	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115822384delC	uc010jck.2	-						SEMA6A_uc003krx.3_Intron	NM_020796	NP_065847			sema domain, transmembrane domain (TM), and						apoptosis|axon guidance|cell surface receptor linked signaling pathway|cytoskeleton organization|organ morphogenesis	axon|integral to membrane|plasma membrane	receptor activity			ovary(2)	2		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)														---	---	---	---
SEMA6A	57556	broad.mit.edu	37	5	115868456	115868456	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115868456delA	uc010jck.2	-						SEMA6A_uc003krx.3_Intron	NM_020796	NP_065847			sema domain, transmembrane domain (TM), and						apoptosis|axon guidance|cell surface receptor linked signaling pathway|cytoskeleton organization|organ morphogenesis	axon|integral to membrane|plasma membrane	receptor activity			ovary(2)	2		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	118103288	118103291	+	IGR	DEL	AAAC	-	-	rs113798912		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118103288_118103291delAAAC								None (None upstream) : DTWD2 (69280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	118120791	118120792	+	IGR	INS	-	G	G	rs143943779	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118120791_118120792insG								None (None upstream) : DTWD2 (51779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	119336656	119336656	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119336656delA								FAM170A (365140 upstream) : PRR16 (463363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	119684073	119684073	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119684073delT								FAM170A (712557 upstream) : PRR16 (115946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121203571	121203572	+	IGR	DEL	AA	-	-	rs149896827		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121203571_121203572delAA								FTMT (15050 upstream) : SRFBP1 (94084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121369712	121369712	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121369712delT								SRFBP1 (5417 upstream) : LOX (30451 downstream)																																			---	---	---	---
SNX24	28966	broad.mit.edu	37	5	122183510	122183510	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122183510delT	uc011cwo.1	+						SNX24_uc003ktf.2_Intron|SNX24_uc010jcy.2_Intron	NM_014035	NP_054754			SBBI31 protein						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	123007515	123007515	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123007515delA								CSNK1G3 (55053 upstream) : ZNF608 (965095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123923696	123923697	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123923696_123923697delCA								CSNK1G3 (971234 upstream) : ZNF608 (48913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124393773	124393773	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124393773delT								ZNF608 (309273 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124511074	124511074	+	IGR	DEL	A	-	-	rs145445633		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124511074delA								ZNF608 (426574 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124536217	124536217	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124536217delC								ZNF608 (451717 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124592858	124592859	+	IGR	INS	-	A	A	rs149679457	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124592858_124592859insA								ZNF608 (508358 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124665743	124665743	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124665743delA								ZNF608 (581243 upstream) : None (None downstream)																																			---	---	---	---
C5orf48	389320	broad.mit.edu	37	5	125967084	125967084	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125967084delT	uc003kub.1	+							NM_207408	NP_997291			hypothetical protein LOC389320											ovary(1)	1																		---	---	---	---
MEGF10	84466	broad.mit.edu	37	5	126688369	126688369	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126688369delA	uc003kuh.3	+						MEGF10_uc010jdc.1_Intron|MEGF10_uc010jdd.1_Intron|MEGF10_uc003kui.3_Intron	NM_032446	NP_115822			multiple EGF-like-domains 10 precursor						cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	128285838	128285838	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128285838delA								FBN2 (411922 upstream) : SLC27A6 (15372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	129160363	129160364	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129160363_129160364delAA								ADAMTS19 (85987 upstream) : CHSY3 (80159 downstream)																																			---	---	---	---
CHSY3	337876	broad.mit.edu	37	5	129515021	129515022	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129515021_129515022insT	uc003kvd.2	+							NM_175856	NP_787052			chondroitin sulfate synthase 3							Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	129549029	129549029	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129549029delT								CHSY3 (26703 upstream) : HINT1 (945846 downstream)																																			---	---	---	---
HINT1	3094	broad.mit.edu	37	5	130499279	130499279	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130499279delT	uc003kve.3	-						HINT1_uc011cxd.1_Intron|HINT1_uc003kvf.3_Intron	NM_005340	NP_005331			histidine triad nucleotide binding protein 1						signal transduction	cytoplasm|cytoskeleton|nucleus	hydrolase activity|protein kinase C binding				0		all_cancers(142;0.0452)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Adenosine monophosphate(DB00131)													---	---	---	---
CDC42SE2	56990	broad.mit.edu	37	5	130611500	130611500	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130611500delT	uc003kvh.2	+						CDC42SE2_uc003kvi.2_Intron|CDC42SE2_uc003kvj.2_Intron|CDC42SE2_uc003kvk.2_Intron	NM_020240	NP_064625			CDC42 small effector 2						phagocytosis|regulation of cell shape|regulation of signal transduction	cell projection|cytoplasm|cytoskeleton|phagocytic cup	protein binding|structural molecule activity				0		all_cancers(142;0.0525)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	131099782	131099782	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131099782delT	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron|FNIP1_uc010jdm.1_Intron|FNIP1_uc003kvu.2_Intron	NM_016340	NP_057424			PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)														---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	131100921	131100921	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131100921delA	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)														---	---	---	---
ACSL6	23305	broad.mit.edu	37	5	131163732	131163732	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131163732delA	uc003kvv.1	-							NM_015256				acyl-CoA synthetase long-chain family member 6						fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane|plasma membrane	ATP binding|long-chain fatty acid-CoA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	131486604	131486604	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131486604delT								CSF2 (74746 upstream) : P4HA2 (41702 downstream)																																			---	---	---	---
RAD50	10111	broad.mit.edu	37	5	131917557	131917557	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131917557delT	uc003kxi.2	+						RAD50_uc003kxh.2_Intron	NM_005732	NP_005723			RAD50 homolog isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase	Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm	ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)										Homologous_recombination					---	---	---	---
Unknown	0	broad.mit.edu	37	5	131980467	131980468	+	IGR	INS	-	T	T	rs138734472	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131980467_131980468insT								RAD50 (874 upstream) : IL13 (13397 downstream)																																			---	---	---	---
AFF4	27125	broad.mit.edu	37	5	132256819	132256820	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132256819_132256820delAA	uc003kyd.2	-						AFF4_uc011cxk.1_Intron|AFF4_uc003kye.1_Intron	NM_014423	NP_055238			ALL1 fused gene from 5q31						transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	132374960	132374960	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132374960delT								ZCCHC10 (12720 upstream) : HSPA4 (12702 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	132380127	132380127	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132380127delA								ZCCHC10 (17887 upstream) : HSPA4 (7535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	133172817	133172817	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133172817delT								FSTL4 (224594 upstream) : C5orf15 (118382 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	133759104	133759104	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133759104delA								CDKN2AIPNL (11515 upstream) : PHF15 (100962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	133932776	133932777	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133932776_133932777delAC								PHF15 (13858 upstream) : SAR1B (9343 downstream)																																			---	---	---	---
DDX46	9879	broad.mit.edu	37	5	134138998	134138998	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134138998delT	uc003kzw.2	+						DDX46_uc003kzv.1_Intron	NM_014829	NP_055644			DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	134486350	134486350	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134486350delC	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	135154784	135154784	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135154784delA								LOC340074 (165160 upstream) : LOC153328 (15581 downstream)																																			---	---	---	---
TRPC7	57113	broad.mit.edu	37	5	135675528	135675530	+	Intron	DEL	CAA	-	-	rs144226582		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135675528_135675530delCAA	uc003lbn.1	-						TRPC7_uc010jef.1_Intron|TRPC7_uc010jeg.1_Intron|TRPC7_uc010jeh.1_Intron|TRPC7_uc010jei.1_Intron|TRPC7_uc010jej.1_Intron	NM_020389	NP_065122			transient receptor potential cation channel,						axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	136292514	136292514	+	IGR	DEL	A	-	-	rs76738475		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136292514delA								TRPC7 (599441 upstream) : SPOCK1 (18474 downstream)																																			---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136394759	136394759	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136394759delA	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	136410383	136410385	+	Intron	DEL	TTG	-	-	rs71845125		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136410383_136410385delTTG	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	136602435	136602436	+	Intron	INS	-	T	T	rs66506051		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136602435_136602436insT	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589			sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
KLHL3	26249	broad.mit.edu	37	5	136976422	136976423	+	Intron	INS	-	C	C	rs147867543	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136976422_136976423insC	uc010jek.2	-						KLHL3_uc011cyc.1_Intron|KLHL3_uc003lbr.3_Intron|KLHL3_uc011cyd.1_Intron|KLHL3_uc010jel.1_Intron|KLHL3_uc010jem.1_Intron	NM_017415	NP_059111			kelch-like 3							cytoplasm|cytoskeleton	actin binding|structural molecule activity				0		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)														---	---	---	---
BRD8	10902	broad.mit.edu	37	5	137431938	137431938	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137431938delA	uc003lcc.1	-							NM_001164326				bromodomain containing 8 isoform 4						cell surface receptor linked signaling pathway|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription from RNA polymerase II promoter	mitochondrion|NuA4 histone acetyltransferase complex	sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
NME5	8382	broad.mit.edu	37	5	137451461	137451461	+	Intron	DEL	A	-	-	rs76717490		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137451461delA	uc003lce.2	-						BRD8_uc003lcc.1_Intron	NM_003551	NP_003542			non-metastatic cells 5, protein expressed in						anti-apoptosis|CTP biosynthetic process|GTP biosynthetic process|multicellular organismal development|spermatid development|UTP biosynthetic process		ATP binding|nucleoside diphosphate kinase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
KDM3B	51780	broad.mit.edu	37	5	137735915	137735915	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137735915delG	uc003lcy.1	+						KDM3B_uc010jew.1_Intron|KDM3B_uc011cys.1_Intron	NM_016604	NP_057688			jumonji domain containing 1B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11																		---	---	---	---
CTNNA1	1495	broad.mit.edu	37	5	138150911	138150911	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138150911delT	uc003ldh.2	+						CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron	NM_001903	NP_001894			catenin, alpha 1						adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
MATR3	9782	broad.mit.edu	37	5	138624336	138624337	+	Intron	INS	-	T	T	rs76794804		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138624336_138624337insT	uc003ldu.2	+						MATR3_uc003lds.2_Intron|MATR3_uc010jfb.2_Intron|MATR3_uc003ldt.2_Intron	NM_199189	NP_954659			matrin 3							nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
CXXC5	51523	broad.mit.edu	37	5	139049332	139049333	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139049332_139049333delAC	uc010jfg.1	+						CXXC5_uc003let.2_Intron	NM_016463	NP_057547			CXXC finger 5						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|nucleus	DNA binding|signal transducer activity|zinc ion binding			central_nervous_system(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	139124233	139124234	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139124233_139124234delAC								CXXC5 (61553 upstream) : PSD2 (51172 downstream)																																			---	---	---	---
PSD2	84249	broad.mit.edu	37	5	139184149	139184150	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139184149_139184150insT	uc003leu.1	+							NM_032289	NP_115665			pleckstrin and Sec7 domain containing 2						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	139447828	139447828	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139447828delA								NRG2 (24949 upstream) : PURA (45880 downstream)																																			---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139841755	139841755	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139841755delT	uc003lfs.1	+						ANKHD1_uc003lfq.1_Intron|ANKHD1_uc003lfr.2_Intron|ANKHD1_uc003lft.1_Intron|ANKHD1_uc003lfu.1_Intron|ANKHD1_uc003lfp.2_Intron|ANKHD1_uc003lfo.2_Intron|ANKHD1_uc010jfk.2_Intron	NM_020690	NP_065741			ANKHD1-EIF4EBP3 protein							cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139917263	139917263	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139917263delA	uc003lfs.1	+						ANKHD1_uc003lfr.2_Intron|ANKHD1-EIF4EBP3_uc011czh.1_Intron|ANKHD1_uc003lfw.2_Intron|ANKHD1_uc010jfl.2_Intron|ANKHD1-EIF4EBP3_uc003lfx.1_Intron	NM_020690	NP_065741			ANKHD1-EIF4EBP3 protein							cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	139995719	139995720	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139995719_139995720insA								SLC35A4 (47036 upstream) : CD14 (15597 downstream)																																			---	---	---	---
ZMAT2	153527	broad.mit.edu	37	5	140083649	140083649	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140083649delT	uc003lgy.1	+							NM_144723	NP_653324			zinc finger, matrin type 2							nucleus	DNA binding|zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	140127378	140127379	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140127378_140127379delTT								VTRNA1-3 (21547 upstream) : PCDHA1 (38497 downstream)																																			---	---	---	---
PCDHGA10	56106	broad.mit.edu	37	5	140812926	140812929	+	Intron	DEL	CTAT	-	-	rs72463976		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140812926_140812929delCTAT	uc003lkl.1	+						PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron	NM_018913	NP_061736			protocadherin gamma subfamily A, 10 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDH1	5097	broad.mit.edu	37	5	141249270	141249270	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141249270delC	uc003llq.2	-						PCDH1_uc003llp.2_Intron|PCDH1_uc011dbf.1_5'Flank	NM_002587	NP_002578			protocadherin 1 isoform 1 precursor						cell-cell signaling|homophilic cell adhesion|nervous system development	cell-cell junction|integral to plasma membrane	calcium ion binding			ovary(5)	5		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	141278765	141278766	+	IGR	DEL	TT	-	-	rs112182037		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141278765_141278766delTT								PCDH1 (20821 upstream) : KIAA0141 (24619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	142085827	142085827	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142085827delA								FGF1 (8192 upstream) : ARHGAP26 (64465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	143102435	143102436	+	IGR	INS	-	TT	TT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143102435_143102436insTT								NR3C1 (287358 upstream) : HMHB1 (89290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	143371774	143371774	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143371774delA								HMHB1 (171492 upstream) : YIPF5 (165957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	144247610	144247611	+	IGR	DEL	AA	-	-	rs67044212		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144247610_144247611delAA								KCTD16 (390666 upstream) : PRELID2 (890971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	144355311	144355311	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144355311delG								KCTD16 (498367 upstream) : PRELID2 (783271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	144702743	144702746	+	IGR	DEL	AAAA	-	-	rs35238834		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144702743_144702746delAAAA								KCTD16 (845799 upstream) : PRELID2 (435836 downstream)																																			---	---	---	---
LARS	51520	broad.mit.edu	37	5	145537471	145537472	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145537471_145537472insT	uc003lnx.1	-						LARS_uc011dbq.1_Intron|LARS_uc011dbr.1_Intron|LARS_uc011dbs.1_Intron	NM_020117	NP_064502			leucyl-tRNA synthetase						leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)													---	---	---	---
DPYSL3	1809	broad.mit.edu	37	5	146810073	146810073	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146810073delA	uc003lon.1	-						DPYSL3_uc003loo.2_Intron	NM_001387	NP_001378			dihydropyrimidinase-like 3						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol|growth cone	dihydropyrimidinase activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	146945198	146945198	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146945198delG	uc003lop.1	+											Homo sapiens cDNA FLJ14672 fis, clone NT2RP2003687.																														---	---	---	---
JAKMIP2	9832	broad.mit.edu	37	5	147110012	147110012	+	Intron	DEL	T	-	-	rs78808956		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147110012delT	uc003loq.1	-						JAKMIP2_uc011dbx.1_Intron|JAKMIP2_uc003lor.1_Intron	NM_014790	NP_055605			janus kinase and microtubule interacting protein							Golgi apparatus				large_intestine(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	147320312	147320313	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147320312_147320313insT								C5orf46 (34211 upstream) : SPINK5 (123222 downstream)																																			---	---	---	---
SPINK5	11005	broad.mit.edu	37	5	147475261	147475261	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147475261delT	uc003lox.2	+						SPINK5_uc010jgq.1_Intron|SPINK5_uc010jgs.1_Intron|SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837			serine peptidase inhibitor, Kazal type 5 isoform						anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
SPINK5	11005	broad.mit.edu	37	5	147486959	147486959	+	Intron	DEL	T	-	-	rs11951425		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147486959delT	uc003lox.2	+						SPINK5_uc010jgs.1_Intron|SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837			serine peptidase inhibitor, Kazal type 5 isoform						anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
HTR4	3360	broad.mit.edu	37	5	147902626	147902626	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147902626delA	uc003lpn.2	-						HTR4_uc010jgu.1_Intron|HTR4_uc003lpi.1_Intron|HTR4_uc003lpj.1_Intron|HTR4_uc003lpk.2_Intron|HTR4_uc011dby.1_Intron|HTR4_uc003lpl.2_Intron|HTR4_uc003lpm.2_Intron|HTR4_uc010jgv.2_Intron|HTR4_uc003lpo.1_Intron	NM_000870	NP_000861			serotonin 5-HT4 receptor isoform b						G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)													---	---	---	---
HTR4	3360	broad.mit.edu	37	5	148012575	148012575	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148012575delA	uc003lpn.2	-						HTR4_uc010jgu.1_Intron|HTR4_uc003lpi.1_Intron|HTR4_uc003lpj.1_Intron|HTR4_uc003lpk.2_Intron|HTR4_uc011dby.1_Intron|HTR4_uc003lpl.2_Intron|HTR4_uc003lpm.2_Intron|HTR4_uc010jgv.2_Intron|HTR4_uc003lpo.1_Intron|SH3TC2_uc003lpp.1_Intron|HTR4_uc003lpq.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	148847977	148847980	+	IGR	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148847977_148847980delAAAA								LOC728264 (35578 upstream) : CSNK1A1 (24969 downstream)																																			---	---	---	---
PDE6A	5145	broad.mit.edu	37	5	149319497	149319497	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149319497delA	uc003lrg.3	-							NM_000440	NP_000431			phosphodiesterase 6A						cytosolic calcium ion homeostasis|GMP metabolic process|platelet activation|signal transduction|visual perception	cytosol|plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)															---	---	---	---
HMGXB3	22993	broad.mit.edu	37	5	149422814	149422814	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149422814delA	uc003lrk.3	+							NM_014983	NP_055798			HMG box domain containing 3							nucleus	DNA binding|kinase activity			kidney(1)|central_nervous_system(1)	2																		---	---	---	---
CD74	972	broad.mit.edu	37	5	149793944	149793944	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149793944delA	uc003lsc.2	-						CD74_uc003lse.2_5'Flank|CD74_uc003lsd.2_5'Flank|CD74_uc003lsf.1_5'Flank	NM_001025159	NP_001020330			CD74 antigen isoform a						antigen processing and presentation of endogenous antigen|cell proliferation|immunoglobulin mediated immune response|intracellular protein transport|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of peptide secretion|positive regulation of B cell proliferation|positive regulation of chemokine (C-X-C motif) ligand 2 production|positive regulation of cytokine-mediated signaling pathway|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|positive regulation of macrophage cytokine production|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation|prostaglandin biosynthetic process|protein complex assembly|regulation of macrophage activation	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|lysosome|receptor complex	beta-amyloid binding|cytokine receptor activity|identical protein binding|MHC class II protein binding			breast(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)					T	ROS1	NSCLC								---	---	---	---
GM2A	2760	broad.mit.edu	37	5	150800814	150800814	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150800814delT	uc011dcs.1	+							NM_000405				GM2 ganglioside activator precursor							lysosome|nucleolus	sphingolipid activator protein activity				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
GLRA1	2741	broad.mit.edu	37	5	151262284	151262284	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151262284delT	uc003lut.2	-						GLRA1_uc003lur.2_Intron|GLRA1_uc003lus.2_Intron	NM_001146040	NP_001139512			glycine receptor, alpha 1 isoform 1 precursor						muscle contraction|negative regulation of transmission of nerve impulse|neuropeptide signaling pathway|positive regulation of acrosome reaction|regulation of membrane potential|startle response	cell junction|chloride channel complex|integral to plasma membrane|intracellular membrane-bounded organelle|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|protein binding|receptor activity|taurine binding|transmitter-gated ion channel activity			ovary(1)|central_nervous_system(1)	2		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	151868105	151868105	+	IGR	DEL	C	-	-	rs13354964	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151868105delC								NMUR2 (83265 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	152425844	152425845	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152425844_152425845delAA								NMUR2 (641004 upstream) : GRIA1 (443330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	152586274	152586277	+	IGR	DEL	TTTG	-	-	rs79365267		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152586274_152586277delTTTG								NMUR2 (801434 upstream) : GRIA1 (282898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	152630780	152630782	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152630780_152630782delTTT								NMUR2 (845940 upstream) : GRIA1 (238393 downstream)																																			---	---	---	---
GALNT10	55568	broad.mit.edu	37	5	153576919	153576919	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153576919delC	uc003lvh.2	+						GALNT10_uc003lvg.1_Intron|GALNT10_uc010jic.2_Intron	NM_198321	NP_938080			GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)													OREG0016966	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
LARP1	23367	broad.mit.edu	37	5	154113728	154113728	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154113728delA	uc003lvo.2	+							NM_015315	NP_056130			la related protein isoform 1								protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
LARP1	23367	broad.mit.edu	37	5	154153610	154153612	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154153610_154153612delTTT	uc003lvp.2	+						LARP1_uc003lvo.2_Intron|LARP1_uc010jie.1_Intron	NM_033551	NP_291029			la related protein isoform 2								protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
GEMIN5	25929	broad.mit.edu	37	5	154292720	154292720	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154292720delT	uc003lvx.3	-						GEMIN5_uc011ddk.1_Intron	NM_015465	NP_056280			gemin 5						ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
GEMIN5	25929	broad.mit.edu	37	5	154293377	154293377	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154293377delA	uc003lvx.3	-						GEMIN5_uc011ddk.1_Intron	NM_015465	NP_056280			gemin 5						ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
KIF4B	285643	broad.mit.edu	37	5	154395578	154395580	+	In_Frame_Del	DEL	AAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154395578_154395580delAAC	uc010jih.1	+	1	2319_2321	c.2159_2161delAAC	c.(2158-2163)AAACAA>AAA	p.Q721del		NM_001099293	NP_001092763	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	721	Interaction with PRC1 (By similarity).|Potential.				axon guidance|blood coagulation|microtubule-based movement	cytosol|microtubule|nuclear matrix	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155654598	155654598	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155654598delT	uc003lwa.1	+							NM_172244	NP_758447			delta-sarcoglycan isoform 2						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155935513	155935514	+	Intron	DEL	AA	-	-	rs111768881		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155935513_155935514delAA	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681			delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	156333517	156333517	+	IGR	DEL	T	-	-	rs75046319		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156333517delT								PPP1R2P3 (53978 upstream) : TIMD4 (12776 downstream)																																			---	---	---	---
CYFIP2	26999	broad.mit.edu	37	5	156734644	156734645	+	Intron	INS	-	GTGTGTGTGT	GTGTGTGTGT	rs144622623	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156734644_156734645insGTGTGTGTGT	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron	NM_001037333	NP_001032410			cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
ADAM19	8728	broad.mit.edu	37	5	156994809	156994809	+	Intron	DEL	A	-	-	rs112813107		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156994809delA	uc003lwz.2	-						ADAM19_uc003lww.1_Intron|ADAM19_uc011ddr.1_Intron	NM_033274	NP_150377			ADAM metallopeptidase domain 19 preproprotein						proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	157305145	157305146	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157305145_157305146delTT								CLINT1 (18977 upstream) : EBF1 (817778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	157635794	157635797	+	IGR	DEL	AGTG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157635794_157635797delAGTG								CLINT1 (349626 upstream) : EBF1 (487127 downstream)																																			---	---	---	---
EBF1	1879	broad.mit.edu	37	5	158308027	158308027	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158308027delA	uc010jip.2	-						EBF1_uc011ddw.1_Intron|EBF1_uc011ddx.1_Intron|EBF1_uc003lxl.3_Intron	NM_024007	NP_076870			early B-cell factor						multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)					T	HMGA2	lipoma								---	---	---	---
RNF145	153830	broad.mit.edu	37	5	158616908	158616908	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158616908delG	uc003lxp.2	-						RNF145_uc011ddy.1_Intron|RNF145_uc003lxo.1_Intron|RNF145_uc011ddz.1_Intron|RNF145_uc010jiq.1_Intron|RNF145_uc011dea.1_Intron	NM_144726	NP_653327			ring finger protein 145							integral to membrane	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	158953827	158953834	+	IGR	DEL	ACACACAC	-	-	rs10528924		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158953827_158953834delACACACAC								LOC285627 (60543 upstream) : ADRA1B (389906 downstream)																																			---	---	---	---
FABP6	2172	broad.mit.edu	37	5	159650441	159650441	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159650441delT	uc003lxx.1	+						FABP6_uc003lxz.1_Intron	NM_001130958	NP_001124430			gastrotropin isoform 1						bile acid and bile salt transport|bile acid metabolic process|negative regulation of cell proliferation	cytosol	transporter activity				0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
SLU7	10569	broad.mit.edu	37	5	159842415	159842415	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159842415delT	uc003lyg.2	-						SLU7_uc003lyh.1_Intron|SLU7_uc003lyi.1_Intron	NM_006425	NP_006416			step II splicing factor SLU7						alternative nuclear mRNA splicing, via spliceosome|nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|cytoplasm|nuclear speck|small nuclear ribonucleoprotein complex	pre-mRNA 3'-splice site binding|second spliceosomal transesterification activity|zinc ion binding			ovary(1)	1	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	159905116	159905116	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159905116delA	uc003lyl.3	+											Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 2005635.																														---	---	---	---
GABRB2	2561	broad.mit.edu	37	5	160875638	160875638	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160875638delT	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron	NM_021911	NP_068711			gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	161937790	161937790	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161937790delA								GABRG2 (355246 upstream) : CCNG1 (926787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	161943101	161943101	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161943101delT								GABRG2 (360557 upstream) : CCNG1 (921476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163027270	163027270	+	IGR	DEL	T	-	-	rs66739629		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163027270delT								MAT2B (80937 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163201512	163201512	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163201512delT								MAT2B (255179 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164013172	164013172	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164013172delA	uc003lzn.2	+											Homo sapiens, clone IMAGE:4479080, mRNA, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	164379996	164379996	+	IGR	DEL	T	-	-	rs148925267		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164379996delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164859940	164859943	+	IGR	DEL	TTTT	-	-	rs34057925		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164859940_164859943delTTTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165449501	165449501	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165449501delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165456894	165456894	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165456894delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165688908	165688910	+	IGR	DEL	AAC	-	-	rs6859158		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165688908_165688910delAAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165873985	165873985	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165873985delC								None (None upstream) : ODZ2 (837858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166096694	166096694	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166096694delT								None (None upstream) : ODZ2 (615149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166240590	166240590	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166240590delA								None (None upstream) : ODZ2 (471253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166327307	166327308	+	IGR	INS	-	AGG	AGG	rs145009687	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166327307_166327308insAGG								None (None upstream) : ODZ2 (384535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166569029	166569029	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166569029delG								None (None upstream) : ODZ2 (142814 downstream)																																			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167200734	167200734	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167200734delT	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
WWC1	23286	broad.mit.edu	37	5	167727379	167727379	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167727379delG	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron	NM_015238	NP_056053			WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	167975040	167975041	+	IGR	INS	-	AC	AC	rs144636603	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167975040_167975041insAC								FBLL1 (17402 upstream) : PANK3 (7589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	168740120	168740120	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168740120delA								SLIT3 (11987 upstream) : CCDC99 (270518 downstream)																																			---	---	---	---
CCDC99	54908	broad.mit.edu	37	5	169015404	169015404	+	5'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169015404delA	uc003mae.3	+	2					CCDC99_uc010jjj.2_5'UTR|CCDC99_uc011deq.1_5'UTR|CCDC99_uc010jjk.2_5'UTR	NM_017785	NP_060255			coiled-coil domain containing 99						cell division|establishment of mitotic spindle orientation|mitotic metaphase plate congression|mitotic prometaphase|protein localization to kinetochore	condensed chromosome outer kinetochore|cytosol|microtubule organizing center|nucleus|spindle pole	kinetochore binding|protein binding			ovary(1)|liver(1)	2	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
GABRP	2568	broad.mit.edu	37	5	170235947	170235947	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170235947delT	uc003mau.2	+						GABRP_uc011dev.1_Intron	NM_014211	NP_055026			gamma-aminobutyric acid (GABA) A receptor, pi							cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			breast(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
RANBP17	64901	broad.mit.edu	37	5	170371072	170371072	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170371072delT	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								---	---	---	---
Unknown	0	broad.mit.edu	37	5	170789991	170789992	+	IGR	INS	-	TG	TG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170789991_170789992insTG								TLX3 (50854 upstream) : NPM1 (24128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	170793009	170793009	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170793009delA								TLX3 (53872 upstream) : NPM1 (21111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	171057977	171057977	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171057977delT								FGF18 (173815 upstream) : FBXW11 (230579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	171269239	171269239	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171269239delC								FGF18 (385077 upstream) : FBXW11 (19317 downstream)																																			---	---	---	---
STK10	6793	broad.mit.edu	37	5	171585286	171585287	+	Intron	INS	-	A	A	rs142254144	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171585286_171585287insA	uc003mbo.1	-							NM_005990	NP_005981			serine/threonine kinase 10								ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
SH3PXD2B	285590	broad.mit.edu	37	5	171862756	171862757	+	Intron	DEL	TA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171862756_171862757delTA	uc003mbr.2	-						SH3PXD2B_uc003mbs.1_Intron	NM_001017995	NP_001017995			SH3 and PX domains 2B						adipose tissue development|bone development|cell communication|cell differentiation|eye development|heart development|podosome assembly	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-5-phosphate binding|SH2 domain binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	172255399	172255400	+	IGR	INS	-	C	C	rs144424687		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172255399_172255400insC								DUSP1 (57196 upstream) : ERGIC1 (5823 downstream)																																			---	---	---	---
ATP6V0E1	8992	broad.mit.edu	37	5	172410147	172410147	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172410147delT	uc003mcd.1	+							NM_003945	NP_003936			ATPase, H+ transporting, lysosomal 9kDa, V0						ATP hydrolysis coupled proton transport|cell growth|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport|vacuolar acidification	endosome membrane|integral to membrane|membrane fraction|proton-transporting V-type ATPase, V0 domain|vacuole	proton-transporting ATPase activity, rotational mechanism				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	172470014	172470014	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172470014delT								ATP6V0E1 (8114 upstream) : C5orf41 (13356 downstream)																																			---	---	---	---
C5orf41	153222	broad.mit.edu	37	5	172484816	172484817	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172484816_172484817delTT	uc003mch.2	+						C5orf41_uc003mcg.2_Intron|C5orf41_uc003mcf.2_Intron|C5orf41_uc011dfd.1_Intron	NM_153607	NP_705835			luman-recruiting factor								protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
C5orf41	153222	broad.mit.edu	37	5	172532229	172532230	+	Intron	DEL	TG	-	-	rs113596042		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172532229_172532230delTG	uc003mch.2	+						C5orf41_uc011dfd.1_Intron	NM_153607	NP_705835			luman-recruiting factor								protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
C5orf41	153222	broad.mit.edu	37	5	172538285	172538285	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172538285delT	uc003mch.2	+						C5orf41_uc011dfd.1_Intron	NM_153607	NP_705835			luman-recruiting factor								protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
BNIP1	662	broad.mit.edu	37	5	172587243	172587244	+	Intron	DEL	TT	-	-	rs10693152		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172587243_172587244delTT	uc003mcj.3	+						BNIP1_uc003mci.3_Intron|BNIP1_uc003mck.3_Intron|BNIP1_uc003mcl.3_Intron	NM_001205	NP_001196			BCL2/adenovirus E1B 19kD interacting protein 1						anti-apoptosis|apoptosis|endoplasmic reticulum membrane fusion|endoplasmic reticulum organization|induction of apoptosis|vesicle-mediated transport	integral to endoplasmic reticulum membrane|nuclear envelope|SNARE complex	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
CPEB4	80315	broad.mit.edu	37	5	173316671	173316671	+	5'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173316671delA	uc003mcs.3	+	1					CPEB4_uc010jju.1_5'UTR|CPEB4_uc010jjv.2_5'UTR|CPEB4_uc011dfg.1_5'UTR	NM_030627	NP_085130			cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	174074922	174074924	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174074922_174074924delAAA								HMP19 (538741 upstream) : MSX2 (76651 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174128042	174128042	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174128042delT								HMP19 (591861 upstream) : MSX2 (23533 downstream)																																			---	---	---	---
DRD1	1812	broad.mit.edu	37	5	174869692	174869692	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174869692delG	uc003mcz.2	-	2	1356	c.411delC	c.(409-411)CCCfs	p.P137fs		NM_000794	NP_000785	P21728	DRD1_HUMAN	dopamine receptor D1	137	Cytoplasmic (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|adult walking behavior|cerebral cortex GABAergic interneuron migration|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|mating behavior|positive regulation of cAMP biosynthetic process|positive regulation of cell migration|positive regulation of potassium ion transport|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of synaptic transmission, glutamatergic|prepulse inhibition|response to drug|synapse assembly|visual learning	endoplasmic reticulum membrane|membrane fraction	protein binding			ovary(2)|skin(1)	3	all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Carphenazine(DB01038)|Chlorprothixene(DB01239)|Clozapine(DB00363)|Cocaine(DB00907)|Dopamine(DB00988)|Fenoldopam(DB00800)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methylergonovine(DB00353)|Minaprine(DB00805)|Olanzapine(DB00334)|Pegademase bovine(DB00061)|Pergolide(DB01186)|Perphenazine(DB00850)|Prochlorperazine(DB00433)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Triflupromazine(DB00508)|Zuclopenthixol(DB01624)													---	---	---	---
C5orf25	375484	broad.mit.edu	37	5	175664700	175664700	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175664700delT	uc003mds.3	+						C5orf25_uc003mdt.3_5'Flank|C5orf25_uc003mdr.3_5'Flank|C5orf25_uc011dfk.1_5'Flank					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)														---	---	---	---
C5orf25	375484	broad.mit.edu	37	5	175768754	175768756	+	Intron	DEL	TGA	-	-	rs112399080		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175768754_175768756delTGA	uc003mds.3	+						C5orf25_uc003mdt.3_Intron|C5orf25_uc003mdr.3_Intron|C5orf25_uc003mdv.2_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	176017749	176017749	+	Intron	DEL	G	-	-	rs73806034	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176017749delG	uc003mem.1	+						CDHR2_uc003men.1_Intron	NM_017675	NP_060145			protocadherin LKC precursor						homophilic cell adhesion|negative regulation of cell growth	apical plasma membrane|cell junction|integral to membrane	calcium ion binding|protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	176044352	176044352	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176044352delT								GPRIN1 (7221 upstream) : SNCB (2859 downstream)																																			---	---	---	---
UIMC1	51720	broad.mit.edu	37	5	176395374	176395375	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176395374_176395375delAA	uc011dfp.1	-						UIMC1_uc003mfc.1_Intron|UIMC1_uc003mfd.1_Intron|UIMC1_uc003mfg.1_Intron|UIMC1_uc003mff.1_Intron	NM_016290	NP_057374			ubiquitin interaction motif containing 1						double-strand break repair|G2/M transition DNA damage checkpoint|histone H2A K63-linked deubiquitination|negative regulation of transcription, DNA-dependent|positive regulation of DNA repair|response to ionizing radiation|transcription, DNA-dependent	BRCA1-A complex	histone binding|K63-linked polyubiquitin binding			ovary(3)|skin(1)	4	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176722543	176722543	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)			---	---	---	---
LMAN2	10960	broad.mit.edu	37	5	176770566	176770567	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176770566_176770567delAC	uc003mge.2	-						LMAN2_uc003mgd.2_Intron	NM_006816	NP_006807			lectin, mannose-binding 2 precursor						protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	metal ion binding|sugar binding				0	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
PDLIM7	9260	broad.mit.edu	37	5	176912620	176912622	+	Intron	DEL	CCT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176912620_176912622delCCT	uc003mhc.1	-						PDLIM7_uc003mha.1_Intron|PDLIM7_uc003mhb.1_Intron|PDLIM7_uc003mhd.1_Intron|PDLIM7_uc003mhe.1_Intron	NM_005451	NP_005442			PDZ and LIM domain 7 isoform 1						cell differentiation|multicellular organismal development|ossification|receptor-mediated endocytosis	cytoplasm|focal adhesion	protein binding|zinc ion binding			breast(1)	1	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	177275506	177275506	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177275506delA								FAM153A (65107 upstream) : LOC728554 (26756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	177402835	177402835	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177402835delA								LOC728554 (91568 upstream) : PROP1 (16401 downstream)																																			---	---	---	---
HNRNPAB	3182	broad.mit.edu	37	5	177633781	177633781	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177633781delA	uc003miu.2	+	4	684	c.427delA	c.(427-429)AAAfs	p.K143fs	HNRNPAB_uc003miv.2_Frame_Shift_Del_p.K143fs|HNRNPAB_uc010jks.2_Frame_Shift_Del_p.K143fs|HNRNPAB_uc003miw.2_Frame_Shift_Del_p.K143fs|HNRNPAB_uc003mix.2_Frame_Shift_Del_p.K143fs	NM_031266	NP_112556	Q99729	ROAA_HUMAN	heterogeneous nuclear ribonucleoprotein A/B	142	RRM 1.				epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding				0																		---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177772457	177772457	+	Intron	DEL	T	-	-	rs78634385		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177772457delT	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	177796746	177796747	+	Intron	INS	-	C	C	rs148597549	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177796746_177796747insC	uc003mje.2	-							NM_173465	NP_775736			collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	178186559	178186559	+	IGR	DEL	T	-	-	rs111822095		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178186559delT								ZNF354A (28856 upstream) : AACSL (5307 downstream)																																			---	---	---	---
AACSL	729522	broad.mit.edu	37	5	178212319	178212319	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178212319delG	uc011dgl.1	-						AACSL_uc003mjk.2_Intron					Homo sapiens acetoacetyl-CoA synthetase-like, mRNA (cDNA clone IMAGE:3945810), partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	178256287	178256292	+	IGR	DEL	ATGTGT	-	-	rs66533568		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178256287_178256292delATGTGT								AACSL (10851 upstream) : ZNF354B (30662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	178515356	178515360	+	IGR	DEL	TTTTA	-	-	rs140765416		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178515356_178515360delTTTTA								ZNF354C (7667 upstream) : ADAMTS2 (25491 downstream)																																			---	---	---	---
ADAMTS2	9509	broad.mit.edu	37	5	178650538	178650541	+	Intron	DEL	CACT	-	-	rs149712134		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178650538_178650541delCACT	uc003mjw.2	-						ADAMTS2_uc011dgm.1_Intron	NM_014244	NP_055059			ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)														---	---	---	---
RUFY1	80230	broad.mit.edu	37	5	179036402	179036404	+	In_Frame_Del	DEL	TCT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179036402_179036404delTCT	uc003mka.1	+	18	2009_2011	c.2009_2011delTCT	c.(2008-2013)ATCTTC>ATC	p.F671del	RUFY1_uc003mkb.1_In_Frame_Del_p.F563del|RUFY1_uc003mkc.1_In_Frame_Del_p.F563del|RUFY1_uc003mkd.1_In_Frame_Del_p.F273del	NM_025158	NP_079434	Q96T51	RUFY1_HUMAN	RUN and FYVE domain-containing 1 isoform a	671	FYVE-type.				endocytosis|protein transport	early endosome membrane	lipid binding|zinc ion binding			ovary(4)|breast(1)	5	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)												HNSCC(44;0.11)			---	---	---	---
MAML1	9794	broad.mit.edu	37	5	179185999	179185999	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179185999delA	uc003mkm.2	+						MAML1_uc003mkn.1_Intron	NM_014757	NP_055572			mastermind-like 1						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	peptide antigen binding|protein kinase binding|transcription coactivator activity			lung(4)|ovary(2)	6	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
TBC1D9B	23061	broad.mit.edu	37	5	179299849	179299849	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179299849delC	uc003mlh.2	-						TBC1D9B_uc003mli.2_Intron|TBC1D9B_uc003mlj.2_Intron|TBC1D9B_uc003mlg.2_5'Flank|TBC1D9B_uc011dgv.1_5'Flank|TBC1D9B_uc011dgw.1_5'Flank|TBC1D9B_uc003mlk.1_5'Flank	NM_198868	NP_942568			TBC1 domain family, member 9B (with GRAM domain)							integral to membrane|intracellular	calcium ion binding|Rab GTPase activator activity			breast(1)|skin(1)	2	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
RNF130	55819	broad.mit.edu	37	5	179471832	179471832	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179471832delA	uc003mll.1	-						RNF130_uc003mlm.1_Intron	NM_018434	NP_060904			ring finger protein 130 precursor						apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	179651053	179651053	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179651053delA								RASGEF1C (14923 upstream) : MAPK9 (9544 downstream)																																			---	---	---	---
MAPK9	5601	broad.mit.edu	37	5	179707339	179707339	+	Intron	DEL	T	-	-	rs138341304	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179707339delT	uc003mls.3	-						MAPK9_uc003mlt.3_Intron|MAPK9_uc010jlc.2_Intron|MAPK9_uc003mlv.3_Intron|MAPK9_uc011dgx.1_Intron	NM_002752	NP_002743			mitogen-activated protein kinase 9 isoform JNK2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|protein binding|protein binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)	4	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
FLT4	2324	broad.mit.edu	37	5	180049928	180049928	+	Intron	DEL	A	-	-	rs307828		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180049928delA	uc003mma.3	-						FLT4_uc003mlz.3_Intron|FLT4_uc003mmb.1_Intron|FLT4_uc011dgy.1_Intron	NM_002020	NP_002011			fms-related tyrosine kinase 4 isoform 2						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)									Congenital_Hereditary_Lymphedema				---	---	---	---
BTNL8	79908	broad.mit.edu	37	5	180367926	180367926	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180367926delA	uc003mmp.2	+						BTNL8_uc003mmq.2_Intron|BTNL8_uc011dhg.1_Intron|BTNL8_uc010jll.2_Intron|BTNL8_uc010jlm.2_Intron|BTNL8_uc011dhh.1_Intron	NM_001040462	NP_001035552			butyrophilin-like 8 isoform 2 precursor							integral to membrane				upper_aerodigestive_tract(1)|skin(1)	2	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	180560193	180560193	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180560193delT								BTNL9 (71671 upstream) : OR2V2 (21750 downstream)																																			---	---	---	---
GNB2L1	10399	broad.mit.edu	37	5	180665799	180665799	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180665799delA	uc003mni.1	-						GNB2L1_uc003mnh.1_Intron|GNB2L1_uc003mnk.1_Intron|GNB2L1_uc003mnj.1_Intron|GNB2L1_uc003mnl.1_Intron|GNB2L1_uc011dhk.1_3'UTR	NM_006098	NP_006089			guanine nucleotide binding protein (G protein),						apoptosis|cell cycle|gastrulation|interspecies interaction between organisms|negative regulation of cell growth|negative regulation of phagocytosis|negative regulation of translation|negative regulation of Wnt receptor signaling pathway|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of gastrulation|positive regulation of GTPase activity|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein homooligomerization|positive regulation of protein phosphorylation|regulation of cell cycle|regulation of cell division|regulation of establishment of cell polarity|regulation of protein localization|rhythmic process	cytoskeleton|dendrite|midbody|nucleus|perikaryon|perinuclear region of cytoplasm|phagocytic cup|small ribosomal subunit	ion channel inhibitor activity|protein kinase C binding|protein phosphatase binding|protein tyrosine kinase inhibitor activity|receptor tyrosine kinase binding|SH2 domain binding				0	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.101)|all cancers(165;0.11)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	388030	388030	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:388030delT								DUSP22 (36677 upstream) : IRF4 (3722 downstream)																																			---	---	---	---
EXOC2	55770	broad.mit.edu	37	6	499431	499438	+	Intron	DEL	ACACACAC	-	-	rs4061197		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:499431_499438delACACACAC	uc003mtd.2	-						EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773			Sec5 protein						exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)														---	---	---	---
LOC285768	285768	broad.mit.edu	37	6	1056853	1056854	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1056853_1056854delAA	uc011dhp.1	-						LOC285768_uc010jnf.1_Intron|LOC285768_uc003mtj.2_Intron	NR_027115				Homo sapiens cDNA clone IMAGE:5272115.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	1255580	1255581	+	IGR	INS	-	AC	AC	rs151239361	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1255580_1255581insAC								LOC285768 (154013 upstream) : FOXQ1 (57094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	1494351	1494351	+	5'Flank	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1494351delG	uc003mto.2	+											Homo sapiens cDNA clone IMAGE:30390216.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	1523111	1523111	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1523111delC								FOXF2 (127280 upstream) : FOXC1 (87570 downstream)																																			---	---	---	---
FOXC1	2296	broad.mit.edu	37	6	1612420	1612420	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1612420delA	uc003mtp.2	+	1						NM_001453	NP_001444			forkhead box C1						anti-apoptosis|artery morphogenesis|blood vessel remodeling|brain development|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|germ cell migration|glycosaminoglycan metabolic process|lacrimal gland development|lymphangiogenesis|metanephros development|negative regulation of mitotic cell cycle|neural crest cell fate commitment|Notch signaling pathway|odontogenesis of dentine-containing tooth|ossification|ovarian follicle development|paraxial mesodermal cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|regulation of blood vessel size|regulation of organ growth|regulation of sequence-specific DNA binding transcription factor activity|somitogenesis|ureteric bud development|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	nuclear heterochromatin|transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)														---	---	---	---
GMDS	2762	broad.mit.edu	37	6	1681384	1681385	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1681384_1681385delAC	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	1929897	1929898	+	Intron	INS	-	AA	AA	rs142983267	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1929897_1929898insAA	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	2240836	2240836	+	Intron	DEL	A	-	-	rs71702006		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2240836delA	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)														---	---	---	---
SERPINB6	5269	broad.mit.edu	37	6	2954697	2954697	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2954697delT	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)													---	---	---	---
RIPK1	8737	broad.mit.edu	37	6	3081034	3081034	+	Intron	DEL	C	-	-	rs3830793		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3081034delC	uc010jni.2	+						RIPK1_uc003muv.3_Intron|RIPK1_uc003muw.3_Intron|RIPK1_uc011dhs.1_Intron|RIPK1_uc003mux.2_Intron	NM_003804	NP_003795			receptor (TNFRSF)-interacting serine-threonine						activation of caspase activity|activation of JUN kinase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of necroptosis by extracellular signals|innate immune response|MyD88-independent toll-like receptor signaling pathway|positive regulation of anti-apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of reactive oxygen species metabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|protein autophosphorylation|regulation of ATP:ADP antiporter activity|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|death-inducing signaling complex|endosome membrane|mitochondrion|receptor complex	ATP binding|death domain binding|death receptor binding|protein serine/threonine kinase activity			large_intestine(3)|lung(1)|skin(1)	5	Ovarian(93;0.0386)	all_hematologic(90;0.0895)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	3597222	3597222	+	IGR	DEL	A	-	-	rs76441038		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3597222delA								SLC22A23 (140429 upstream) : C6orf145 (125614 downstream)																																			---	---	---	---
PECI	10455	broad.mit.edu	37	6	4124198	4124198	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4124198delA	uc003mwf.2	-						C6orf201_uc003mwa.3_Intron|C6orf201_uc003mvz.3_Intron|C6orf201_uc011dhw.1_Intron|C6orf201_uc003mwb.3_Intron|PECI_uc003mwc.2_Intron|PECI_uc003mwd.2_Intron|PECI_uc003mwe.2_Intron|PECI_uc010jnr.1_Intron	NM_206836	NP_996667			peroxisomal D3,D2-enoyl-CoA isomerase isoform 2						fatty acid metabolic process	mitochondrion|peroxisomal matrix	dodecenoyl-CoA delta-isomerase activity|fatty-acyl-CoA binding				0	Ovarian(93;0.0925)	all_hematologic(90;0.0895)																---	---	---	---
CDYL	9425	broad.mit.edu	37	6	4746994	4746994	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4746994delG	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)														---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5327044	5327045	+	Intron	INS	-	T	T	rs149288618	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5327044_5327045insT	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558			phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)													---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5610540	5610540	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5610540delT	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558			phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)													---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5732713	5732713	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5732713delC	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558			phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	6116063	6116064	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6116063_6116064insG								NRN1 (108430 upstream) : F13A1 (28248 downstream)																																			---	---	---	---
LOC285780	285780	broad.mit.edu	37	6	6434266	6434266	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6434266delA	uc003mww.3	-						LOC285780_uc003mwx.2_Intron	NR_026970				Homo sapiens cDNA FLJ33708 fis, clone BRAWH2007862.												0																		---	---	---	---
LY86	9450	broad.mit.edu	37	6	6605072	6605072	+	Intron	DEL	A	-	-	rs33984109		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6605072delA	uc003mwy.1	+						LOC285780_uc003mww.3_Intron|LOC285780_uc003mwx.2_Intron	NM_004271	NP_004262			MD-1, RP105-associated precursor						apoptosis|cell proliferation|humoral immune response|inflammatory response|innate immune response	extracellular space|plasma membrane					0	Ovarian(93;0.0377)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	6677813	6677813	+	IGR	DEL	T	-	-	rs77788259		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6677813delT								LY86 (22597 upstream) : RREB1 (430375 downstream)																																			---	---	---	---
RREB1	6239	broad.mit.edu	37	6	7132097	7132097	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7132097delT	uc003mxc.2	+						RREB1_uc010jnw.2_Intron|RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron|RREB1_uc003mxd.2_Intron	NM_001003698	NP_001003698			ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)																---	---	---	---
RREB1	6239	broad.mit.edu	37	6	7218721	7218722	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7218721_7218722delAA	uc003mxc.2	+						RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron|RREB1_uc003mxd.2_3'UTR	NM_001003698	NP_001003698			ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)																---	---	---	---
SSR1	6745	broad.mit.edu	37	6	7288158	7288159	+	3'UTR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7288158_7288159delAA	uc003mxf.3	-	8					SSR1_uc003mxg.3_3'UTR|SSR1_uc010jny.2_3'UTR	NM_003144	NP_003135			signal sequence receptor, alpha precursor						cotranslational protein targeting to membrane|positive regulation of cell proliferation	endoplasmic reticulum membrane|integral to membrane	signal sequence binding				0	Ovarian(93;0.0398)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	7474540	7474541	+	IGR	DEL	TT	-	-	rs111752639		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7474540_7474541delTT								RIOK1 (56272 upstream) : DSP (67329 downstream)																																			---	---	---	---
DSP	1832	broad.mit.edu	37	6	7582771	7582771	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7582771delT	uc003mxp.1	+						DSP_uc003mxq.1_Intron	NM_004415	NP_004406			desmoplakin isoform I						cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)														---	---	---	---
TXNDC5	81567	broad.mit.edu	37	6	7954888	7954891	+	Intron	DEL	CAAT	-	-	rs150063753		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7954888_7954891delCAAT	uc003mxw.2	-							NM_001145549	NP_001139021			thioredoxin domain containing 5 isoform 3						anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)																	---	---	---	---
EEF1E1	9521	broad.mit.edu	37	6	8103720	8103720	+	5'Flank	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8103720delG	uc003mxz.2	-						EEF1E1_uc011dic.1_5'Flank	NM_004280	NP_004271			eukaryotic translation elongation factor 1						negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of DNA damage response, signal transduction by p53 class mediator|tRNA aminoacylation for protein translation	cytosol|nucleus					0	Ovarian(93;0.0398)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	8463531	8463531	+	Intron	DEL	T	-	-	rs75573907		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8463531delT	uc003mye.2	+											Homo sapiens, clone IMAGE:5539086, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	8719558	8719558	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8719558delA								HULC (65481 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9046564	9046564	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9046564delA								HULC (392487 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9361850	9361850	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9361850delT								HULC (707773 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9882436	9882438	+	Intron	DEL	AAA	-	-	rs141405335		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9882436_9882438delAAA	uc003myg.1	-						uc010jog.1_Intron|uc003myh.1_Intron|uc003myi.2_Intron|uc003myj.1_Intron|uc003myk.1_Intron|uc010joh.1_Intron					Homo sapiens clone 958LR MRDS1 protein (MRDS1) mRNA, complete cds.																														---	---	---	---
TFAP2A	7020	broad.mit.edu	37	6	10400158	10400159	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10400158_10400159delTG	uc003myr.2	-						TFAP2A_uc003myq.2_Intron|TFAP2A_uc003mys.2_Intron|TFAP2A_uc011dih.1_Intron|TFAP2A_uc003myt.2_Intron	NM_003220	NP_003211			transcription factor AP-2 alpha isoform a						ectoderm development|positive regulation of bone mineralization|positive regulation of tooth mineralization|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	centrosome|Golgi apparatus|nucleus	chromatin binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)	1	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)																---	---	---	---
TMEM14B	81853	broad.mit.edu	37	6	10750407	10750407	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10750407delT	uc003mzk.3	+						SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jor.2_Intron|TMEM14B_uc010jos.1_Intron	NM_030969	NP_112231			transmembrane protein 14B isoform a							integral to membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)																---	---	---	---
SYCP2L	221711	broad.mit.edu	37	6	10762752	10762752	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10762752delG	uc011dim.1	+						TMEM14B_uc010jos.1_Intron					Homo sapiens cDNA FLJ46251 fis, clone TESTI4021713, weakly  similar to Homo sapiens synaptonemal complex protein 2 (SYCP2).							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)															---	---	---	---
MAK	4117	broad.mit.edu	37	6	10814129	10814129	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10814129delT	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)																---	---	---	---
SYCP2L	221711	broad.mit.edu	37	6	10889103	10889103	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10889103delT	uc003mzo.2	+						SYCP2L_uc011dim.1_Intron	NM_001040274	NP_001035364			synaptonemal complex protein 2-like							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)															---	---	---	---
ELOVL2	54898	broad.mit.edu	37	6	11005392	11005392	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11005392delA	uc003mzp.3	-							NM_017770	NP_060240			elongation of very long chain fatty acids-like						fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)															---	---	---	---
NEDD9	4739	broad.mit.edu	37	6	11319852	11319853	+	Intron	INS	-	CG	CG	rs146003449		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11319852_11319853insCG	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	11396527	11396528	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11396527_11396528delTT								NEDD9 (13946 upstream) : TMEM170B (141983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	11400798	11400798	+	IGR	DEL	A	-	-	rs139092649	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11400798delA								NEDD9 (18217 upstream) : TMEM170B (137713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	11646121	11646121	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11646121delT								TMEM170B (62365 upstream) : C6orf105 (67769 downstream)																																			---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12033556	12033557	+	Intron	DEL	TG	-	-	rs58465582		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)																---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	12723721	12723721	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12723721delT	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	12842941	12842942	+	Intron	DEL	TT	-	-	rs34373946		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12842941_12842942delTT	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	13066185	13066185	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13066185delA	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron	NM_030948	NP_112210			phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)															---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13194714	13194714	+	Intron	DEL	A	-	-	rs72179745		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13194714delA	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron	NM_030948	NP_112210			phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	13357406	13357406	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13357406delA								TBC1D7 (28636 upstream) : GFOD1 (6413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	13903585	13903586	+	IGR	DEL	TG	-	-	rs112419846		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13903585_13903586delTG								CCDC90A (88796 upstream) : RNF182 (21617 downstream)																																			---	---	---	---
RNF182	221687	broad.mit.edu	37	6	13956544	13956546	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13956544_13956546delTTT	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	14078308	14078308	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14078308delC								RNF182 (98075 upstream) : CD83 (39557 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14332244	14332244	+	IGR	DEL	T	-	-	rs71828170		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14332244delT								CD83 (195098 upstream) : JARID2 (913490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14402762	14402763	+	IGR	INS	-	GTT	GTT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14402762_14402763insGTT								CD83 (265616 upstream) : JARID2 (842971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14710891	14710891	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14710891delA								CD83 (573745 upstream) : JARID2 (534843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14990206	14990206	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14990206delA								CD83 (853060 upstream) : JARID2 (255528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15040893	15040900	+	IGR	DEL	TTTTTTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15040893_15040900delTTTTTTTT								CD83 (903747 upstream) : JARID2 (204834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15186378	15186378	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15186378delA								None (None upstream) : JARID2 (59356 downstream)																																			---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15495834	15495834	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15495834delT	uc003nbj.2	+						JARID2_uc011diu.1_Intron|JARID2_uc011div.1_Intron|JARID2_uc011diw.1_Intron	NM_004973	NP_004964			jumonji, AT rich interactive domain 2 protein						central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)																---	---	---	---
DTNBP1	84062	broad.mit.edu	37	6	15580842	15580844	+	Intron	DEL	GAT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15580842_15580844delGAT	uc003nbm.2	-						DTNBP1_uc003nbl.2_Intron|DTNBP1_uc003nbn.2_Intron|DTNBP1_uc003nbo.2_Intron|DTNBP1_uc003nbp.2_Intron|DTNBP1_uc010jph.2_Intron	NM_032122	NP_115498			dystrobrevin binding protein 1 isoform a						actin cytoskeleton reorganization|cellular membrane organization|neuron projection morphogenesis|post-Golgi vesicle-mediated transport|regulation of dopamine receptor signaling pathway	axon part|BLOC-1 complex|cell junction|dendritic spine|endoplasmic reticulum membrane|endosome membrane|growth cone|melanosome membrane|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|synaptic vesicle membrane|synaptosome	identical protein binding				0	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)											Hermansky-Pudlak_syndrome				---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16763356	16763356	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16763356delT	uc003nbt.2	-						ATXN1_uc010jpi.2_5'Flank|ATXN1_uc003nbv.1_5'Flank|ATXN1_uc003nbw.1_5'Flank	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	16825192	16825192	+	IGR	DEL	A	-	-	rs35423385		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16825192delA								ATXN1 (63471 upstream) : RBM24 (456617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	16838049	16838050	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16838049_16838050delTT								ATXN1 (76328 upstream) : RBM24 (443759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	16881591	16881591	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16881591delT								ATXN1 (119870 upstream) : RBM24 (400218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	16949258	16949259	+	IGR	INS	-	TCA	TCA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16949258_16949259insTCA								ATXN1 (187537 upstream) : RBM24 (332550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	17014387	17014388	+	IGR	INS	-	T	T	rs150763231	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17014387_17014388insT								ATXN1 (252666 upstream) : RBM24 (267421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	17015341	17015341	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17015341delT								ATXN1 (253620 upstream) : RBM24 (266468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	17587095	17587098	+	IGR	DEL	ACAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17587095_17587098delACAC								CAP2 (29074 upstream) : FAM8A1 (13420 downstream)																																			---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17983726	17983726	+	Intron	DEL	T	-	-	rs60982346		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17983726delT	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron|KIF13A_uc003nck.2_Intron	NM_022113	NP_071396			kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)															---	---	---	---
KDM1B	221656	broad.mit.edu	37	6	18194108	18194109	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18194108_18194109delTT	uc003nco.1	+						KDM1B_uc003ncn.1_Intron	NM_153042	NP_694587			amine oxidase (flavin containing) domain 1						multicellular organismal development|regulation of DNA methylation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-monomethyl-K4 specific)|oxidoreductase activity|zinc ion binding			skin(1)	1																		---	---	---	---
DEK	7913	broad.mit.edu	37	6	18263751	18263751	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18263751delA	uc003ncr.1	-						DEK_uc011djf.1_Intron|DEK_uc011djg.1_Intron	NM_003472	NP_003463			DEK oncogene isoform 1						chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|histone binding			kidney(1)	1	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)					T	NUP214	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	6	19568355	19568355	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19568355delA								MIR548A1 (996244 upstream) : ID4 (269262 downstream)																																			---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20734352	20734352	+	Intron	DEL	C	-	-	rs71538802		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20734352delC	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20792055	20792056	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20792055_20792056delTT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	21108618	21108619	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21108618_21108619insT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron|CDKAL1_uc003ndf.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	21729657	21729658	+	Intron	DEL	TT	-	-	rs72119227		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21729657_21729658delTT	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	21982309	21982310	+	Intron	INS	-	AG	AG	rs150978201	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21982309_21982310insAG	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	22206609	22206610	+	Intron	DEL	TT	-	-	rs144103692		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22206609_22206610delTT	uc003ndl.2	+											Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	22920588	22920588	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22920588delT								HDGFL1 (349839 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	24075000	24075000	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24075000delT								None (None upstream) : NRSN1 (51414 downstream)																																			---	---	---	---
C6orf62	81688	broad.mit.edu	37	6	24705739	24705739	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24705739delA	uc003nel.2	-	5						NM_030939	NP_112201			hypothetical protein LOC81688							intracellular					0																		---	---	---	---
FAM65B	9750	broad.mit.edu	37	6	24852702	24852702	+	Intron	DEL	A	-	-	rs75350718		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24852702delA	uc003neo.1	-						FAM65B_uc011djs.1_Intron|FAM65B_uc011dju.1_Intron|FAM65B_uc003nep.2_Intron|FAM65B_uc011djt.1_Intron	NM_014722	NP_055537			hypothetical protein LOC9750 isoform 1						cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1																		---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25415379	25415379	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25415379delT	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110			leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	25750862	25750863	+	IGR	DEL	AG	-	-	rs67217551		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25750862_25750863delAG								HIST1H2BA (23290 upstream) : SLC17A4 (4064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	25903959	25903959	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25903959delA								SLC17A3 (29488 upstream) : SLC17A2 (9032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	25939953	25939953	+	IGR	DEL	T	-	-	rs67827987		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25939953delT								SLC17A2 (9114 upstream) : TRIM38 (23118 downstream)																																			---	---	---	---
TRIM38	10475	broad.mit.edu	37	6	25974975	25974975	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25974975delT	uc003nfm.2	+						TRIM38_uc003nfn.2_Intron|TRIM38_uc010jqd.2_Intron	NM_006355	NP_006346			tripartite motif-containing 38						positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular	signal transducer activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	26670370	26670371	+	IGR	INS	-	ACAT	ACAT	rs141090413	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26670370_26670371insACAT								ZNF322A (10407 upstream) : GUSBL1 (168895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	26681865	26681866	+	IGR	DEL	CA	-	-	rs72404755		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26681865_26681866delCA								ZNF322A (21902 upstream) : GUSBL1 (157400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27055803	27055803	+	IGR	DEL	A	-	-	rs111743899		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27055803delA								C6orf41 (64051 upstream) : HIST1H2BJ (36959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27555683	27555684	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27555683_27555684insA								ZNF184 (114786 upstream) : HIST1H2BL (219574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27686448	27686449	+	IGR	INS	-	AAC	AAC	rs143174277	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27686448_27686449insAAC								ZNF184 (245551 upstream) : HIST1H2BL (88809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	29068729	29068729	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29068729delA								OR2B3 (13639 upstream) : OR2J3 (10939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	29655446	29655448	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29655446_29655448delTTT								ZFP57 (6559 upstream) : HLA-F (35669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	29677361	29677362	+	IGR	INS	-	C	C	rs141016482	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29677361_29677362insC								ZFP57 (28474 upstream) : HLA-F (13755 downstream)																																			---	---	---	---
HLA-G	3135	broad.mit.edu	37	6	29898272	29898273	+	Intron	DEL	AG	-	-	rs150832294		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29898272_29898273delAG	uc011dmb.1	+						HCG4P6_uc003nog.1_Intron	NM_002127	NP_002118			major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
TRIM15	89870	broad.mit.edu	37	6	30132886	30132886	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30132886delT	uc010jrx.2	+							NM_033229	NP_150232			tripartite motif protein 15						mesodermal cell fate determination	intracellular	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	30354914	30354914	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30354914delA								TRIM39 (40282 upstream) : HLA-E (102357 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	30663872	30663873	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30663872_30663873delTT								NRM (4814 upstream) : MDC1 (3712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	30781189	30781190	+	3'UTR	INS	-	GT	GT	rs140684064	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30781189_30781190insGT	uc003nrp.1	-	2										RecName: Full=Putative uncharacterized protein C6orf214;																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	30813367	30813367	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30813367delT								IER3 (101040 upstream) : DDR1 (37327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	31042907	31042907	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31042907delT								HCG22 (15254 upstream) : C6orf15 (36093 downstream)																																			---	---	---	---
C2	717	broad.mit.edu	37	6	31891266	31891266	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31891266delT	uc011dop.1	+						C2_uc003nyc.2_Intron|C2_uc011doo.1_Intron	NM_001145903	NP_001139375			complement component 2 isoform 2 preproprotein						complement activation, classical pathway|innate immune response|proteolysis	extracellular space	serine-type endopeptidase activity			ovary(1)|skin(1)	2		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	32201149	32201149	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32201149delT								NOTCH4 (9305 upstream) : C6orf10 (55154 downstream)																																			---	---	---	---
C6orf10	10665	broad.mit.edu	37	6	32306184	32306184	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32306184delT	uc011dpy.1	-							NM_006781	NP_006772			chromosome 6 open reading frame 10							integral to membrane				skin(1)	1																		---	---	---	---
ITPR3	3710	broad.mit.edu	37	6	33616682	33616683	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33616682_33616683delTT	uc011drk.1	+							NM_002224	NP_002215			inositol 1,4,5-triphosphate receptor, type 3						activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	33918368	33918371	+	IGR	DEL	GTGT	-	-	rs147700351		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33918368_33918371delGTGT								MLN (146575 upstream) : MIR1275 (49378 downstream)																																			---	---	---	---
C6orf106	64771	broad.mit.edu	37	6	34585595	34585595	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34585595delA	uc003ojr.2	-						C6orf106_uc003ojs.2_Intron	NM_024294	NP_077270			chromosome 6 open reading frame 106 isoform a											skin(2)|ovary(1)	3																		---	---	---	---
C6orf106	64771	broad.mit.edu	37	6	34654281	34654282	+	Intron	DEL	AA	-	-	rs74753449		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34654281_34654282delAA	uc003ojr.2	-						C6orf106_uc003ojs.2_Intron	NM_024294	NP_077270			chromosome 6 open reading frame 106 isoform a											skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	34712497	34712497	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34712497delA								C6orf106 (47872 upstream) : SNRPC (12815 downstream)																																			---	---	---	---
UHRF1BP1	54887	broad.mit.edu	37	6	34787943	34787943	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34787943delA	uc003oju.3	+						UHRF1BP1_uc010jvm.1_Intron|UHRF1BP1_uc010jvn.2_Intron	NM_017754	NP_060224			ICBP90 binding protein 1											ovary(3)	3																		---	---	---	---
ANKS1A	23294	broad.mit.edu	37	6	34974885	34974885	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34974885delG	uc003ojx.3	+						ANKS1A_uc011dss.1_Intron|ANKS1A_uc011dst.1_Intron|ANKS1A_uc010jvp.1_Intron	NM_015245	NP_056060			ankyrin repeat and sterile alpha motif domain							cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
ANKS1A	23294	broad.mit.edu	37	6	35071115	35071115	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35071115delA	uc010jvp.1	+											SubName: Full=ANKS1A protein;							cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	35162052	35162052	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35162052delA								TCP11 (52865 upstream) : SCUBE3 (20138 downstream)																																			---	---	---	---
PPARD	5467	broad.mit.edu	37	6	35321313	35321313	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35321313delA	uc003okm.2	+						PPARD_uc003okl.2_Intron|PPARD_uc003okn.2_Intron|PPARD_uc011dtb.1_Intron|PPARD_uc011dtc.1_Intron	NM_006238	NP_006229			peroxisome proliferative activated 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)													---	---	---	---
FANCE	2178	broad.mit.edu	37	6	35421090	35421090	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35421090delT	uc003oko.1	+						FANCE_uc010jvw.1_Intron	NM_021922	NP_068741			Fanconi anemia, complementation group E						DNA repair	nucleoplasm	protein binding			ovary(1)|lung(1)|skin(1)	3								N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
Unknown	0	broad.mit.edu	37	6	35761203	35761205	+	IGR	DEL	AAA	-	-	rs145998764		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35761203_35761205delAAA								C6orf127 (5363 upstream) : CLPS (1555 downstream)																																			---	---	---	---
STK38	11329	broad.mit.edu	37	6	36482982	36482982	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36482982delA	uc003omg.2	-						STK38_uc003omh.2_Intron|STK38_uc003omi.2_Intron	NM_007271	NP_009202			serine/threonine kinase 38						intracellular protein kinase cascade|negative regulation of MAP kinase activity	cytoplasm|MLL5-L complex	ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	36698913	36698913	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36698913delC	uc010jwm.1	+											Homo sapiens cDNA FLJ43093 fis, clone CORDB1000140.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	37114881	37114882	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37114881_37114882delTT								FGD2 (118036 upstream) : PIM1 (23040 downstream)																																			---	---	---	---
TBC1D22B	55633	broad.mit.edu	37	6	37265827	37265827	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37265827delG	uc003onn.2	+						TBC1D22B_uc010jwt.2_Intron	NM_017772	NP_060242			TBC1 domain family, member 22B							intracellular	Rab GTPase activator activity				0			OV - Ovarian serous cystadenocarcinoma(102;0.241)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	37509314	37509315	+	IGR	DEL	GT	-	-	rs67487920	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37509314_37509315delGT								C6orf129 (41614 upstream) : MDGA1 (90969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	37550722	37550722	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37550722delT								C6orf129 (83022 upstream) : MDGA1 (49562 downstream)																																			---	---	---	---
MDGA1	266727	broad.mit.edu	37	6	37617647	37617647	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37617647delT	uc003onu.1	-						MDGA1_uc003onv.1_5'Flank	NM_153487	NP_705691			MAM domain containing						brain development|neuron migration|spinal cord association neuron differentiation	anchored to plasma membrane				central_nervous_system(2)	2																		---	---	---	---
ZFAND3	60685	broad.mit.edu	37	6	37897540	37897540	+	Intron	DEL	T	-	-	rs5875603		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37897540delT	uc003onx.2	+							NM_021943	NP_068762			zinc finger, AN1-type domain 3								DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZFAND3	60685	broad.mit.edu	37	6	37956687	37956687	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37956687delT	uc003onx.2	+							NM_021943	NP_068762			zinc finger, AN1-type domain 3								DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
BTBD9	114781	broad.mit.edu	37	6	38181159	38181159	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38181159delA	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																		---	---	---	---
BTBD9	114781	broad.mit.edu	37	6	38212254	38212254	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38212254delT	uc003ooa.3	-						BTBD9_uc003ony.3_Intron|BTBD9_uc010jwv.2_Intron|BTBD9_uc010jww.2_Intron|BTBD9_uc010jwx.2_Intron	NM_052893	NP_443125			BTB (POZ) domain containing 9 isoform a						cell adhesion						0																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38825529	38825529	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38825529delT	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
GLP1R	2740	broad.mit.edu	37	6	39031703	39031710	+	Intron	DEL	ACACACAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39031703_39031710delACACACAC	uc003ooj.3	+						GLP1R_uc003ooh.2_Intron|GLP1R_uc003ooi.2_Intron	NM_002062	NP_002053			glucagon-like peptide 1 receptor precursor						activation of adenylate cyclase activity|cAMP-mediated signaling|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	glucagon receptor activity|peptide receptor activity, G-protein coupled			lung(3)|breast(1)|pancreas(1)	5					Exenatide(DB01276)|Glucagon recombinant(DB00040)													---	---	---	---
GLP1R	2740	broad.mit.edu	37	6	39033314	39033315	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39033314_39033315delGT	uc003ooj.3	+						GLP1R_uc003ooh.2_Intron|GLP1R_uc003ooi.2_Intron	NM_002062	NP_002053			glucagon-like peptide 1 receptor precursor						activation of adenylate cyclase activity|cAMP-mediated signaling|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	glucagon receptor activity|peptide receptor activity, G-protein coupled			lung(3)|breast(1)|pancreas(1)	5					Exenatide(DB01276)|Glucagon recombinant(DB00040)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	39065659	39065659	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39065659delT								GLP1R (10140 upstream) : C6orf64 (6181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40765586	40765587	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40765586_40765587insG								LRFN2 (210460 upstream) : UNC5CL (229185 downstream)																																			---	---	---	---
TFEB	7942	broad.mit.edu	37	6	41694187	41694187	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41694187delT	uc003oqs.1	-						TFEB_uc003oqt.1_Intron|TFEB_uc003oqu.1_Intron|TFEB_uc003oqv.1_Intron|TFEB_uc010jxo.1_Intron|TFEB_uc003oqx.1_Intron|TFEB_uc003oqy.1_5'Flank|TFEB_uc003oqz.1_Intron|TFEB_uc010jxq.1_Intron	NM_007162	NP_009093			transcription factor EB						embryonic placenta development|humoral immune response|positive regulation of transcription from RNA polymerase II promoter	cytoplasm	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)					T	ALPHA	renal (childhood epithelioid)								---	---	---	---
USP49	25862	broad.mit.edu	37	6	41825764	41825765	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41825764_41825765delGT	uc003ori.2	-							NM_018561	NP_061031			ubiquitin thioesterase 49						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
MED20	9477	broad.mit.edu	37	6	41888527	41888527	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41888527delA	uc003ork.2	-						MED20_uc003orj.2_Intron|MED20_uc011duh.1_Intron|MED20_uc011dui.1_Intron|MED20_uc011duj.1_Intron|BYSL_uc003orl.2_5'Flank	NM_004275	NP_004266			Trf (TATA binding protein-related						regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	mediator complex	DNA-directed RNA polymerase activity|protein binding				0	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000367)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
TRERF1	55809	broad.mit.edu	37	6	42401159	42401160	+	Intron	DEL	AA	-	-	rs113663769		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42401159_42401160delAA	uc003osd.2	-						TRERF1_uc003osb.2_Intron|TRERF1_uc003osc.2_Intron|TRERF1_uc003ose.2_Intron|TRERF1_uc010jxu.1_Intron	NM_033502	NP_277037			transcriptional regulating factor 1						cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	42733537	42733537	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42733537delT								TBCC (19653 upstream) : KIAA0240 (16253 downstream)																																			---	---	---	---
KIAA0240	23506	broad.mit.edu	37	6	42796222	42796222	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42796222delT	uc003osn.1	+						KIAA0240_uc003osm.1_Intron|KIAA0240_uc011duw.1_Intron|KIAA0240_uc003oso.1_Intron|KIAA0240_uc003osp.1_Intron	NM_015349	NP_056164			hypothetical protein LOC23506											ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)															---	---	---	---
MRPL2	51069	broad.mit.edu	37	6	43022057	43022057	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43022057delG	uc003ots.1	-	7	996	c.873delC	c.(871-873)CCCfs	p.P291fs	CUL7_uc011dvb.1_5'Flank|CUL7_uc003otq.2_5'Flank|CUL7_uc010jyh.2_5'Flank|KLC4_uc003otr.1_Intron	NM_015950	NP_057034	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2 precursor	291					translation	mitochondrion|ribosome	structural constituent of ribosome				0		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)														---	---	---	---
KLC4	89953	broad.mit.edu	37	6	43041398	43041399	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43041398_43041399delAA	uc003otv.1	+						PTK7_uc003oub.1_5'Flank|PTK7_uc003ouc.1_5'Flank|PTK7_uc003oud.1_5'Flank|PTK7_uc003oue.1_5'Flank|PTK7_uc003ouf.1_5'Flank|PTK7_uc003oug.1_5'Flank|KLC4_uc003otr.1_Intron|KLC4_uc011dvd.1_Intron|KLC4_uc003otw.1_Intron|KLC4_uc003otx.1_Intron|KLC4_uc003oty.1_Intron|KLC4_uc003otz.1_Intron|PTK7_uc003oua.2_5'Flank	NM_201521	NP_958929			kinesin-like 8 isoform a							cytoplasm|kinesin complex|microtubule	microtubule motor activity|protein binding			skin(3)|ovary(1)	4			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)															---	---	---	---
PTK7	5754	broad.mit.edu	37	6	43122929	43122930	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43122929_43122930delTT	uc003oub.1	+						PTK7_uc003ouc.1_Intron|PTK7_uc003oud.1_Intron|PTK7_uc003oue.1_Intron|PTK7_uc003ouf.1_Intron|PTK7_uc003oug.1_Intron|PTK7_uc011dve.1_Intron|PTK7_uc010jyj.1_Intron	NM_002821	NP_002812			PTK7 protein tyrosine kinase 7 isoform a						actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration	cell-cell junction|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			ovary(2)|large_intestine(1)	3			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)															---	---	---	---
ZNF318	24149	broad.mit.edu	37	6	43310013	43310013	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43310013delT	uc003oux.2	-						ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160			zinc finger protein 318						meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)															---	---	---	---
XPO5	57510	broad.mit.edu	37	6	43496093	43496093	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43496093delA	uc003ovp.2	-						POLR1C_uc003ovo.1_Intron	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)															---	---	---	---
RSPH9	221421	broad.mit.edu	37	6	43635519	43635519	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43635519delT	uc003ovw.1	+						RSPH9_uc003ovx.1_Intron	NM_152732	NP_689945			radial spoke head 9 homolog						cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton				upper_aerodigestive_tract(1)|skin(1)	2														Kartagener_syndrome		OREG0017454	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
LOC100132354	100132354	broad.mit.edu	37	6	43873936	43873936	+	Intron	DEL	T	-	-	rs71778111		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43873936delT	uc011dvm.1	+							NR_024478				Homo sapiens cDNA FLJ38229 fis, clone FCBBF2004256.												0																		---	---	---	---
TMEM63B	55362	broad.mit.edu	37	6	44120321	44120321	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44120321delC	uc003owr.2	+						TMEM63B_uc003ows.2_Intron|TMEM63B_uc010jyz.2_Intron	NM_018426	NP_060896			transmembrane protein 63B							integral to membrane	nucleotide binding|protein binding			pancreas(2)|central_nervous_system(1)	3	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)													OREG0017465	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SPATS1	221409	broad.mit.edu	37	6	44339989	44339992	+	Intron	DEL	CAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44339989_44339992delCAAA	uc003oxk.2	+						SPATS1_uc003oxg.2_Intron|SPATS1_uc010jzb.2_Intron	NM_145026	NP_659463			spermatogenesis associated, serine-rich 1											skin(1)	1	all_lung(25;0.00469)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	44730395	44730395	+	IGR	DEL	A	-	-	rs1338907	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44730395delA								CDC5L (315616 upstream) : SUPT3H (46659 downstream)																																			---	---	---	---
RUNX2	860	broad.mit.edu	37	6	45514482	45514482	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45514482delT	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	45731134	45731134	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45731134delA								RUNX2 (212316 upstream) : CLIC5 (135056 downstream)																																			---	---	---	---
CLIC5	53405	broad.mit.edu	37	6	45877872	45877872	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45877872delT	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	46121102	46121102	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46121102delA								ENPP4 (6667 upstream) : ENPP5 (6660 downstream)																																			---	---	---	---
TNFRSF21	27242	broad.mit.edu	37	6	47272031	47272031	+	Intron	DEL	A	-	-	rs5876021		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47272031delA	uc003oyv.2	-							NM_014452	NP_055267			tumor necrosis factor receptor superfamily,						cellular lipid metabolic process	cytoplasm|integral to membrane	protein binding|receptor activity				0			Lung(136;0.189)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	47361556	47361556	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47361556delA								TNFRSF21 (83876 upstream) : CD2AP (83969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	49002574	49002574	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49002574delA								C6orf138 (923631 upstream) : MUT (396420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	49395243	49395243	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49395243delA								None (None upstream) : MUT (3751 downstream)																																			---	---	---	---
MUT	4594	broad.mit.edu	37	6	49408202	49408202	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49408202delT	uc003ozg.3	-							NM_000255	NP_000246			methylmalonyl Coenzyme A mutase precursor						fatty acid beta-oxidation	mitochondrial matrix	cobalamin binding|metal ion binding|methylmalonyl-CoA mutase activity				0	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
MUT	4594	broad.mit.edu	37	6	49427150	49427151	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49427150_49427151insA	uc003ozg.3	-	2	284_285	c.29_30insT	c.(28-30)TTAfs	p.L10fs		NM_000255	NP_000246	P22033	MUTA_HUMAN	methylmalonyl Coenzyme A mutase precursor	10					fatty acid beta-oxidation	mitochondrial matrix	cobalamin binding|metal ion binding|methylmalonyl-CoA mutase activity				0	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
C6orf141	135398	broad.mit.edu	37	6	49525773	49525775	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49525773_49525775delTTT	uc003ozj.2	+							NM_001145652				hypothetical protein LOC135398												0																		---	---	---	---
RHAG	6005	broad.mit.edu	37	6	49579454	49579456	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49579454_49579456delTTT	uc003ozk.3	-						RHAG_uc010jzl.2_Intron|RHAG_uc010jzm.2_Intron	NM_000324	NP_000315			Rh-associated glycoprotein						carbon dioxide transport|cellular ion homeostasis	integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			breast(1)|skin(1)	2	Lung NSC(77;0.0255)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	50112958	50112958	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50112958delA								DEFB112 (96594 upstream) : TFAP2D (568299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	50173584	50173584	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50173584delA								DEFB112 (157220 upstream) : TFAP2D (507673 downstream)																																			---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51771356	51771356	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51771356delA	uc003pah.1	-						PKHD1_uc010jzn.1_Intron|PKHD1_uc003pai.2_Intron	NM_138694	NP_619639			fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51823612	51823613	+	Intron	INS	-	AC	AC	rs141366130	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51823612_51823613insAC	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	51934378	51934378	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51934378delT	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639			fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	52812231	52812232	+	IGR	DEL	CA	-	-	rs34786247		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52812231_52812232delCA								GSTA3 (37735 upstream) : GSTA4 (30515 downstream)																																			---	---	---	---
KLHL31	401265	broad.mit.edu	37	6	53520114	53520114	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53520114delA	uc003pcb.3	-							NM_001003760	NP_001003760			kelch repeat and BTB (POZ) domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent					ovary(1)	1	Lung NSC(77;0.0158)																	---	---	---	---
LRRC1	55227	broad.mit.edu	37	6	53784276	53784276	+	Intron	DEL	A	-	-	rs45473902	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53784276delA	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	54455809	54455809	+	IGR	DEL	T	-	-	rs113501642		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54455809delT								TINAG (200859 upstream) : FAM83B (255760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	54500961	54500961	+	IGR	DEL	T	-	-	rs113821969		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54500961delT								TINAG (246011 upstream) : FAM83B (210608 downstream)																																			---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	55932072	55932072	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55932072delA	uc003pcs.2	-						COL21A1_uc010jzz.2_Intron|COL21A1_uc011dxg.1_Intron|COL21A1_uc011dxh.1_Intron|COL21A1_uc003pcr.2_Intron	NM_030820	NP_110447			collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)															---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	56047463	56047463	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)															---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	56201565	56201566	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56201565_56201566delTT	uc003pcu.1	-							NM_030820	NP_110447			collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)															---	---	---	---
DST	667	broad.mit.edu	37	6	56720745	56720745	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56720745delT	uc003pdf.2	-							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)															---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57210304	57210305	+	Intron	INS	-	TACA	TACA	rs148422338	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57210304_57210305insTACA	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	57212885	57212885	+	Intron	DEL	A	-	-	rs3839583		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57212885delA	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	57274779	57274779	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57274779delT	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	57293417	57293418	+	Intron	INS	-	T	T	rs149853195	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57293417_57293418insT	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	57306094	57306094	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57306094delT	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	57371112	57371113	+	Intron	INS	-	ACTT	ACTT	rs147044801	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57371112_57371113insACTT	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57377539	57377540	+	Intron	INS	-	TCTG	TCTG	rs138307214		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57377539_57377540insTCTG	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57391533	57391534	+	Intron	INS	-	A	A	rs66613378		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57391533_57391534insA	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	57411112	57411114	+	Intron	DEL	AAA	-	-	rs10531855		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57411112_57411114delAAA	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	57453972	57453974	+	Intron	DEL	AAA	-	-	rs79498351		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57453972_57453974delAAA	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	57466685	57466686	+	Intron	INS	-	T	T	rs150786912		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57466685_57466686insT	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	57502183	57502186	+	Intron	DEL	GAGA	-	-	rs113607514		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57502183_57502186delGAGA	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	57511818	57511818	+	Intron	DEL	G	-	-	rs11310474		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57511818delG	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	57564479	57564480	+	IGR	INS	-	A	A	rs33964245		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57564479_57564480insA								PRIM2 (51104 upstream) : GUSBL2 (681679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	58066472	58066473	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58066472_58066473insT								PRIM2 (553097 upstream) : GUSBL2 (179686 downstream)																																			---	---	---	---
GUSBL2	375513	broad.mit.edu	37	6	58283393	58283393	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58283393delA	uc011dxq.1	-						GUSBL2_uc011dxp.1_Intron|GUSBL2_uc003peb.3_Intron|GUSBL2_uc003pec.3_Intron|GUSBL2_uc003ped.3_Intron|GUSBL2_uc003pee.3_Intron					SubName: Full=Putative uncharacterized protein ENSP00000348869; Flags: Fragment;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	58433518	58433519	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58433518_58433519delCA								GUSBL2 (145794 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	58699110	58699111	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58699110_58699111delAA								GUSBL2 (411386 upstream) : None (None downstream)																																			---	---	---	---
KHDRBS2	202559	broad.mit.edu	37	6	62963495	62963495	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62963495delA	uc003peg.2	-							NM_152688	NP_689901			KH domain-containing, RNA-binding, signal						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			skin(7)|ovary(3)|liver(1)	11				BRCA - Breast invasive adenocarcinoma(397;0.149)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	63450404	63450404	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63450404delC								KHDRBS2 (454304 upstream) : LGSN (535453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63536283	63536286	+	IGR	DEL	AGAG	-	-	rs150526318		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63536283_63536286delAGAG								KHDRBS2 (540183 upstream) : LGSN (449571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	64194943	64194943	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64194943delT								LGSN (165061 upstream) : PTP4A1 (36708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	64215076	64215076	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64215076delT								LGSN (185194 upstream) : PTP4A1 (16575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	64221989	64221989	+	IGR	DEL	T	-	-	rs71764405		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64221989delT								LGSN (192107 upstream) : PTP4A1 (9662 downstream)																																			---	---	---	---
EYS	346007	broad.mit.edu	37	6	65194254	65194254	+	Intron	DEL	A	-	-	rs112366576		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65194254delA	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	65278920	65278923	+	Intron	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65278920_65278923delAAAA	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	65818200	65818200	+	Intron	DEL	T	-	-	rs112118943		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65818200delT	uc011dxu.1	-							NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	66556446	66556447	+	IGR	INS	-	TT	TT	rs11412450		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66556446_66556447insTT								MCART3P (57071 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67670924	67670926	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67670924_67670926delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67991754	67991754	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67991754delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68891444	68891444	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68891444delA								None (None upstream) : BAI3 (454188 downstream)																																			---	---	---	---
BAI3	577	broad.mit.edu	37	6	70092934	70092935	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70092934_70092935insA	uc003pev.3	+						BAI3_uc010kak.2_Intron|BAI3_uc011dxx.1_Intron	NM_001704	NP_001695			brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)																---	---	---	---
LMBRD1	55788	broad.mit.edu	37	6	70459210	70459210	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70459210delA	uc003pfa.2	-						LMBRD1_uc003pez.2_Intron|LMBRD1_uc010kal.2_Intron|LMBRD1_uc003pfb.2_Intron	NM_018368	NP_060838			liver regeneration p-53 related protein						interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1																		---	---	---	---
COL19A1	1310	broad.mit.edu	37	6	70897224	70897225	+	Intron	INS	-	CACACACAAACATG	CACACACAAACATG	rs140149836	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70897224_70897225insCACACACAAACATG	uc003pfc.1	+							NM_001858	NP_001849			alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	71110851	71110851	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71110851delA								COL9A1 (98065 upstream) : FAM135A (12256 downstream)																																			---	---	---	---
SMAP1	60682	broad.mit.edu	37	6	71442051	71442051	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71442051delT	uc003pfr.2	+						SMAP1_uc011dxy.1_Intron|SMAP1_uc003pfs.2_Intron|SMAP1_uc010kao.2_Intron|SMAP1_uc010kap.2_Intron	NM_001044305	NP_001037770			stromal membrane-associated GTPase-activating						regulation of ARF GTPase activity	plasma membrane	ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	71933677	71933677	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71933677delG								B3GAT2 (266889 upstream) : OGFRL1 (64800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	72294601	72294601	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72294601delG								C6orf155 (164153 upstream) : RIMS1 (302049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	72506106	72506106	+	IGR	DEL	T	-	-	rs72099385		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72506106delT								C6orf155 (375658 upstream) : RIMS1 (90544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	72529749	72529750	+	IGR	DEL	AA	-	-	rs72353358		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72529749_72529750delAA								C6orf155 (399301 upstream) : RIMS1 (66900 downstream)																																			---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72635774	72635776	+	Intron	DEL	TTG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72635774_72635776delTTG	uc003pga.2	+							NM_014989	NP_055804			regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72961148	72961148	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72961148delT	uc003pga.2	+						RIMS1_uc011dyb.1_Intron|RIMS1_uc003pgc.2_Intron|RIMS1_uc010kaq.2_Intron|RIMS1_uc011dyc.1_Intron|RIMS1_uc010kar.2_Intron|RIMS1_uc011dyd.1_Intron|RIMS1_uc003pgf.2_Intron|RIMS1_uc003pgg.2_Intron|RIMS1_uc003pgi.2_Intron|RIMS1_uc003pgh.2_Intron|RIMS1_uc003pgd.2_Intron|RIMS1_uc003pge.2_Intron|RIMS1_uc011dye.1_5'Flank|RIMS1_uc003pgb.3_Intron|RIMS1_uc010kas.1_Intron	NM_014989	NP_055804			regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72983964	72983964	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72983964delT	uc003pga.2	+						RIMS1_uc011dyb.1_Intron|RIMS1_uc003pgc.2_Intron|RIMS1_uc010kaq.2_Intron|RIMS1_uc011dyc.1_Intron|RIMS1_uc010kar.2_Intron|RIMS1_uc011dyd.1_Intron|RIMS1_uc003pgf.2_Intron|RIMS1_uc003pgg.2_Intron|RIMS1_uc003pgi.2_Intron|RIMS1_uc003pgh.2_Intron|RIMS1_uc003pgd.2_Intron|RIMS1_uc003pge.2_Intron|RIMS1_uc011dye.1_Intron|RIMS1_uc011dyf.1_Intron	NM_014989	NP_055804			regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	73104634	73104634	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73104634delA	uc003pga.2	+						RIMS1_uc011dyb.1_Intron|RIMS1_uc003pgc.2_Intron|RIMS1_uc010kaq.2_Intron|RIMS1_uc011dyc.1_Intron|RIMS1_uc010kar.2_Intron|RIMS1_uc011dyd.1_Intron|RIMS1_uc003pgf.2_Intron|RIMS1_uc003pgg.2_Intron|RIMS1_uc003pgi.2_Intron|RIMS1_uc003pgh.2_Intron|RIMS1_uc003pgd.2_Intron|RIMS1_uc003pge.2_Intron|RIMS1_uc011dye.1_Intron|RIMS1_uc011dyf.1_Intron|RIMS1_uc011dyg.1_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	73433507	73433507	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73433507delA	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	73625424	73625425	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73625424_73625425delCA	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	73743903	73743903	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73743903delT	uc003pgk.2	+						KCNQ5_uc003pgj.3_Intron|KCNQ5_uc011dyh.1_Intron|KCNQ5_uc011dyi.1_Intron|KCNQ5_uc010kat.2_Intron|KCNQ5_uc011dyj.1_Intron|KCNQ5_uc011dyk.1_Intron	NM_019842	NP_062816			potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)														---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73787656	73787656	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73787656delT	uc003pgk.2	+						KCNQ5_uc003pgj.3_Intron|KCNQ5_uc011dyh.1_Intron|KCNQ5_uc011dyi.1_Intron|KCNQ5_uc010kat.2_Intron|KCNQ5_uc011dyj.1_Intron|KCNQ5_uc011dyk.1_Intron	NM_019842	NP_062816			potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)														---	---	---	---
C6orf150	115004	broad.mit.edu	37	6	74152128	74152129	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74152128_74152129delTT	uc003pgx.1	-							NM_138441	NP_612450			hypothetical protein LOC115004												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	74267752	74267752	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74267752delG								EEF1A1 (36461 upstream) : SLC17A5 (35351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	74296455	74296456	+	IGR	DEL	TT	-	-	rs76446168		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74296455_74296456delTT								EEF1A1 (65164 upstream) : SLC17A5 (6647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	74938685	74938689	+	Intron	DEL	CTTTC	-	-	rs71806693		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74938685_74938689delCTTTC	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
COX7A2	1347	broad.mit.edu	37	6	75949818	75949818	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75949818delA	uc003phv.1	-							NM_001865	NP_001856			cytochrome c oxidase subunit VIIa polypeptide 2							mitochondrial respiratory chain	cytochrome-c oxidase activity|electron carrier activity				0																		---	---	---	---
SENP6	26054	broad.mit.edu	37	6	76331349	76331349	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76331349delT	uc003pid.3	+						SENP6_uc003pie.3_Intron|SENP6_uc003pic.2_Intron	NM_015571	NP_056386			SUMO1/sentrin specific peptidase 6 isoform 1						proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)																---	---	---	---
MYO6	4646	broad.mit.edu	37	6	76527432	76527432	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76527432delT	uc003pih.1	+						MYO6_uc003pig.1_Intron|MYO6_uc003pii.1_Intron	NM_004999	NP_004990			myosin VI						actin filament-based movement|DNA damage response, signal transduction by p53 class mediator|endocytosis|intracellular protein transport|positive regulation of transcription from RNA polymerase II promoter|regulation of secretion|sensory perception of sound|synaptic transmission	cell cortex|clathrin coated vesicle membrane|coated pit|cytosol|DNA-directed RNA polymerase II, holoenzyme|filamentous actin|Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|ruffle membrane|unconventional myosin complex	actin filament binding|ADP binding|ATP binding|calmodulin binding|minus-end directed microfilament motor activity|protein binding			kidney(1)|pancreas(1)	2		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)														---	---	---	---
MYO6	4646	broad.mit.edu	37	6	76551241	76551242	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76551241_76551242delAA	uc003pih.1	+						MYO6_uc003pig.1_Intron|MYO6_uc003pii.1_Intron	NM_004999	NP_004990			myosin VI						actin filament-based movement|DNA damage response, signal transduction by p53 class mediator|endocytosis|intracellular protein transport|positive regulation of transcription from RNA polymerase II promoter|regulation of secretion|sensory perception of sound|synaptic transmission	cell cortex|clathrin coated vesicle membrane|coated pit|cytosol|DNA-directed RNA polymerase II, holoenzyme|filamentous actin|Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|ruffle membrane|unconventional myosin complex	actin filament binding|ADP binding|ATP binding|calmodulin binding|minus-end directed microfilament motor activity|protein binding			kidney(1)|pancreas(1)	2		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	77750957	77750958	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77750957_77750958delTT								IMPG1 (968622 upstream) : HTR1B (420990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	77785925	77785925	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77785925delA								None (None upstream) : HTR1B (386023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	77814546	77814546	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77814546delT								None (None upstream) : HTR1B (357402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78127677	78127677	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78127677delA								None (None upstream) : HTR1B (44271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79444012	79444012	+	IGR	DEL	A	-	-	rs74929957		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79444012delA								None (None upstream) : IRAK1BP1 (133177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79842924	79842924	+	IGR	DEL	A	-	-	rs75146563	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79842924delA								PHIP (54913 upstream) : HMGN3 (68040 downstream)																																			---	---	---	---
HMGN3	9324	broad.mit.edu	37	6	79939596	79939597	+	Intron	DEL	AA	-	-	rs79408040		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79939596_79939597delAA	uc003pit.2	-						HMGN3_uc003pis.2_Intron|HMGN3_uc003piu.1_Intron	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	80062640	80062640	+	IGR	DEL	A	-	-	rs11347872		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80062640delA								HMGN3 (118185 upstream) : LCA5 (132069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	80419477	80419477	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80419477delT								SH3BGRL2 (6108 upstream) : RNY4 (32159 downstream)																																			---	---	---	---
TTK	7272	broad.mit.edu	37	6	80751910	80751910	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80751910delA	uc003pjc.2	+	22	2639	c.2565delA	c.(2563-2565)GGAfs	p.G855fs	TTK_uc003pjb.3_Frame_Shift_Del_p.G854fs	NM_003318	NP_003309	P33981	TTK_HUMAN	TTK protein kinase	855					mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1)	11		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)														---	---	---	---
BCKDHB	594	broad.mit.edu	37	6	81021263	81021263	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81021263delT	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	82389147	82389147	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82389147delA								None (None upstream) : FAM46A (66301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82700752	82700752	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82700752delT								FAM46A (238324 upstream) : IBTK (179204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82766333	82766334	+	IGR	DEL	GT	-	-	rs34587764		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82766333_82766334delGT								FAM46A (303905 upstream) : IBTK (113622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82846558	82846558	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82846558delT								FAM46A (384130 upstream) : IBTK (33398 downstream)																																			---	---	---	---
ME1	4199	broad.mit.edu	37	6	83939716	83939716	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83939716delT	uc003pjy.2	-						ME1_uc011dzb.1_Intron|ME1_uc011dzc.1_Intron	NM_002395	NP_002386			cytosolic malic enzyme 1						carbohydrate metabolic process|cellular lipid metabolic process|malate metabolic process|NADP biosynthetic process|response to carbohydrate stimulus|response to hormone stimulus	cytosol	ADP binding|electron carrier activity|malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|manganese ion binding|NAD binding|NADP binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)	NADH(DB00157)													---	---	---	---
ME1	4199	broad.mit.edu	37	6	84061934	84061934	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84061934delT	uc003pjy.2	-						ME1_uc011dzb.1_Intron|ME1_uc011dzc.1_Intron	NM_002395	NP_002386			cytosolic malic enzyme 1						carbohydrate metabolic process|cellular lipid metabolic process|malate metabolic process|NADP biosynthetic process|response to carbohydrate stimulus|response to hormone stimulus	cytosol	ADP binding|electron carrier activity|malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|manganese ion binding|NAD binding|NADP binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)	NADH(DB00157)													---	---	---	---
ME1	4199	broad.mit.edu	37	6	84139426	84139428	+	Intron	DEL	ATC	-	-	rs141489388	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84139426_84139428delATC	uc003pjy.2	-						ME1_uc011dzb.1_Intron|ME1_uc011dzc.1_Intron	NM_002395	NP_002386			cytosolic malic enzyme 1						carbohydrate metabolic process|cellular lipid metabolic process|malate metabolic process|NADP biosynthetic process|response to carbohydrate stimulus|response to hormone stimulus	cytosol	ADP binding|electron carrier activity|malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|manganese ion binding|NAD binding|NADP binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)	NADH(DB00157)													---	---	---	---
ME1	4199	broad.mit.edu	37	6	84139427	84139430	+	Intron	DEL	TCAC	-	-	rs140361413		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84139427_84139430delTCAC	uc003pjy.2	-						ME1_uc011dzb.1_Intron|ME1_uc011dzc.1_Intron	NM_002395	NP_002386			cytosolic malic enzyme 1						carbohydrate metabolic process|cellular lipid metabolic process|malate metabolic process|NADP biosynthetic process|response to carbohydrate stimulus|response to hormone stimulus	cytosol	ADP binding|electron carrier activity|malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|manganese ion binding|NAD binding|NADP binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)	NADH(DB00157)													---	---	---	---
CYB5R4	51167	broad.mit.edu	37	6	84634231	84634231	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84634231delA	uc003pkf.2	+	10	866	c.734delA	c.(733-735)CAAfs	p.Q245fs		NM_016230	NP_057314	Q7L1T6	NB5R4_HUMAN	cytochrome b5 reductase 4	245	CS.				cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process	endoplasmic reticulum|perinuclear region of cytoplasm	cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity			breast(2)	2		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	84713315	84713315	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84713315delT								CYB5R4 (43171 upstream) : MRAP2 (30105 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87236085	87236086	+	IGR	INS	-	A	A	rs142668680	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87236085_87236086insA								SNHG5 (847634 upstream) : HTR1E (410938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87516044	87516045	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87516044_87516045insT								None (None upstream) : HTR1E (130979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87855665	87855665	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87855665delA								CGA (50841 upstream) : ZNF292 (6886 downstream)																																			---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87954956	87954956	+	Intron	DEL	A	-	-	rs75723743		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87954956delA	uc003plm.3	+							NM_015021	NP_055836			zinc finger protein 292						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87955207	87955207	+	Intron	DEL	T	-	-	rs72438234		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87955207delT	uc003plm.3	+							NM_015021	NP_055836			zinc finger protein 292						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
ORC3L	23595	broad.mit.edu	37	6	88330898	88330899	+	Intron	INS	-	A	A	rs146557982	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88330898_88330899insA	uc003pmh.2	+						ORC3L_uc011dzl.1_Intron|ORC3L_uc011dzm.1_Intron|ORC3L_uc011dzn.1_Intron|ORC3L_uc003pmg.2_Intron|ORC3L_uc003pmi.2_Intron|ORC3L_uc011dzo.1_Intron|ORC3L_uc011dzp.1_Intron	NM_012381	NP_036513			origin recognition complex, subunit 3 isoform 2						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)														---	---	---	---
AKIRIN2	55122	broad.mit.edu	37	6	88400865	88400865	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88400865delA	uc003pmk.2	-							NM_018064	NP_060534			akirin 2						innate immune response|transcription, DNA-dependent	transcriptional repressor complex					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	88510396	88510396	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88510396delT	uc003pmm.2	+											Homo sapiens mRNA sequence.																														---	---	---	---
RNGTT	8732	broad.mit.edu	37	6	89481995	89481995	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89481995delA	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)														---	---	---	---
RNGTT	8732	broad.mit.edu	37	6	89586088	89586088	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89586088delA	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)														---	---	---	---
ANKRD6	22881	broad.mit.edu	37	6	90240112	90240113	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90240112_90240113delAA	uc003pni.3	+						ANKRD6_uc003pne.3_Intron|ANKRD6_uc003pnf.3_Intron	NM_014942	NP_055757			ankyrin repeat domain 6								protein binding			ovary(2)|pancreas(1)	3		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)														---	---	---	---
ANKRD6	22881	broad.mit.edu	37	6	90261396	90261397	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90261396_90261397delCA	uc003pni.3	+						ANKRD6_uc003pne.3_Intron|ANKRD6_uc003pnf.3_Intron	NM_014942	NP_055757			ankyrin repeat domain 6								protein binding			ovary(2)|pancreas(1)	3		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90417112	90417115	+	Frame_Shift_Del	DEL	CTCT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90417112_90417115delCTCT	uc003pnn.1	-	52	8095_8098	c.7979_7982delAGAG	c.(7978-7983)GAGAGTfs	p.E2660fs		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	2660_2661					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	90496797	90496798	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90496797_90496798delAA	uc003pnn.1	-						MDN1_uc003pno.1_5'Flank|MDN1_uc003pnp.1_Intron	NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90784580	90784580	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90784580delC	uc011eab.1	-						BACH2_uc003pnw.2_Intron|BACH2_uc010kch.2_Intron	NM_021813	NP_068585			BTB and CNC homology 1, basic leucine zipper							nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)														---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90865707	90865707	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90865707delT	uc011eab.1	-						BACH2_uc003pnw.2_Intron|BACH2_uc010kch.2_Intron	NM_021813	NP_068585			BTB and CNC homology 1, basic leucine zipper							nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)														---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90946653	90946653	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90946653delT	uc011eab.1	-						BACH2_uc003pnw.2_Intron|BACH2_uc010kch.2_Intron	NM_021813	NP_068585			BTB and CNC homology 1, basic leucine zipper							nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)														---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90981980	90981980	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90981980delT	uc011eab.1	-						BACH2_uc003pnw.2_Intron|BACH2_uc010kch.2_Intron	NM_021813	NP_068585			BTB and CNC homology 1, basic leucine zipper							nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	91584649	91584649	+	IGR	DEL	T	-	-	rs67171247		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91584649delT								MAP3K7 (287742 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91765927	91765927	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91765927delT								MAP3K7 (469020 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92838371	92838372	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92838371_92838372delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92951448	92951448	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92951448delG								None (None upstream) : EPHA7 (998294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93210293	93210293	+	IGR	DEL	T	-	-	rs67248231		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93210293delT								None (None upstream) : EPHA7 (739449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93257730	93257730	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93257730delT								None (None upstream) : EPHA7 (692012 downstream)																																			---	---	---	---
EPHA7	2045	broad.mit.edu	37	6	94130975	94130975	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94130975delA	uc003poe.2	-						EPHA7_uc003pof.2_5'Flank|EPHA7_uc011eac.1_5'Flank|EPHA7_uc003pog.3_5'Flank	NM_004440	NP_004431			ephrin receptor EphA7 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	94267158	94267158	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94267158delA								EPHA7 (137858 upstream) : TSG1 (149643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	94494193	94494193	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94494193delT								TSG1 (7994 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	94560474	94560474	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94560474delT								TSG1 (74275 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	94684403	94684403	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94684403delA								TSG1 (198204 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	97072121	97072121	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97072121delT								FHL5 (7609 upstream) : GPR63 (173768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	97225759	97225759	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97225759delA								FHL5 (161247 upstream) : GPR63 (20130 downstream)																																			---	---	---	---
GPR63	81491	broad.mit.edu	37	6	97246258	97246258	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97246258delA	uc010kcl.2	-	3					GPR63_uc003pou.2_3'UTR	NM_001143957	NP_001137429			G protein-coupled receptor 63							integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)														---	---	---	---
KLHL32	114792	broad.mit.edu	37	6	97500960	97500961	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97500960_97500961delAC	uc010kcm.1	+						KLHL32_uc003poy.2_Intron|KLHL32_uc011ead.1_Intron|KLHL32_uc003poz.2_Intron|KLHL32_uc011eae.1_Intron|KLHL32_uc003ppa.2_Intron	NM_052904	NP_443136			kelch-like 32											ovary(3)|skin(1)	4		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)														---	---	---	---
C6orf167	253714	broad.mit.edu	37	6	97629570	97629570	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97629570delT	uc003ppb.2	-						C6orf167_uc011eaf.1_Intron	NM_198468	NP_940870			hypothetical protein LOC253714						double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	98496883	98496883	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98496883delT								MIR2113 (24386 upstream) : POU3F2 (785697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	99547224	99547224	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99547224delT								FBXL4 (151375 upstream) : C6orf168 (173570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	99981264	99981264	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99981264delA	uc003pqc.2	+											Homo sapiens, clone IMAGE:5785547, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	100075364	100075364	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100075364delT								PRDM13 (11910 upstream) : MCHR2 (292422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	100505626	100505626	+	IGR	DEL	T	-	-	rs34305276		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100505626delT								MCHR2 (63512 upstream) : SIM1 (331125 downstream)																																			---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101064868	101064869	+	Intron	INS	-	GTT	GTT	rs141000454	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101064868_101064869insGTT	uc003pqk.2	-							NM_006828	NP_006819			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101080337	101080337	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101080337delA	uc003pqk.2	-							NM_006828	NP_006819			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	101376831	101376836	+	IGR	DEL	ATTCAG	-	-	rs71778217		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101376831_101376836delATTCAG								ASCC3 (47607 upstream) : GRIK2 (470069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	101802793	101802793	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101802793delA								ASCC3 (473569 upstream) : GRIK2 (44112 downstream)																																			---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102437425	102437428	+	Intron	DEL	TTAG	-	-	rs71837450		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102437425_102437428delTTAG	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	102733168	102733169	+	IGR	INS	-	AA	AA	rs143625482	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102733168_102733169insAA								GRIK2 (215211 upstream) : None (None downstream)																																			---	---	---	---
BVES	11149	broad.mit.edu	37	6	105585978	105585978	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105585978delA	uc003pqw.2	-						BVES_uc003pqx.2_5'Flank|BVES_uc003pqy.2_5'Flank|uc003pqz.2_Intron	NM_147147	NP_671488			blood vessel epicardial substance isoform 5						epithelial cell-cell adhesion|muscle organ development|positive regulation of locomotion|positive regulation of receptor recycling|regulation of Cdc42 GTPase activity|regulation of cell shape|regulation of Rac GTPase activity|substrate adhesion-dependent cell spreading|vesicle-mediated transport	integral to membrane|lateral plasma membrane|tight junction	structural molecule activity				0		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	106174299	106174300	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106174299_106174300insA								PREP (323330 upstream) : PRDM1 (359895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106205022	106205022	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106205022delA								PREP (354053 upstream) : PRDM1 (329173 downstream)																																			---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107756317	107756317	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107756317delA	uc003prt.2	-						PDSS2_uc011eak.1_Intron|PDSS2_uc011eal.1_Intron|PDSS2_uc003pru.2_Intron|PDSS2_uc003prv.2_Intron	NM_020381	NP_065114			prenyl diphosphate synthase, subunit 2						isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)														---	---	---	---
SOBP	55084	broad.mit.edu	37	6	107838620	107838621	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107838620_107838621delGA	uc003prx.2	+						SOBP_uc003prw.1_Intron	NM_018013	NP_060483			sine oculis binding protein homolog								metal ion binding			ovary(1)	1		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)														---	---	---	---
SOBP	55084	broad.mit.edu	37	6	107847155	107847155	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107847155delT	uc003prx.2	+						SOBP_uc003prw.1_Intron	NM_018013	NP_060483			sine oculis binding protein homolog								metal ion binding			ovary(1)	1		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	109637804	109637804	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109637804delA								C6orf182 (152691 upstream) : CD164 (49914 downstream)																																			---	---	---	---
AKD1	221264	broad.mit.edu	37	6	109816485	109816487	+	Intron	DEL	AAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109816485_109816487delAAG	uc003ptn.2	-						AKD1_uc011eas.1_Intron	NM_001145128	NP_001138600			adenylate kinase domain containing 1 isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1																		---	---	---	---
AKD1	221264	broad.mit.edu	37	6	109909280	109909281	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109909280_109909281insT	uc003ptn.2	-							NM_001145128	NP_001138600			adenylate kinase domain containing 1 isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1																		---	---	---	---
CDC40	51362	broad.mit.edu	37	6	110528894	110528894	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110528894delT	uc003pua.2	+							NM_015891	NP_056975			cell division cycle 40 homolog						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|nucleoplasm					0		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)														---	---	---	---
SLC22A16	85413	broad.mit.edu	37	6	110763982	110763982	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110763982delA	uc003puf.2	-						SLC22A16_uc003pue.2_Intron	NM_033125	NP_149116			solute carrier family 22, member 16						acid secretion|cell differentiation|multicellular organismal development|single fertilization|sperm motility|spermatogenesis	integral to membrane	carnitine transporter activity			ovary(1)	1		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)														---	---	---	---
CDK19	23097	broad.mit.edu	37	6	111077593	111077596	+	Intron	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111077593_111077596delAAAA	uc003puh.1	-						CDK19_uc003pui.1_Intron	NM_015076	NP_055891			cell division cycle 2-like 6 (CDK8-like)								ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
CDK19	23097	broad.mit.edu	37	6	111102524	111102526	+	Intron	DEL	CAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111102524_111102526delCAG	uc003puh.1	-						CDK19_uc003pui.1_Intron	NM_015076	NP_055891			cell division cycle 2-like 6 (CDK8-like)								ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
CDK19	23097	broad.mit.edu	37	6	111108575	111108576	+	Intron	INS	-	AAAA	AAAA	rs145416437	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111108575_111108576insAAAA	uc003puh.1	-						CDK19_uc003pui.1_Intron	NM_015076	NP_055891			cell division cycle 2-like 6 (CDK8-like)								ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
AMD1	262	broad.mit.edu	37	6	111185169	111185169	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111185169delT	uc011eay.1	+							NM_001033059	NP_001028231			adenosylmethionine decarboxylase 1 isoform 2						spermidine biosynthetic process|spermine biosynthetic process	cytosol	adenosylmethionine decarboxylase activity			upper_aerodigestive_tract(1)	1		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)													---	---	---	---
SLC16A10	117247	broad.mit.edu	37	6	111542949	111542950	+	Intron	DEL	AA	-	-	rs77308070		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111542949_111542950delAA	uc003pus.2	+						SLC16A10_uc003put.2_Intron	NM_018593	NP_061063			solute carrier family 16, member 10						aromatic amino acid transport|cellular nitrogen compound metabolic process|ion transport	basolateral plasma membrane|integral to membrane	amino acid transmembrane transporter activity				0		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)														---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111641279	111641279	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111641279delT	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	111839605	111839605	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111839605delA								REV3L (34687 upstream) : TRAF3IP2 (40540 downstream)																																			---	---	---	---
FYN	2534	broad.mit.edu	37	6	112024291	112024291	+	Intron	DEL	T	-	-	rs66624251		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112024291delT	uc003pvj.2	-						FYN_uc003pvi.2_Intron|FYN_uc003pvk.2_Intron|FYN_uc003pvh.2_Intron|FYN_uc010kdy.1_5'Flank	NM_002037	NP_002028			protein-tyrosine kinase fyn isoform a						axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)													---	---	---	---
WISP3	8838	broad.mit.edu	37	6	112389434	112389434	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112389434delA	uc003pvm.2	+	5	726	c.616delA	c.(616-618)AAAfs	p.K206fs	WISP3_uc003pvn.2_RNA|WISP3_uc003pvo.2_Frame_Shift_Del_p.K224fs	NM_003880	NP_003871	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	206					cell-cell signaling|regulation of cell growth|signal transduction	extracellular region|soluble fraction	growth factor activity|insulin-like growth factor binding				0		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	112845465	112845465	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112845465delA								RFPL4B (172967 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	113314132	113314132	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113314132delC								RFPL4B (641634 upstream) : MARCKS (864395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	113390745	113390745	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113390745delA								RFPL4B (718247 upstream) : MARCKS (787782 downstream)																																			---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114455136	114455137	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114455136_114455137delGA	uc003pwh.3	-						uc003pwf.2_Intron	NM_153612	NP_705840			heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)														---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114602764	114602765	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114602764_114602765delGA	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	115780998	115780998	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115780998delA								None (None upstream) : FRK (481695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116393694	116393695	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116393694_116393695delAC								FRK (11773 upstream) : NT5DC1 (28304 downstream)																																			---	---	---	---
RSPH4A	345895	broad.mit.edu	37	6	116935480	116935480	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116935480delA	uc003pxe.2	+						RSPH4A_uc010kee.2_5'Flank	NM_001010892	NP_001010892			radial spoke head 4 homolog A isoform 1						cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton|radial spoke					0														Kartagener_syndrome				---	---	---	---
RSPH4A	345895	broad.mit.edu	37	6	116937274	116937275	+	5'Flank	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116937274_116937275delTC	uc003pxe.2	+						RSPH4A_uc010kee.2_5'Flank	NM_001010892	NP_001010892			radial spoke head 4 homolog A isoform 1						cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton|radial spoke					0														Kartagener_syndrome				---	---	---	---
GOPC	57120	broad.mit.edu	37	6	117758291	117758292	+	Intron	INS	-	TTG	TTG	rs148674813	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117758291_117758292insTTG	uc003pxq.1	-							NM_001017408	NP_001017408			golgi associated PDZ and coiled-coil motif						apical protein localization|cytoplasmic sequestering of CFTR protein|ER to Golgi vesicle-mediated transport|Golgi to plasma membrane transport|protein homooligomerization|protein transport	cell junction|dendrite|Golgi membrane|postsynaptic density|postsynaptic membrane|trans-Golgi network transport vesicle	cystic fibrosis transmembrane conductance regulator binding			ovary(1)	1		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)				O	ROS1	glioblastoma								---	---	---	---
GOPC	57120	broad.mit.edu	37	6	117910789	117910789	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117910789delT	uc003pxu.2	-						GOPC_uc003pxv.2_Intron	NM_020399	NP_065132			golgi associated PDZ and coiled-coil motif						apical protein localization|cytoplasmic sequestering of CFTR protein|ER to Golgi vesicle-mediated transport|Golgi to plasma membrane transport|protein homooligomerization|protein transport	cell junction|dendrite|Golgi membrane|postsynaptic density|postsynaptic membrane|trans-Golgi network transport vesicle	cystic fibrosis transmembrane conductance regulator binding			ovary(1)	1		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)				O	ROS1	glioblastoma								---	---	---	---
Unknown	0	broad.mit.edu	37	6	118219541	118219541	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118219541delA								NUS1 (187657 upstream) : SLC35F1 (9148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	119280704	119280705	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119280704_119280705delAA								MCM9 (24401 upstream) : FAM184A (293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	120581796	120581796	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120581796delA								MAN1A1 (910870 upstream) : C6orf170 (818831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	121901159	121901159	+	IGR	DEL	A	-	-	rs148833150	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121901159delA								GJA1 (130287 upstream) : HSF2 (819537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	121903131	121903132	+	IGR	DEL	TG	-	-	rs35211610		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121903131_121903132delTG								GJA1 (132259 upstream) : HSF2 (817564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122009974	122009974	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122009974delA								GJA1 (239102 upstream) : HSF2 (710722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122629235	122629235	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122629235delA								GJA1 (858363 upstream) : HSF2 (91461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122696282	122696283	+	IGR	DEL	AA	-	-	rs67994769		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122696282_122696283delAA								GJA1 (925410 upstream) : HSF2 (24413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	123412927	123412927	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123412927delA								CLVS2 (27864 upstream) : TRDN (124556 downstream)																																			---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124431284	124431285	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124431284_124431285insT	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	124676217	124676217	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124676217delA	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304			T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)														---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	125118989	125118989	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125118989delA	uc003pzo.2	+						NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304			T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	125634577	125634577	+	IGR	DEL	A	-	-	rs74398538		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125634577delA								HDDC2 (11295 upstream) : HEY2 (434203 downstream)																																			---	---	---	---
NCOA7	135112	broad.mit.edu	37	6	126215915	126215915	+	Intron	DEL	T	-	-	rs111496290		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126215915delT	uc010kes.2	+						NCOA7_uc003qae.3_Intron|NCOA7_uc003qah.2_Intron|NCOA7_uc003qai.2_Intron|NCOA7_uc010ket.2_Intron	NM_181782	NP_861447			nuclear receptor coactivator 7 isoform 1						cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127176551	127176552	+	Intron	DEL	AC	-	-	rs67232084		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127176551_127176552delAC	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
ECHDC1	55862	broad.mit.edu	37	6	127616098	127616099	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127616098_127616099delTT	uc003qax.2	-						ECHDC1_uc003qaz.3_Intron|ECHDC1_uc010key.2_Intron|ECHDC1_uc003qay.3_Intron|ECHDC1_uc010kez.2_Intron|ECHDC1_uc010kex.2_Intron	NM_001139510	NP_001132982			enoyl Coenzyme A hydratase domain containing 1								catalytic activity				0				GBM - Glioblastoma multiforme(226;0.0423)|all cancers(137;0.156)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127877053	127877054	+	IGR	INS	-	TG	TG	rs138170893	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127877053_127877054insTG								C6orf174 (36553 upstream) : C6orf58 (21265 downstream)																																			---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128525802	128525802	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128525802delA	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
ARHGAP18	93663	broad.mit.edu	37	6	129952538	129952538	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129952538delA	uc003qbr.2	-						ARHGAP18_uc011ebw.1_Intron	NM_033515	NP_277050			Rho GTPase activating protein 18						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	130121233	130121233	+	IGR	DEL	T	-	-	rs74675073		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130121233delT								ARHGAP18 (89863 upstream) : C6orf191 (31158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	130244077	130244079	+	IGR	DEL	TCT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130244077_130244079delTCT								C6orf191 (61661 upstream) : L3MBTL3 (95655 downstream)																																			---	---	---	---
L3MBTL3	84456	broad.mit.edu	37	6	130357044	130357044	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130357044delA	uc003qbt.2	+						L3MBTL3_uc003qbu.2_Intron	NM_032438	NP_115814			l(3)mbt-like 3 isoform a						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	130956974	130956974	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130956974delT								TMEM200A (192766 upstream) : LOC285733 (191350 downstream)																																			---	---	---	---
MED23	9439	broad.mit.edu	37	6	131915530	131915530	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131915530delA	uc003qcs.1	-						MED23_uc003qcq.2_Intron|MED23_uc003qcr.1_5'Flank|MED23_uc011eca.1_Intron	NM_004830	NP_004821			mediator complex subunit 23 isoform a						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)														---	---	---	---
MED23	9439	broad.mit.edu	37	6	131920884	131920884	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131920884delT	uc003qcs.1	-						MED23_uc003qcq.2_Intron|MED23_uc011eca.1_Intron|MED23_uc003qct.1_Intron	NM_004830	NP_004821			mediator complex subunit 23 isoform a						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)														---	---	---	---
MED23	9439	broad.mit.edu	37	6	131942899	131942899	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131942899delT	uc003qcs.1	-						MED23_uc003qcq.2_Intron|MED23_uc003qct.1_Intron|MED23_uc011ecb.1_Intron	NM_004830	NP_004821			mediator complex subunit 23 isoform a						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)														---	---	---	---
MED23	9439	broad.mit.edu	37	6	131948297	131948298	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131948297_131948298delTT	uc003qcs.1	-						ENPP3_uc010kfn.1_5'Flank|ENPP3_uc003qcu.3_5'Flank|MED23_uc003qcq.2_Intron|MED23_uc003qct.1_Intron|MED23_uc011ecb.1_Intron	NM_004830	NP_004821			mediator complex subunit 23 isoform a						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	132102621	132102621	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132102621delC								ENPP3 (34072 upstream) : ENPP1 (26535 downstream)																																			---	---	---	---
ENPP1	5167	broad.mit.edu	37	6	132163851	132163851	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132163851delC	uc011ecf.1	+							NM_006208	NP_006199			ectonucleotide pyrophosphatase/phosphodiesterase						3'-phosphoadenosine 5'-phosphosulfate metabolic process|biomineral tissue development|cellular phosphate ion homeostasis|cellular response to insulin stimulus|generation of precursor metabolites and energy|immune response|inorganic diphosphate transport|negative regulation of cell growth|negative regulation of fat cell differentiation|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of protein autophosphorylation|nucleoside triphosphate catabolic process|phosphate metabolic process|sequestering of triglyceride|water-soluble vitamin metabolic process	basolateral plasma membrane|cell surface|extracellular space|integral to membrane	ATP binding|insulin receptor binding|metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|protein homodimerization activity|scavenger receptor activity			upper_aerodigestive_tract(2)|ovary(2)	4	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)													---	---	---	---
ENPP1	5167	broad.mit.edu	37	6	132190481	132190481	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132190481delT	uc011ecf.1	+						ENPP1_uc003qcy.2_Intron	NM_006208	NP_006199			ectonucleotide pyrophosphatase/phosphodiesterase						3'-phosphoadenosine 5'-phosphosulfate metabolic process|biomineral tissue development|cellular phosphate ion homeostasis|cellular response to insulin stimulus|generation of precursor metabolites and energy|immune response|inorganic diphosphate transport|negative regulation of cell growth|negative regulation of fat cell differentiation|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of protein autophosphorylation|nucleoside triphosphate catabolic process|phosphate metabolic process|sequestering of triglyceride|water-soluble vitamin metabolic process	basolateral plasma membrane|cell surface|extracellular space|integral to membrane	ATP binding|insulin receptor binding|metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|protein homodimerization activity|scavenger receptor activity			upper_aerodigestive_tract(2)|ovary(2)	4	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	132231037	132231037	+	IGR	DEL	T	-	-	rs10708840		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132231037delT								ENPP1 (14744 upstream) : CTGF (38282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	132243219	132243219	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132243219delT								ENPP1 (26926 upstream) : CTGF (26100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	132320952	132320953	+	IGR	DEL	AG	-	-	rs140524031	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132320952_132320953delAG								CTGF (48434 upstream) : MOXD1 (296242 downstream)																																			---	---	---	---
VNN3	55350	broad.mit.edu	37	6	133052340	133052340	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133052340delA	uc003qdp.2	-						VNN3_uc010kfs.2_Intron|VNN3_uc011ecl.1_Intron|VNN3_uc011ecm.1_Intron|VNN3_uc011ecn.1_Intron|VNN3_uc010kfu.2_Intron|VNN3_uc010kfv.2_Intron|VNN3_uc010kfw.2_Intron|VNN3_uc010kfx.2_Intron|VNN3_uc010kfy.2_Intron|VNN3_uc010kfz.2_Intron	NM_078625	NP_523239			SubName: Full=PAGEL-beta;												0	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00242)|GBM - Glioblastoma multiforme(226;0.0168)														---	---	---	---
EYA4	2070	broad.mit.edu	37	6	133564228	133564231	+	Intron	DEL	GTGT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133564228_133564231delGTGT	uc003qec.3	+						EYA4_uc011ecq.1_Intron|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_Intron|EYA4_uc003qee.3_Intron|EYA4_uc011ecs.1_Intron	NM_004100	NP_004091			eyes absent 4 isoform a						anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)														---	---	---	---
EYA4	2070	broad.mit.edu	37	6	133606127	133606127	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133606127delT	uc003qec.3	+						EYA4_uc011ecq.1_Intron|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_Intron|EYA4_uc003qee.3_Intron|EYA4_uc011ecs.1_Intron	NM_004100	NP_004091			eyes absent 4 isoform a						anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	134489086	134489086	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134489086delA								SLC2A12 (115297 upstream) : SGK1 (1299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	134687741	134687741	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134687741delA								SGK1 (48545 upstream) : ALDH8A1 (550788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	134763257	134763257	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134763257delT	uc003qeq.1	-						uc003qer.1_Intron|uc003qes.1_Intron|uc003qet.1_Intron					Homo sapiens cDNA clone IMAGE:4837072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	135459192	135459192	+	IGR	DEL	T	-	-	rs71955144		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135459192delT								HBS1L (83156 upstream) : MYB (43261 downstream)																																			---	---	---	---
AHI1	54806	broad.mit.edu	37	6	135751150	135751150	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135751150delA	uc003qgi.2	-						AHI1_uc003qgf.2_Intron|AHI1_uc003qgg.2_Intron|AHI1_uc003qgh.2_Intron|AHI1_uc003qgj.2_Intron|AHI1_uc003qgk.3_Intron|AHI1_uc003qgl.3_Intron	NM_001134831	NP_001128303			Abelson helper integration site 1 isoform a							adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	136154729	136154729	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136154729delA								C6orf217 (117537 upstream) : PDE7B (18105 downstream)																																			---	---	---	---
FAM54A	113115	broad.mit.edu	37	6	136566111	136566111	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136566111delT	uc010kgp.1	-						FAM54A_uc003qgt.1_Intron|FAM54A_uc003qgu.1_Intron	NM_001099286	NP_001092756			DUF729 domain containing 1											skin(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00228)|OV - Ovarian serous cystadenocarcinoma(155;0.00504)														---	---	---	---
IFNGR1	3459	broad.mit.edu	37	6	137524613	137524614	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137524613_137524614insA	uc003qho.2	-						IFNGR1_uc011edm.1_Intron	NM_000416	NP_000407			interferon gamma receptor 1 precursor						regulation of interferon-gamma-mediated signaling pathway|response to virus	integral to plasma membrane	interferon-gamma receptor activity			upper_aerodigestive_tract(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	137848608	137848608	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137848608delT								OLIG3 (33077 upstream) : TNFAIP3 (339973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138094847	138094847	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138094847delA								OLIG3 (279316 upstream) : TNFAIP3 (93734 downstream)																																			---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138524042	138524043	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138524042_138524043delCA	uc003qhu.2	+							NM_020340	NP_065073			brefeldin A-inhibited guanine						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)														---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138548181	138548181	+	Intron	DEL	T	-	-	rs112834247		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138548181delT	uc003qhu.2	+							NM_020340	NP_065073			brefeldin A-inhibited guanine						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)														---	---	---	---
NHSL1	57224	broad.mit.edu	37	6	138768907	138768907	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138768907delA	uc003qhx.2	-						NHSL1_uc011edp.1_Intron|NHSL1_uc003qhy.2_Intron	NM_020464	NP_065197			NHS-like 1 isoform 1												0																		---	---	---	---
NHSL1	57224	broad.mit.edu	37	6	138848399	138848399	+	Intron	DEL	A	-	-	rs67722254		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138848399delA	uc003qhx.2	-							NM_020464	NP_065197			NHS-like 1 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	138941190	138941190	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138941190delT								NHSL1 (47522 upstream) : CCDC28A (153467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	139088636	139088636	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139088636delT	uc003qid.1	-											Homo sapiens cDNA FLJ35273 fis, clone PROST2006020.																														---	---	---	---
ECT2L	345930	broad.mit.edu	37	6	139135710	139135710	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139135710delT	uc003qif.1	+	2	252	c.149delT	c.(148-150)ATTfs	p.I50fs	ECT2L_uc011edq.1_5'UTR	NM_001077706	NP_001071174	Q008S8	ECT2L_HUMAN	epithelial cell transforming sequence 2	50					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
ECT2L	345930	broad.mit.edu	37	6	139207261	139207261	+	Intron	DEL	A	-	-	rs145289720		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139207261delA	uc003qif.1	+						ECT2L_uc011edq.1_Intron	NM_001077706	NP_001071174			epithelial cell transforming sequence 2						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	140202699	140202699	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140202699delA								CITED2 (506914 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	140955635	140955635	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140955635delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	142613820	142613820	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142613820delT								VTA1 (71737 upstream) : GPR126 (9236 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	144563933	144563933	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144563933delT								STX11 (50858 upstream) : UTRN (43557 downstream)																																			---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144710745	144710745	+	Intron	DEL	C	-	-	rs6939205	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144710745delC	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	145093031	145093031	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	145167776	145167776	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145167776delA	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	145202455	145202455	+	IGR	DEL	A	-	-	rs71744293		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145202455delA								UTRN (28287 upstream) : EPM2A (743991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	145288155	145288156	+	IGR	DEL	AA	-	-	rs113801165		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145288155_145288156delAA								UTRN (113987 upstream) : EPM2A (658290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	145540676	145540676	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145540676delA								UTRN (366508 upstream) : EPM2A (405770 downstream)																																			---	---	---	---
EPM2A	7957	broad.mit.edu	37	6	146047967	146047967	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146047967delA	uc003qkw.2	-						EPM2A_uc003qkv.2_Intron|EPM2A_uc010khr.2_Intron|EPM2A_uc003qkx.2_Intron	NM_005670	NP_005661			laforin isoform a						glycogen metabolic process	cytosol|endoplasmic reticulum|nucleus|plasma membrane|polysome	carbohydrate binding|identical protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)														---	---	---	---
FBXO30	84085	broad.mit.edu	37	6	146126435	146126435	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146126435delT	uc003qla.2	-	2	1306	c.1107delA	c.(1105-1107)AAAfs	p.K369fs	uc003qky.1_Intron	NM_032145	NP_115521	Q8TB52	FBX30_HUMAN	F-box only protein 30	369							ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)														---	---	---	---
STXBP5	134957	broad.mit.edu	37	6	147561081	147561081	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147561081delT	uc003qlz.2	+						STXBP5_uc010khz.1_Intron|STXBP5_uc003qlx.2_Intron|STXBP5_uc003qly.2_Intron	NM_001127715	NP_001121187			syntaxin binding protein 5 (tomosyn) isoform b						exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)														---	---	---	---
SAMD5	389432	broad.mit.edu	37	6	147836793	147836793	+	Intron	DEL	C	-	-	rs72289918		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147836793delC	uc003qmc.1	+							NM_001030060	NP_001025231			sterile alpha motif domain containing 5												0		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.55e-10)|GBM - Glioblastoma multiforme(68;0.112)														---	---	---	---
SAMD5	389432	broad.mit.edu	37	6	147879732	147879733	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147879732_147879733insC	uc003qmc.1	+							NM_001030060	NP_001025231			sterile alpha motif domain containing 5												0		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.55e-10)|GBM - Glioblastoma multiforme(68;0.112)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	148148454	148148454	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148148454delA								SAMD5 (257297 upstream) : SASH1 (515275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	148617263	148617264	+	IGR	INS	-	TTG	TTG	rs141110755	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148617263_148617264insTTG								SAMD5 (726106 upstream) : SASH1 (46465 downstream)																																			---	---	---	---
SASH1	23328	broad.mit.edu	37	6	148687261	148687261	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148687261delA	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	149055980	149055980	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149055980delA								SASH1 (182796 upstream) : UST (12291 downstream)																																			---	---	---	---
PPIL4	85313	broad.mit.edu	37	6	149862317	149862318	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149862317_149862318delTT	uc003qmo.1	-						PPIL4_uc010kic.2_Intron|PPIL4_uc003qmp.1_Intron	NM_139126	NP_624311			peptidylprolyl isomerase-like 4						protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)														---	---	---	---
LATS1	9113	broad.mit.edu	37	6	149993033	149993033	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149993033delT	uc003qmu.1	-						LATS1_uc010kif.1_Intron	NM_004690	NP_004681			LATS homolog 1						cell division|cytoplasmic sequestering of protein|G2/M transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|positive regulation of peptidyl-serine phosphorylation|regulation of actin filament polymerization|sister chromatid segregation	microtubule organizing center|spindle pole	ATP binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)														---	---	---	---
PCMT1	5110	broad.mit.edu	37	6	150073018	150073018	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150073018delT	uc003qne.2	+						PCMT1_uc003qna.2_Intron|PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)														---	---	---	---
PCMT1	5110	broad.mit.edu	37	6	150092137	150092137	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150092137delA	uc003qne.2	+						PCMT1_uc003qna.2_Intron|PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	150411388	150411389	+	IGR	DEL	TG	-	-	rs143649978		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150411388_150411389delTG								ULBP3 (21105 upstream) : PPP1R14C (52799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	150648156	150648157	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150648156_150648157delCT								PPP1R14C (76630 upstream) : IYD (41871 downstream)																																			---	---	---	---
PLEKHG1	57480	broad.mit.edu	37	6	151141344	151141346	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151141344_151141346delAAA	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron|PLEKHG1_uc011eem.1_Intron|PLEKHG1_uc003qnz.2_Intron	NM_001029884	NP_001025055			pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)														---	---	---	---
ESR1	2099	broad.mit.edu	37	6	152098259	152098259	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152098259delT	uc003qom.3	+							NM_001122742	NP_001116214			estrogen receptor alpha isoform 4						positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	152429361	152429368	+	IGR	DEL	CACTCATC	-	-	rs112430028		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152429361_152429368delCACTCATC								ESR1 (4955 upstream) : SYNE1 (13455 downstream)																																			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152755214	152755214	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152755214delA	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qow.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)			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153923795	153923795	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153923795delC								RGS17 (471406 upstream) : OPRM1 (407841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	154001609	154001609	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154001609delA								RGS17 (549220 upstream) : OPRM1 (330027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	154255347	154255350	+	IGR	DEL	CTGT	-	-	rs71690099		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154255347_154255350delCTGT								RGS17 (802958 upstream) : OPRM1 (76286 downstream)																																			---	---	---	---
RBM16	22828	broad.mit.edu	37	6	155088511	155088511	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155088511delT	uc003qqa.2	+						RBM16_uc011efj.1_Intron|RBM16_uc011efk.1_Intron|RBM16_uc003qpz.2_Intron|RBM16_uc010kji.2_Intron	NM_014892	NP_055707			RNA-binding motif protein 16						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	155181651	155181651	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155181651delT	uc003qqb.2	+							NM_012454	NP_036586			T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155186164	155186164	+	Intron	DEL	T	-	-	rs68160515		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155186164delT	uc003qqb.2	+						uc003qqc.1_Intron	NM_012454	NP_036586			T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
NOX3	50508	broad.mit.edu	37	6	155761308	155761308	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155761308delA	uc003qqm.2	-							NM_015718	NP_056533			NADPH oxidase 3								electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	156469413	156469413	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156469413delA								MIR1202 (201400 upstream) : ARID1B (629673 downstream)																																			---	---	---	---
TULP4	56995	broad.mit.edu	37	6	158923753	158923753	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158923753delG	uc003qrf.2	+	13	4415	c.3058delG	c.(3058-3060)GGGfs	p.G1020fs	TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	1020					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)														---	---	---	---
SYTL3	94120	broad.mit.edu	37	6	159085938	159085938	+	Intron	DEL	A	-	-	rs11442844		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159085938delA	uc003qrp.2	+						SYTL3_uc011efp.1_Intron|SYTL3_uc003qro.2_Intron|SYTL3_uc003qrq.2_Intron|SYTL3_uc003qrr.2_Intron|SYTL3_uc003qrs.2_Intron|SYTL3_uc011efq.1_Intron	NM_001009991	NP_001009991			synaptotagmin-like 3						intracellular protein transport	endomembrane system|membrane	Rab GTPase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	159293956	159293956	+	IGR	DEL	C	-	-	rs112522523		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159293956delC								OSTCL (15292 upstream) : RSPH3 (104312 downstream)																																			---	---	---	---
FNDC1	84624	broad.mit.edu	37	6	159660894	159660895	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159660894_159660895insC	uc010kjv.2	+	14	4726_4727	c.4526_4527insC	c.(4525-4527)ATCfs	p.I1509fs	FNDC1_uc010kjw.1_Frame_Shift_Ins_p.I1394fs	NM_032532	NP_115921	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1509	Thr-rich.					extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)														---	---	---	---
PNLDC1	154197	broad.mit.edu	37	6	160223520	160223520	+	Intron	DEL	T	-	-	rs74710112		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160223520delT	uc003qsx.1	+						PNLDC1_uc003qsy.1_Intron	NM_173516	NP_775787			poly(A)-specific ribonuclease (PARN)-like domain							integral to membrane|nucleus	nucleic acid binding				0		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)														---	---	---	---
LPA	4018	broad.mit.edu	37	6	160960478	160960478	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160960478delT	uc003qtl.2	-							NM_005577	NP_005568			lipoprotein Lp(a) precursor						blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|skin(2)|pancreas(1)	6		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)													---	---	---	---
PARK2	5071	broad.mit.edu	37	6	161869726	161869726	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161869726delG	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	162112075	162112076	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162112075_162112076insT	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	162463483	162463483	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162463483delT	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	163131796	163131796	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163131796delA	uc003qtx.3	-						PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163222160	163222160	+	Intron	DEL	T	-	-	rs67557919		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163222160delT	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623			parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163538784	163538787	+	Intron	DEL	AAAA	-	-	rs113463417		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163538784_163538787delAAAA	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623			parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
QKI	9444	broad.mit.edu	37	6	163899920	163899920	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163899920delA	uc003qui.2	+	3	945	c.394delA	c.(394-396)AAAfs	p.K132fs	QKI_uc003que.2_Frame_Shift_Del_p.K132fs|QKI_uc003quf.2_Frame_Shift_Del_p.K132fs|QKI_uc003qug.2_Frame_Shift_Del_p.K132fs|QKI_uc003quh.2_Frame_Shift_Del_p.K132fs|QKI_uc003quj.2_Frame_Shift_Del_p.K132fs	NM_006775	NP_006766	Q96PU8	QKI_HUMAN	quaking homolog, KH domain RNA binding isoform	132	KH.				mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	164033039	164033039	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164033039delA								QKI (38147 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164231490	164231491	+	IGR	INS	-	AT	AT	rs140577253	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164231490_164231491insAT								QKI (236598 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164276301	164276301	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164276301delA								QKI (281409 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164418764	164418766	+	IGR	DEL	TTT	-	-	rs79538593		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164418764_164418766delTTT								QKI (423872 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	165542144	165542145	+	IGR	INS	-	G	G	rs149398463	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165542144_165542145insG								None (None upstream) : C6orf118 (151010 downstream)																																			---	---	---	---
PDE10A	10846	broad.mit.edu	37	6	165755094	165755094	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165755094delA	uc003qun.2	-						PDE10A_uc011egj.1_Intron|PDE10A_uc011egk.1_Intron|PDE10A_uc003quo.2_Intron	NM_006661	NP_006652			phosphodiesterase 10A isoform 2						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	166165464	166165464	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166165464delA								PDE10A (89880 upstream) : C6orf176 (172072 downstream)																																			---	---	---	---
C6orf176	90632	broad.mit.edu	37	6	166384628	166384628	+	Intron	DEL	A	-	-	rs66602976		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
C6orf176	90632	broad.mit.edu	37	6	166385943	166385943	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166385943delA	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	166692740	166692741	+	IGR	DEL	TT	-	-	rs71920586		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166692740_166692741delTT								T (110609 upstream) : PRR18 (26427 downstream)																																			---	---	---	---
CCR6	1235	broad.mit.edu	37	6	167550898	167550898	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167550898delA	uc003qvl.2	+	13					CCR6_uc010kkm.2_3'UTR|CCR6_uc003qvn.3_3'UTR|CCR6_uc003qvm.3_3'UTR	NM_031409	NP_113597			chemokine (C-C motif) receptor 6						cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|humoral immune response	integral to plasma membrane	C-C chemokine receptor activity			ovary(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	167831652	167831652	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167831652delT								TCP10 (33654 upstream) : C6orf123 (353569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	167880106	167880107	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167880106_167880107delCT								TCP10 (82108 upstream) : C6orf123 (305114 downstream)																																			---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168276400	168276400	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168276400delA	uc003qwd.2	+						MLLT4_uc003qwb.1_Intron|MLLT4_uc003qwc.1_Intron	NM_001040001	NP_001035090			myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
Unknown	0	broad.mit.edu	37	6	168784310	168784311	+	IGR	INS	-	GCAA	GCAA	rs28698540		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168784310_168784311insGCAA								DACT2 (63908 upstream) : SMOC2 (57720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	169594924	169594925	+	IGR	DEL	TG	-	-	rs34338636		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169594924_169594925delTG								SMOC2 (526253 upstream) : THBS2 (20951 downstream)																																			---	---	---	---
WDR27	253769	broad.mit.edu	37	6	170070554	170070554	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170070554delA	uc003qwx.2	-						WDR27_uc010kkw.1_Intron|WDR27_uc003qwy.2_Intron|WDR27_uc011egw.1_Intron|WDR27_uc010kkx.2_3'UTR					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)														---	---	---	---
C6orf70	55780	broad.mit.edu	37	6	170181412	170181412	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170181412delT	uc003qxg.1	+						C6orf70_uc011ehb.1_Intron|C6orf70_uc003qxh.1_Intron|C6orf70_uc010kky.1_Intron|C6orf70_uc003qxi.1_Intron	NM_018341	NP_060811			hypothetical protein LOC55780							integral to membrane				ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.2e-22)|BRCA - Breast invasive adenocarcinoma(81;1.49e-07)|GBM - Glioblastoma multiforme(31;0.00191)														---	---	---	---
TBP	6908	broad.mit.edu	37	6	170873745	170873745	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170873745delT	uc003qxt.2	+						TBP_uc003qxu.2_Intron|TBP_uc011ehf.1_Intron	NM_003194	NP_003185			TATA box binding protein						cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	59814	59815	+	IGR	INS	-	CTC	CTC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:59814_59815insCTC								None (None upstream) : FAM20C (133154 downstream)																																			---	---	---	---
FAM20C	56975	broad.mit.edu	37	7	195852	195854	+	Intron	DEL	CCT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:195852_195854delCCT	uc003sip.2	+							NM_020223	NP_064608			family with sequence similarity 20, member C							extracellular region					0		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.57e-17)|Epithelial(4;1.26e-16)|all cancers(6;4.79e-14)														---	---	---	---
PDGFA	5154	broad.mit.edu	37	7	542405	542406	+	Intron	INS	-	CA	CA	rs72169903		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:542405_542406insCA	uc003sir.2	-						PDGFA_uc003sis.2_Intron|PDGFA_uc003sit.1_Intron	NM_002607	NP_002598			platelet-derived growth factor alpha isoform 1						actin cytoskeleton organization|angiogenesis|cell projection assembly|embryo development|hair follicle development|lung alveolus development|negative chemotaxis|negative regulation of phosphatidylinositol biosynthetic process|negative regulation of platelet activation|organ morphogenesis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of DNA replication|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|positive regulation of MAP kinase activity|positive regulation of mesenchymal cell proliferation|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein autophosphorylation|positive regulation of protein kinase B signaling cascade|regulation of actin cytoskeleton organization|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling|regulation of peptidyl-tyrosine phosphorylation|regulation of smooth muscle cell migration|skin development	cell surface|endoplasmic reticulum lumen|extracellular space|Golgi membrane|microvillus|platelet alpha granule lumen	collagen binding|eukaryotic cell surface binding|growth factor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein heterodimerization activity|protein homodimerization activity				0		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)														---	---	---	---
ADAP1	11033	broad.mit.edu	37	7	977795	977795	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:977795delT	uc003sjo.3	-						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																		---	---	---	---
C7orf50	84310	broad.mit.edu	37	7	1167118	1167119	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1167118_1167119delAA	uc003sju.2	-						C7orf50_uc011jvt.1_Intron|C7orf50_uc011jvu.1_Intron	NM_032350	NP_115726			hypothetical protein LOC84310								protein binding				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0216)|OV - Ovarian serous cystadenocarcinoma(56;1.3e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	1228461	1228463	+	IGR	DEL	GAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1228461_1228463delGAA								ZFAND2A (28606 upstream) : UNCX (44191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1356557	1356557	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1356557delT								UNCX (79945 upstream) : MICALL2 (117439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1380705	1380706	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1380705_1380706insC								UNCX (104093 upstream) : MICALL2 (93290 downstream)																																			---	---	---	---
MICALL2	79778	broad.mit.edu	37	7	1488150	1488150	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1488150delG	uc003skj.3	-							NM_182924	NP_891554			MICAL-like 2 isoform 1							cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	2294444	2294444	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2294444delT								NUDT1 (3664 upstream) : SNX8 (197 downstream)																																			---	---	---	---
SNX8	29886	broad.mit.edu	37	7	2303067	2303068	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2303067_2303068insC	uc003slw.2	-							NM_013321	NP_037453			sorting nexin 8						cell communication|early endosome to Golgi transport|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)														---	---	---	---
SNX8	29886	broad.mit.edu	37	7	2338921	2338921	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2338921delA	uc003slw.2	-							NM_013321	NP_037453			sorting nexin 8						cell communication|early endosome to Golgi transport|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)														---	---	---	---
GNA12	2768	broad.mit.edu	37	7	2877475	2877475	+	Intron	DEL	A	-	-	rs34262163		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2877475delA	uc003smu.2	-						GNA12_uc011jwb.1_Intron	NM_007353	NP_031379			guanine nucleotide binding protein (G protein)						G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|Rho protein signal transduction	brush border membrane|heterotrimeric G-protein complex	D5 dopamine receptor binding|G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)														---	---	---	---
CARD11	84433	broad.mit.edu	37	7	2987516	2987516	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2987516delA	uc003smv.2	-							NM_032415	NP_115791			caspase recruitment domain family, member 11						positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)				Mis		DLBCL								---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3892779	3892779	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3892779delA	uc003smx.2	+							NM_152744	NP_689957			sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	4094376	4094376	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4094376delT	uc003smx.2	+						SDK1_uc010kso.2_Intron	NM_152744	NP_689957			sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	4352385	4352385	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4352385delA								SDK1 (43756 upstream) : FOXK1 (331003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	4436385	4436385	+	IGR	DEL	T	-	-	rs71535109		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4436385delT								SDK1 (127756 upstream) : FOXK1 (247003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	4605511	4605511	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4605511delA								SDK1 (296882 upstream) : FOXK1 (77877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	4926623	4926623	+	IGR	DEL	T	-	-	rs111594042		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4926623delT								RADIL (3288 upstream) : MMD2 (5253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	5201519	5201519	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5201519delT								LOC389458 (88666 upstream) : WIPI2 (28316 downstream)																																			---	---	---	---
TNRC18	84629	broad.mit.edu	37	7	5367244	5367244	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5367244delA	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)														---	---	---	---
TNRC18	84629	broad.mit.edu	37	7	5425929	5425929	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5425929delA	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	5563348	5563348	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5563348delT	uc003sop.1	+											Homo sapiens hypothetical protein LOC221946, mRNA (cDNA clone IMAGE:4829407).																														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5767575	5767575	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5767575delA	uc003soy.1	-						RNF216_uc010ksz.1_Intron|RNF216_uc010kta.1_Intron|RNF216_uc011jwj.1_Intron|RNF216_uc003sox.1_Intron	NM_207116	NP_996999			ring finger protein 216 isoform b						apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5819824	5819824	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5819824delT	uc003soy.1	-						RNF216_uc003sox.1_Intron|uc003spb.2_RNA	NM_207116	NP_996999			ring finger protein 216 isoform b						apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	5826510	5826511	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5826510_5826511delAA								RNF216 (5218 upstream) : ZNF815 (36280 downstream)																																			---	---	---	---
OCM	654231	broad.mit.edu	37	7	5925245	5925246	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5925245_5925246delTT	uc003spe.3	+							NM_001097622	NP_001091091			oncomodulin								calcium ion binding				0		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0978)|OV - Ovarian serous cystadenocarcinoma(56;2.11e-14)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	6104123	6104123	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6104123delT								EIF2AK1 (5263 upstream) : USP42 (40427 downstream)																																			---	---	---	---
CYTH3	9265	broad.mit.edu	37	7	6302594	6302594	+	Intron	DEL	A	-	-	rs71531371		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6302594delA	uc003spt.2	-							NM_004227	NP_004218			cytohesin 3						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|membrane fraction|plasma membrane	1-phosphatidylinositol binding|ARF guanyl-nucleotide exchange factor activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	6405398	6405398	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6405398delA								C7orf70 (16808 upstream) : RAC1 (8728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	6444342	6444342	+	IGR	DEL	T	-	-	rs11290060		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6444342delT								RAC1 (745 upstream) : DAGLB (4406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	6594655	6594655	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6594655delA								GRID2IP (3588 upstream) : ZDHHC4 (22410 downstream)																																			---	---	---	---
PMS2CL	441194	broad.mit.edu	37	7	6775133	6775133	+	Intron	DEL	T	-	-	rs138405905		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6775133delT	uc011jxb.1	+						PMS2CL_uc003squ.2_Intron|PMS2CL_uc003sqv.1_Intron					SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	6975495	6975495	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6975495delG								C7orf28B (109634 upstream) : C1GALT1 (246751 downstream)																																			---	---	---	---
RPA3	6119	broad.mit.edu	37	7	7738188	7738188	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7738188delT	uc003sri.2	-						uc011jxf.1_Intron	NM_002947	NP_002938			replication protein A3, 14kDa						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	cytoplasm|DNA replication factor A complex|nucleoplasm	protein binding|single-stranded DNA binding			large_intestine(1)	1		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.202)									Direct_reversal_of_damage|NER					---	---	---	---
Unknown	0	broad.mit.edu	37	7	9496382	9496382	+	IGR	DEL	T	-	-	rs113850901		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9496382delT								NXPH1 (703790 upstream) : PER4 (177518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10230102	10230103	+	IGR	INS	-	T	T	rs149656600	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10230102_10230103insT								PER4 (554655 upstream) : NDUFA4 (742712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10260760	10260761	+	IGR	DEL	TT	-	-	rs111331783		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10260760_10260761delTT								PER4 (585313 upstream) : NDUFA4 (712054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10333417	10333418	+	IGR	INS	-	GT	GT	rs146453198	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10333417_10333418insGT								PER4 (657970 upstream) : NDUFA4 (639397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10348529	10348529	+	IGR	DEL	G	-	-	rs62456429		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10348529delG								PER4 (673082 upstream) : NDUFA4 (624286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10552694	10552695	+	IGR	INS	-	C	C	rs145088331	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10552694_10552695insC								PER4 (877247 upstream) : NDUFA4 (420120 downstream)																																			---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11491335	11491339	+	Intron	DEL	GCTGA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11491335_11491339delGCTGA	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	11583968	11583968	+	Intron	DEL	A	-	-	rs139692181	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11583968delA	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)			---	---	---	---
ARL4A	10124	broad.mit.edu	37	7	12724371	12724374	+	5'Flank	DEL	TTTT	-	-	rs111294056		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12724371_12724374delTTTT	uc003ssp.2	+						ARL4A_uc003ssq.2_5'Flank|ARL4A_uc003ssr.2_5'Flank|ARL4A_uc003sss.2_5'Flank	NM_001037164	NP_001032241			ADP-ribosylation factor-like 4A						small GTPase mediated signal transduction	cytoplasm|nucleolus|plasma membrane	GTP binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (126;0.176)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	12737457	12737458	+	IGR	INS	-	TTG	TTG	rs144696331	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12737457_12737458insTTG								ARL4A (6901 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13079705	13079705	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13079705delA								ARL4A (349149 upstream) : ETV1 (851153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13369620	13369620	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13369620delT								ARL4A (639064 upstream) : ETV1 (561238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13861281	13861281	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13861281delA								None (None upstream) : ETV1 (69577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	15235843	15235843	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15235843delT								DGKB (293293 upstream) : TMEM195 (4100 downstream)																																			---	---	---	---
ISPD	729920	broad.mit.edu	37	7	16317860	16317861	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16317860_16317861delAA	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	16456307	16456307	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16456307delA	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)			---	---	---	---
AGR3	155465	broad.mit.edu	37	7	16905487	16905487	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16905487delT	uc003sts.2	-							NM_176813	NP_789783			breast cancer membrane protein 11 precursor							extracellular region					0	Lung NSC(10;0.0376)|all_lung(11;0.0721)|all_epithelial(12;0.202)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)														---	---	---	---
AHR	196	broad.mit.edu	37	7	17349519	17349519	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17349519delT	uc011jxz.1	+						AHR_uc003stt.3_Intron	NM_001621	NP_001612			aryl hydrocarbon receptor precursor						apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)																	---	---	---	---
AHR	196	broad.mit.edu	37	7	17379998	17379998	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17379998delT	uc011jxz.1	+						AHR_uc003stt.3_Intron	NM_001621	NP_001612			aryl hydrocarbon receptor precursor						apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)																	---	---	---	---
SNX13	23161	broad.mit.edu	37	7	17930126	17930126	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17930126delA	uc003stw.1	-						SNX13_uc003stv.2_Intron|SNX13_uc010kuc.2_Intron|SNX13_uc003stx.1_Intron|SNX13_uc003sty.2_Intron					SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;						cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	19148353	19148354	+	IGR	DEL	GT	-	-	rs147796633		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19148353_19148354delGT								HDAC9 (111369 upstream) : TWIST1 (6739 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20144723	20144723	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20144723delT								TMEM196 (331507 upstream) : MACC1 (29565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	21376662	21376662	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21376662delC								RPL23P8 (509223 upstream) : SP4 (91027 downstream)																																			---	---	---	---
CDCA7L	55536	broad.mit.edu	37	7	21977265	21977266	+	Intron	DEL	AA	-	-	rs77273447		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21977265_21977266delAA	uc010kuk.2	-						CDCA7L_uc003sve.3_Intron|CDCA7L_uc010kul.2_Intron|CDCA7L_uc003svf.3_Intron|CDCA7L_uc011jyk.1_Intron	NM_018719	NP_061189			cell division cycle associated 7-like isoform 1						positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	22035134	22035134	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22035134delA								CDCA7L (49592 upstream) : RAPGEF5 (122775 downstream)																																			---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22336209	22336210	+	Intron	INS	-	A	A	rs148470472	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22336209_22336210insA	uc003svg.2	-							NM_012294	NP_036426			Rap guanine nucleotide exchange factor (GEF) 5						nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22357672	22357672	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22357672delA	uc003svg.2	-							NM_012294	NP_036426			Rap guanine nucleotide exchange factor (GEF) 5						nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
FAM126A	84668	broad.mit.edu	37	7	23033305	23033306	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23033305_23033306delAC	uc003svm.3	-						FAM126A_uc003svn.3_Intron|FAM126A_uc011jyr.1_Intron	NM_032581	NP_115970			family with sequence similarity 126, member A							cytoplasm|membrane	signal transducer activity			central_nervous_system(1)	1																		---	---	---	---
KLHL7	55975	broad.mit.edu	37	7	23167755	23167757	+	Intron	DEL	AAA	-	-	rs72119383		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23167755_23167757delAAA	uc003svs.3	+						KLHL7_uc003svr.3_Intron|KLHL7_uc011jys.1_Intron|KLHL7_uc011jyt.1_Intron|KLHL7_uc003svt.2_Intron	NM_001031710	NP_001026880			kelch-like 7 isoform 1							Golgi apparatus|nucleolus|plasma membrane					0																		---	---	---	---
KLHL7	55975	broad.mit.edu	37	7	23180198	23180198	+	Intron	DEL	A	-	-	rs36052612		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23180198delA	uc003svs.3	+						KLHL7_uc003svr.3_Intron|KLHL7_uc011jys.1_Intron|KLHL7_uc011jyt.1_Intron|KLHL7_uc003svt.2_Intron|KLHL7_uc011jyv.1_5'Flank	NM_001031710	NP_001026880			kelch-like 7 isoform 1							Golgi apparatus|nucleolus|plasma membrane					0																		---	---	---	---
C7orf30	115416	broad.mit.edu	37	7	23346049	23346049	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23346049delT	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	23359538	23359538	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23359538delT	uc003swg.2	-						IGF2BP3_uc003swf.2_Intron	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	23376573	23376573	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23376573delA	uc003swg.2	-						IGF2BP3_uc003swf.2_Intron	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	23379653	23379653	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23379653delT	uc003swg.2	-						IGF2BP3_uc003swf.2_Intron	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-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	23539683	23539683	+	IGR	DEL	T	-	-	rs141349514		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23539683delT								RPS2P32 (8654 upstream) : TRA2A (4719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	24489162	24489163	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24489162_24489163insT								NPY (157685 upstream) : MPP6 (123922 downstream)																																			---	---	---	---
MPP6	51678	broad.mit.edu	37	7	24617731	24617731	+	Intron	DEL	A	-	-	rs74368912		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24617731delA	uc003swx.2	+						MPP6_uc003swy.2_Intron	NM_016447	NP_057531			membrane protein, palmitoylated 6						protein complex assembly		protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	25258512	25258512	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25258512delT								C7orf31 (38695 upstream) : NPVF (5681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25337977	25337977	+	IGR	DEL	T	-	-	rs11300761		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25337977delT								NPVF (69872 upstream) : MIR148A (651562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25471187	25471187	+	IGR	DEL	A	-	-	rs72322021		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25471187delA								NPVF (203082 upstream) : MIR148A (518352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25504493	25504493	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25504493delA								NPVF (236388 upstream) : MIR148A (485046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25727195	25727198	+	IGR	DEL	TCTC	-	-	rs148759560		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25727195_25727198delTCTC								NPVF (459090 upstream) : MIR148A (262341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25729106	25729106	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25729106delT								NPVF (461001 upstream) : MIR148A (260433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	26006352	26006352	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26006352delG								MIR148A (16746 upstream) : NFE2L3 (185495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	26324487	26324487	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26324487delA								CBX3 (71513 upstream) : SNX10 (7028 downstream)																																			---	---	---	---
SNX10	29887	broad.mit.edu	37	7	26339870	26339870	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26339870delT	uc003sxx.2	+						SNX10_uc011jzg.1_Intron|SNX10_uc010kuu.2_Intron	NM_013322	NP_037454			sorting nexin 10						cell communication|endosome organization|protein transport	extrinsic to endosome membrane	1-phosphatidylinositol binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	27308926	27308926	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27308926delT								EVX1 (22734 upstream) : HIBADH (256137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	27353757	27353757	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27353757delT								EVX1 (67565 upstream) : HIBADH (211306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	27456651	27456652	+	IGR	DEL	TT	-	-	rs72490001		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27456651_27456652delTT								EVX1 (170459 upstream) : HIBADH (108411 downstream)																																			---	---	---	---
HIBADH	11112	broad.mit.edu	37	7	27668706	27668706	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27668706delA	uc003szf.2	-						HIBADH_uc003szg.2_Intron|HIBADH_uc003szh.2_Intron|HIBADH_uc003szi.2_Intron	NM_152740	NP_689953			3-hydroxyisobutyrate dehydrogenase precursor						branched chain family amino acid catabolic process|pentose-phosphate shunt|valine metabolic process	mitochondrial matrix	3-hydroxyisobutyrate dehydrogenase activity|NAD binding|phosphogluconate dehydrogenase (decarboxylating) activity			ovary(2)	2			GBM - Glioblastoma multiforme(3;0.0368)		NADH(DB00157)													---	---	---	---
CREB5	9586	broad.mit.edu	37	7	28855672	28855673	+	Intron	INS	-	CACA	CACA	rs139523614	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28855672_28855673insCACA	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																		---	---	---	---
CREB5	9586	broad.mit.edu	37	7	28855744	28855744	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28855744delT	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	29599321	29599322	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29599321_29599322delTG	uc003tab.2	-											Homo sapiens, clone IMAGE:4347271, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	29760233	29760233	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29760233delT	uc003tai.2	+											Homo sapiens DPY-19-like 2 pseudogene 3 (DPY19L2P3) pseudogene mRNA, complete sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	30255257	30255258	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30255257_30255258insA								C7orf41 (52876 upstream) : ZNRF2 (68665 downstream)																																			---	---	---	---
INMT	11185	broad.mit.edu	37	7	30754637	30754638	+	Intron	INS	-	A	A	rs138069915	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30754637_30754638insA	uc010kwc.1	+											Homo sapiens indolethylamine N-methyltransferase (INMT) mRNA, INMT-1 allele, complete cds.							cytoplasm	amine N-methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	31148361	31148362	+	RNA	DEL	TG	-	-	rs113237427		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31148361_31148362delTG	uc003tcg.2	+	1		c.920_921delTG								Homo sapiens cDNA FLJ39226 fis, clone OCBBF2007232.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	31489981	31489981	+	IGR	DEL	T	-	-	rs35899147		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31489981delT								NEUROD6 (109443 upstream) : CCDC129 (63704 downstream)																																			---	---	---	---
CCDC129	223075	broad.mit.edu	37	7	31630238	31630238	+	Intron	DEL	A	-	-	rs76682865		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31630238delA	uc003tcj.1	+						CCDC129_uc011kad.1_Intron|CCDC129_uc003tci.1_Intron|CCDC129_uc011kae.1_Intron|CCDC129_uc003tck.1_Intron	NM_194300	NP_919276			coiled-coil domain containing 129												0																		---	---	---	---
PDE1C	5137	broad.mit.edu	37	7	32246968	32246970	+	Intron	DEL	AAA	-	-	rs76198550		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32246968_32246970delAAA	uc003tco.1	-							NM_005020	NP_005011			phosphodiesterase 1C						activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)															---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33604220	33604220	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33604220delT	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc003tdr.1_Intron|BBS9_uc003tds.1_Intron|BBS9_uc003tdt.2_Intron	NM_198428	NP_940820			parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
BMPER	168667	broad.mit.edu	37	7	34118338	34118339	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34118338_34118339delTT	uc011kap.1	+							NM_133468	NP_597725			BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	34991681	34991682	+	Intron	DEL	AA	-	-	rs67358186		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34991681_34991682delAA	uc003tem.3	-							NM_015283	NP_056098			dpy-19-like 1							integral to membrane					0																		---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	35003221	35003222	+	Intron	DEL	GT	-	-	rs150409920		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35003221_35003222delGT	uc003tem.3	-							NM_015283	NP_056098			dpy-19-like 1							integral to membrane					0																		---	---	---	---
DPY19L2P1	554236	broad.mit.edu	37	7	35204311	35204311	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35204311delA	uc003teq.1	-						DPY19L2P1_uc010kwz.1_5'Flank					RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	36011827	36011827	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36011827delT								SEPT7 (66912 upstream) : EEPD1 (181009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	36027639	36027639	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36027639delA								SEPT7 (82724 upstream) : EEPD1 (165197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	36095169	36095170	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36095169_36095170delTT								SEPT7 (150254 upstream) : EEPD1 (97666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	36350925	36350925	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36350925delT								EEPD1 (9774 upstream) : KIAA0895 (12834 downstream)																																			---	---	---	---
ANLN	54443	broad.mit.edu	37	7	36466411	36466411	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36466411delT	uc003tff.2	+						ANLN_uc011kaz.1_Intron|ANLN_uc003tfg.2_Intron|ANLN_uc010kxe.2_Intron	NM_018685	NP_061155			anillin, actin binding protein						cytokinesis|mitosis|regulation of exit from mitosis|septin ring assembly	actomyosin contractile ring|nucleus	actin binding			ovary(2)|skin(1)	3																		---	---	---	---
AOAH	313	broad.mit.edu	37	7	36618774	36618774	+	Intron	DEL	A	-	-	rs11342055		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36618774delA	uc003tfh.3	-						AOAH_uc010kxf.2_Intron|AOAH_uc011kba.1_Intron	NM_001637	NP_001628			acyloxyacyl hydrolase precursor						inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	36806349	36806349	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36806349delG								AOAH (42196 upstream) : ELMO1 (87612 downstream)																																			---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37151700	37151700	+	Intron	DEL	A	-	-	rs34490695		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37151700delA	uc003tfk.1	-						ELMO1_uc011kbc.1_Intron|ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615			engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
SFRP4	6424	broad.mit.edu	37	7	37953935	37953937	+	Intron	DEL	GAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37953935_37953937delGAG	uc003tfo.3	-							NM_003014	NP_003005			secreted frizzled-related  protein 4 precursor						brain development|cell differentiation|decidualization|embryo development|epithelium development|gonad development|mammary gland involution|menstrual cycle phase|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell proliferation|negative regulation of JNK cascade|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of sodium-dependent phosphate transport|phosphate ion homeostasis|positive regulation of apoptosis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of epidermal cell differentiation|positive regulation of gene expression|positive regulation of receptor internalization|vasculature development|Wnt receptor signaling pathway	cell surface|cytoplasm|extracellular space|nucleus	PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	38133435	38133435	+	IGR	DEL	A	-	-	rs149521025		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38133435delA								EPDR1 (141896 upstream) : STARD3NL (84498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	38277816	38277817	+	IGR	INS	-	TGTGTG	TGTGTG	rs146563544	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38277816_38277817insTGTGTG								STARD3NL (7547 upstream) : TARP (21427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	38373496	38373497	+	5'Flank	DEL	AT	-	-	rs34215527		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38373496_38373497delAT	uc010kxj.1	-						uc010kxk.1_Intron					SubName: Full=Putative uncharacterized protein ENSP00000374866;																														---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39111687	39111688	+	Intron	INS	-	GTA	GTA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39111687_39111688insGTA	uc003thb.1	+						POU6F2_uc010kxo.2_Intron	NM_007252	NP_009183			POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1																		---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39300665	39300666	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39300665_39300666delCA	uc003thb.1	+						POU6F2_uc010kxo.2_Intron	NM_007252	NP_009183			POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1																		---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39363707	39363707	+	Intron	DEL	A	-	-	rs71908329		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39363707delA	uc003thb.1	+						POU6F2_uc010kxo.2_Intron	NM_007252	NP_009183			POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40192303	40192304	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40192303_40192304delTT	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	40328817	40328817	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40328817delA	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	40352060	40352060	+	Intron	DEL	A	-	-	rs34196397		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40352060delA	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	40544038	40544038	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40544038delT	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	41162827	41162827	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41162827delA								C7orf10 (262470 upstream) : INHBA (565776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41413699	41413700	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41413699_41413700delTT								C7orf10 (513342 upstream) : INHBA (314903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41657452	41657453	+	IGR	DEL	AA	-	-	rs77276786		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41657452_41657453delAA								C7orf10 (757095 upstream) : INHBA (71150 downstream)																																			---	---	---	---
LOC285954	285954	broad.mit.edu	37	7	41812236	41812236	+	Intron	DEL	T	-	-	rs148468129		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41812236delT	uc003tht.3	+							NR_027118				Homo sapiens cDNA FLJ38947 fis, clone NT2NE2017792.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	41833309	41833310	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41833309_41833310delAG								LOC285954 (14335 upstream) : GLI3 (167240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	42410459	42410459	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42410459delT								GLI3 (133841 upstream) : C7orf25 (538415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	43041198	43041198	+	IGR	DEL	T	-	-	rs35532323		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43041198delT								MRPL32 (63747 upstream) : HECW1 (111000 downstream)																																			---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43156939	43156939	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43156939delT	uc003tid.1	+						HECW1_uc011kbi.1_Intron|HECW1_uc003tie.1_Intron|uc003tif.1_5'Flank	NM_015052	NP_055867			NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43249181	43249182	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43249181_43249182insT	uc003tid.1	+						HECW1_uc011kbi.1_Intron|HECW1_uc003tie.1_Intron	NM_015052	NP_055867			NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43358092	43358092	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43358092delT	uc003tid.1	+						HECW1_uc011kbi.1_Intron|HECW1_uc003tie.1_Intron	NM_015052	NP_055867			NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
CAMK2B	816	broad.mit.edu	37	7	44336907	44336909	+	Intron	DEL	AAG	-	-	rs145713689		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44336907_44336909delAAG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	45473392	45473392	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45473392delT								RAMP3 (249545 upstream) : ADCY1 (140347 downstream)																																			---	---	---	---
SEPT7P2	641977	broad.mit.edu	37	7	45798706	45798706	+	RNA	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45798706delG	uc003tnh.2	-	2		c.427delC			SEPT7P2_uc003tnf.3_RNA	NR_024271				Homo sapiens mRNA; cDNA DKFZp313J1114 (from clone DKFZp313J1114).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	45873000	45873000	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45873000delA								SEPT7P2 (64383 upstream) : IGFBP1 (54959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46531306	46531306	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46531306delT								IGFBP3 (570435 upstream) : TNS3 (783447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46679590	46679591	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46679590_46679591delAA								IGFBP3 (718719 upstream) : TNS3 (635162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	47148843	47148843	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47148843delT								None (None upstream) : TNS3 (165910 downstream)																																			---	---	---	---
TNS3	64759	broad.mit.edu	37	7	47546545	47546545	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47546545delG	uc003tnv.2	-						TNS3_uc003tnw.2_Intron|TNS3_uc010kyo.1_Intron	NM_022748	NP_073585			tensin 3							focal adhesion	protein binding			ovary(4)	4																		---	---	---	---
PKD1L1	168507	broad.mit.edu	37	7	47826951	47826951	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47826951delC	uc003tny.1	-							NM_138295	NP_612152			polycystin-1L1						cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48348631	48348632	+	Intron	DEL	CA	-	-	rs33986865		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48348631_48348632delCA	uc003toq.2	+						ABCA13_uc010kys.1_Intron	NM_152701	NP_689914			ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48494327	48494329	+	Intron	DEL	GAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48494327_48494329delGAG	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc010kyt.1_Intron|ABCA13_uc010kyu.1_5'Flank	NM_152701	NP_689914			ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	49226009	49226009	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49226009delA								CDC14C (258960 upstream) : VWC2 (587248 downstream)																																			---	---	---	---
C7orf72	100130988	broad.mit.edu	37	7	50191940	50191940	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50191940delA	uc011kcj.1	+							NM_001161834	NP_001155306			hypothetical protein LOC100130988											ovary(1)	1																		---	---	---	---
IKZF1	10320	broad.mit.edu	37	7	50437465	50437465	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50437465delT	uc003tow.3	+						IKZF1_uc003tox.3_Intron|IKZF1_uc003toy.3_Intron|IKZF1_uc011kck.1_Intron|IKZF1_uc003toz.3_Intron|IKZF1_uc010kyx.2_Intron	NM_006060	NP_006051			zinc finger protein, subfamily 1A, 1 (Ikaros)						cell cycle|chromatin modification|mesoderm development	cytoplasm|nucleus	zinc ion binding	p.?(14)		haematopoietic_and_lymphoid_tissue(147)|lung(1)	148	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)						D		ALL								---	---	---	---
GRB10	2887	broad.mit.edu	37	7	50687623	50687624	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50687623_50687624delAC	uc003tpi.2	-						GRB10_uc003tph.3_Intron|GRB10_uc003tpj.2_Intron|GRB10_uc003tpk.2_Intron|GRB10_uc010kzb.2_Intron|GRB10_uc003tpl.2_Intron|GRB10_uc003tpm.2_Intron|GRB10_uc003tpn.2_Intron	NM_005311	NP_005302			growth factor receptor-bound protein 10 isoform						insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			lung(3)|ovary(2)|upper_aerodigestive_tract(1)	6	Glioma(55;0.08)|all_neural(89;0.245)													Russell-Silver_syndrome				---	---	---	---
GRB10	2887	broad.mit.edu	37	7	50735361	50735362	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50735361_50735362delAA	uc003tpi.2	-						GRB10_uc003tph.3_Intron|GRB10_uc003tpj.2_Intron|GRB10_uc003tpk.2_Intron|GRB10_uc010kzb.2_Intron|GRB10_uc003tpl.2_Intron|GRB10_uc003tpm.2_Intron|GRB10_uc003tpn.2_Intron	NM_005311	NP_005302			growth factor receptor-bound protein 10 isoform						insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			lung(3)|ovary(2)|upper_aerodigestive_tract(1)	6	Glioma(55;0.08)|all_neural(89;0.245)													Russell-Silver_syndrome				---	---	---	---
GRB10	2887	broad.mit.edu	37	7	50779794	50779795	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50779794_50779795delAA	uc003tpi.2	-						GRB10_uc003tpj.2_Intron|GRB10_uc003tpk.2_Intron|GRB10_uc010kzb.2_Intron|GRB10_uc003tpl.2_Intron|GRB10_uc003tpm.2_Intron|GRB10_uc003tpn.2_Intron	NM_005311	NP_005302			growth factor receptor-bound protein 10 isoform						insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			lung(3)|ovary(2)|upper_aerodigestive_tract(1)	6	Glioma(55;0.08)|all_neural(89;0.245)													Russell-Silver_syndrome				---	---	---	---
GRB10	2887	broad.mit.edu	37	7	50854629	50854629	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50854629delG	uc003tpl.2	-						GRB10_uc003tpm.2_Intron|GRB10_uc003tpn.2_Intron	NM_001001555	NP_001001555			growth factor receptor-bound protein 10 isoform						insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			lung(3)|ovary(2)|upper_aerodigestive_tract(1)	6	Glioma(55;0.08)|all_neural(89;0.245)													Russell-Silver_syndrome				---	---	---	---
COBL	23242	broad.mit.edu	37	7	51304759	51304760	+	Intron	INS	-	CG	CG	rs145686715	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51304759_51304760insCG	uc003tpr.3	-						COBL_uc003tps.2_Intron|COBL_uc011kcl.1_Intron|COBL_uc010kzc.2_Intron|COBL_uc003tpt.2_Intron	NM_015198	NP_056013			cordon-bleu homolog											skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	51570473	51570474	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51570473_51570474delTT								COBL (185958 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	51970454	51970454	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51970454delA								COBL (585939 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52706441	52706442	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52706441_52706442delTG								None (None upstream) : POM121L12 (396907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53644526	53644526	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53644526delT								POM121L12 (539909 upstream) : HPVC1 (624391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53646835	53646835	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53646835delG								POM121L12 (542218 upstream) : HPVC1 (622082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53718143	53718143	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53718143delC								POM121L12 (613526 upstream) : HPVC1 (550774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54509290	54509290	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54509290delA								HPVC1 (239176 upstream) : VSTM2A (100729 downstream)																																			---	---	---	---
EGFR	1956	broad.mit.edu	37	7	55259059	55259059	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55259059delC	uc003tqk.2	+						EGFR_uc010kzg.1_Intron|EGFR_uc011kco.1_Intron|uc003tqo.2_5'Flank	NM_005228	NP_005219			epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	55859302	55859302	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55859302delA								FKBP9L (87042 upstream) : SEPT14 (1935 downstream)																																			---	---	---	---
GBAS	2631	broad.mit.edu	37	7	56039331	56039331	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56039331delT	uc003tre.1	+						GBAS_uc003trf.1_Intron	NM_001483	NP_001474			nipsnap homolog 2							integral to plasma membrane|membrane fraction|mitochondrion	protein binding			central_nervous_system(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
PSPH	5723	broad.mit.edu	37	7	56091127	56091127	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56091127delT	uc003trg.2	-						PSPH_uc003trh.2_Intron|PSPH_uc003tri.2_Intron|PSPH_uc003trj.2_Intron	NM_004577	NP_004568			phosphoserine phosphatase						L-serine biosynthetic process	cytoplasm	calcium ion binding|magnesium ion binding|phosphoserine phosphatase activity|protein homodimerization activity			ovary(1)|skin(1)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
PSPH	5723	broad.mit.edu	37	7	56103037	56103037	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56103037delA	uc003trg.2	-						PSPH_uc003trh.2_Intron|PSPH_uc003tri.2_Intron|PSPH_uc003trj.2_Intron	NM_004577	NP_004568			phosphoserine phosphatase						L-serine biosynthetic process	cytoplasm	calcium ion binding|magnesium ion binding|phosphoserine phosphatase activity|protein homodimerization activity			ovary(1)|skin(1)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
PSPH	5723	broad.mit.edu	37	7	56175136	56175137	+	Intron	DEL	TT	-	-	rs34470930		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56175136_56175137delTT	uc003trj.2	-						CHCHD2_uc003tsa.2_5'Flank	NM_004577	NP_004568			phosphoserine phosphatase						L-serine biosynthetic process	cytoplasm	calcium ion binding|magnesium ion binding|phosphoserine phosphatase activity|protein homodimerization activity			ovary(1)|skin(1)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	56231403	56231403	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56231403delA								PSPH (47313 upstream) : DKFZp434L192 (332513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56518705	56518705	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56518705delA								PSPH (334615 upstream) : DKFZp434L192 (45211 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56636647	56636652	+	IGR	DEL	TTTTTT	-	-	rs145866655		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56636647_56636652delTTTTTT								DKFZp434L192 (71670 upstream) : ZNF479 (550676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56755407	56755408	+	IGR	INS	-	A	A	rs113398711		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56755407_56755408insA								DKFZp434L192 (190430 upstream) : ZNF479 (431920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56769764	56769764	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56769764delA								DKFZp434L192 (204787 upstream) : ZNF479 (417564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56804254	56804256	+	IGR	DEL	CTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56804254_56804256delCTT								DKFZp434L192 (239277 upstream) : ZNF479 (383072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57413951	57413952	+	IGR	DEL	AA	-	-	rs113181567		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57413951_57413952delAA								ZNF479 (206380 upstream) : ZNF716 (95931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57619159	57619160	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57619159_57619160delAA								ZNF716 (85894 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57647928	57647929	+	IGR	INS	-	T	T	rs143924577	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57647928_57647929insT								ZNF716 (114663 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57656414	57656414	+	IGR	DEL	C	-	-	rs113908815		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57656414delC								ZNF716 (123149 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57723992	57723993	+	IGR	DEL	AG	-	-	rs142987140		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57723992_57723993delAG								ZNF716 (190727 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57730324	57730325	+	IGR	INS	-	A	A	rs112384627	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57730324_57730325insA								ZNF716 (197059 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61073890	61073890	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61073890delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61761559	61761559	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61761559delA								None (None upstream) : LOC643955 (990113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62983561	62983561	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62983561delT								LOC100287704 (171410 upstream) : ZNF727 (522260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63324301	63324301	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63324301delT								LOC100287704 (512150 upstream) : ZNF727 (181520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63486854	63486854	+	RNA	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63486854delT	uc003tsw.1	-	4		c.833delA								Homo sapiens cDNA clone IMAGE:4837429.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	63550927	63550927	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63550927delT								ZNF727 (12002 upstream) : ZNF735 (116654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63782487	63782487	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63782487delT	uc011kdo.1	+											SubName: Full=cDNA FLJ57041, moderately similar to Zinc finger protein 92;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	63808454	63808454	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63808454delT	uc011kdo.1	+											SubName: Full=cDNA FLJ57041, moderately similar to Zinc finger protein 92;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	64054897	64054898	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64054897_64054898delAA	uc003ttc.1	+											Homo sapiens cDNA FLJ43440 fis, clone OCBBF2030517.																														---	---	---	---
INTS4L1	285905	broad.mit.edu	37	7	64639184	64639184	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64639184delT	uc003ttw.2	+							NR_027393				Homo sapiens cDNA FLJ25037 fis, clone CBL03066.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	64981948	64981948	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64981948delT								ZNF92 (115951 upstream) : INTS4L2 (130829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65211291	65211293	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65211291_65211293delAAA	uc003tud.1	-						uc003tuf.2_Intron					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																														---	---	---	---
VKORC1L1	154807	broad.mit.edu	37	7	65386346	65386346	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65386346delC	uc003tul.2	+						VKORC1L1_uc011kds.1_Intron	NM_173517	NP_775788			vitamin K epoxide reductase complex, subunit							integral to membrane					0		Lung NSC(55;0.197)			Menadione(DB00170)|Warfarin(DB00682)													---	---	---	---
VKORC1L1	154807	broad.mit.edu	37	7	65392284	65392284	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65392284delA	uc003tul.2	+						VKORC1L1_uc011kds.1_Intron	NM_173517	NP_775788			vitamin K epoxide reductase complex, subunit							integral to membrane					0		Lung NSC(55;0.197)			Menadione(DB00170)|Warfarin(DB00682)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	65622419	65622420	+	IGR	DEL	AG	-	-	rs144340434	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65622419_65622420delAG								CRCP (2868 upstream) : TPST1 (47839 downstream)																																			---	---	---	---
TPST1	8460	broad.mit.edu	37	7	65776088	65776088	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65776088delT	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	65949067	65949067	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65949067delA								NCRNA00174 (83672 upstream) : LOC493754 (44379 downstream)																																			---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66482557	66482557	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66482557delT	uc003tvn.2	+						TYW1_uc010lai.2_Intron	NM_018264	NP_060734			radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66527554	66527555	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66527554_66527555delAA	uc003tvn.2	+						TYW1_uc010lai.2_Intron	NM_018264	NP_060734			radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
PMS2L4	5382	broad.mit.edu	37	7	66723862	66723862	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66723862delA	uc003tvo.2	-											Homo sapiens cDNA clone IMAGE:4081618.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	66818722	66818722	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66818722delA								STAG3L4 (32210 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	66819693	66819693	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66819693delT								STAG3L4 (33181 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67317835	67317843	+	IGR	DEL	GGAGGAGGG	-	-	rs13238498		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67317835_67317843delGGAGGAGGG								STAG3L4 (531323 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67809501	67809502	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67809501_67809502delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67934546	67934547	+	IGR	INS	-	A	A	rs140147156	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67934546_67934547insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68100580	68100580	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68100580delT								None (None upstream) : AUTS2 (963325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68242751	68242751	+	IGR	DEL	A	-	-	rs141785048		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68242751delA								None (None upstream) : AUTS2 (821154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68255659	68255659	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68255659delT								None (None upstream) : AUTS2 (808246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	69047893	69047893	+	IGR	DEL	A	-	-	rs79786892		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69047893delA								None (None upstream) : AUTS2 (16012 downstream)																																			---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69491964	69491964	+	Intron	DEL	T	-	-	rs72301604		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69491964delT	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	70248867	70248867	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70248867delA	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron|AUTS2_uc011keg.1_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	70977000	70977001	+	Intron	DEL	TT	-	-	rs71984653		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70977000_70977001delTT	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	71041515	71041518	+	Intron	DEL	TGTG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71041515_71041518delTGTG	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	71086197	71086197	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71086197delT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924			UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)																---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71701974	71701974	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71701974delT	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	71716382	71716382	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71716382delT	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440			calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	71953677	71953677	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71953677delT								CALN1 (41541 upstream) : TYW1B (70052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	71977628	71977628	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71977628delT								CALN1 (65492 upstream) : TYW1B (46101 downstream)																																			---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72211813	72211814	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72211813_72211814insA	uc011kej.1	-						TYW1B_uc011keh.1_Intron|TYW1B_uc011kei.1_5'Flank|TYW1B_uc011kek.1_Intron	NM_001145440	NP_001138912			tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0																		---	---	---	---
TRIM50	135892	broad.mit.edu	37	7	72733298	72733298	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72733298delT	uc010lbd.1	-						FKBP6_uc003twz.2_Intron|TRIM50_uc003txy.1_Intron|TRIM50_uc003txz.1_Intron	NM_178125	NP_835226			tripartite motif protein 50A							cytoplasm|intracellular membrane-bounded organelle	ligase activity|zinc ion binding			skin(1)	1																		---	---	---	---
BAZ1B	9031	broad.mit.edu	37	7	72865483	72865483	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)																---	---	---	---
TBL2	26608	broad.mit.edu	37	7	72989623	72989624	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72989623_72989624delTT	uc003tyh.2	-						TBL2_uc011kex.1_Intron|TBL2_uc010lbg.2_Intron|TBL2_uc003tyi.2_Intron|TBL2_uc011key.1_Intron|TBL2_uc010lbh.2_Intron	NM_012453	NP_036585			transducin (beta)-like 2												0		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
MLXIPL	51085	broad.mit.edu	37	7	73010422	73010422	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73010422delG	uc003tyn.1	-						MLXIPL_uc003tyj.1_Intron|MLXIPL_uc003tyk.1_Intron|MLXIPL_uc003tyl.1_Intron|MLXIPL_uc003tym.1_Intron|MLXIPL_uc003tyo.1_Intron|MLXIPL_uc003typ.1_Intron	NM_032951	NP_116569			Williams Beuren syndrome chromosome region 14						anatomical structure morphogenesis|energy reserve metabolic process|glucose mediated signaling pathway|intracellular protein kinase cascade|negative regulation of cell cycle arrest|negative regulation of oxidative phosphorylation|negative regulation of peptidyl-serine phosphorylation|positive regulation of cell proliferation|positive regulation of fatty acid biosynthetic process|positive regulation of glycolysis|positive regulation of transcription from RNA polymerase II promoter|triglyceride homeostasis	cytosol|transcription factor complex	carbohydrate response element binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	73076384	73076385	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73076384_73076385delAC								MLXIPL (37514 upstream) : VPS37D (5789 downstream)																																			---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73321654	73321654	+	Intron	DEL	T	-	-	rs112831501		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73321654delT	uc011kfa.1	-							NM_181471				replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
ELN	2006	broad.mit.edu	37	7	73443533	73443534	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73443533_73443534delTG	uc003tzw.2	+						RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_Intron|ELN_uc011kfe.1_Intron|ELN_uc003tzn.2_Intron|ELN_uc003tzz.2_Intron|ELN_uc003tzo.2_Intron|ELN_uc003tzp.2_Intron|ELN_uc003tzq.2_Intron|ELN_uc003tzr.2_Intron|ELN_uc003tzs.2_Intron|ELN_uc003tzt.2_Intron|ELN_uc003tzu.2_Intron|ELN_uc003tzv.2_Intron|ELN_uc003tzx.2_Intron|ELN_uc011kff.1_Intron|ELN_uc003tzy.2_Intron	NM_000501	NP_001075224			elastin isoform a precursor						blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						---	---	---	---
Unknown	0	broad.mit.edu	37	7	73860274	73860274	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73860274delA								CLIP2 (40002 upstream) : GTF2IRD1 (7846 downstream)																																			---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73874748	73874749	+	Intron	DEL	TT	-	-	rs68052458		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73874748_73874749delTT	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	74027382	74027382	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74027382delT								GTF2IRD1 (10464 upstream) : GTF2I (44648 downstream)																																			---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74074952	74074952	+	Intron	DEL	T	-	-	rs147152973		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74074952delT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74121006	74121006	+	Intron	DEL	T	-	-	rs80185889		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74121006delT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron|uc003uaz.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
RHBDD2	57414	broad.mit.edu	37	7	75513219	75513220	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75513219_75513220delTT	uc003udw.1	+						RHBDD2_uc003udv.1_Intron	NM_001040456	NP_001035546			rhomboid domain containing 2 isoform a							integral to membrane	serine-type endopeptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	75519759	75519759	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75519759delA								RHBDD2 (1515 upstream) : POR (24661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	75530740	75530740	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75530740delA								RHBDD2 (12496 upstream) : POR (13680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	75804673	75804673	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75804673delA								MDH2 (108745 upstream) : SRRM3 (26543 downstream)																																			---	---	---	---
SRRM3	222183	broad.mit.edu	37	7	75837824	75837825	+	Intron	DEL	AA	-	-	rs112442379		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75837824_75837825delAA	uc010ldi.2	+							NM_001110199	NP_001103669			serine/arginine repetitive matrix 3												0																		---	---	---	---
POMZP3	22932	broad.mit.edu	37	7	76242239	76242240	+	Intron	INS	-	T	T	rs140682358		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76242239_76242240insT	uc003uft.2	-						uc003ufs.1_Intron|POMZP3_uc003ufu.2_Intron|POMZP3_uc003ufv.2_Intron|POMZP3_uc011kgm.1_Intron	NM_012230	NP_036362			POMZP3 fusion protein isoform 1												0		Myeloproliferative disorder(862;0.204)																---	---	---	---
PMS2L11	441263	broad.mit.edu	37	7	76625161	76625161	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76625161delA	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0																		---	---	---	---
PMS2L11	441263	broad.mit.edu	37	7	76634275	76634280	+	Intron	DEL	TGCTGT	-	-	rs67390349		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76634275_76634280delTGCTGT	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0																		---	---	---	---
RSBN1L	222194	broad.mit.edu	37	7	77333964	77333965	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77333964_77333965delTT	uc010ldt.1	+						RSBN1L_uc003ugm.2_Intron	NM_198467	NP_940869			round spermatid basic protein 1-like							nucleus				ovary(1)	1																		---	---	---	---
PHTF2	57157	broad.mit.edu	37	7	77523208	77523208	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77523208delT	uc003ugs.3	+						PHTF2_uc003ugo.3_Intron|PHTF2_uc003ugp.2_Intron|PHTF2_uc003ugq.3_Intron|PHTF2_uc010ldv.2_Intron|PHTF2_uc003ugr.3_Intron|PHTF2_uc003ugt.3_Intron|PHTF2_uc003ugu.3_Intron	NM_001127357	NP_001120829			putative homeodomain transcription factor 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1																		---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	78343405	78343406	+	Intron	INS	-	GG	GG	rs139501832	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78343405_78343406insGG	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	78383034	78383034	+	Intron	DEL	A	-	-	rs79257544		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78383034delA	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	78415455	78415456	+	Intron	INS	-	A	A	rs111883361		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78415455_78415456insA	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	78556146	78556146	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78556146delT	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	78869503	78869503	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78869503delC	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	79266462	79266462	+	IGR	DEL	T	-	-	rs111277625		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79266462delT								MAGI2 (183572 upstream) : GNAI1 (497678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79494586	79494586	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79494586delA								MAGI2 (411696 upstream) : GNAI1 (269554 downstream)																																			---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	81619865	81619865	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81619865delA	uc003uhr.1	-							NM_000722	NP_000713			calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)													---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	81664661	81664662	+	Intron	INS	-	A	A	rs151299752	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81664661_81664662insA	uc003uhr.1	-							NM_000722	NP_000713			calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)													---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	82058717	82058717	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82058717delA	uc003uhr.1	-							NM_000722	NP_000713			calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	82147865	82147865	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82147865delA								CACNA2D1 (74834 upstream) : PCLO (235456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	82874741	82874741	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82874741delT								PCLO (82544 upstream) : SEMA3E (118481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	83525425	83525425	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83525425delT								SEMA3E (247101 upstream) : SEMA3A (62240 downstream)																																			---	---	---	---
SEMA3A	10371	broad.mit.edu	37	7	83591153	83591153	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83591153delA	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	84104493	84104493	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84104493delT								SEMA3A (280276 upstream) : SEMA3D (520381 downstream)																																			---	---	---	---
SEMA3D	223117	broad.mit.edu	37	7	84666354	84666354	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84666354delA	uc003uic.2	-						SEMA3D_uc010led.2_Intron|SEMA3D_uc003uib.2_Intron	NM_152754	NP_689967			semaphorin 3D precursor						cell differentiation|nervous system development	extracellular region|membrane	receptor activity			ovary(3)|large_intestine(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	85328978	85328978	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85328978delA								SEMA3D (512807 upstream) : GRM3 (944252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	86124104	86124104	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86124104delA								None (None upstream) : GRM3 (149126 downstream)																																			---	---	---	---
KIAA1324L	222223	broad.mit.edu	37	7	86542523	86542523	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86542523delA	uc011kha.1	-						KIAA1324L_uc003uif.1_Intron|KIAA1324L_uc011kgz.1_Intron|KIAA1324L_uc003uie.2_Intron	NM_001142749	NP_001136221			hypothetical protein LOC222223 isoform 1							integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)																	---	---	---	---
KIAA1324L	222223	broad.mit.edu	37	7	86569608	86569608	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86569608delA	uc011kha.1	-						KIAA1324L_uc003uif.1_Intron|KIAA1324L_uc011kgz.1_Intron|KIAA1324L_uc003uie.2_Intron	NM_001142749	NP_001136221			hypothetical protein LOC222223 isoform 1							integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)																	---	---	---	---
ABCB1	5243	broad.mit.edu	37	7	87155481	87155482	+	Intron	DEL	TT	-	-	rs111465883		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87155481_87155482delTT	uc003uiz.1	-						ABCB1_uc011khc.1_Intron	NM_000927	NP_000918			ATP-binding cassette, subfamily B, member 1						G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	88141302	88141302	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88141302delT								STEAP4 (205093 upstream) : ZNF804B (247451 downstream)																																			---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88676108	88676108	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88676108delT	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	89601823	89601823	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89601823delT								ZNF804B (635479 upstream) : DPY19L2P4 (146891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	89733144	89733144	+	IGR	DEL	T	-	-	rs78545735		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89733144delT								ZNF804B (766800 upstream) : DPY19L2P4 (15570 downstream)																																			---	---	---	---
C7orf63	79846	broad.mit.edu	37	7	89884729	89884729	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89884729delT	uc010lep.2	+						C7orf63_uc003ukf.2_Intron|C7orf63_uc003ukg.2_Intron|C7orf63_uc011khj.1_Intron|C7orf63_uc010leo.2_Intron	NM_001039706	NP_001034795			hypothetical protein LOC79846 isoform 1								binding			ovary(1)	1																		---	---	---	---
GTPBP10	85865	broad.mit.edu	37	7	90007438	90007438	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90007438delT	uc003ukm.1	+						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	90127347	90127347	+	Intron	DEL	T	-	-	rs112917496		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90127347delT	uc003ukt.1	+							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	90465903	90465903	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90465903delT	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
MTERF	7978	broad.mit.edu	37	7	91509449	91509449	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91509449delA	uc003ulb.1	-						MTERF_uc010let.1_Intron|MTERF_uc003ulc.1_Intron|MTERF_uc011khm.1_Intron|MTERF_uc010leu.1_Intron	NM_006980	NP_008911			mitochondrial transcription termination factor						DNA geometric change|regulation of transcription, DNA-dependent|termination of mitochondrial transcription	mitochondrial nucleoid	double-stranded DNA binding				0	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)															---	---	---	---
ANKIB1	54467	broad.mit.edu	37	7	91989754	91989755	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91989754_91989755delGT	uc003ulw.2	+							NM_019004	NP_061877			ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)															---	---	---	---
ANKIB1	54467	broad.mit.edu	37	7	92027348	92027348	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92027348delT	uc003ulw.2	+						ANKIB1_uc010lew.1_Intron	NM_019004	NP_061877			ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)															---	---	---	---
PEX1	5189	broad.mit.edu	37	7	92118782	92118782	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92118782delA	uc003uly.2	-						PEX1_uc011khr.1_Intron|PEX1_uc010ley.2_Intron|PEX1_uc011khs.1_Intron	NM_000466	NP_000457			peroxin1						microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)															---	---	---	---
CDK6	1021	broad.mit.edu	37	7	92316105	92316105	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92316105delT	uc011khw.1	-						CDK6_uc010lez.2_Intron	NM_001259	NP_001250			cyclin-dependent kinase 6						cell dedifferentiation|cell division|G1 phase of mitotic cell cycle|gliogenesis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|negative regulation of osteoblast differentiation|positive regulation of cell-matrix adhesion|positive regulation of fibroblast proliferation|regulation of erythrocyte differentiation|regulation of gene expression|response to virus	cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleus|ruffle	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			central_nervous_system(1)|skin(1)	2	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)					T	MLLT10	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	7	92480820	92480820	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92480820delT								CDK6 (14879 upstream) : SAMD9 (248012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	92619171	92619171	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92619171delA								CDK6 (153230 upstream) : SAMD9 (109661 downstream)																																			---	---	---	---
CALCR	799	broad.mit.edu	37	7	93067237	93067237	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93067237delT	uc003umv.1	-						CALCR_uc011kia.1_Intron|CALCR_uc003ums.1_Intron|CALCR_uc003umt.1_Intron|CALCR_uc003umu.1_Intron|CALCR_uc003umw.2_Intron	NM_001742	NP_001733			calcitonin receptor isoform 2 precursor						activation of adenylate cyclase activity by G-protein signaling pathway|elevation of cytosolic calcium ion concentration|positive regulation of adenylate cyclase activity|response to glucocorticoid stimulus	integral to plasma membrane	calcitonin binding|calcitonin binding|calcitonin receptor activity|calcitonin receptor activity|protein binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Salmon Calcitonin(DB00017)													---	---	---	---
GNGT1	2792	broad.mit.edu	37	7	93415829	93415831	+	Intron	DEL	AAA	-	-	rs2724089	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93415829_93415831delAAA	uc003umx.1	+											Homo sapiens guanine nucleotide binding protein gamma 1 (GNG1) mRNA, complete cds.						G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|signal transducer activity				0	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	93799747	93799747	+	IGR	DEL	T	-	-	rs10261798		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93799747delT								BET1 (166057 upstream) : COL1A2 (224126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	93834246	93834246	+	IGR	DEL	T	-	-	rs67217932		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93834246delT								BET1 (200556 upstream) : COL1A2 (189627 downstream)																																			---	---	---	---
CASD1	64921	broad.mit.edu	37	7	94176572	94176572	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94176572delT	uc003uni.3	+						CASD1_uc003unj.3_Intron	NM_022900	NP_075051			CAS1 domain containing 1 precursor							integral to membrane				ovary(2)	2	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)															---	---	---	---
PEG10	23089	broad.mit.edu	37	7	94285913	94285913	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94285913delT	uc011kie.1	+						SGCE_uc003unm.2_5'Flank|SGCE_uc003unl.2_5'Flank|SGCE_uc003unn.2_5'Flank|SGCE_uc011kic.1_5'Flank|SGCE_uc011kid.1_5'Flank	NM_001040152	NP_001035242			paternally expressed 10 isoform RF1						apoptosis|cell differentiation|negative regulation of transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			central_nervous_system(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)													OREG0018170	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PPP1R9A	55607	broad.mit.edu	37	7	94570923	94570924	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94570923_94570924delTT	uc003unp.2	+						PPP1R9A_uc010lfj.2_Intron|PPP1R9A_uc011kif.1_Intron|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_Intron	NM_017650	NP_060120			protein phosphatase 1, regulatory (inhibitor)							cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)												HNSCC(28;0.073)			---	---	---	---
PPP1R9A	55607	broad.mit.edu	37	7	94864174	94864174	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94864174delA	uc003unp.2	+						PPP1R9A_uc010lfj.2_Intron|PPP1R9A_uc011kif.1_Intron|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_Intron	NM_017650	NP_060120			protein phosphatase 1, regulatory (inhibitor)							cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)												HNSCC(28;0.073)			---	---	---	---
DYNC1I1	1780	broad.mit.edu	37	7	95685349	95685349	+	Intron	DEL	T	-	-	rs10712465		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95685349delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	96115478	96115478	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96115478delT	uc003uoh.1	-						uc011kil.1_Intron					RecName: Full=Putative uncharacterized protein FLJ42280;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	96120415	96120416	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96120415_96120416insT	uc003uoh.1	-						uc011kil.1_Intron					RecName: Full=Putative uncharacterized protein FLJ42280;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	96223722	96223723	+	IGR	INS	-	A	A	rs150083062	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96223722_96223723insA								SLC25A13 (272263 upstream) : SHFM1 (78514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96422293	96422293	+	IGR	DEL	A	-	-	rs34721351		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96422293delA								SHFM1 (83090 upstream) : DLX6AS (175535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96729321	96729321	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96729321delA								DLX5 (75178 upstream) : ACN9 (16584 downstream)																																			---	---	---	---
ACN9	57001	broad.mit.edu	37	7	96764377	96764380	+	Intron	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96764377_96764380delTTTT	uc003uoo.3	+							NM_020186	NP_064571			ACN9 homolog precursor						regulation of gluconeogenesis	mitochondrial intermembrane space					0	all_cancers(62;2.54e-08)|all_epithelial(64;2.24e-08)|Esophageal squamous(72;0.00507)|all_lung(186;0.154)|Lung NSC(181;0.159)																	---	---	---	---
ACN9	57001	broad.mit.edu	37	7	96796618	96796618	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96796618delA	uc003uoo.3	+							NM_020186	NP_064571			ACN9 homolog precursor						regulation of gluconeogenesis	mitochondrial intermembrane space					0	all_cancers(62;2.54e-08)|all_epithelial(64;2.24e-08)|Esophageal squamous(72;0.00507)|all_lung(186;0.154)|Lung NSC(181;0.159)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	97064817	97064817	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97064817delA								ACN9 (253744 upstream) : TAC1 (296454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97215783	97215783	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97215783delA								ACN9 (404710 upstream) : TAC1 (145488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97353815	97353818	+	IGR	DEL	TTTG	-	-	rs78162656		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97353815_97353818delTTTG								ACN9 (542742 upstream) : TAC1 (7453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97634173	97634173	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97634173delA								OCM2 (14757 upstream) : LMTK2 (102024 downstream)																																			---	---	---	---
LMTK2	22853	broad.mit.edu	37	7	97752279	97752279	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97752279delT	uc003upd.1	+							NM_014916	NP_055731			lemur tyrosine kinase 2 precursor						early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)																	---	---	---	---
BAIAP2L1	55971	broad.mit.edu	37	7	97972550	97972550	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97972550delA	uc003upj.2	-							NM_018842	NP_061330			BAI1-associated protein 2-like 1						filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
SMURF1	57154	broad.mit.edu	37	7	98628456	98628457	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98628456_98628457insT	uc003upu.1	-						SMURF1_uc003upv.1_Intron|SMURF1_uc003upt.2_Intron|TRRAP_uc003ups.2_Intron	NM_020429	NP_065162			Smad ubiquitination regulatory factor 1 isoform						BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)															---	---	---	---
SMURF1	57154	broad.mit.edu	37	7	98654616	98654617	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98654616_98654617delAA	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)															---	---	---	---
BUD31	8896	broad.mit.edu	37	7	99014637	99014637	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99014637delT	uc003uqf.2	+						BUD31_uc011kiu.1_Intron|BUD31_uc011kiv.1_Intron|BUD31_uc003uqg.3_Intron	NM_003910	NP_003901			G10 protein						regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_cancers(62;1.76e-08)|all_epithelial(64;1.63e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
PTCD1	26024	broad.mit.edu	37	7	99039953	99039953	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99039953delT	uc011kiw.1	-						CPSF4_uc003uqi.2_Intron|CPSF4_uc003uqj.2_Intron|CPSF4_uc003uqk.2_Intron|CPSF4_uc011kix.1_Intron	NM_015545	NP_056360			pentatricopeptide repeat domain 1											ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ZKSCAN1	7586	broad.mit.edu	37	7	99616833	99616833	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99616833delT	uc003usk.1	+						ZKSCAN1_uc003usj.2_Intron|ZKSCAN1_uc003usl.1_Intron|ZKSCAN1_uc003usm.1_Intron	NM_003439	NP_003430			zinc finger protein 36						viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
COPS6	10980	broad.mit.edu	37	7	99687409	99687409	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99687409delA	uc003usu.2	+						COPS6_uc011kjf.1_Frame_Shift_Del_p.*125fs	NM_006833	NP_006824			COP9 signalosome subunit 6						cullin deneddylation|interspecies interaction between organisms	cytoplasm|signalosome	protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
C7orf59	389541	broad.mit.edu	37	7	99750774	99750775	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99750774_99750775delAA	uc003utq.2	+							NM_001008395	NP_001008396			hypothetical protein LOC389541												0																		---	---	---	---
GATS	352954	broad.mit.edu	37	7	99850736	99850736	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99850736delT	uc003uua.3	-						GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc010lgt.2_Intron|GATS_uc010lgu.2_Intron	NM_178831	NP_849153			GATS, stromal antigen 3 opposite strand												0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
GATS	352954	broad.mit.edu	37	7	99851096	99851096	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99851096delT	uc003uua.3	-						GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc010lgt.2_Intron|GATS_uc010lgu.2_Intron	NM_178831	NP_849153			GATS, stromal antigen 3 opposite strand												0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100092883	100092884	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100092883_100092884delAA								C7orf51 (461 upstream) : AGFG2 (43950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	100133751	100133751	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100133751delT								C7orf51 (41329 upstream) : AGFG2 (3083 downstream)																																			---	---	---	---
EPHB4	2050	broad.mit.edu	37	7	100422562	100422562	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100422562delG	uc003uwn.1	-						EPHB4_uc003uwm.1_5'UTR|EPHB4_uc010lhj.1_Intron|EPHB4_uc011kkf.1_Intron|EPHB4_uc011kkg.1_Intron|EPHB4_uc011kkh.1_Intron	NM_004444	NP_004435			EPH receptor B4 precursor						cell proliferation|organ morphogenesis|regulation of angiogenesis	cell surface|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(4)|stomach(3)|skin(3)|central_nervous_system(2)|ovary(2)|breast(1)	15	Lung NSC(181;0.041)|all_lung(186;0.0581)																	---	---	---	---
SLC12A9	56996	broad.mit.edu	37	7	100448345	100448345	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100448345delT	uc003uwp.2	+						SLC12A9_uc003uwo.1_5'Flank|SLC12A9_uc003uwq.2_5'Flank|SLC12A9_uc011kki.1_5'Flank	NM_020246	NP_064631			solute carrier family 12 (potassium/chloride							integral to membrane|plasma membrane	cation:chloride symporter activity				0	Lung NSC(181;0.041)|all_lung(186;0.0581)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100911868	100911868	+	IGR	DEL	A	-	-	rs34186969		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100911868delA								FIS1 (16275 upstream) : RABL5 (44781 downstream)																																			---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101138693	101138694	+	Intron	DEL	TT	-	-	rs35590022		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101138693_101138694delTT	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	101476666	101476666	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101476666delA	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530			cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101664588	101664588	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101664588delT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530			cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101883014	101883014	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101883014delT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530			cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	102131221	102131240	+	5'Flank	DEL	CATTCCCACAGCACCCAGGG	-	-	rs140450517	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102131221_102131240delCATTCCCACAGCACCCAGGG	uc003uzr.1	-						uc011kkt.1_Intron|uc003uzs.1_Intron|uc010lia.1_Intron|uc003uzt.1_Intron|uc003uzu.1_Intron|POLR2J3_uc011kku.1_Intron|uc003uzv.1_Intron|uc010lib.1_Intron|uc011kkv.1_5'Flank					Homo sapiens mRNA for KIAA0538 protein, partial cds.																														---	---	---	---
DNAJC2	27000	broad.mit.edu	37	7	102971412	102971412	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102971412delT	uc003vbo.2	-						DNAJC2_uc003vbn.2_Intron|DNAJC2_uc010lix.2_Intron|DNAJC2_uc003vbp.2_Intron|DNAJC2_uc003vbq.1_Intron	NM_014377	NP_055192			DnaJ (Hsp40) homolog, subfamily C, member 2						'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1																		---	---	---	---
SLC26A5	375611	broad.mit.edu	37	7	103015124	103015125	+	Intron	DEL	TT	-	-	rs72245175		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103015124_103015125delTT	uc003vbz.2	-						SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|SLC26A5_uc003vbw.2_Intron|SLC26A5_uc003vbx.2_Intron|SLC26A5_uc003vby.2_Intron|SLC26A5_uc010liy.2_Intron	NM_198999	NP_945350			prestin isoform a						regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity			ovary(1)	1																		---	---	---	---
SLC26A5	375611	broad.mit.edu	37	7	103051094	103051094	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103051094delT	uc003vbz.2	-						SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|SLC26A5_uc003vbw.2_Intron|SLC26A5_uc003vbx.2_Intron|SLC26A5_uc003vby.2_Intron|SLC26A5_uc010liy.2_Intron	NM_198999	NP_945350			prestin isoform a						regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity			ovary(1)	1																		---	---	---	---
RELN	5649	broad.mit.edu	37	7	103129651	103129652	+	Intron	DEL	GT	-	-	rs111672292		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103129651_103129652delGT	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	104064563	104064563	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104064563delA	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	104430915	104430915	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104430915delT	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
SRPK2	6733	broad.mit.edu	37	7	104875248	104875248	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104875248delA	uc003vct.2	-						SRPK2_uc003vcu.2_Intron|SRPK2_uc003vcv.2_Intron|SRPK2_uc003vcw.1_Intron	NM_182691	NP_872633			serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	105054869	105054869	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105054869delA								SRPK2 (15071 upstream) : PUS7 (42093 downstream)																																			---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105248197	105248198	+	3'UTR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105248197_105248198delAG	uc003vde.2	-	12					ATXN7L1_uc003vdf.2_3'UTR	NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
CDHR3	222256	broad.mit.edu	37	7	105672824	105672824	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105672824delT	uc003vdl.3	+						CDHR3_uc003vdk.2_Intron|CDHR3_uc003vdm.3_Intron|CDHR3_uc011klt.1_Intron|CDHR3_uc003vdn.2_Intron	NM_152750	NP_689963			hypothetical protein LOC222256 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	106289571	106289572	+	Intron	INS	-	AC	AC	rs149714036	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106289571_106289572insAC	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	106291575	106291576	+	Intron	INS	-	AGT	AGT	rs151282190	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106291575_106291576insAGT	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	106345289	106345290	+	Intron	DEL	TC	-	-	rs141676976		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106345289_106345290delTC	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	106369639	106369639	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106369639delA	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																														---	---	---	---
LAMB4	22798	broad.mit.edu	37	7	107698419	107698419	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107698419delA	uc010ljo.1	-						LAMB4_uc003vey.2_Intron|LAMB4_uc010ljp.1_Intron	NM_007356	NP_031382			laminin, beta 4 precursor						cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8																		---	---	---	---
LAMB4	22798	broad.mit.edu	37	7	107749452	107749452	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107749452delT	uc010ljo.1	-						LAMB4_uc003vey.2_Intron	NM_007356	NP_031382			laminin, beta 4 precursor						cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108103777	108103777	+	IGR	DEL	A	-	-	rs1859771	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108103777delA								NRCAM (6951 upstream) : PNPLA8 (8294 downstream)																																			---	---	---	---
PNPLA8	50640	broad.mit.edu	37	7	108154532	108154532	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108154532delT	uc003vff.1	-						PNPLA8_uc003vfg.1_Intron|PNPLA8_uc003vfh.1_Intron|PNPLA8_uc003vfi.1_Intron|PNPLA8_uc003vfj.1_Intron|PNPLA8_uc003vfk.1_Intron	NM_015723	NP_056538			patatin-like phospholipase domain containing 8						fatty acid metabolic process|lipid catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|membrane fraction|perinuclear region of cytoplasm|peroxisomal membrane	ATP binding|calcium-independent phospholipase A2 activity|lysophospholipase activity			breast(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108255193	108255194	+	IGR	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108255193_108255194delGA								DNAJB9 (39901 upstream) : C7orf66 (268846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108536206	108536207	+	IGR	INS	-	A	A	rs74944127	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108536206_108536207insA								C7orf66 (11569 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	109742146	109742146	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109742146delA								EIF3IP1 (141876 upstream) : IMMP2L (560964 downstream)																																			---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	110393807	110393808	+	Intron	DEL	GG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110393807_110393808delGG	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	110415306	110415317	+	Intron	DEL	TGTGTGTGTGTG	-	-	rs112351441		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110415306_110415317delTGTGTGTGTGTG	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron	NM_032549	NP_115938			IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)														---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	110543833	110543833	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110543833delT	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	110633173	110633173	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110633173delT	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938			IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)														---	---	---	---
LRRN3	54674	broad.mit.edu	37	7	110764989	110764989	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110764989delA	uc003vft.3	+	4					IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_3'UTR|LRRN3_uc003vfs.3_3'UTR	NM_001099660	NP_001093130			leucine rich repeat neuronal 3 precursor							integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)														---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111688782	111688782	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111688782delA	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron|DOCK4_uc010ljt.1_Intron	NM_014705	NP_055520			dedicator of cytokinesis 4						cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)																---	---	---	---
ZNF277	11179	broad.mit.edu	37	7	111892686	111892686	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111892686delT	uc003vge.2	+						ZNF277_uc003vgd.2_Intron|ZNF277_uc003vgf.2_Intron|ZNF277_uc003vgc.2_Intron	NM_021994	NP_068834			zinc finger protein (C2H2 type) 277							nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|breast(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	112320054	112320054	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112320054delA								C7orf53 (189119 upstream) : TMEM168 (85735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	112361898	112361899	+	IGR	DEL	TT	-	-	rs138841321	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112361898_112361899delTT								C7orf53 (230963 upstream) : TMEM168 (43890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	112827633	112827635	+	IGR	DEL	TTT	-	-	rs111522596		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112827633_112827635delTTT								LOC401397 (68996 upstream) : PPP1R3A (689247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	112934198	112934199	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112934198_112934199delAA								LOC401397 (175561 upstream) : PPP1R3A (582683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	113408254	113408254	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113408254delT								LOC401397 (649617 upstream) : PPP1R3A (108628 downstream)																																			---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	113900900	113900900	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113900900delA	uc003vgu.2	+						FOXP2_uc003vgt.1_Intron					Homo sapiens full length insert cDNA clone YX52E07.						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8																		---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	113937110	113937110	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113937110delT	uc003vgv.1	+						FOXP2_uc003vgu.2_Intron|FOXP2_uc003vgt.1_Intron	NM_014491	NP_055306			forkhead box P2 isoform I						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8																		---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	114210823	114210823	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114210823delA	uc003vhb.2	+						FOXP2_uc003vgu.2_Intron|FOXP2_uc003vgz.2_Intron|FOXP2_uc003vha.2_Intron|FOXP2_uc011kmu.1_Intron|FOXP2_uc011kmv.1_Intron|FOXP2_uc003vgt.1_Intron|FOXP2_uc003vgv.1_Intron|FOXP2_uc003vgw.2_Intron|FOXP2_uc003vgx.2_Intron|FOXP2_uc003vhd.2_Intron|FOXP2_uc003vhc.2_Intron	NM_014491	NP_055306			forkhead box P2 isoform I						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8																		---	---	---	---
MDFIC	29969	broad.mit.edu	37	7	114655528	114655528	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114655528delT	uc003vhf.2	+							NM_199072	NP_951038			MyoD family inhibitor domain containing protein						activation of JUN kinase activity|interspecies interaction between organisms|negative regulation of protein import into nucleus|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|regulation of Wnt receptor signaling pathway|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleolus|nucleolus|nucleus	cyclin binding|Tat protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	114731286	114731287	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114731286_114731287insA	uc003vhh.1	+											Homo sapiens, clone IMAGE:4276820, mRNA.																														---	---	---	---
TFEC	22797	broad.mit.edu	37	7	115679476	115679477	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115679476_115679477delTG	uc011kmw.1	-											SubName: Full=cDNA FLJ55256, highly similar to Homo sapiens transcription factor EC (TFEC), transcript variant 1, mRNA;							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			large_intestine(1)	1			STAD - Stomach adenocarcinoma(10;0.00878)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	115837913	115837913	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115837913delT								TFEC (37963 upstream) : TES (12668 downstream)																																			---	---	---	---
CAV1	857	broad.mit.edu	37	7	115943275	115943275	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115943275delA	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|uc003vhu.1_Intron|uc003vhs.1_Intron|uc003vht.1_Intron|uc003vhy.1_Intron	NM_001753	NP_001744			caveolin 1						blood coagulation|calcium ion transport|caveola assembly|cellular response to starvation|cholesterol homeostasis|cytosolic calcium ion homeostasis|inactivation of MAPK activity|interspecies interaction between organisms|leukocyte migration|lipid storage|maintenance of protein location in cell|mammary gland involution|membrane depolarization|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of endothelial cell proliferation|negative regulation of epithelial cell differentiation|negative regulation of nitric oxide biosynthetic process|negative regulation of peptidyl-serine phosphorylation|negative regulation of protein binding|negative regulation of transcription from RNA polymerase II promoter|nitric oxide homeostasis|nitric oxide metabolic process|positive regulation of calcium ion transport into cytosol|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of metalloenzyme activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of vasoconstriction|protein homooligomerization|receptor internalization|regulation of blood coagulation|regulation of fatty acid metabolic process|regulation of nitric-oxide synthase activity|regulation of smooth muscle contraction|response to calcium ion|response to estrogen stimulus|response to hypoxia|response to progesterone stimulus|skeletal muscle tissue development|T cell costimulation|triglyceride metabolic process|vasculogenesis|vesicle organization	apical plasma membrane|basolateral plasma membrane|caveola|caveola|cytosol|endoplasmic reticulum|endosome|Golgi membrane|lipid particle|perinuclear region of cytoplasm	cholesterol binding|nitric-oxide synthase binding|peptidase activator activity|protein binding|protein complex scaffold|receptor binding				0	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	116270014	116270015	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116270014_116270015delAA								CAV1 (68784 upstream) : MET (42444 downstream)																																			---	---	---	---
ST7	7982	broad.mit.edu	37	7	116621169	116621169	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116621169delT	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron	NM_021908	NP_068708			suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)														---	---	---	---
ST7	7982	broad.mit.edu	37	7	116841615	116841617	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116841615_116841617delTTT	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_Intron|ST7_uc003vir.2_Intron|ST7_uc011knn.1_Intron|ST7OT3_uc003viy.1_Intron	NM_021908	NP_068708			suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)														---	---	---	---
WNT2	7472	broad.mit.edu	37	7	116924682	116924682	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116924682delT	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)														---	---	---	---
ASZ1	136991	broad.mit.edu	37	7	117057242	117057242	+	Intron	DEL	A	-	-	rs5886856		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117057242delA	uc003vjb.2	-						ASZ1_uc011kno.1_Intron|ASZ1_uc011knp.1_Intron	NM_130768	NP_570124			ankyrin repeat, SAM and basic leucine zipper						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)															---	---	---	---
CFTR	1080	broad.mit.edu	37	7	117188929	117188929	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117188929delT	uc003vjd.2	+						CFTR_uc011knq.1_Intron	NM_000492	NP_000483			cystic fibrosis transmembrane conductance						respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)									Cystic_Fibrosis				---	---	---	---
Unknown	0	broad.mit.edu	37	7	117339404	117339404	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117339404delT								CFTR (30688 upstream) : CTTNBP2 (11304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118018798	118018799	+	IGR	INS	-	TC	TC	rs145250726	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118018798_118018799insTC								ANKRD7 (136016 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118233861	118233861	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118233861delA								ANKRD7 (351079 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	119530619	119530620	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119530619_119530620delAC								None (None upstream) : KCND2 (383102 downstream)																																			---	---	---	---
KCND2	3751	broad.mit.edu	37	7	120072556	120072559	+	Intron	DEL	CACA	-	-	rs149747676		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120072556_120072559delCACA	uc003vjj.1	+							NM_012281	NP_036413			potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
PTPRZ1	5803	broad.mit.edu	37	7	121602629	121602629	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121602629delT	uc003vjy.2	+						PTPRZ1_uc003vjz.2_Intron	NM_002851	NP_002842			protein tyrosine phosphatase, receptor-type,						central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9																		---	---	---	---
PTPRZ1	5803	broad.mit.edu	37	7	121674544	121674544	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121674544delT	uc003vjy.2	+						PTPRZ1_uc003vjz.2_Intron|PTPRZ1_uc011knt.1_Intron	NM_002851	NP_002842			protein tyrosine phosphatase, receptor-type,						central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9																		---	---	---	---
FEZF1	389549	broad.mit.edu	37	7	121941782	121941782	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121941782delA	uc003vkd.2	-	4					FEZF1_uc003vkc.2_3'UTR|uc010lko.1_5'Flank	NM_001024613	NP_001019784			FEZ family zinc finger 1 isoform 1						cell differentiation|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|breast(1)	3																		---	---	---	---
CADPS2	93664	broad.mit.edu	37	7	122366828	122366829	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122366828_122366829delAA	uc010lkp.2	-						CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424			Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	122594429	122594429	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122594429delT								CADPS2 (67875 upstream) : TAS2R16 (40330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	123478610	123478610	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123478610delA								HYALP1 (19126 upstream) : HYAL4 (6613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	123548375	123548375	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123548375delA								HYAL4 (30846 upstream) : SPAM1 (16954 downstream)																																			---	---	---	---
SPAM1	6677	broad.mit.edu	37	7	123573917	123573918	+	Intron	DEL	AT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123573917_123573918delAT	uc003vld.2	+						SPAM1_uc003vle.2_Intron|SPAM1_uc003vlf.3_Intron|SPAM1_uc010lku.2_Intron	NM_153189	NP_694859			sperm adhesion molecule 1 isoform 2						binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	123716894	123716894	+	Intron	DEL	C	-	-	rs4731140	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123716894delC	uc011koc.1	+											Homo sapiens disrupted in Rett 1 mRNA sequence.																														---	---	---	---
POT1	25913	broad.mit.edu	37	7	124514788	124514788	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124514788delA	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	125015755	125015755	+	IGR	DEL	A	-	-	rs67827223		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125015755delA								POT1 (445718 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	125049986	125049986	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125049986delC								POT1 (479949 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	125494489	125494500	+	IGR	DEL	GACCATAGCCTA	-	-	rs72004011		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125494489_125494500delGACCATAGCCTA								POT1 (924452 upstream) : GRM8 (584152 downstream)																																			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126125338	126125338	+	Intron	DEL	A	-	-	rs11347674		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126125338delA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)										HNSCC(24;0.065)			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126806332	126806332	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126806332delT	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)										HNSCC(24;0.065)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	127242859	127242859	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127242859delA								FSCN3 (1016 upstream) : PAX4 (7487 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	127784982	127784982	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127784982delT								SND1 (52324 upstream) : MIR129-1 (62943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	127794664	127794664	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127794664delA								SND1 (62006 upstream) : MIR129-1 (53261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	127904696	127904697	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127904696_127904697delAC								LEP (7014 upstream) : RBM28 (45739 downstream)																																			---	---	---	---
RBM28	55131	broad.mit.edu	37	7	127968572	127968572	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127968572delT	uc003vmp.2	-						RBM28_uc003vmo.2_Intron|RBM28_uc011koj.1_Intron|RBM28_uc011kok.1_Intron	NM_018077	NP_060547			RNA binding motif protein 28						mRNA processing|RNA splicing	Golgi apparatus|nucleolus|spliceosomal complex	nucleotide binding|RNA binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	128249447	128249447	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128249447delT								METTL2B (106470 upstream) : FLJ45340 (31848 downstream)																																			---	---	---	---
FAM71F2	346653	broad.mit.edu	37	7	128312236	128312236	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128312236delT	uc003vnk.3	+						FAM71F2_uc010llm.1_5'Flank|FAM71F2_uc003vnl.2_5'Flank|FAM71F2_uc010lln.1_5'Flank	NM_001012454	NP_001012457			hypothetical protein LOC346653 isoform a												0																		---	---	---	---
CALU	813	broad.mit.edu	37	7	128404783	128404783	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128404783delT	uc003vns.2	+						CALU_uc003vnq.2_Intron|CALU_uc003vnr.2_Intron	NM_001130674	NP_001124146			calumenin isoform b precursor						platelet activation|platelet degranulation	extracellular region|Golgi apparatus|melanosome|sarcoplasmic reticulum lumen	calcium ion binding|protein binding				0																		---	---	---	---
CALU	813	broad.mit.edu	37	7	128408006	128408006	+	Intron	DEL	T	-	-	rs79883365		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128408006delT	uc003vns.2	+						CALU_uc003vnq.2_Intron|CALU_uc003vnr.2_Intron	NM_001130674	NP_001124146			calumenin isoform b precursor						platelet activation|platelet degranulation	extracellular region|Golgi apparatus|melanosome|sarcoplasmic reticulum lumen	calcium ion binding|protein binding				0																		---	---	---	---
TNPO3	23534	broad.mit.edu	37	7	128650396	128650396	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128650396delT	uc003vol.1	-						TNPO3_uc003vom.1_Intron|TNPO3_uc010lly.1_Intron|TNPO3_uc010llz.1_Intron	NM_012470	NP_036602			transportin 3						splicing factor protein import into nucleus	cytoplasm|nucleus	protein binding|receptor activity			ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
TSPAN33	340348	broad.mit.edu	37	7	128783684	128783684	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128783684delT	uc003vop.1	+							NM_178562	NP_848657			tetraspanin 33							integral to membrane				ovary(1)	1																		---	---	---	---
AHCYL2	23382	broad.mit.edu	37	7	128919231	128919231	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128919231delC	uc011kov.1	+						AHCYL2_uc003vot.2_Intron	NM_015328	NP_056143			S-adenosylhomocysteine hydrolase-like 2 isoform						one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2																		---	---	---	---
FAM40B	57464	broad.mit.edu	37	7	129097774	129097774	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129097774delA	uc011koy.1	+						FAM40B_uc003vow.2_Intron|FAM40B_uc011koz.1_5'Flank	NM_020704	NP_065755			hypothetical protein LOC57464 isoform a												0																		---	---	---	---
NRF1	4899	broad.mit.edu	37	7	129357028	129357028	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129357028delT	uc003voz.2	+						NRF1_uc003vpa.2_Intron|NRF1_uc011kpa.1_Intron|NRF1_uc003vpb.2_Intron	NM_005011	NP_005002			nuclear respiratory factor 1						generation of precursor metabolites and energy|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1																		---	---	---	---
UBE2H	7328	broad.mit.edu	37	7	129497297	129497297	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129497297delT	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)																	---	---	---	---
TMEM209	84928	broad.mit.edu	37	7	129813798	129813798	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129813798delT	uc003vpn.2	-						TMEM209_uc010lmc.1_Intron	NM_032842	NP_116231			transmembrane protein 209							integral to membrane				ovary(2)|large_intestine(1)	3	Melanoma(18;0.0435)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	129968020	129968020	+	IGR	DEL	A	-	-	rs9690202	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129968020delA								CPA4 (4001 upstream) : CPA5 (16610 downstream)																																			---	---	---	---
CPA5	93979	broad.mit.edu	37	7	129989560	129989592	+	Intron	DEL	CAAAAATTAAAAATTACAAAAAAACCTGTATCC	-	-	rs11272432	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129989560_129989592delCAAAAATTAAAAATTACAAAAAAACCTGTATCC	uc010lmd.1	+						CPA5_uc003vps.2_Intron|CPA5_uc003vpt.2_Intron|CPA5_uc010lme.1_Intron|CPA5_uc003vpu.1_Intron	NM_001127441	NP_001120913			carboxypeptidase A5 isoform 1						proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2	Melanoma(18;0.0435)																	---	---	---	---
TSGA14	95681	broad.mit.edu	37	7	130039100	130039100	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130039100delT	uc003vpz.2	-						TSGA14_uc003vpy.2_Intron|TSGA14_uc010lmf.2_Intron|TSGA14_uc003vqa.2_Intron|TSGA14_uc011kpg.1_Intron	NM_018718	NP_061188			testis specific, 14						G2/M transition of mitotic cell cycle	centrosome|cytosol					0	Melanoma(18;0.0435)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	130085917	130085917	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130085917delT								TSGA14 (5063 upstream) : MEST (40129 downstream)																																			---	---	---	---
COPG2	26958	broad.mit.edu	37	7	130147428	130147429	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130147428_130147429delTT	uc003vqh.1	-							NM_012133	NP_036265			coatomer protein complex, subunit gamma 2						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)																	---	---	---	---
COPG2	26958	broad.mit.edu	37	7	130283027	130283027	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130283027delT	uc003vqh.1	-							NM_012133	NP_036265			coatomer protein complex, subunit gamma 2						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)																	---	---	---	---
TSGA13	114960	broad.mit.edu	37	7	130357306	130357307	+	Intron	DEL	TT	-	-	rs71960059		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130357306_130357307delTT	uc003vqi.2	-						TSGA13_uc003vqj.2_Intron	NM_052933	NP_443165			testis specific, 13											ovary(2)	2	Melanoma(18;0.0435)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	130552245	130552245	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130552245delT	uc003vql.1	+											full-length cDNA clone CS0DI009YJ20 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
FLJ43663	378805	broad.mit.edu	37	7	130661521	130661523	+	Intron	DEL	AAC	-	-	rs143787980		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130661521_130661523delAAC	uc011kpk.1	-						FLJ43663_uc003vqo.1_Intron|FLJ43663_uc003vqp.2_Intron|FLJ43663_uc003vqq.2_Intron	NR_024153				Homo sapiens cDNA FLJ43663 fis, clone SYNOV4005989.												0																		---	---	---	---
FLJ43663	378805	broad.mit.edu	37	7	130776448	130776448	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130776448delA	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	130905211	130905212	+	Intron	INS	-	A	A	rs72581250		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130905211_130905212insA	uc011kpl.1	+							NM_001145354	NP_001138826			muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	131361032	131361032	+	IGR	DEL	T	-	-	rs66906080		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131361032delT								PODXL (119656 upstream) : PLXNA4 (447060 downstream)																																			---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	131810378	131810378	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131810378delT	uc003vra.3	-	32					PLXNA4_uc003vqz.3_3'UTR	NM_020911	NP_065962			plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
CHCHD3	54927	broad.mit.edu	37	7	132570508	132570508	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132570508delA	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																		---	---	---	---
CHCHD3	54927	broad.mit.edu	37	7	132682212	132682212	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132682212delA	uc003vre.2	-						CHCHD3_uc010lmi.2_Intron|CHCHD3_uc003vrf.2_Intron|CHCHD3_uc010lmj.2_Intron|CHCHD3_uc011kpn.1_Intron	NM_017812	NP_060282			coiled-coil-helix-coiled-coil-helix domain						inner mitochondrial membrane organization|mitochondrial fusion	mitochondrial inner membrane	protein complex scaffold				0																		---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	132975788	132975788	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132975788delT	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vri.2_Intron|EXOC4_uc003vrj.2_Intron	NM_021807	NP_068579			SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)																---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133310961	133310961	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133310961delA	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	133586048	133586048	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133586048delT	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)																---	---	---	---
WDR91	29062	broad.mit.edu	37	7	134874036	134874036	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134874036delA	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																		---	---	---	---
CNOT4	4850	broad.mit.edu	37	7	135157789	135157789	+	Intron	DEL	A	-	-	rs112724701		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135157789delA	uc003vsv.1	-						CNOT4_uc003vss.2_Intron|CNOT4_uc011kpz.1_Intron|CNOT4_uc003vst.2_Intron|CNOT4_uc003vsu.1_Intron	NM_001008225	NP_001008226			CCR4-NOT transcription complex, subunit 4						nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	135208384	135208384	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135208384delA								CNOT4 (13533 upstream) : NUP205 (34278 downstream)																																			---	---	---	---
SLC13A4	26266	broad.mit.edu	37	7	135411319	135411323	+	Intron	DEL	AGGGA	-	-	rs66494820		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135411319_135411323delAGGGA	uc003vta.2	-						SLC13A4_uc003vtb.2_Intron|SLC13A4_uc003vtc.1_Intron	NM_012450	NP_036582			solute carrier family 13 (sodium/sulfate							integral to plasma membrane	sodium:sulfate symporter activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	136912087	136912088	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136912087_136912088insT								CHRM2 (210316 upstream) : PTN (4 downstream)																																			---	---	---	---
PTN	5764	broad.mit.edu	37	7	136932811	136932811	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136932811delA	uc003vtq.2	-						PTN_uc010lmx.2_Intron|PTN_uc003vtr.1_Intron	NM_002825	NP_002816			pleiotrophin						nervous system development|positive regulation of cell division|positive regulation of cell proliferation|transmembrane receptor protein tyrosine phosphatase signaling pathway	endoplasmic reticulum|extracellular space	growth factor activity|heparin binding|protein phosphatase inhibitor activity			upper_aerodigestive_tract(1)|pancreas(1)	2																		---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137294115	137294115	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137294115delT	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																		---	---	---	---
TRIM24	8805	broad.mit.edu	37	7	138186730	138186730	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138186730delA	uc003vuc.2	+						TRIM24_uc003vub.2_Intron	NM_015905	NP_056989			transcriptional intermediary factor 1 alpha						cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter	cytoplasm	chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1)	8																		---	---	---	---
UBN2	254048	broad.mit.edu	37	7	138989453	138989454	+	3'UTR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138989453_138989454delGT	uc011kqr.1	+	18						NM_173569	NP_775840			ubinuclein 2											ovary(1)|skin(1)	2																		---	---	---	---
LUC7L2	51631	broad.mit.edu	37	7	139081022	139081022	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139081022delA	uc003vux.2	+						LUC7L2_uc011kqs.1_Intron|LUC7L2_uc011kqt.1_Intron|LUC7L2_uc003vuy.2_Intron|LUC7L2_uc003vuz.1_Intron|LUC7L2_uc003vva.2_Intron	NM_016019	NP_057103			LUC7-like 2								enzyme binding|metal ion binding				0	Melanoma(164;0.242)																	---	---	---	---
JHDM1D	80853	broad.mit.edu	37	7	139820179	139820179	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139820179delA	uc003vvm.2	-						JHDM1D_uc010lng.2_5'Flank	NM_030647	NP_085150			jumonji C domain containing histone demethylase						midbrain development|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1	Melanoma(164;0.0142)																	---	---	---	---
JHDM1D	80853	broad.mit.edu	37	7	139826263	139826263	+	Intron	DEL	A	-	-	rs79442932		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139826263delA	uc003vvm.2	-							NM_030647	NP_085150			jumonji C domain containing histone demethylase						midbrain development|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1	Melanoma(164;0.0142)																	---	---	---	---
JHDM1D	80853	broad.mit.edu	37	7	139844511	139844512	+	Intron	DEL	AC	-	-	rs35190810		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139844511_139844512delAC	uc003vvm.2	-							NM_030647	NP_085150			jumonji C domain containing histone demethylase						midbrain development|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1	Melanoma(164;0.0142)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	139958829	139958829	+	IGR	DEL	T	-	-	rs2471302	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139958829delT								LOC100134229 (79390 upstream) : SLC37A3 (74725 downstream)																																			---	---	---	---
SLC37A3	84255	broad.mit.edu	37	7	140053520	140053521	+	Intron	INS	-	T	T	rs111484557		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140053520_140053521insT	uc003vvo.2	-						SLC37A3_uc003vvp.2_Intron|SLC37A3_uc010lnh.2_Intron|SLC37A3_uc011kqz.1_Intron|SLC37A3_uc011kra.1_Intron|SLC37A3_uc011krb.1_Intron	NM_207113	NP_996996			solute carrier family 37 (glycerol-3-phosphate						carbohydrate transport|transmembrane transport	integral to membrane				ovary(3)	3	Melanoma(164;0.0142)																	---	---	---	---
SLC37A3	84255	broad.mit.edu	37	7	140064059	140064059	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140064059delA	uc003vvo.2	-						SLC37A3_uc003vvp.2_Intron|SLC37A3_uc010lnh.2_Intron|SLC37A3_uc011kqz.1_Intron|SLC37A3_uc011kra.1_Intron|SLC37A3_uc011krb.1_Intron	NM_207113	NP_996996			solute carrier family 37 (glycerol-3-phosphate						carbohydrate transport|transmembrane transport	integral to membrane				ovary(3)	3	Melanoma(164;0.0142)																	---	---	---	---
RAB19	401409	broad.mit.edu	37	7	140102019	140102019	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140102019delT	uc010lni.2	+						uc003vvq.1_RNA	NM_001008749	NP_001008749			RAB19, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0	Melanoma(164;0.0142)																	---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140249024	140249024	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140249024delA	uc010lnj.2	-						DENND2A_uc011kre.1_Intron|DENND2A_uc010lnk.2_Intron|DENND2A_uc003vvw.2_Intron|DENND2A_uc003vvx.2_Intron	NM_015689	NP_056504			DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140327489	140327489	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140327489delT	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)																	---	---	---	---
ADCK2	90956	broad.mit.edu	37	7	140370192	140370192	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140370192delT	uc003vvy.1	+						ADCK2_uc003vvz.2_5'Flank	NM_052853	NP_443085			aarF domain containing kinase 2							integral to membrane	ATP binding|protein serine/threonine kinase activity				0	Melanoma(164;0.00956)																	---	---	---	---
ADCK2	90956	broad.mit.edu	37	7	140379951	140379951	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140379951delT	uc003vvy.1	+						ADCK2_uc003vvz.2_Intron	NM_052853	NP_443085			aarF domain containing kinase 2							integral to membrane	ATP binding|protein serine/threonine kinase activity				0	Melanoma(164;0.00956)																	---	---	---	---
BRAF	673	broad.mit.edu	37	7	140549865	140549865	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140549865delT	uc003vwc.3	-							NM_004333	NP_004324			B-Raf						activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				---	---	---	---
AGK	55750	broad.mit.edu	37	7	141314051	141314051	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141314051delT	uc003vwi.2	+						AGK_uc011krg.1_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	141564490	141564491	+	IGR	INS	-	TC	TC	rs147660813	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141564490_141564491insTC								PRSS37 (23205 upstream) : OR9A4 (54185 downstream)																																			---	---	---	---
TAS2R38	5726	broad.mit.edu	37	7	141673000	141673001	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141673000_141673001insA	uc003vwx.1	-	1	573_574	c.489_490insT	c.(487-492)TTTAGCfs	p.F163fs		NM_176817	NP_789787	P59533	T2R38_HUMAN	taste receptor, type 2, member 38	163_164	Extracellular (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			kidney(1)|skin(1)	2	Melanoma(164;0.0171)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	141947300	141947301	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141947300_141947301insC								LOC100124692 (26212 upstream) : TRYX3 (4663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	142142824	142142824	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142142824delA	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	142392452	142392452	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142392452delA	uc011krp.1	+						uc011krr.1_Intron|uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc011ksg.1_Intron					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																														---	---	---	---
C7orf34	135927	broad.mit.edu	37	7	142636600	142636601	+	5'Flank	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142636600_142636601insG	uc003wca.2	+							NM_178829	NP_849151			hypothetical protein LOC135927							extracellular region					0	Melanoma(164;0.059)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	142895760	142895760	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142895760delT								TAS2R39 (14233 upstream) : TAS2R40 (23412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	143610924	143610924	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143610924delT								FAM115A (11705 upstream) : OR2F2 (21402 downstream)																																			---	---	---	---
OR2A2	442361	broad.mit.edu	37	7	143806449	143806449	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143806449delT	uc011ktz.1	+							NM_001005480	NP_001005480			olfactory receptor, family 2, subfamily A,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	Melanoma(164;0.0783)																	---	---	---	---
TPK1	27010	broad.mit.edu	37	7	144174371	144174371	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144174371delA	uc003weq.2	-						TPK1_uc003weo.2_Intron|TPK1_uc003wep.2_Intron|TPK1_uc003wer.2_Intron|TPK1_uc003wes.2_Intron	NM_022445	NP_071890			thiamin pyrophosphokinase 1 isoform a						thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	144631522	144631524	+	IGR	DEL	TTT	-	-	rs111506956		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144631522_144631524delTTT								TPK1 (98376 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145159623	145159623	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145159623delT								TPK1 (626477 upstream) : CNTNAP2 (653830 downstream)																																			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146193756	146193756	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146193756delT	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	146693763	146693763	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146693763delT	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	147023024	147023024	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147023024delT	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	147454537	147454537	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147454537delT	uc003weu.1	+							NM_014141	NP_054860			cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	148243434	148243434	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148243434delA								CNTNAP2 (125348 upstream) : C7orf33 (44223 downstream)																																			---	---	---	---
EZH2	2146	broad.mit.edu	37	7	148516252	148516252	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148516252delA	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	149438160	149438161	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149438160_149438161delAA								KRBA1 (6498 upstream) : ZNF467 (23112 downstream)																																			---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149526342	149526342	+	Intron	DEL	C	-	-	rs72369277		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149526342delC	uc010lpk.2	+						SSPO_uc003wgh.2_Intron	NM_198455	NP_940857			SCO-spondin precursor						cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
ABP1	26	broad.mit.edu	37	7	150552119	150552126	+	Intron	DEL	TATGAAAA	-	-	rs144136244		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150552119_150552126delTATGAAAA	uc003why.1	+						ABP1_uc003whz.1_Intron|ABP1_uc003wia.1_Intron	NM_001091	NP_001082			amiloride binding protein 1 precursor						amine metabolic process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)|skin(2)	6	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	150592029	150592029	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150592029delT								ABP1 (33650 upstream) : KCNH2 (50021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	150629786	150629786	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150629786delA								ABP1 (71407 upstream) : KCNH2 (12264 downstream)																																			---	---	---	---
ATG9B	285973	broad.mit.edu	37	7	150721484	150721484	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150721484delC	uc011kvc.1	-	1	103	c.27delG	c.(25-27)GGGfs	p.G9fs	ATG9B_uc003wig.3_5'Flank	NM_173681	NP_775952	Q674R7	ATG9B_HUMAN	ATG9 autophagy related 9 homolog B	9	Cytoplasmic (By similarity).				autophagic vacuole assembly	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane				ovary(1)	1	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
NUB1	51667	broad.mit.edu	37	7	151053367	151053367	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151053367delT	uc003wjx.2	+						NUB1_uc003wjv.2_Intron|NUB1_uc003wjw.2_Intron|NUB1_uc010lqb.2_Intron|NUB1_uc003wjy.2_Intron|NUB1_uc011kvj.1_Intron|NUB1_uc010lqc.2_Intron	NM_016118	NP_057202			NEDD8 ultimate buster-1						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|response to interferon-gamma|response to tumor necrosis factor|ubiquitin-dependent protein catabolic process	nucleus	protein binding				0			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)														---	---	---	---
GALNTL5	168391	broad.mit.edu	37	7	151707205	151707205	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151707205delT	uc003wkp.2	+						GALNTL5_uc003wkq.2_Intron|GALNTL5_uc003wkr.2_Intron|GALNTL5_uc003wks.2_Intron|GALNTL5_uc010lqf.2_Intron	NM_145292	NP_660335			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151949945	151949946	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151949945_151949946delTT	uc003wla.2	-							NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	152101372	152101373	+	Intron	INS	-	TTTAG	TTTAG	rs149946595		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152101372_152101373insTTTAG	uc003wla.2	-							NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	152106492	152106495	+	Intron	DEL	AAGA	-	-	rs76883025		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152106492_152106495delAAGA	uc003wla.2	-							NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	152106898	152106898	+	Intron	DEL	A	-	-	rs10707629		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152106898delA	uc003wla.2	-							NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
Unknown	0	broad.mit.edu	37	7	152252007	152252008	+	IGR	DEL	TG	-	-	rs72462568		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152252007_152252008delTG								LOC100128822 (89379 upstream) : XRCC2 (91581 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	152304693	152304693	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152304693delT								LOC100128822 (142065 upstream) : XRCC2 (38896 downstream)																																			---	---	---	---
DPP6	1804	broad.mit.edu	37	7	153827185	153827185	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153827185delA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	153983890	153983892	+	Intron	DEL	TTT	-	-	rs113416741	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153983890_153983892delTTT	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	154645548	154645548	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154645548delT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	154971006	154971006	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154971006delA								HTR5A (93547 upstream) : INSIG1 (118480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155227387	155227387	+	IGR	DEL	T	-	-	rs71694457		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155227387delT								INSIG1 (125445 upstream) : EN2 (23437 downstream)																																			---	---	---	---
RBM33	155435	broad.mit.edu	37	7	155473256	155473256	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155473256delT	uc010lqk.1	+						RBM33_uc003wme.2_Intron	NM_053043	NP_444271			RNA binding motif protein 33								nucleotide binding|RNA binding			ovary(1)	1	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	155697394	155697394	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155697394delT								SHH (92427 upstream) : C7orf4 (635791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155808829	155808829	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155808829delT								SHH (203862 upstream) : C7orf4 (524356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	156739163	156739163	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156739163delA								LMBR1 (53261 upstream) : NOM1 (3254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	156832797	156832798	+	IGR	INS	-	G	G	rs142762771	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156832797_156832798insG								MNX1 (29450 upstream) : UBE3C (98857 downstream)																																			---	---	---	---
DNAJB6	10049	broad.mit.edu	37	7	157131031	157131033	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157131031_157131033delTTT	uc003wnk.2	+						DNAJB6_uc003wnj.2_Intron|DNAJB6_uc003wnl.2_Intron|DNAJB6_uc011kvy.1_Intron|DNAJB6_uc011kvz.1_Intron|DNAJB6_uc010lqt.2_Intron	NM_058246	NP_490647			DnaJ (Hsp40) homolog, subfamily B, member 6						intermediate filament organization|negative regulation of caspase activity|protein folding|response to unfolded protein	nucleus|perinuclear region of cytoplasm	ATPase activator activity|chaperone binding|heat shock protein binding|unfolded protein binding			ovary(2)	2	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)														---	---	---	---
DNAJB6	10049	broad.mit.edu	37	7	157133229	157133229	+	Intron	DEL	T	-	-	rs68038505		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157133229delT	uc003wnk.2	+						DNAJB6_uc003wnj.2_Intron|DNAJB6_uc003wnl.2_Intron|DNAJB6_uc011kvy.1_Intron|DNAJB6_uc011kvz.1_Intron|DNAJB6_uc010lqt.2_Intron	NM_058246	NP_490647			DnaJ (Hsp40) homolog, subfamily B, member 6						intermediate filament organization|negative regulation of caspase activity|protein folding|response to unfolded protein	nucleus|perinuclear region of cytoplasm	ATPase activator activity|chaperone binding|heat shock protein binding|unfolded protein binding			ovary(2)	2	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)												OREG0018485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157954519	157954520	+	Intron	INS	-	ATATCTG	ATATCTG	rs143227273	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157954519_157954520insATATCTG	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
WDR60	55112	broad.mit.edu	37	7	158706914	158706914	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158706914delT	uc003woe.3	+						WDR60_uc010lqv.2_Intron|WDR60_uc010lqw.2_Intron	NM_018051	NP_060521			WD repeat domain 60											ovary(2)|breast(1)|central_nervous_system(1)	4	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)														---	---	---	---
RPL23AP53	644128	broad.mit.edu	37	8	173263	173263	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:173263delC	uc010lra.2	-						RPL23AP53_uc003woq.3_Intron|RPL23AP53_uc010lrb.2_Intron	NR_003572				Homo sapiens cDNA FLJ45055 fis, clone BRAWH3022900.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	848653	848656	+	Intron	DEL	CTCA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:848653_848656delCTCA	uc003wpj.1	+						uc003wpk.2_Intron					Homo sapiens cDNA clone IMAGE:4824304.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	881076	881077	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:881076_881077delTT	uc003wpj.1	+						uc003wpk.2_Intron					Homo sapiens cDNA clone IMAGE:4824304.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1246345	1246347	+	IGR	DEL	CAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1246345_1246347delCAC								ERICH1 (565119 upstream) : DLGAP2 (203222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1363475	1363475	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1363475delT								ERICH1 (682249 upstream) : DLGAP2 (86094 downstream)																																			---	---	---	---
MYOM2	9172	broad.mit.edu	37	8	2050911	2050914	+	Intron	DEL	TGGG	-	-	rs113617267		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2050911_2050914delTGGG	uc003wpx.3	+						MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961			myomesin 2						muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	2096698	2096698	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2096698delC								MYOM2 (3319 upstream) : CSMD1 (696178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2551777	2551777	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2551777delA								MYOM2 (458398 upstream) : CSMD1 (241099 downstream)																																			---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2971577	2971580	+	Intron	DEL	AAAC	-	-	rs145392550		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2971577_2971580delAAAC	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	3081758	3081758	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3081758delA	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	3460238	3460239	+	Intron	INS	-	AC	AC	rs144275628	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3460238_3460239insAC	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	3720674	3720674	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3720674delT	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	4692188	4692188	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4692188delA	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	4986003	4986004	+	IGR	INS	-	T	T	rs143803132	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4986003_4986004insT								CSMD1 (133675 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5057520	5057521	+	IGR	DEL	GT	-	-	rs140618785		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5057520_5057521delGT								CSMD1 (205192 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5546195	5546195	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5546195delA								CSMD1 (693867 upstream) : MCPH1 (717926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5704232	5704232	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5704232delG								CSMD1 (851904 upstream) : MCPH1 (559889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5789923	5789923	+	IGR	DEL	C	-	-	rs11360160		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5789923delC								CSMD1 (937595 upstream) : MCPH1 (474198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5822316	5822316	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5822316delT								CSMD1 (969988 upstream) : MCPH1 (441805 downstream)																																			---	---	---	---
AGPAT5	55326	broad.mit.edu	37	8	6576748	6576748	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6576748delT	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)														---	---	---	---
AGPAT5	55326	broad.mit.edu	37	8	6612540	6612540	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6612540delA	uc003wqo.2	+						AGPAT5_uc011kwm.1_Intron	NM_018361	NP_060831			1-acylglycerol-3-phosphate O-acyltransferase 5						phospholipid biosynthetic process	integral to membrane|mitochondrion	1-acylglycerol-3-phosphate O-acyltransferase activity				0			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	6967158	6967159	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6967158_6967159insT								DEFA5 (52899 upstream) : LOC349196 (150983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	7004876	7004876	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7004876delT								DEFA5 (90617 upstream) : LOC349196 (113266 downstream)																																			---	---	---	---
SPAG11A	653423	broad.mit.edu	37	8	7709843	7709843	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7709843delT	uc003wrx.2	+						SPAG11A_uc003wry.2_Intron|SPAG11A_uc003wrz.2_Intron|SPAG11A_uc003wsa.2_Intron|SPAG11A_uc003wsb.2_Intron	NM_001081552	NP_001075021			sperm associated antigen 11A							extracellular region					0				COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.236)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	8285322	8285323	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8285322_8285323insT								SGK223 (46065 upstream) : CLDN23 (274343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8308147	8308147	+	IGR	DEL	A	-	-	rs75720425		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8308147delA								SGK223 (68890 upstream) : CLDN23 (251519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8310341	8310342	+	IGR	INS	-	GT	GT	rs148002557	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8310341_8310342insGT								SGK223 (71084 upstream) : CLDN23 (249324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8626927	8626928	+	IGR	INS	-	T	T	rs143421587	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8626927_8626928insT								CLDN23 (65311 upstream) : MFHAS1 (15071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8628616	8628616	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8628616delT								CLDN23 (67000 upstream) : MFHAS1 (13383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9042184	9042187	+	IGR	DEL	AAAC	-	-	rs34513922		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9042184_9042187delAAAC								PPP1R3B (33100 upstream) : TNKS (371258 downstream)																																			---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9592835	9592835	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9592835delT	uc003wss.2	+						TNKS_uc011kww.1_Intron|TNKS_uc010lrt.1_Intron	NM_003747	NP_003738			tankyrase, TRF1-interacting ankyrin-related						mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)														---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9605523	9605523	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9605523delT	uc003wss.2	+						TNKS_uc011kww.1_Intron|TNKS_uc010lrt.1_Intron	NM_003747	NP_003738			tankyrase, TRF1-interacting ankyrin-related						mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	9723593	9723593	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9723593delT								TNKS (83738 upstream) : LOC157627 (33981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9784178	9784179	+	IGR	DEL	TT	-	-	rs113580749		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9784178_9784179delTT								MIR124-1 (23196 upstream) : MSRA (127651 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9899388	9899388	+	IGR	DEL	A	-	-	rs35072523		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9899388delA								MIR124-1 (138406 upstream) : MSRA (12442 downstream)																																			---	---	---	---
MSRA	4482	broad.mit.edu	37	8	9946248	9946248	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9946248delA	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)													---	---	---	---
PRSS55	203074	broad.mit.edu	37	8	10393762	10393762	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10393762delA	uc003wta.2	+						uc010lru.2_Intron|PRSS55_uc003wtb.2_Intron	NM_198464	NP_940866			hypothetical protein LOC203074 precursor						proteolysis	integral to membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
SOX7	83595	broad.mit.edu	37	8	10608185	10608185	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10608185delT	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)														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	10755310	10755310	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10755310delT	uc003wtk.1	-	3						NM_173683	NP_775954			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	10990278	10990279	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10990278_10990279delCA	uc003wtk.1	-							NM_173683	NP_775954			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	11082953	11082953	+	IGR	DEL	A	-	-	rs112503075		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11082953delA								XKR6 (24078 upstream) : MTMR9 (59047 downstream)																																			---	---	---	---
FAM167A	83648	broad.mit.edu	37	8	11281015	11281015	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11281015delA	uc010lry.1	-	3					C8orf12_uc003wtu.2_Intron|C8orf12_uc003wtv.2_Intron|FAM167A_uc003wtw.2_3'UTR	NM_053279	NP_444509			hypothetical protein LOC83648												0																		---	---	---	---
FAM167A	83648	broad.mit.edu	37	8	11316295	11316295	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	11462300	11462300	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11462300delG								BLK (40193 upstream) : GATA4 (72168 downstream)																																			---	---	---	---
GATA4	2626	broad.mit.edu	37	8	11546033	11546034	+	Intron	INS	-	CA	CA	rs145128130	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11546033_11546034insCA	uc003wub.1	+						GATA4_uc011kxb.1_Intron	NM_002052	NP_002043			GATA binding protein 4						atrial septum primum morphogenesis|atrial septum secundum morphogenesis|blood coagulation|cardiac right ventricle morphogenesis|cell-cell signaling|embryonic foregut morphogenesis|embryonic heart tube anterior/posterior pattern formation|endocardial cushion development|endoderm development|heart looping|intestinal epithelial cell differentiation|male gonad development|positive regulation of angiogenesis|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|response to drug|transcription from RNA polymerase II promoter|ventricular septum development	nucleoplasm	activating transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	12440147	12440147	+	Intron	DEL	T	-	-	rs141399472		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12440147delT	uc003wvy.3	-											Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	12450124	12450124	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12450124delC	uc003wvy.3	-											Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14238380	14238380	+	Intron	DEL	A	-	-	rs80280544		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14238380delA	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	14809850	14809850	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14809850delT	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	15508060	15508060	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15508060delA	uc003wwt.2	+						TUSC3_uc003wwr.2_Intron|TUSC3_uc003wws.2_Intron|TUSC3_uc003wwu.2_Intron|TUSC3_uc003wwv.2_Intron|TUSC3_uc003www.2_Intron|TUSC3_uc003wwx.2_Intron|TUSC3_uc003wwy.2_Intron	NM_006765	NP_006756			tumor suppressor candidate 3 isoform a						cell redox homeostasis|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				ovary(2)|central_nervous_system(1)	3				Colorectal(111;0.113)														---	---	---	---
MSR1	4481	broad.mit.edu	37	8	15999333	15999333	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15999333delA	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_Intron|MSR1_uc003wxb.2_Intron|MSR1_uc011kxz.1_Intron	NM_138715	NP_619729			macrophage scavenger receptor 1 isoform type 1						cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)														---	---	---	---
MSR1	4481	broad.mit.edu	37	8	16035613	16035614	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16035613_16035614delTT	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_Intron|MSR1_uc003wxb.2_Intron|MSR1_uc011kxz.1_Intron	NM_138715	NP_619729			macrophage scavenger receptor 1 isoform type 1						cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	16314239	16314250	+	IGR	DEL	AGGGAGGAAGGG	-	-	rs34234178		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16314239_16314250delAGGGAGGAAGGG								MSR1 (263939 upstream) : FGF20 (536084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16400637	16400637	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16400637delT								MSR1 (350337 upstream) : FGF20 (449697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16829810	16829811	+	IGR	INS	-	TT	TT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16829810_16829811insTT								MSR1 (779510 upstream) : FGF20 (20523 downstream)																																			---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17643663	17643663	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17643663delA	uc003wxv.2	-						MTUS1_uc003wxw.2_Intron|MTUS1_uc010lsz.2_Intron	NM_001001924	NP_001001924			mitochondrial tumor suppressor 1 isoform 1							Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)														---	---	---	---
PCM1	5108	broad.mit.edu	37	8	17812946	17812946	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17812946delA	uc003wyi.3	+						PCM1_uc011kyh.1_Intron|PCM1_uc003wyj.3_Intron|PCM1_uc003wyh.2_Intron|PCM1_uc010lta.1_Intron	NM_006197	NP_006188			pericentriolar material 1						centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome	centriolar satellite|cytosol|nuclear membrane|pericentriolar material	identical protein binding		PCM1/JAK2(30)	haematopoietic_and_lymphoid_tissue(30)|breast(4)|ovary(2)	36				Colorectal(111;0.0789)				T	RET|JAK2	papillary thyroid|CML|MPD								---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18519501	18519501	+	Intron	DEL	T	-	-	rs76022889		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18519501delT	uc003wza.2	-						PSD3_uc003wyx.3_Intron|PSD3_uc003wyy.2_Intron|PSD3_uc003wyz.2_Intron	NM_015310	NP_056125			ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18736562	18736563	+	Intron	DEL	AC	-	-	rs34794501		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18736562_18736563delAC	uc003wza.2	-							NM_015310	NP_056125			ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)														---	---	---	---
SH2D4A	63898	broad.mit.edu	37	8	19168821	19168821	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19168821delT	uc003wzb.2	+						SH2D4A_uc011kym.1_5'Flank|SH2D4A_uc003wzc.2_5'Flank	NM_022071	NP_071354			SH2 domain containing 4A							cytoplasm|nucleus	protein binding				0				Colorectal(111;0.0732)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	19624040	19624041	+	IGR	INS	-	TAT	TAT	rs7016728		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19624040_19624041insTAT								CSGALNACT1 (8658 upstream) : INTS10 (50877 downstream)																																			---	---	---	---
SLC18A1	6570	broad.mit.edu	37	8	20011178	20011178	+	Intron	DEL	A	-	-	rs112441023		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20011178delA	uc011kyq.1	-						SLC18A1_uc003wzl.2_Intron|SLC18A1_uc003wzm.2_Intron|SLC18A1_uc011kyr.1_Intron|SLC18A1_uc003wzn.2_Intron|SLC18A1_uc010ltf.2_Intron|SLC18A1_uc003wzo.2_Intron	NM_001135691	NP_001129163			solute carrier family 18 (vesicular monoamine),						neurotransmitter transport	clathrin sculpted monoamine transport vesicle membrane|integral to membrane|membrane fraction	drug transmembrane transporter activity|monoamine transmembrane transporter activity			ovary(2)	2				Colorectal(74;0.0747)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	20189337	20189337	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20189337delA								LZTS1 (76534 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20190980	20190980	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20190980delA								LZTS1 (78177 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20377797	20377798	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20377797_20377798insC								LZTS1 (264994 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20451441	20451441	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20451441delG								LZTS1 (338638 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21034347	21034347	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21034347delC								LZTS1 (921544 upstream) : GFRA2 (515183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21091759	21091759	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21091759delA								LZTS1 (978956 upstream) : GFRA2 (457771 downstream)																																			---	---	---	---
GFRA2	2675	broad.mit.edu	37	8	21550684	21550684	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21550684delT	uc003wzu.1	-	9					GFRA2_uc003wzv.1_3'UTR|GFRA2_uc003wzw.1_3'UTR	NM_001495	NP_001486			GDNF family receptor alpha 2 isoform a							anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity				0				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)														---	---	---	---
SLC39A14	23516	broad.mit.edu	37	8	22238188	22238188	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22238188delT	uc003xbq.3	+						SLC39A14_uc011kzg.1_Intron|SLC39A14_uc003xbp.3_Intron|SLC39A14_uc011kzh.1_Intron	NM_001128431	NP_001121903			solute carrier family 39 (zinc transporter),							endoplasmic reticulum|Golgi apparatus|integral to membrane|lamellipodium|plasma membrane	zinc ion transmembrane transporter activity				0				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)														---	---	---	---
PPP3CC	5533	broad.mit.edu	37	8	22363782	22363782	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22363782delA	uc003xbs.2	+						PPP3CC_uc003xbr.1_Intron|PPP3CC_uc011kzi.1_Intron|PPP3CC_uc003xbt.2_Intron	NM_005605	NP_005596			protein phosphatase 3, catalytic subunit, gamma						activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	cytosol	calmodulin binding|metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)														---	---	---	---
KIAA1967	57805	broad.mit.edu	37	8	22469459	22469459	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22469459delT	uc003xch.2	+						KIAA1967_uc003xci.2_Intron|KIAA1967_uc003xcj.1_Intron	NM_199205	NP_954675			p30 DBC protein						apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
PEBP4	157310	broad.mit.edu	37	8	22638965	22638965	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22638965delT	uc003xcn.1	-							NM_144962	NP_659399			phosphatidylethanolamine-binding protein 4							lysosome				ovary(1)|large_intestine(1)|breast(1)|skin(1)	4		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)														---	---	---	---
PEBP4	157310	broad.mit.edu	37	8	22710310	22710310	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22710310delA	uc003xcn.1	-							NM_144962	NP_659399			phosphatidylethanolamine-binding protein 4							lysosome				ovary(1)|large_intestine(1)|breast(1)|skin(1)	4		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)														---	---	---	---
PEBP4	157310	broad.mit.edu	37	8	22722205	22722205	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22722205delT	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)												OREG0018622	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SLC25A37	51312	broad.mit.edu	37	8	23386770	23386771	+	Intron	DEL	GC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23386770_23386771delGC	uc003xdo.2	+						SLC25A37_uc003xdn.1_Intron|SLC25A37_uc003xdp.2_Intron|SLC25A37_uc010ltz.2_Intron	NM_016612	NP_057696			solute carrier family 25, member 37						ion transport|iron ion homeostasis	integral to membrane|mitochondrial inner membrane					0		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)														---	---	---	---
SLC25A37	51312	broad.mit.edu	37	8	23396036	23396037	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23396036_23396037delGT	uc003xdo.2	+						SLC25A37_uc003xdn.1_Intron|SLC25A37_uc003xdp.2_Intron|SLC25A37_uc010ltz.2_Intron	NM_016612	NP_057696			solute carrier family 25, member 37						ion transport|iron ion homeostasis	integral to membrane|mitochondrial inner membrane					0		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	24433653	24433654	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24433653_24433654delTG								ADAM7 (49172 upstream) : NEFM (337620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24973549	24973549	+	IGR	DEL	A	-	-	rs111674286		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24973549delA								NEFL (159418 upstream) : DOCK5 (68738 downstream)																																			---	---	---	---
CDCA2	157313	broad.mit.edu	37	8	25352938	25352938	+	Intron	DEL	T	-	-	rs72510411		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25352938delT	uc003xep.1	+						PPP2R2A_uc003xek.2_Intron|CDCA2_uc011lae.1_Intron|CDCA2_uc003xeq.1_Intron|CDCA2_uc003xer.1_Intron	NM_152562	NP_689775			cell division cycle associated 2						cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25415236	25415236	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25415236delT	uc003xek.2	+							NM_002717	NP_002708			alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)														---	---	---	---
EBF2	64641	broad.mit.edu	37	8	25847705	25847708	+	Intron	DEL	ACAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25847705_25847708delACAC	uc003xes.1	-						PPP2R2A_uc003xek.2_Intron	NM_022659	NP_073150			early B-cell factor 2						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)														---	---	---	---
EBF2	64641	broad.mit.edu	37	8	25888087	25888087	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25888087delA	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	25929994	25929995	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25929994_25929995delAG	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	25975471	25975472	+	Intron	INS	-	A	A	rs72583828	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25975471_25975472insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	26281266	26281267	+	IGR	DEL	AA	-	-	rs113857282		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26281266_26281267delAA								BNIP3L (10622 upstream) : PNMA2 (80929 downstream)																																			---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27173811	27173811	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27173811delT	uc003xfn.1	+						PTK2B_uc003xfo.1_Intron	NM_173174	NP_775266			PTK2B protein tyrosine kinase 2 beta isoform a						apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			lung(3)|ovary(1)|skin(1)	5		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	27446318	27446319	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27446318_27446319delTG								EPHX2 (43834 upstream) : CLU (8132 downstream)																																			---	---	---	---
CCDC25	55246	broad.mit.edu	37	8	27607186	27607186	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27607186delA	uc003xgc.2	-						CCDC25_uc003xgd.2_Intron|CCDC25_uc011lan.1_Intron|CCDC25_uc011lao.1_Intron|CCDC25_uc003xge.2_Intron|CCDC25_uc003xgf.1_Intron	NM_018246	NP_060716			coiled-coil domain containing 25												0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)														---	---	---	---
ESCO2	157570	broad.mit.edu	37	8	27653603	27653603	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27653603delT	uc003xgg.2	+						ESCO2_uc010luy.1_Intron	NM_001017420	NP_001017420			establishment of cohesion 1 homolog 2						cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding			central_nervous_system(1)	1		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)										SC_Phocomelia_syndrome				---	---	---	---
PBK	55872	broad.mit.edu	37	8	27690542	27690542	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27690542delA	uc003xgi.2	-						PBK_uc011lap.1_Intron	NM_018492	NP_060962			PDZ binding kinase						mitosis		ATP binding|protein binding|protein serine/threonine kinase activity				0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)														---	---	---	---
SCARA5	286133	broad.mit.edu	37	8	27745582	27745582	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27745582delT	uc003xgj.2	-						SCARA5_uc010luz.2_Intron|hsa-mir-4287|MI0015895_5'Flank	NM_173833	NP_776194			scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)														---	---	---	---
ELP3	55140	broad.mit.edu	37	8	27989691	27989691	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27989691delT	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)														---	---	---	---
PNOC	5368	broad.mit.edu	37	8	28182805	28182806	+	Intron	INS	-	T	T	rs148496405	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28182805_28182806insT	uc010lva.2	+						PNOC_uc003xgp.2_Intron	NM_006228	NP_006219			prepronociceptin precursor						neuropeptide signaling pathway|sensory perception|synaptic transmission	extracellular region	neuropeptide hormone activity|opioid peptide activity			central_nervous_system(1)	1		Ovarian(32;0.000953)		KIRC - Kidney renal clear cell carcinoma(542;0.104)|Kidney(114;0.125)|Colorectal(74;0.145)|BRCA - Breast invasive adenocarcinoma(99;0.245)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	28431221	28431223	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28431221_28431223delAAA								FZD3 (9262 upstream) : EXTL3 (127930 downstream)																																			---	---	---	---
INTS9	55756	broad.mit.edu	37	8	28628716	28628716	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28628716delT	uc003xha.2	-						INTS9_uc011lav.1_Intron|INTS9_uc011law.1_Intron|INTS9_uc011lax.1_Intron|INTS9_uc010lvc.2_Intron	NM_018250	NP_060720			integrator complex subunit 9 isoform 1						snRNA processing	integrator complex	protein binding			central_nervous_system(1)|pancreas(1)	2		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)														---	---	---	---
HMBOX1	79618	broad.mit.edu	37	8	28795947	28795947	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28795947delT	uc003xhd.3	+						HMBOX1_uc010lvd.2_Intron|HMBOX1_uc003xhc.3_Intron|HMBOX1_uc010lve.2_Intron|HMBOX1_uc003xhe.2_Intron	NM_001135726	NP_001129198			homeobox containing 1						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)														---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	29063610	29063610	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29063610delA	uc003xhh.3	-						KIF13B_uc003xhj.2_Intron|KIF13B_uc010lvf.1_Intron|KIF13B_uc003xhk.2_Intron	NM_015254	NP_056069			kinesin family member 13B						microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)														---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	29114857	29114857	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29114857delT	uc003xhh.3	-						KIF13B_uc003xhj.2_Intron|KIF13B_uc010lvf.1_Intron|KIF13B_uc003xhk.2_Intron	NM_015254	NP_056069			kinesin family member 13B						microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	29129914	29129914	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29129914delA								KIF13B (9304 upstream) : DUSP4 (63703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30235252	30235255	+	IGR	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30235252_30235255delTTTT								DCTN6 (194193 upstream) : RBPMS (6689 downstream)																																			---	---	---	---
RBPMS	11030	broad.mit.edu	37	8	30294442	30294442	+	Intron	DEL	T	-	-	rs72385384		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30294442delT	uc003xic.1	+						RBPMS_uc003xid.1_Intron|RBPMS_uc003xie.1_Intron|RBPMS_uc011lba.1_Intron|RBPMS_uc003xib.2_Intron	NM_006867	NP_006858			RNA-binding protein with multiple splicing						positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)														---	---	---	---
PPP2CB	5516	broad.mit.edu	37	8	30657033	30657033	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30657033delA	uc003xik.2	-							NM_004156	NP_004147			protein phosphatase 2, catalytic subunit, beta						protein dephosphorylation	chromosome, centromeric region|cytoplasm|nucleus|protein phosphatase type 2A complex|spindle pole	metal ion binding				0				KIRC - Kidney renal clear cell carcinoma(542;0.095)|Kidney(114;0.114)	Vitamin E(DB00163)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	30815271	30815272	+	IGR	INS	-	AT	AT	rs151190316	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30815271_30815272insAT								TEX15 (69049 upstream) : PURG (38049 downstream)																																			---	---	---	---
WRN	7486	broad.mit.edu	37	8	30958600	30958601	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30958600_30958601insT	uc003xio.3	+						WRN_uc010lvk.2_Intron	NM_000553	NP_000544			Werner syndrome protein						base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)				Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				---	---	---	---
NRG1	3084	broad.mit.edu	37	8	31592347	31592347	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31592347delT	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	31698406	31698406	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31698406delT	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	32620721	32620721	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32620721delT	uc003xiv.2	+						NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc011lbg.1_Intron|NRG1_uc011lbh.1_Intron|NRG1_uc003xja.2_Intron	NM_013964	NP_039258			neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	33439875	33439875	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33439875delT								RNF122 (15232 upstream) : DUSP26 (8981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33490659	33490659	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33490659delC								DUSP26 (33220 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34051495	34051495	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34051495delT								DUSP26 (594056 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34255847	34255848	+	IGR	INS	-	A	A	rs78303677		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34255847_34255848insA								DUSP26 (798408 upstream) : UNC5D (837127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34426165	34426165	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34426165delT								DUSP26 (968726 upstream) : UNC5D (666810 downstream)																																			---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35150235	35150236	+	Intron	DEL	TT	-	-	rs71916312		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35150235_35150236delTT	uc003xjr.1	+							NM_080872	NP_543148			unc-5 homolog D precursor						apoptosis|axon guidance	integral to membrane	receptor activity			upper_aerodigestive_tract(2)|ovary(2)|pancreas(1)|skin(1)	6				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	36244094	36244097	+	IGR	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36244094_36244097delTTTT								UNC5D (591914 upstream) : KCNU1 (397745 downstream)																																			---	---	---	---
KCNU1	157855	broad.mit.edu	37	8	36763445	36763445	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36763445delA	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	36873539	36873539	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36873539delA								KCNU1 (79898 upstream) : ZNF703 (679762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37565038	37565039	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37565038_37565039delAA								ZNF703 (8642 upstream) : ERLIN2 (29058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37649458	37649458	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37649458delA								PROSC (12173 upstream) : GPR124 (4966 downstream)																																			---	---	---	---
RAB11FIP1	80223	broad.mit.edu	37	8	37725231	37725231	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)															---	---	---	---
ASH2L	9070	broad.mit.edu	37	8	37970484	37970485	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37970484_37970485delTT	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)																---	---	---	---
PPAPDC1B	84513	broad.mit.edu	37	8	38121588	38121588	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38121588delA	uc003xlf.3	-	7					PPAPDC1B_uc003xle.3_3'UTR	NM_001102559	NP_001096029			phosphatidic acid phosphatase type 2 domain						phospholipid dephosphorylation	cytoplasm|integral to membrane|plasma membrane	phosphatidate phosphatase activity				0	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)	BRCA - Breast invasive adenocarcinoma(5;3.04e-26)|COAD - Colon adenocarcinoma(9;0.188)															---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38678721	38678722	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38678721_38678722delAA	uc010lwp.2	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc011lbz.1_Intron|TACC1_uc003xmb.3_Intron|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron|TACC1_uc003xmf.3_Intron|TACC1_uc011lca.1_Intron|TACC1_uc011lcb.1_Intron|TACC1_uc011lcc.1_Intron|TACC1_uc011lcd.1_Intron|TACC1_uc003xmh.3_Intron|TACC1_uc010lwq.2_Intron	NM_006283	NP_006274			transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38687048	38687048	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38687048delC	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_uc011lcd.1_Intron|TACC1_uc003xmh.3_Intron|TACC1_uc010lwq.2_Intron	NM_006283	NP_006274			transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38692772	38692773	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38692772_38692773delAA	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_uc010lwo.1_Intron|TACC1_uc003xmf.3_Intron|TACC1_uc011lca.1_Intron|TACC1_uc011lcb.1_Intron|TACC1_uc011lcd.1_Intron|TACC1_uc003xmh.3_Intron|TACC1_uc010lwq.2_Intron	NM_006283	NP_006274			transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
PLEKHA2	59339	broad.mit.edu	37	8	38768763	38768763	+	Intron	DEL	T	-	-	rs33940133		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38768763delT	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	38814989	38814990	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38814989_38814990insT	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)															---	---	---	---
HTRA4	203100	broad.mit.edu	37	8	38834465	38834466	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38834465_38834466insT	uc003xmj.2	+							NM_153692	NP_710159			HtrA serine peptidase 4 precursor						proteolysis|regulation of cell growth	extracellular region	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)															---	---	---	---
ADAM32	203102	broad.mit.edu	37	8	39128387	39128387	+	Intron	DEL	C	-	-	rs4733994	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39128387delC	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)															---	---	---	---
ADAM32	203102	broad.mit.edu	37	8	39131820	39131820	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39131820delT	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	40162147	40162147	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40162147delT								C8orf4 (149326 upstream) : ZMAT4 (225969 downstream)																																			---	---	---	---
GINS4	84296	broad.mit.edu	37	8	41392258	41392260	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41392258_41392260delTTT	uc003xnx.2	+						GINS4_uc003xny.2_Intron	NM_032336	NP_115712			GINS complex subunit 4						DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	cytoplasm|nucleoplasm				skin(1)	1	Ovarian(28;0.014)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.00732)|Lung NSC(58;0.0207)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00329)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)															---	---	---	---
GINS4	84296	broad.mit.edu	37	8	41400167	41400167	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41400167delA	uc003xnx.2	+	8					GINS4_uc003xny.2_Intron	NM_032336	NP_115712			GINS complex subunit 4						DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	cytoplasm|nucleoplasm				skin(1)	1	Ovarian(28;0.014)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.00732)|Lung NSC(58;0.0207)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00329)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)															---	---	---	---
AGPAT6	137964	broad.mit.edu	37	8	41433673	41433673	+	5'Flank	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41433673delG	uc003xnz.2	+							NM_178819	NP_848934			lysophosphatidic acid acyltransferase zeta						acyl-CoA metabolic process|lactation|phosphatidylcholine biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|membrane fraction	glycerol-3-phosphate O-acyltransferase activity				0	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)															---	---	---	---
ANK1	286	broad.mit.edu	37	8	41559913	41559913	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41559913delG	uc003xok.2	-						NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Intron|ANK1_uc003xoi.2_Intron|ANK1_uc003xoj.2_Intron|ANK1_uc003xol.2_Intron|ANK1_uc003xom.2_Intron	NM_020476	NP_065209			ankyrin 1 isoform 1						axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)													OREG0018740	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ANK1	286	broad.mit.edu	37	8	41595325	41595325	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41595325delA	uc003xok.2	-						NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoi.2_Intron|ANK1_uc003xoj.2_Intron|ANK1_uc003xol.2_Intron|ANK1_uc003xom.2_Intron	NM_020476	NP_065209			ankyrin 1 isoform 1						axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)															---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41803550	41803550	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41803550delA	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	41924811	41924812	+	IGR	DEL	TT	-	-	rs145502292		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41924811_41924812delTT								MYST3 (15306 upstream) : AP3M2 (85652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42111743	42111743	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42111743delT								PLAT (46549 upstream) : IKBKB (17086 downstream)																																			---	---	---	---
IKBKB	3551	broad.mit.edu	37	8	42171989	42171989	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42171989delT	uc003xow.1	+						IKBKB_uc003xov.2_Intron|IKBKB_uc010lxh.1_Intron|IKBKB_uc011lco.1_Intron|IKBKB_uc010lxj.1_Intron|IKBKB_uc003xox.1_Intron|IKBKB_uc011lcp.1_Intron|IKBKB_uc011lcq.1_Intron|IKBKB_uc010lxi.1_Intron|IKBKB_uc011lcr.1_Intron	NM_001556	NP_001547			inhibitor of nuclear factor kappa B kinase beta						anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)													---	---	---	---
POLB	5423	broad.mit.edu	37	8	42195936	42195937	+	5'Flank	INS	-	GCCCC	GCCCC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42195936_42195937insGCCCC	uc003xoz.1	+						POLB_uc003xpa.1_5'Flank|POLB_uc011lcs.1_5'Flank	NM_002690	NP_002681			DNA-directed DNA polymerase beta						DNA-dependent DNA replication	cytoplasm|nucleoplasm|spindle microtubule	DNA-(apurinic or apyrimidinic site) lyase activity|DNA-directed DNA polymerase activity|enzyme binding|metal ion binding|microtubule binding			ovary(1)|breast(1)	2	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)								DNA_polymerases_(catalytic_subunits)					---	---	---	---
SLC20A2	6575	broad.mit.edu	37	8	42325440	42325440	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42325440delT	uc010lxl.2	-						SLC20A2_uc010lxm.2_Intron|SLC20A2_uc003xpe.2_Intron	NM_006749	NP_006740			solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	42676851	42676851	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42676851delA								CHRNA6 (53232 upstream) : THAP1 (14967 downstream)																																			---	---	---	---
HOOK3	84376	broad.mit.edu	37	8	42852638	42852638	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42852638delA	uc003xpr.2	+						HOOK3_uc010lxq.1_Intron	NM_032410	NP_115786			golgi-associated microtubule-binding protein						cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)					T	RET	papillary thyroid								---	---	---	---
FNTA	2339	broad.mit.edu	37	8	42917317	42917320	+	Intron	DEL	TGTG	-	-	rs71646249		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42917317_42917320delTGTG	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)															---	---	---	---
HGSNAT	138050	broad.mit.edu	37	8	43008200	43008200	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43008200delA	uc003xpx.3	+							NM_152419	NP_689632			heparan-alpha-glucosaminide N-acetyltransferase						lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	46942065	46942065	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46942065delA								None (None upstream) : BEYLA (810443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47452644	47452645	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47452644_47452645insT								None (None upstream) : BEYLA (299863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47457487	47457488	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47457487_47457488delTC								None (None upstream) : BEYLA (295020 downstream)																																			---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48306239	48306248	+	Intron	DEL	TTTCCTTTCC	-	-	rs150623579		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48306239_48306248delTTTCCTTTCC	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48554978	48554979	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48554978_48554979delAA	uc003xqd.2	+						KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48719577	48719577	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48719577delA	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835			protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)											NHEJ					---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48841969	48841969	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48841969delC	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835			protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)											NHEJ					---	---	---	---
Unknown	0	broad.mit.edu	37	8	48991469	48991470	+	IGR	DEL	AA	-	-	rs112741171		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48991469_48991470delAA								UBE2V2 (17017 upstream) : EFCAB1 (631881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49611051	49611051	+	IGR	DEL	A	-	-	rs112894157		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49611051delA								UBE2V2 (636599 upstream) : EFCAB1 (12300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49671139	49671140	+	IGR	DEL	GT	-	-	rs71824754		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49671139_49671140delGT								EFCAB1 (23269 upstream) : SNAI2 (159099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49909310	49909310	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49909310delT								SNAI2 (75322 upstream) : C8orf22 (75593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50182405	50182406	+	IGR	INS	-	G	G	rs144312068	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50182405_50182406insG								C8orf22 (193764 upstream) : SNTG1 (639943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50461243	50461243	+	IGR	DEL	T	-	-	rs34222144		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50461243delT								C8orf22 (472602 upstream) : SNTG1 (361106 downstream)																																			---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	50971295	50971296	+	Intron	DEL	TG	-	-	rs33928043		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50971295_50971296delTG	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron	NM_018967	NP_061840			syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)																---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51090919	51090919	+	Intron	DEL	T	-	-	rs112121506		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51090919delT	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	51461084	51461087	+	Intron	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51461084_51461087delTTTT	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	52053872	52053875	+	IGR	DEL	TTTG	-	-	rs141009294	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52053872_52053875delTTTG								SNTG1 (348445 upstream) : PXDNL (178269 downstream)																																			---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52609429	52609430	+	Intron	DEL	AT	-	-	rs56347711		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52609429_52609430delAT	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	52968900	52968900	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52968900delG								PCMTD1 (157165 upstream) : ST18 (54492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53502591	53502591	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53502591delT								FAM150A (24570 upstream) : RB1CC1 (32428 downstream)																																			---	---	---	---
ATP6V1H	51606	broad.mit.edu	37	8	54736558	54736558	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54736558delA	uc003xrl.2	-						ATP6V1H_uc003xrk.2_Intron|ATP6V1H_uc003xrm.2_Intron|ATP6V1H_uc003xrn.2_Intron|ATP6V1H_uc011ldv.1_Intron|ATP6V1H_uc010lyd.2_Intron	NM_213620	NP_998785			ATPase, H+ transporting, lysosomal 50/57kDa, V1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|endocytosis|insulin receptor signaling pathway|interspecies interaction between organisms|regulation of defense response to virus by virus|transferrin transport|vacuolar acidification|viral reproduction	cytosol|plasma membrane|vacuolar proton-transporting V-type ATPase, V1 domain	enzyme regulator activity|protein binding|proton-transporting ATPase activity, rotational mechanism				0		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)															---	---	---	---
RGS20	8601	broad.mit.edu	37	8	54816687	54816687	+	Intron	DEL	T	-	-	rs112423385		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54816687delT	uc003xrp.2	+						RGS20_uc003xrq.2_Intron|RGS20_uc010lye.2_Intron|RGS20_uc010lyf.2_Intron|RGS20_uc003xrr.2_Intron|RGS20_uc003xrs.2_Intron|RGS20_uc003xrt.2_Intron	NM_170587	NP_733466			regulator of G-protein signaling 20 isoform a						negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|nucleus|plasma membrane	GTPase activator activity|protein binding|signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	55150897	55150898	+	IGR	DEL	CA	-	-	rs143354181	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55150897_55150898delCA								MRPL15 (89823 upstream) : SOX17 (219597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55163702	55163703	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55163702_55163703delTC								MRPL15 (102628 upstream) : SOX17 (206792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55375114	55375114	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55375114delC								SOX17 (1659 upstream) : RP1 (153513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55396600	55396600	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55396600delA								SOX17 (23145 upstream) : RP1 (132027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55898073	55898073	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55898073delA								RP1 (215542 upstream) : XKR4 (116944 downstream)																																			---	---	---	---
LYN	4067	broad.mit.edu	37	8	56858977	56858977	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56858977delT	uc003xsk.3	+						LYN_uc003xsl.3_Intron	NM_002350	NP_002341			Yamaguchi sarcoma viral (v-yes-1) oncogene						erythrocyte differentiation|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of cellular component movement|positive regulation of stress-activated protein kinase signaling cascade|positive regulation of tyrosine phosphorylation of STAT protein|response to DNA damage stimulus|T cell costimulation	cytosol|Golgi apparatus|membrane raft|nucleus|perinuclear region of cytoplasm	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|receptor signaling protein tyrosine kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	56927057	56927057	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56927057delA								LYN (3121 upstream) : RPS20 (53682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57019554	57019554	+	IGR	DEL	A	-	-	rs79815830		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57019554delA								RPS20 (32414 upstream) : MOS (5948 downstream)																																			---	---	---	---
FAM110B	90362	broad.mit.edu	37	8	58944554	58944554	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58944554delA	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)																---	---	---	---
NSMAF	8439	broad.mit.edu	37	8	59500894	59500895	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59500894_59500895delTT	uc003xtt.2	-						NSMAF_uc011lee.1_Intron	NM_003580	NP_003571			neutral sphingomyelinase (N-SMase) activation						ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	59577063	59577063	+	IGR	DEL	T	-	-	rs113981763		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59577063delT								NSMAF (4659 upstream) : TOX (140914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59597972	59597973	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59597972_59597973delGT								NSMAF (25568 upstream) : TOX (120004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59706786	59706787	+	IGR	DEL	AG	-	-	rs59172653		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59706786_59706787delAG								NSMAF (134382 upstream) : TOX (11190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60283399	60283399	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60283399delT								TOX (251632 upstream) : CA8 (818024 downstream)																																			---	---	---	---
CA8	767	broad.mit.edu	37	8	61141720	61141720	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61141720delT	uc003xtz.1	-						CA8_uc003xua.1_Intron	NM_004056	NP_004047			carbonic anhydrase VIII						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)																---	---	---	---
CA8	767	broad.mit.edu	37	8	61189919	61189919	+	Intron	DEL	T	-	-	rs113659462		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61189919delT	uc003xtz.1	-						CA8_uc003xua.1_Intron|CA8_uc003xub.2_Intron	NM_004056	NP_004047			carbonic anhydrase VIII						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	61376787	61376788	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61376787_61376788delGT								CA8 (182833 upstream) : RAB2A (52771 downstream)																																			---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61714076	61714076	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	61740109	61740109	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61740109delA	uc003xue.2	+							NM_017780	NP_060250			chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
ASPH	444	broad.mit.edu	37	8	62496486	62496486	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62496486delA	uc003xuj.2	-						ASPH_uc011leg.1_Intron|ASPH_uc003xuo.2_Intron	NM_004318	NP_004309			aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)													---	---	---	---
NKAIN3	286183	broad.mit.edu	37	8	63164697	63164697	+	Intron	DEL	T	-	-	rs72430703		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63164697delT	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	63374877	63374877	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63374877delT	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	63477924	63477925	+	Intron	INS	-	GT	GT	rs143240903	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63477924_63477925insGT	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	63781559	63781560	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63781559_63781560delCT	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)																---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65642786	65642786	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65642786delT	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	65974604	65974604	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65974604delA								CYP7B1 (263256 upstream) : ARMC1 (540468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65992946	65992946	+	IGR	DEL	A	-	-	rs71938282		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65992946delA								CYP7B1 (281598 upstream) : ARMC1 (522126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66481565	66481565	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66481565delA								CYP7B1 (770217 upstream) : ARMC1 (33507 downstream)																																			---	---	---	---
TRIM55	84675	broad.mit.edu	37	8	67057266	67057266	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67057266delT	uc003xvv.2	+						TRIM55_uc003xvu.2_Intron|TRIM55_uc003xvw.2_Intron|TRIM55_uc003xvx.2_Intron	NM_184085	NP_908973			tripartite motif-containing 55 isoform 1							cytoplasm|microtubule|nucleus	signal transducer activity|zinc ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	67129573	67129573	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67129573delT								CRH (38875 upstream) : RRS1 (211690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	67281855	67281857	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67281855_67281857delAAA								CRH (191157 upstream) : RRS1 (59406 downstream)																																			---	---	---	---
ADHFE1	137872	broad.mit.edu	37	8	67354989	67354989	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67354989delT	uc003xwb.3	+						ADHFE1_uc003xwd.3_Intron|ADHFE1_uc003xwc.3_Intron|ADHFE1_uc003xwe.3_Intron|ADHFE1_uc003xwf.3_Intron|ADHFE1_uc011les.1_Intron|ADHFE1_uc011leq.1_Intron|ADHFE1_uc011ler.1_Intron	NM_144650	NP_653251			alcohol dehydrogenase, iron containing, 1						2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)															---	---	---	---
SGK3	23678	broad.mit.edu	37	8	67643080	67643080	+	Intron	DEL	T	-	-	rs113173320		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67643080delT	uc003xwr.2	+						SGK3_uc003xwp.2_Intron	NM_001033578	NP_001028750			serum/glucocorticoid regulated kinase 3 isoform						cell communication|response to stress	cytoplasmic membrane-bounded vesicle|early endosome	ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity			ovary(1)|large_intestine(1)|lung(1)|breast(1)	4	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
C8orf45	157777	broad.mit.edu	37	8	67828378	67828378	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67828378delT	uc003xwz.3	+						C8orf45_uc011lew.1_Intron|C8orf45_uc011lex.1_Intron	NM_173518	NP_775789			minichromosome maintenance complex						DNA replication		ATP binding|DNA binding			ovary(1)	1	Breast(64;0.186)		Epithelial(68;0.00384)|OV - Ovarian serous cystadenocarcinoma(28;0.00913)|all cancers(69;0.0175)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
SNHG6	641638	broad.mit.edu	37	8	67840245	67840245	+	5'Flank	DEL	T	-	-	rs11357514		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67840245delT	uc003xxa.1	-							NR_002599				Homo sapiens cDNA FLJ32554 fis, clone SPLEN1000106.												0																		---	---	---	---
COPS5	10987	broad.mit.edu	37	8	67963608	67963608	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67963608delA	uc003xxe.2	-						COPS5_uc003xxd.2_Intron|COPS5_uc003xxf.2_Intron|COPS5_uc010lyu.1_Intron|COPS5_uc010lyv.1_Intron	NM_006837	NP_006828			COP9 signalosome subunit 5						cullin deneddylation|transcription from RNA polymerase II promoter	eukaryotic translation initiation factor 3 complex|signalosome	metal ion binding|metallopeptidase activity|protein binding|transcription coactivator activity|translation initiation factor activity			ovary(1)|skin(1)	2	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68044403	68044403	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68236040	68236041	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68236040_68236041delTT	uc003xxo.1	-							NM_006421	NP_006412			brefeldin A-inhibited guanine						exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
CPA6	57094	broad.mit.edu	37	8	68383748	68383748	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68383748delT	uc003xxq.3	-						CPA6_uc003xxr.3_Intron	NM_020361	NP_065094			carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	69838216	69838217	+	Intron	INS	-	T	T	rs146407151	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69838216_69838217insT	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	70348706	70348707	+	IGR	INS	-	AG	AG	rs111607377		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70348706_70348707insAG								C8orf34 (617450 upstream) : SULF1 (30152 downstream)																																			---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70570543	70570543	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70570543delT	uc010lza.1	+						SULF1_uc003xyd.2_Intron|SULF1_uc003xye.2_Intron|SULF1_uc003xyf.2_Intron|SULF1_uc003xyg.2_Intron|SULF1_uc003xyh.1_Intron|SULF1_uc003xyi.1_Intron|SULF1_uc003xyj.1_Intron	NM_015170	NP_055985			sulfatase 1 precursor						apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	70775079	70775079	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70775079delA								SLCO5A1 (27780 upstream) : PRDM14 (188946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	70924567	70924567	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70924567delT								SLCO5A1 (177268 upstream) : PRDM14 (39458 downstream)																																			---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71036596	71036596	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71036596delT	uc003xyn.1	-						NCOA2_uc011lfb.1_Intron	NM_006540	NP_006531			nuclear receptor coactivator 2						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)					T	RUNXBP2	AML								---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71130435	71130437	+	Intron	DEL	TTT	-	-	rs34322124		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71130435_71130437delTTT	uc003xyn.1	-							NM_006540	NP_006531			nuclear receptor coactivator 2						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)					T	RUNXBP2	AML								---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71237673	71237674	+	Intron	DEL	TT	-	-	rs78987789		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71237673_71237674delTT	uc003xyn.1	-							NM_006540	NP_006531			nuclear receptor coactivator 2						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)					T	RUNXBP2	AML								---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71269978	71269978	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71269978delA	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	71984235	71984235	+	IGR	DEL	T	-	-	rs71566281		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71984235delT								XKR9 (336059 upstream) : EYA1 (125435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	72559088	72559088	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72559088delT								EYA1 (284621 upstream) : MSC (194689 downstream)																																			---	---	---	---
TRPA1	8989	broad.mit.edu	37	8	72969431	72969432	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72969431_72969432delTG	uc003xza.2	-							NM_007332	NP_015628			ankyrin-like protein 1							integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)													---	---	---	---
TRPA1	8989	broad.mit.edu	37	8	72982027	72982028	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72982027_72982028delGA	uc003xza.2	-							NM_007332	NP_015628			ankyrin-like protein 1							integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	73006297	73006297	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73006297delT								TRPA1 (18478 upstream) : KCNB2 (443329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	73040168	73040168	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73040168delT								TRPA1 (52349 upstream) : KCNB2 (409458 downstream)																																			---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73603723	73603723	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73603723delT	uc003xzb.2	+							NM_004770	NP_004761			potassium voltage-gated channel, Shab-related						regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)															---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73645226	73645226	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73645226delA	uc003xzb.2	+							NM_004770	NP_004761			potassium voltage-gated channel, Shab-related						regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	74019155	74019156	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74019155_74019156delAC								C8orf84 (13648 upstream) : RPL7 (183719 downstream)																																			---	---	---	---
UBE2W	55284	broad.mit.edu	37	8	74751962	74751962	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74751962delT	uc003xzv.2	-						UBE2W_uc003xzt.2_Intron|UBE2W_uc003xzu.2_Intron|UBE2W_uc003xzw.2_Intron	NM_018299	NP_060769			ubiquitin-conjugating enzyme E2W (putative)						protein K11-linked ubiquitination|protein monoubiquitination		ATP binding|protein binding|ubiquitin-protein ligase activity				0	Breast(64;0.0311)		Epithelial(68;0.0235)|all cancers(69;0.0687)|BRCA - Breast invasive adenocarcinoma(89;0.069)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	75034131	75034132	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75034131_75034132delTT								LY96 (92826 upstream) : JPH1 (112809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75617884	75617884	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75617884delA	uc003yaj.1	+						MIR2052_hsa-mir-2052|MI0010486_5'Flank					Homo sapiens cDNA FLJ39080 fis, clone NT2RP7018197.																														---	---	---	---
PI15	51050	broad.mit.edu	37	8	75743532	75743532	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75743532delT	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)															---	---	---	---
ZFHX4	79776	broad.mit.edu	37	8	77595636	77595636	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77595636delC	uc003yav.2	+						LOC100192378_uc003yas.3_5'Flank|ZFHX4_uc003yat.1_Intron|ZFHX4_uc003yau.1_Intron	NM_024721	NP_078997			zinc finger homeodomain 4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)												HNSCC(33;0.089)			---	---	---	---
ZFHX4	79776	broad.mit.edu	37	8	77661807	77661808	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77661807_77661808insT	uc003yav.2	+						ZFHX4_uc003yau.1_Intron|ZFHX4_uc003yaw.1_Intron	NM_024721	NP_078997			zinc finger homeodomain 4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)												HNSCC(33;0.089)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78543671	78543671	+	IGR	DEL	A	-	-	rs75514868		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78543671delA								PEX2 (631147 upstream) : PKIA (884665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79220924	79220924	+	IGR	DEL	A	-	-	rs34659085		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79220924delA								None (None upstream) : PKIA (207412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80637196	80637196	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80637196delA								STMN2 (58802 upstream) : HEY1 (39050 downstream)																																			---	---	---	---
TPD52	7163	broad.mit.edu	37	8	80999371	80999371	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80999371delT	uc003ybs.1	-						TPD52_uc010lzs.1_Intron|TPD52_uc003ybt.1_Intron	NM_001025253	NP_001020424			tumor protein D52 isoform 2						anatomical structure morphogenesis|B cell differentiation|secretion	endoplasmic reticulum|perinuclear region of cytoplasm	calcium ion binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	81173486	81173486	+	IGR	DEL	T	-	-	rs9969433	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81173486delT								TPD52 (89650 upstream) : ZBTB10 (224368 downstream)																																			---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81553805	81553806	+	Intron	DEL	AA	-	-	rs78833157	by1000genomes;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81553805_81553806delAA	uc003yby.1	-							NM_001033723	NP_001028895			zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)															---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81710494	81710495	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81710494_81710495delTT	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)															---	---	---	---
PAG1	55824	broad.mit.edu	37	8	81995147	81995148	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81995147_81995148delTT	uc003ybz.2	-							NM_018440	NP_060910			phosphoprotein associated with glycosphingolipid						epidermal growth factor receptor signaling pathway|intracellular signal transduction|T cell receptor signaling pathway	integral to membrane|intracellular|membrane raft|plasma membrane	SH2 domain binding|SH3/SH2 adaptor activity				0	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	82516124	82516124	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82516124delT								FABP12 (72574 upstream) : IMPA1 (53027 downstream)																																			---	---	---	---
IMPA1	3612	broad.mit.edu	37	8	82594390	82594390	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82594390delA	uc003ych.2	-						IMPA1_uc011lfq.1_Intron|IMPA1_uc011lfr.1_Intron	NM_005536	NP_005527			inositol(myo)-1(or 4)-monophosphatase 1 isoform						inositol phosphate dephosphorylation|phosphatidylinositol biosynthetic process|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(1)	1					Lithium(DB01356)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	82776628	82776628	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82776628delA								SNX16 (22107 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83177794	83177794	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83177794delT								SNX16 (423273 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83280814	83280814	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83280814delG								SNX16 (526293 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83419332	83419332	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83419332delA								SNX16 (664811 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84871118	84871118	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84871118delA								None (None upstream) : RALYL (224335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84882341	84882341	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84882341delT								None (None upstream) : RALYL (213112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	85919980	85919980	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85919980delT								RALYL (85909 upstream) : LRRCC1 (99397 downstream)																																			---	---	---	---
CA13	377677	broad.mit.edu	37	8	86305176	86305176	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86305176delT	uc003ydf.1	+											Homo sapiens cDNA FLJ36434 fis, clone THYMU2012002.						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0																		---	---	---	---
CA2	760	broad.mit.edu	37	8	86386666	86386666	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86386666delT	uc003ydk.2	+							NM_000067	NP_000058			carbonic anhydrase II						one-carbon metabolic process	apical part of cell	carbonate dehydratase activity|zinc ion binding			central_nervous_system(1)	1					Acetazolamide(DB00819)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Dorzolamide(DB00869)|Ethinamate(DB01031)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Topiramate(DB00273)|Trichlormethiazide(DB01021)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	86975357	86975358	+	IGR	DEL	GT	-	-	rs35460093		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86975357_86975358delGT								REXO1L1 (400089 upstream) : PSKH2 (85335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	87103992	87103995	+	IGR	DEL	GGAA	-	-	rs72136292		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87103992_87103995delGGAA								PSKH2 (22141 upstream) : ATP6V0D2 (7144 downstream)																																			---	---	---	---
ATP6V0D2	245972	broad.mit.edu	37	8	87125362	87125363	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87125362_87125363delTT	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																		---	---	---	---
WWP1	11059	broad.mit.edu	37	8	87414524	87414525	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87414524_87414525insT	uc003ydt.2	+						WWP1_uc010mai.2_Intron	NM_007013	NP_008944			WW domain containing E3 ubiquitin protein ligase						central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction	cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			lung(1)|liver(1)	2																		---	---	---	---
CNBD1	168975	broad.mit.edu	37	8	88218493	88218494	+	Intron	DEL	GG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88218493_88218494delGG	uc003ydy.2	+							NM_173538	NP_775809			cyclic nucleotide binding domain containing 1											ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	88398385	88398386	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88398385_88398386insG								CNBD1 (3430 upstream) : DCAF4L2 (484587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88453304	88453304	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88453304delT								CNBD1 (58349 upstream) : DCAF4L2 (429669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88540988	88540988	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88540988delT								CNBD1 (146033 upstream) : DCAF4L2 (341985 downstream)																																			---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89192511	89192511	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89192511delA	uc003yeb.3	-						MMP16_uc003yec.2_Intron	NM_005941	NP_005932			matrix metalloproteinase 16 isoform 1						collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)|kidney(1)	8																		---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89227550	89227551	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89227550_89227551delAA	uc003yeb.3	-						MMP16_uc003yec.2_Intron	NM_005941	NP_005932			matrix metalloproteinase 16 isoform 1						collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)|kidney(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	90538484	90538485	+	IGR	DEL	TG	-	-	rs72231171		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90538484_90538485delTG								None (None upstream) : RIPK2 (231490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90629402	90629402	+	IGR	DEL	A	-	-	rs35607385		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90629402delA								None (None upstream) : RIPK2 (140573 downstream)																																			---	---	---	---
RIPK2	8767	broad.mit.edu	37	8	90773605	90773605	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90773605delT	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	90811110	90811110	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90811110delA								RIPK2 (7819 upstream) : OSGIN2 (102986 downstream)																																			---	---	---	---
NBN	4683	broad.mit.edu	37	8	90976819	90976819	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90976819delT	uc003yej.1	-						NBN_uc003yei.1_Intron|NBN_uc011lgb.1_Intron	NM_002485	NP_002476			nibrin						cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance	Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm	protein N-terminus binding|transcription factor binding			central_nervous_system(3)|kidney(3)|lung(1)	7			BRCA - Breast invasive adenocarcinoma(11;0.0344)										Direct_reversal_of_damage|Homologous_recombination	Nijmegen_Breakage_syndrome				---	---	---	---
TMEM64	169200	broad.mit.edu	37	8	91681336	91681336	+	Intron	DEL	T	-	-	rs67806159		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91681336delT	uc003yeo.2	-							NM_001008495	NP_001008495			transmembrane protein 64 isoform 1							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(11;0.0598)															---	---	---	---
NECAB1	64168	broad.mit.edu	37	8	91884332	91884332	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91884332delT	uc011lgg.1	+							NM_022351	NP_071746			N-terminal EF-hand calcium binding protein 1						antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity			central_nervous_system(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.0499)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	92522653	92522654	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92522653_92522654delGT								SLC26A7 (112273 upstream) : RUNX1T1 (448498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	92624281	92624281	+	IGR	DEL	A	-	-	rs34342084		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92624281delA								SLC26A7 (213901 upstream) : RUNX1T1 (346871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	92698861	92698862	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92698861_92698862insA								SLC26A7 (288481 upstream) : RUNX1T1 (272290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	92792431	92792432	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92792431_92792432delTT								SLC26A7 (382051 upstream) : RUNX1T1 (178720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93156235	93156235	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93156235delT								RUNX1T1 (48529 upstream) : C8orf83 (739630 downstream)																																			---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94745548	94745548	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94745548delA	uc003yfz.2	-	3						NM_203390	NP_976324			RNA binding motif protein 12B								nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
TMEM67	91147	broad.mit.edu	37	8	94770691	94770691	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94770691delT	uc011lgk.1	+						TMEM67_uc010mav.2_Intron|TMEM67_uc010mat.1_Intron|TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Intron	NM_153704	NP_714915			meckelin isoform 1						cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)															---	---	---	---
TMEM67	91147	broad.mit.edu	37	8	94800262	94800262	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94800262delT	uc011lgk.1	+						TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Intron	NM_153704	NP_714915			meckelin isoform 1						cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	95095476	95095476	+	IGR	DEL	A	-	-	rs67380687		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95095476delA								PDP1 (157182 upstream) : CDH17 (43918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	95137545	95137545	+	IGR	DEL	T	-	-	rs35859318		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95137545delT								PDP1 (199251 upstream) : CDH17 (1849 downstream)																																			---	---	---	---
CDH17	1015	broad.mit.edu	37	8	95198478	95198479	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95198478_95198479delCT	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	95372929	95372929	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95372929delA								GEM (98372 upstream) : RAD54B (11260 downstream)																																			---	---	---	---
RAD54B	25788	broad.mit.edu	37	8	95429936	95429936	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95429936delA	uc003ygk.2	-						RAD54B_uc010may.1_Intron|RAD54B_uc003ygl.1_Intron	NM_012415	NP_036547			RAD54 homolog B						double-strand break repair via homologous recombination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA translocase activity|protein binding			kidney(2)|lung(1)|skin(1)	4	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RAD54B	25788	broad.mit.edu	37	8	95454593	95454594	+	Intron	INS	-	G	G	rs142857926	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95454593_95454594insG	uc003ygk.2	-						RAD54B_uc003ygl.1_Intron|RAD54B_uc003ygn.1_Intron	NM_012415	NP_036547			RAD54 homolog B						double-strand break repair via homologous recombination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA translocase activity|protein binding			kidney(2)|lung(1)|skin(1)	4	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
KIAA1429	25962	broad.mit.edu	37	8	95531563	95531563	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95531563delA	uc003ygo.1	-	9	2176	c.2163delT	c.(2161-2163)TTTfs	p.F721fs	KIAA1429_uc003ygp.2_Frame_Shift_Del_p.F721fs|KIAA1429_uc010maz.1_RNA	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	721					mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)															---	---	---	---
KIAA1429	25962	broad.mit.edu	37	8	95541687	95541687	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95541687delA	uc003ygo.1	-						KIAA1429_uc003ygp.2_Intron|KIAA1429_uc010maz.1_5'Flank	NM_015496	NP_056311			hypothetical protein LOC25962 isoform 1						mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)															---	---	---	---
KIAA1429	25962	broad.mit.edu	37	8	95545397	95545397	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95545397delA	uc003ygo.1	-						KIAA1429_uc003ygp.2_Intron	NM_015496	NP_056311			hypothetical protein LOC25962 isoform 1						mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	96247402	96247403	+	IGR	DEL	TT	-	-	rs34643974		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96247402_96247403delTT								PLEKHF2 (78491 upstream) : C8orf37 (10832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96636047	96636048	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96636047_96636048delAG								C8orf37 (354610 upstream) : GDF6 (518512 downstream)																																			---	---	---	---
UQCRB	7381	broad.mit.edu	37	8	97242849	97242849	+	3'UTR	DEL	C	-	-	rs7836698	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97242849delC	uc003yhq.3	-	4					UQCRB_uc011lgt.1_RNA|UQCRB_uc010mbc.2_RNA	NM_006294	NP_006285			ubiquinol-cytochrome c reductase binding						aerobic respiration|mitochondrial electron transport, ubiquinol to cytochrome c	mitochondrial respiratory chain	ubiquinol-cytochrome-c reductase activity			ovary(1)	1	Breast(36;5.16e-05)																	---	---	---	---
PTDSS1	9791	broad.mit.edu	37	8	97291747	97291747	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97291747delA	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	97353698	97353699	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97353698_97353699delAA								PTDSS1 (6924 upstream) : SDC2 (152183 downstream)																																			---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97971141	97971141	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97971141delA	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	98147536	98147536	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	98319254	98319255	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98319254_98319255insG								TSPYL5 (29078 upstream) : MTDH (337152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98363392	98363392	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98363392delA								TSPYL5 (73216 upstream) : MTDH (293015 downstream)																																			---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98978386	98978386	+	Intron	DEL	A	-	-	rs75427563		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98978386delA	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron|MATN2_uc010mbi.1_Intron	NM_002380	NP_002371			matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98999070	98999070	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98999070delT	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron|MATN2_uc010mbi.1_Intron	NM_002380	NP_002371			matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	99006489	99006490	+	Intron	INS	-	GAAGAAGGAGAA	GAAGAAGGAGAA	rs146393102	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99006489_99006490insGAAGAAGGAGAA	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron|MATN2_uc010mbi.1_Intron	NM_002380	NP_002371			matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
RPL30	6156	broad.mit.edu	37	8	99037501	99037502	+	3'UTR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99037501_99037502delCA	uc010mbk.1	-	4					MATN2_uc010mbh.1_Intron|MATN2_uc003yic.2_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron|MATN2_uc010mbi.1_Intron|MATN2_uc010mbj.1_Intron	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)															---	---	---	---
POP1	10940	broad.mit.edu	37	8	99148630	99148630	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99148630delA	uc003yij.3	+						POP1_uc011lgv.1_Intron|POP1_uc003yik.2_Intron	NM_001145860	NP_001139332			processing of precursor 1						tRNA 5'-leader removal|tRNA catabolic process	nucleolar ribonuclease P complex|ribonuclease MRP complex	identical protein binding|ribonuclease MRP activity|ribonuclease P activity			ovary(1)|breast(1)	2	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)															---	---	---	---
NIPAL2	79815	broad.mit.edu	37	8	99247386	99247386	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99247386delA	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	99351758	99351759	+	IGR	INS	-	G	G	rs138388915	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99351758_99351759insG								NIPAL2 (45137 upstream) : KCNS2 (87491 downstream)																																			---	---	---	---
STK3	6788	broad.mit.edu	37	8	99592020	99592020	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99592020delA	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	99607998	99607998	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99607998delA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
OSR2	116039	broad.mit.edu	37	8	99962748	99962748	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99962748delA	uc003yir.2	+						OSR2_uc010mbn.2_Intron|OSR2_uc003yiq.2_Intron|OSR2_uc011lgx.1_Intron	NM_001142462	NP_001135934			odd-skipped related 2 isoform a						bone morphogenesis|chondrocyte differentiation|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic hindlimb morphogenesis|embryonic leg joint morphogenesis|embryonic skeletal joint morphogenesis|eyelid development in camera-type eye|head development|mesonephros development|metanephros development|middle ear morphogenesis|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|osteoblast proliferation|palate development|positive regulation of bone mineralization|positive regulation of epithelial cell proliferation|positive regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|zinc ion binding			central_nervous_system(1)	1	Breast(36;4.14e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.0136)															---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100270022	100270023	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100270022_100270023delTT	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)															---	---	---	---
FBXO43	286151	broad.mit.edu	37	8	101157158	101157158	+	Intron	DEL	A	-	-	rs74811222		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101157158delA	uc003yjd.2	-						FBXO43_uc003yje.2_Intron|FBXO43_uc010mbp.1_Intron	NM_001029860	NP_001025031			F-box protein 43 isoform b						meiosis		zinc ion binding			kidney(1)|skin(1)	2	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	101438774	101438776	+	IGR	DEL	ATT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101438774_101438776delATT								RNF19A (116447 upstream) : ANKRD46 (83211 downstream)																																			---	---	---	---
SNX31	169166	broad.mit.edu	37	8	101604192	101604192	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101604192delA	uc003yjr.2	-						SNX31_uc011lha.1_Intron|SNX31_uc011lhb.1_Intron	NM_152628	NP_689841			sorting nexin 31						cell communication|protein transport		phosphatidylinositol binding				0	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)															---	---	---	---
NCALD	83988	broad.mit.edu	37	8	102859464	102859464	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)															---	---	---	---
NCALD	83988	broad.mit.edu	37	8	102900815	102900815	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102900815delT	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718			neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)															---	---	---	---
NCALD	83988	broad.mit.edu	37	8	102923500	102923500	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102923500delA	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718			neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)															---	---	---	---
NCALD	83988	broad.mit.edu	37	8	102980069	102980072	+	Intron	DEL	ACAC	-	-	rs72380627		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102980069_102980072delACAC	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	103447219	103447219	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103447219delA								UBR5 (22724 upstream) : ODF1 (116629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103508735	103508735	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103508735delA								UBR5 (84240 upstream) : ODF1 (55113 downstream)																																			---	---	---	---
AZIN1	51582	broad.mit.edu	37	8	103854346	103854346	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103854346delA	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)															---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104613061	104613061	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104613061delT	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)			---	---	---	---
LRP12	29967	broad.mit.edu	37	8	105578089	105578089	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105578089delA	uc003yma.2	-						LRP12_uc003ymb.2_Intron|LRP12_uc003ymc.3_Intron	NM_013437	NP_038465			low density lipoprotein-related protein 12						endocytosis|regulation of growth	coated pit|integral to plasma membrane	low-density lipoprotein receptor activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	105655590	105655591	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105655590_105655591delTC								LRP12 (54370 upstream) : ZFPM2 (675556 downstream)																																			---	---	---	---
ZFPM2	23414	broad.mit.edu	37	8	106497518	106497518	+	Intron	DEL	T	-	-	rs79935635		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106497518delT	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	106735386	106735386	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106735386delT	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)															---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107395220	107395220	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107395220delT	uc003ymf.2	+							NM_018002	NP_060472			oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107688817	107688817	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107688817delT	uc011lht.1	+						OXR1_uc003ymf.2_Intron|OXR1_uc011lhu.1_Intron|OXR1_uc010mcg.2_Intron|OXR1_uc003ymg.1_Intron|OXR1_uc003ymi.1_Intron	NM_018002	NP_060472			oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	107989266	107989266	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107989266delC								ABRA (206794 upstream) : ANGPT1 (272445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108154315	108154315	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108154315delT								ABRA (371843 upstream) : ANGPT1 (107396 downstream)																																			---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108315770	108315770	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108315770delA	uc003ymn.2	-						ANGPT1_uc011lhv.1_Intron|ANGPT1_uc003ymo.2_Intron|ANGPT1_uc003ymp.3_Intron	NM_001146	NP_001137			angiopoietin 1 precursor						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)															---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108379606	108379606	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108379606delT	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)															---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108440861	108440862	+	Intron	DEL	TG	-	-	rs66954670		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108440861_108440862delTG	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	109113219	109113220	+	IGR	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109113219_109113220delGA								RSPO2 (17306 upstream) : EIF3E (100753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109871800	109871800	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109871800delA								TMEM74 (72030 upstream) : TRHR (227939 downstream)																																			---	---	---	---
SYBU	55638	broad.mit.edu	37	8	110644160	110644160	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110644160delT	uc003ynj.3	-						SYBU_uc003yni.3_Intron|SYBU_uc003ynk.3_Intron|SYBU_uc010mco.2_Intron|SYBU_uc003ynl.3_Intron|SYBU_uc010mcp.2_Intron|SYBU_uc010mcq.2_Intron|SYBU_uc003yno.3_Intron|SYBU_uc010mcr.2_Intron|SYBU_uc003ynm.3_Intron|SYBU_uc003ynn.3_Intron|SYBU_uc010mcs.2_Intron|SYBU_uc010mct.2_Intron|SYBU_uc010mcu.2_Intron|SYBU_uc003ynp.3_Intron|SYBU_uc010mcv.2_Intron	NM_001099754	NP_001093224			Golgi-localized syntaphilin-related protein							cytoplasmic membrane-bounded vesicle|cytoskeleton|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	110748690	110748691	+	IGR	DEL	TT	-	-	rs150015279	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110748690_110748691delTT								SYBU (44670 upstream) : KCNV1 (230544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111637151	111637151	+	IGR	DEL	T	-	-	rs150606555		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111637151delT								KCNV1 (649075 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112564891	112564891	+	IGR	DEL	T	-	-	rs71817530		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112564891delT								None (None upstream) : CSMD3 (670270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112672287	112672287	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112672287delA								None (None upstream) : CSMD3 (562874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112749340	112749340	+	IGR	DEL	T	-	-	rs71566007		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112749340delT								None (None upstream) : CSMD3 (485821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112976797	112976797	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112976797delT								None (None upstream) : CSMD3 (258364 downstream)																																			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113411150	113411152	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113411150_113411152delTTT	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115777951	115777951	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115777951delT								None (None upstream) : TRPS1 (642774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115932523	115932523	+	IGR	DEL	A	-	-	rs76662548		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115932523delA								None (None upstream) : TRPS1 (488202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116236667	116236668	+	IGR	INS	-	AC	AC	rs149953520	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116236667_116236668insAC								None (None upstream) : TRPS1 (184057 downstream)																																			---	---	---	---
EIF3H	8667	broad.mit.edu	37	8	117702619	117702619	+	Intron	DEL	A	-	-	rs139887539		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117702619delA	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	117931035	117931038	+	IGR	DEL	AAAA	-	-	rs72306671		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117931035_117931038delAAAA								RAD21 (43930 upstream) : C8orf85 (19426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118557223	118557223	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118557223delA								MED30 (4724 upstream) : EXT1 (254379 downstream)																																			---	---	---	---
EXT1	2131	broad.mit.edu	37	8	119003351	119003352	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119003351_119003352delTT	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	119105775	119105775	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119105775delT	uc003yok.1	-							NM_000127	NP_000118			exostosin 1						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)					Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119598584	119598585	+	Intron	DEL	TT	-	-	rs11311659		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119598584_119598585delTT	uc003yom.2	-						SAMD12_uc010mda.1_Intron|SAMD12_uc010mdb.1_Intron	NM_207506	NP_997389			sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	119654513	119654513	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119654513delT								SAMD12 (20279 upstream) : TNFRSF11B (281284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120301263	120301263	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120301263delT								MAL2 (43352 upstream) : NOV (127289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	121132994	121132994	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121132994delT								DEPDC6 (69838 upstream) : COL14A1 (4358 downstream)																																			---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121183171	121183171	+	Intron	DEL	A	-	-	rs74825767		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121183171delA	uc003yox.2	+							NM_021110	NP_066933			collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121200324	121200324	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121200324delT	uc003yox.2	+							NM_021110	NP_066933			collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121330983	121330983	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121330983delA	uc003yox.2	+						COL14A1_uc003yoz.2_Intron	NM_021110	NP_066933			collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
MRPL13	28998	broad.mit.edu	37	8	121426426	121426427	+	Intron	DEL	GT	-	-	rs139055716		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121426426_121426427delGT	uc003ypa.2	-						MRPL13_uc010mdf.2_Intron	NM_014078	NP_054797			mitochondrial ribosomal protein L13						translation	mitochondrial large ribosomal subunit	protein binding|structural constituent of ribosome			central_nervous_system(1)	1	Lung NSC(37;1.69e-07)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
MTBP	27085	broad.mit.edu	37	8	121508948	121508948	+	Intron	DEL	A	-	-	rs34444618		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121508948delA	uc003ypc.1	+							NM_022045	NP_071328			Mdm2, transformed 3T3 cell double minute 2, p53						cell cycle arrest					skin(2)|ovary(1)	3	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	122186320	122186320	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122186320delA								SNTB1 (362011 upstream) : HAS2 (438951 downstream)																																			---	---	---	---
HAS2	3037	broad.mit.edu	37	8	122629827	122629827	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122629827delA	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	122684455	122684455	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122684455delT								HAS2AS (27522 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122702988	122702988	+	IGR	DEL	T	-	-	rs111330293		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122702988delT								HAS2AS (46055 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123009172	123009172	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123009172delT	uc003ypj.2	-											Homo sapiens, clone IMAGE:5466006, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	123783742	123783742	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123783742delA								None (None upstream) : ZHX2 (10159 downstream)																																			---	---	---	---
ZHX2	22882	broad.mit.edu	37	8	123821766	123821766	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123821766delA	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)															---	---	---	---
DERL1	79139	broad.mit.edu	37	8	124048097	124048097	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124048097delT	uc003ypl.2	-						DERL1_uc003ypm.2_Intron|DERL1_uc011lif.1_Intron|DERL1_uc003ypn.2_Intron	NM_024295	NP_077271			Der1-like domain family, member 1 isoform a						endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|intracellular transport of viral proteins in host cell|retrograde protein transport, ER to cytosol	integral to endoplasmic reticulum membrane	MHC class I protein binding|receptor activity				0	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
ANXA13	312	broad.mit.edu	37	8	124706232	124706233	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124706232_124706233delTT	uc003yqu.2	-						ANXA13_uc003yqt.2_Intron	NM_004306	NP_004297			annexin A13 isoform a						cell differentiation	plasma membrane	calcium ion binding|calcium-dependent phospholipid binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
ANXA13	312	broad.mit.edu	37	8	124708147	124708147	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124708147delC	uc003yqu.2	-						ANXA13_uc003yqt.2_Intron	NM_004306	NP_004297			annexin A13 isoform a						cell differentiation	plasma membrane	calcium ion binding|calcium-dependent phospholipid binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	124915859	124915859	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124915859delT	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)															---	---	---	---
TATDN1	83940	broad.mit.edu	37	8	125534493	125534493	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125534493delT	uc003yrd.2	-						TATDN1_uc003yre.2_Intron|TATDN1_uc010mdm.2_Intron|TATDN1_uc003yrf.2_Intron	NM_032026	NP_114415			TatD DNase domain containing 1 isoform a							nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
TATDN1	83940	broad.mit.edu	37	8	125544322	125544322	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125544322delG	uc003yrd.2	-						TATDN1_uc003yre.2_Intron|TATDN1_uc010mdm.2_Intron|TATDN1_uc003yrf.2_Intron	NM_032026	NP_114415			TatD DNase domain containing 1 isoform a							nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	125818228	125818229	+	IGR	DEL	TT	-	-	rs80118619		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125818228_125818229delTT								MTSS1 (77498 upstream) : LOC157381 (133655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125908109	125908110	+	IGR	INS	-	A	A	rs147050745	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125908109_125908110insA								MTSS1 (167379 upstream) : LOC157381 (43774 downstream)																																			---	---	---	---
KIAA0196	9897	broad.mit.edu	37	8	126059687	126059688	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126059687_126059688delTT	uc003yrt.2	-						KIAA0196_uc011lir.1_Intron|KIAA0196_uc003yru.1_Intron	NM_014846	NP_055661			strumpellin						cell death	WASH complex				ovary(2)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)															---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126180589	126180589	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126180589delA	uc003yrw.2	+						NSMCE2_uc003yrv.2_Intron	NM_173685	NP_775956			non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)															---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126317126	126317126	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126317126delA	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	126388558	126388560	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126388558_126388560delAAA								NSMCE2 (9191 upstream) : TRIB1 (54003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126402097	126402097	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126402097delA								NSMCE2 (22730 upstream) : TRIB1 (40466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126876426	126876426	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126876426delT								TRIB1 (425784 upstream) : FAM84B (688261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126972652	126972653	+	IGR	INS	-	TGTT	TGTT	rs148959870	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126972652_126972653insTGTT								TRIB1 (522010 upstream) : FAM84B (592034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127103829	127103829	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127103829delT								TRIB1 (653187 upstream) : FAM84B (460858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127418305	127418320	+	IGR	DEL	CTTCCTTCCTTCCTTT	-	-	rs60488715		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127418305_127418320delCTTCCTTCCTTCCTTT								TRIB1 (967663 upstream) : FAM84B (146367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127427656	127427656	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127427656delT								TRIB1 (977014 upstream) : FAM84B (137031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128177923	128177924	+	IGR	INS	-	T	T	rs147309872	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128177923_128177924insT								FAM84B (607457 upstream) : LOC727677 (124138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128718505	128718505	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128718505delA	uc003ysg.2	-											Homo sapiens, clone IMAGE:5554747, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	128743844	128743844	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128743844delA	uc003ysg.2	-											Homo sapiens, clone IMAGE:5554747, mRNA.																														---	---	---	---
PVT1	5820	broad.mit.edu	37	8	128828372	128828373	+	Intron	INS	-	ACAA	ACAA	rs143337914	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128828372_128828373insACAA	uc003ysj.2	+						PVT1_uc010mdq.2_Intron|PVT1_uc010mdp.1_Intron					Human proto-oncogene myc mRNA, 5' end, clone DMmyc.												0																		---	---	---	---
PVT1	5820	broad.mit.edu	37	8	129112116	129112116	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129112116delT	uc010mdq.2	+						PVT1_uc003ysl.2_Intron	NR_003367				Homo sapiens Pvt1 oncogene (non-protein coding), mRNA (cDNA clone IMAGE:5517530), with apparent retained intron.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	129189139	129189141	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129189139_129189141delTTT								MIR1208 (26705 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129191386	129191387	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129191386_129191387delCA								MIR1208 (28952 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129419313	129419313	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129419313delT	uc003ysn.2	-											Homo sapiens cDNA clone IMAGE:3877235, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	129665301	129665301	+	IGR	DEL	T	-	-	rs111334282		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129665301delT								MIR1208 (502867 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129737987	129737988	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129737987_129737988insA								MIR1208 (575553 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130037650	130037651	+	IGR	INS	-	AA	AA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130037650_130037651insAA								MIR1208 (875216 upstream) : GSDMC (722792 downstream)																																			---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131165270	131165271	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131165270_131165271insT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	132136349	132136349	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132136349delA								ADCY8 (83514 upstream) : EFR3A (780010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132345949	132345950	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132345949_132345950insA								ADCY8 (293114 upstream) : EFR3A (570409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132487080	132487080	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132487080delT								ADCY8 (434245 upstream) : EFR3A (429279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132597336	132597336	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132597336delT								ADCY8 (544501 upstream) : EFR3A (319023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132640472	132640472	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132640472delA								ADCY8 (587637 upstream) : EFR3A (275887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132657491	132657491	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132657491delA								ADCY8 (604656 upstream) : EFR3A (258868 downstream)																																			---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133379500	133379501	+	Intron	INS	-	T	T	rs140244174	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133379500_133379501insT	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	133423886	133423887	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133423886_133423887delAC	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)															---	---	---	---
TG	7038	broad.mit.edu	37	8	134028162	134028162	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134028162delT	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron	NM_003235	NP_003226			thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)														---	---	---	---
ST3GAL1	6482	broad.mit.edu	37	8	134491451	134491451	+	Intron	DEL	G	-	-	rs34451956		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134491451delG	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	134820525	134820525	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134820525delA								ST3GAL1 (236342 upstream) : ZFAT (669508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135140582	135140582	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135140582delT								ST3GAL1 (556399 upstream) : ZFAT (349451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135378655	135378656	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135378655_135378656insT								ST3GAL1 (794472 upstream) : ZFAT (111377 downstream)																																			---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135602252	135602252	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135602252delC	uc003yup.2	-						ZFAT_uc003yun.2_Intron|ZFAT_uc003yuo.2_Intron|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron	NM_020863	NP_065914			zinc finger protein 406 isoform ZFAT-1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	135754100	135754100	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135754100delA								ZFAT (28819 upstream) : MIR30B (58663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136181134	136181134	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136181134delA								MIR30D (363946 upstream) : LOC286094 (65240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136451189	136451190	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136451189_136451190delAG								LOC286094 (139230 upstream) : KHDRBS3 (18526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136744509	136744509	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136744509delC								KHDRBS3 (84663 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140170847	140170848	+	IGR	INS	-	A	A	rs143572403	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140170847_140170848insA								COL22A1 (244611 upstream) : KCNK9 (442234 downstream)																																			---	---	---	---
KCNK9	51305	broad.mit.edu	37	8	140713681	140713681	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140713681delT	uc003yvf.1	-						KCNK9_uc003yvg.1_Intron	NM_016601	NP_057685			potassium channel, subfamily K, member 9							integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)															---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	140968457	140968457	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140968457delT	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844			trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	141016006	141016008	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141016006_141016008delAAA	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																		---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141774119	141774119	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141774119delA	uc003yvu.2	-						PTK2_uc003yvo.2_Intron|PTK2_uc011ljq.1_Intron|PTK2_uc003yvp.2_Intron|PTK2_uc003yvq.2_Intron|PTK2_uc003yvr.2_Intron|PTK2_uc003yvs.2_Intron|PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560			PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141815705	141815705	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141815705delA	uc003yvu.2	-						PTK2_uc003yvq.2_Intron|PTK2_uc003yvr.2_Intron|PTK2_uc003yvs.2_Intron|PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560			PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141910828	141910828	+	Intron	DEL	G	-	-	rs3952980	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141910828delG	uc003yvu.2	-						PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560			PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	142022603	142022603	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142022603delT								PTK2 (11271 upstream) : DENND3 (116117 downstream)																																			---	---	---	---
DENND3	22898	broad.mit.edu	37	8	142148044	142148045	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142148044_142148045delTG	uc003yvy.2	+						DENND3_uc003yvw.1_Intron|DENND3_uc003yvx.2_Intron|DENND3_uc010mep.2_Intron	NM_014957	NP_055772			DENN/MADD domain containing 3											ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
SLC45A4	57210	broad.mit.edu	37	8	142229177	142229177	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142229177delG	uc003ywd.1	-						SLC45A4_uc003ywc.1_Intron|SLC45A4_uc010meq.1_Intron	NM_001080431	NP_001073900			solute carrier family 45, member 4						transport	integral to membrane				ovary(2)	2	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	142945315	142945315	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142945315delG								MIR1302-7 (77641 upstream) : NCRNA00051 (334402 downstream)																																			---	---	---	---
BAI1	575	broad.mit.edu	37	8	143611593	143611594	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143611593_143611594delGT	uc003ywm.2	+							NM_001702	NP_001693			brain-specific angiogenesis inhibitor 1						axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1)	8	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
C8orf55	51337	broad.mit.edu	37	8	143811137	143811137	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143811137delA	uc003yww.1	+						C8orf55_uc011ljy.1_Intron	NM_016647	NP_057731			mesenchymal stem cell protein DSCD75 precursor							extracellular region					0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
LY6H	4062	broad.mit.edu	37	8	144240077	144240077	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144240077delG	uc011lka.1	-						LY6H_uc011lkb.1_Intron|LY6H_uc003yxt.2_Intron|LY6H_uc011lkc.1_Intron	NM_002347	NP_002338			lymphocyte antigen 6 complex, locus H isoform a						nervous system development|organ morphogenesis	anchored to membrane|plasma membrane					0	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
TOP1MT	116447	broad.mit.edu	37	8	144437034	144437034	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144437034delA	uc011lkd.1	-						TOP1MT_uc011lke.1_Intron|uc003yya.2_Intron	NM_052963	NP_443195			mitochondrial topoisomerase I precursor						DNA topological change	chromosome|mitochondrial nucleoid	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	144486115	144486116	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144486115_144486116delAG								RHPN1 (19726 upstream) : MAFA (25399 downstream)																																			---	---	---	---
C8orf73	642475	broad.mit.edu	37	8	144649891	144649891	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144649891delG	uc010mff.2	-							NM_001100878	NP_001094348			hypothetical protein LOC642475								binding			ovary(1)	1	all_cancers(97;6.49e-11)|all_epithelial(106;4.73e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.014)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
PLEC	5339	broad.mit.edu	37	8	145009585	145009586	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145009585_145009586insC	uc003zaf.1	-						PLEC_uc003zab.1_Intron|PLEC_uc003zac.1_Intron|PLEC_uc003zad.2_Intron|PLEC_uc003zae.1_Intron|PLEC_uc003zag.1_Intron|PLEC_uc003zah.2_Intron|PLEC_uc003zaj.2_Intron	NM_201380	NP_958782			plectin isoform 1						cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9																		---	---	---	---
MAF1	84232	broad.mit.edu	37	8	145160201	145160202	+	Intron	INS	-	TCT	TCT	rs150096970	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145160201_145160202insTCT	uc003zbc.1	+						SHARPIN_uc003zba.2_5'Flank|SHARPIN_uc003zbb.2_5'Flank|KIAA1875_uc003zbd.3_5'Flank	NM_032272	NP_115648			MAF1 protein						negative regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	cytoplasm|nucleus					0	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.1e-42)|Epithelial(56;1.23e-40)|all cancers(56;4.84e-36)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
ZNF250	58500	broad.mit.edu	37	8	146112292	146112292	+	Intron	DEL	A	-	-	rs72451532		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146112292delA	uc003zeq.3	-						COMMD5_uc010mgf.2_Intron|ZNF250_uc003zer.3_Intron|ZNF250_uc010mgg.2_Intron	NM_021061	NP_066405			zinc finger protein 250 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	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)		Epithelial(56;2.53e-38)|OV - Ovarian serous cystadenocarcinoma(54;4.07e-38)|all cancers(56;2.27e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.0654)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	146233916	146233916	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146233916delT								C8orf77 (2485 upstream) : C8orf33 (43908 downstream)																																			---	---	---	---
KANK1	23189	broad.mit.edu	37	9	541632	541632	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:541632delA	uc003zgl.1	+						KANK1_uc003zgm.2_Intron|KANK1_uc003zgn.1_Intron	NM_015158	NP_055973			KN motif and ankyrin repeat domains 1 isoform a						negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)														---	---	---	---
DMRT1	1761	broad.mit.edu	37	9	876529	876529	+	Intron	DEL	T	-	-	rs112659992		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:876529delT	uc003zgv.2	+						DMRT1_uc003zgu.1_Intron	NM_021951	NP_068770			doublesex and mab-3 related transcription factor						cell differentiation|male gonad development|sex determination	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(10;2.66e-10)|Lung NSC(10;2.82e-10)|Breast(48;0.232)		Lung(218;0.037)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	1104613	1104613	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1104613delT								DMRT2 (47060 upstream) : SMARCA2 (910729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1244647	1244647	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1244647delA								DMRT2 (187094 upstream) : SMARCA2 (770695 downstream)																																			---	---	---	---
FLJ35024	401491	broad.mit.edu	37	9	2440516	2440516	+	Intron	DEL	T	-	-	rs113939336		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2440516delT	uc003zhh.1	-						FLJ35024_uc003zhi.2_Intron					Homo sapiens cDNA FLJ35024 fis, clone OCBBF2015233.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	2694396	2694397	+	IGR	DEL	GT	-	-	rs5895991		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2694396_2694397delGT								VLDLR (39911 upstream) : KCNV2 (23129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	2803160	2803160	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2803160delT								KCNV2 (73403 upstream) : KIAA0020 (995 downstream)																																			---	---	---	---
RFX3	5991	broad.mit.edu	37	9	3271277	3271277	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3271277delA	uc003zhr.2	-						RFX3_uc010mhd.2_Intron|RFX3_uc003zhs.1_Intron|RFX3_uc003zht.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	4084291	4084295	+	Intron	DEL	ACACA	-	-	rs58533132		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4084291_4084295delACACA	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)														---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	4132051	4132051	+	Intron	DEL	A	-	-	rs60581804		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4132051delA	uc003zhw.1	-						GLIS3_uc003zhx.1_Intron|GLIS3_uc003zic.1_Intron|GLIS3_uc003zie.1_Intron|GLIS3_uc010mhh.1_Intron|GLIS3_uc003zid.1_Intron|GLIS3_uc010mhi.1_Intron|GLIS3_uc003zif.1_Intron|GLIS3_uc003zig.1_Intron|GLIS3_uc003zih.1_Intron|GLIS3_uc003zib.1_Intron|GLIS3_uc010mhg.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	4148068	4148068	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4148068delT	uc003zhw.1	-						GLIS3_uc003zhx.1_Intron|GLIS3_uc003zic.1_Intron|GLIS3_uc003zie.1_Intron|GLIS3_uc010mhh.1_Intron|GLIS3_uc003zid.1_Intron|GLIS3_uc010mhi.1_Intron|GLIS3_uc003zif.1_Intron|GLIS3_uc003zig.1_Intron|GLIS3_uc003zih.1_Intron|GLIS3_uc003zib.1_5'Flank|GLIS3_uc010mhg.1_5'Flank	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)														---	---	---	---
RCL1	10171	broad.mit.edu	37	9	4820283	4820283	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4820283delA	uc003zis.2	+						RCL1_uc003zit.2_Intron|RCL1_uc010mhk.1_Intron	NM_005772	NP_005763			RNA terminal phosphate cyclase-like 1						ribosome biogenesis|RNA processing	nucleolus	RNA-3'-phosphate cyclase activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0206)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0244)														---	---	---	---
RCL1	10171	broad.mit.edu	37	9	4834472	4834475	+	Intron	DEL	TTTT	-	-	rs144793993		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4834472_4834475delTTTT	uc003zis.2	+						RCL1_uc003zit.2_Intron|RCL1_uc010mhk.1_Intron	NM_005772	NP_005763			RNA terminal phosphate cyclase-like 1						ribosome biogenesis|RNA processing	nucleolus	RNA-3'-phosphate cyclase activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0206)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0244)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	4924298	4924299	+	IGR	INS	-	A	A	rs142336974	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4924298_4924299insA								RCL1 (38381 upstream) : JAK2 (60787 downstream)																																	OREG0019088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PDCD1LG2	80380	broad.mit.edu	37	9	5550700	5550700	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5550700delT	uc003zjg.3	+						C9orf46_uc003zjd.2_Intron|PDCD1LG2_uc011lmc.1_Intron|PDCD1LG2_uc011lmd.1_Intron|PDCD1LG2_uc010mhp.1_Intron|PDCD1LG2_uc010mho.1_Intron	NM_025239	NP_079515			programmed cell death 1 ligand 2 precursor						immune response|T cell costimulation	endomembrane system|extracellular region|integral to membrane|plasma membrane	receptor activity				0	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000767)|Lung(218;0.112)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	6020949	6020949	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6020949delC								RANBP6 (5309 upstream) : IL33 (194858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	6349648	6349648	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6349648delA								TPD52L3 (17748 upstream) : UHRF2 (63503 downstream)																																			---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6582521	6582521	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6582521delA	uc003zkc.2	-							NM_000170	NP_000161			glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6638219	6638219	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6638219delT	uc003zkc.2	-							NM_000170	NP_000161			glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	6736050	6736051	+	Intron	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6736050_6736051insG	uc010mhu.2	+							NM_001146696	NP_001140168			jumonji domain containing 2C isoform 4						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	6990352	6990353	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6990352_6990353delTT	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876			jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	7893013	7893013	+	IGR	DEL	A	-	-	rs75695657		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7893013delA								C9orf123 (93214 upstream) : PTPRD (421234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	7954272	7954272	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7954272delA								C9orf123 (154473 upstream) : PTPRD (359975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	8114848	8114848	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8114848delA								C9orf123 (315049 upstream) : PTPRD (199399 downstream)																																			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	9629981	9629981	+	Intron	DEL	T	-	-	rs113984434		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9629981delT	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	12134852	12134852	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12134852delA								None (None upstream) : TYRP1 (558534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12540783	12540784	+	IGR	INS	-	CTAA	CTAA	rs147670786	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12540783_12540784insCTAA								None (None upstream) : TYRP1 (152602 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12838095	12838095	+	IGR	DEL	A	-	-	rs112251490		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12838095delA								C9orf150 (15037 upstream) : MPDZ (267614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	13373297	13373297	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13373297delT								MPDZ (93734 upstream) : NFIB (708551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	13951294	13951296	+	IGR	DEL	AAA	-	-	rs75724920		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13951294_13951296delAAA								MPDZ (671731 upstream) : NFIB (130552 downstream)																																			---	---	---	---
NFIB	4781	broad.mit.edu	37	9	14200709	14200709	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14200709delC	uc003zle.2	-						NFIB_uc003zlf.2_Intron|NFIB_uc011lmo.1_Intron	NM_005596	NP_005587			nuclear factor I/B						anterior commissure morphogenesis|chondrocyte differentiation|Clara cell differentiation|commissural neuron axon guidance|DNA replication|glial cell differentiation|lung ciliated cell differentiation|negative regulation of DNA binding|negative regulation of epithelial cell proliferation involved in lung morphogenesis|negative regulation of mesenchymal cell proliferation involved in lung development|positive regulation of transcription from RNA polymerase II promoter|principal sensory nucleus of trigeminal nerve development|Type I pneumocyte differentiation|Type II pneumocyte differentiation	cerebellar mossy fiber|nucleolus|nucleus	RNA polymerase II transcription corepressor activity|sequence-specific DNA binding RNA polymerase II transcription factor activity				0				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)				T	MYB|HGMA2	adenoid cystic carcinoma|lipoma								---	---	---	---
Unknown	0	broad.mit.edu	37	9	14405613	14405613	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14405613delA								NFIB (91668 upstream) : ZDHHC21 (149868 downstream)																																			---	---	---	---
TTC39B	158219	broad.mit.edu	37	9	15278003	15278003	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15278003delA	uc003zlr.1	-						TTC39B_uc010mie.1_Intron|TTC39B_uc011lmq.1_Intron|TTC39B_uc011lmr.1_Intron|TTC39B_uc010mif.1_Intron|TTC39B_uc011lms.1_Intron	NM_152574	NP_689787			tetratricopeptide repeat domain 39B								binding			ovary(1)	1																		---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15965653	15965653	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15965653delA	uc003zmd.2	+						C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	17066111	17066111	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17066111delC								BNC2 (195325 upstream) : CNTLN (68927 downstream)																																			---	---	---	---
CNTLN	54875	broad.mit.edu	37	9	17199603	17199603	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17199603delT	uc003zmz.2	+						CNTLN_uc003zmx.3_Intron|CNTLN_uc003zmy.2_Intron	NM_017738	NP_060208			centlein isoform 1							centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)														---	---	---	---
SH3GL2	6456	broad.mit.edu	37	9	17786723	17786723	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17786723delC	uc003zna.2	+						SH3GL2_uc011lmx.1_Intron|SH3GL2_uc011lmy.1_Intron	NM_003026	NP_003017			SH3-domain GRB2-like 2						axon guidance|central nervous system development|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	cytosol|Golgi membrane|plasma membrane	identical protein binding|lipid binding			skin(1)	1				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	18077745	18077745	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18077745delA								SH3GL2 (280625 upstream) : ADAMTSL1 (396359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	18199890	18199890	+	IGR	DEL	T	-	-	rs67163837		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18199890delT								SH3GL2 (402770 upstream) : ADAMTSL1 (274214 downstream)																																			---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18684298	18684298	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18684298delA	uc003zne.3	+						ADAMTSL1_uc003znc.3_Intron	NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
FAM154A	158297	broad.mit.edu	37	9	18946646	18946646	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18946646delA	uc003zni.1	-						FAM154A_uc010mip.1_Intron	NM_153707	NP_714918			hypothetical protein LOC158297											pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)														---	---	---	---
FAM154A	158297	broad.mit.edu	37	9	18955041	18955041	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18955041delA	uc003zni.1	-						FAM154A_uc010mip.1_Intron	NM_153707	NP_714918			hypothetical protein LOC158297											pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)														---	---	---	---
HAUS6	54801	broad.mit.edu	37	9	19078117	19078119	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19078117_19078119delAAA	uc003znk.2	-						HAUS6_uc011lmz.1_Intron|HAUS6_uc003znl.1_Intron|HAUS6_uc003znm.1_Intron	NM_017645	NP_060115			HAUS augmin-like complex, subunit 6						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleus|spindle				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	19138401	19138402	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19138401_19138402insA	uc003znp.1	-											Homo sapiens cDNA FLJ36877 fis, clone BEAST2000454.																														---	---	---	---
DENND4C	55667	broad.mit.edu	37	9	19372238	19372238	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19372238delT	uc003znq.2	+	28					DENND4C_uc011lnc.1_3'UTR|DENND4C_uc011lnd.1_3'UTR|DENND4C_uc003znr.2_3'UTR|DENND4C_uc003zns.2_3'UTR	NM_017925	NP_060395			DENN/MADD domain containing 4C							integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
MLLT3	4300	broad.mit.edu	37	9	20506077	20506078	+	Intron	INS	-	T	T	rs36070031		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20506077_20506078insT	uc003zoe.2	-						MLLT3_uc011lne.1_Intron|MLLT3_uc011lnf.1_Intron|MLLT3_uc003zof.2_Intron|MLLT3_uc011lng.1_Intron	NM_004529	NP_004520			myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)				T	MLL	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	9	21725180	21725180	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21725180delG								LOC554202 (165348 upstream) : MTAP (77455 downstream)														p.0(1)|p.0?(1)																					---	---	---	---
MTAP	4507	broad.mit.edu	37	9	21954474	21954474	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21954474delT	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)													---	---	---	---
CDKN2BAS	100048912	broad.mit.edu	37	9	22051050	22051050	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22051050delT	uc010miw.1	+						CDKN2BAS_uc010mix.1_Intron|CDKN2BAS_uc003zpm.2_Intron					Homo sapiens hypothetical methylthioadenosine phosphorylase fusion protein mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	22413895	22413900	+	IGR	DEL	GAAGAG	-	-	rs150758816	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22413895_22413900delGAAGAG								CDKN2BAS (292804 upstream) : DMRTA1 (32940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	22707339	22707339	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22707339delA	uc003zpq.1	+											Homo sapiens cDNA FLJ35282 fis, clone PROST2007328.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	23083676	23083676	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23083676delT								DMRTA1 (631204 upstream) : ELAVL2 (606429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23271150	23271150	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23271150delA								DMRTA1 (818678 upstream) : ELAVL2 (418955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23493371	23493372	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23493371_23493372delAC								None (None upstream) : ELAVL2 (196733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	24786698	24786698	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24786698delT								ELAVL2 (960635 upstream) : TUSC1 (889696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25249600	25249600	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25249600delA								None (None upstream) : TUSC1 (426794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26047424	26047424	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26047424delA								TUSC1 (368568 upstream) : C9orf82 (793260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26477991	26477992	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26477991_26477992delTC								TUSC1 (799135 upstream) : C9orf82 (362692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26632182	26632183	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26632182_26632183insA								TUSC1 (953326 upstream) : C9orf82 (208501 downstream)																																			---	---	---	---
PLAA	9373	broad.mit.edu	37	9	26909616	26909616	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26909616delT	uc003zqd.2	-						PLAA_uc003zqe.2_Intron	NM_001031689	NP_001026859			phospholipase A2-activating protein						phospholipid metabolic process|signal transduction		phospholipase A2 activator activity				0		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)														---	---	---	---
C9orf72	203228	broad.mit.edu	37	9	27548847	27548848	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27548847_27548848delTT	uc003zqq.2	-							NM_018325	NP_060795			hypothetical protein LOC203228 isoform a											ovary(3)|central_nervous_system(1)	4		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)														---	---	---	---
C9orf72	203228	broad.mit.edu	37	9	27558227	27558228	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27558227_27558228delAA	uc003zqq.2	-							NM_018325	NP_060795			hypothetical protein LOC203228 isoform a											ovary(3)|central_nervous_system(1)	4		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	27745811	27745811	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27745811delT								C9orf72 (171969 upstream) : LINGO2 (202717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	27842413	27842413	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27842413delT	uc003zqs.1	+											full-length cDNA clone CS0DC011YE23 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28182013	28182013	+	Intron	DEL	A	-	-	rs114784349	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28182013delA	uc003zqu.1	-						LINGO2_uc010mjf.1_Intron|LINGO2_uc003zqv.1_Intron	NM_152570	NP_689783			leucine rich repeat and Ig domain containing 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	29146381	29146382	+	IGR	DEL	AC	-	-	rs144167665	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29146381_29146382delAC								MIR873 (257428 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	31645188	31645188	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31645188delA								None (None upstream) : ACO1 (739413 downstream)																																			---	---	---	---
DDX58	23586	broad.mit.edu	37	9	32457558	32457558	+	Intron	DEL	A	-	-	rs7865082	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32457558delA	uc003zra.2	-						DDX58_uc010mjj.2_Intron|DDX58_uc010mji.2_Intron	NM_014314	NP_055129			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide						detection of virus|innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	cytosol	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|protein binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)														---	---	---	---
DDX58	23586	broad.mit.edu	37	9	32476513	32476513	+	Intron	DEL	A	-	-	rs77031042		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32476513delA	uc003zra.2	-						DDX58_uc010mjj.2_Intron|DDX58_uc010mjk.1_Intron|DDX58_uc011lnr.1_Intron|DDX58_uc010mji.2_Intron	NM_014314	NP_055129			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide						detection of virus|innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	cytosol	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|protein binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	32830818	32830818	+	IGR	DEL	T	-	-	rs114395230	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32830818delT								TMEM215 (41621 upstream) : APTX (141791 downstream)																																			---	---	---	---
APTX	54840	broad.mit.edu	37	9	32977842	32977842	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32977842delA	uc003zrm.2	-						APTX_uc010mjm.2_Intron|APTX_uc003zrj.2_Intron|APTX_uc011lns.1_Intron|APTX_uc003zrl.2_Intron|APTX_uc003zrn.2_Intron|APTX_uc003zro.2_Intron|APTX_uc003zrp.2_Intron|APTX_uc003zrq.2_Intron|APTX_uc003zrr.2_Intron|APTX_uc003zrs.2_Intron|APTX_uc003zrt.2_Intron|APTX_uc003zru.2_Intron|APTX_uc003zrv.2_Intron|APTX_uc003zrw.2_Intron|APTX_uc003zrx.2_Intron|APTX_uc003zry.2_Intron|APTX_uc003zrz.2_Intron	NM_175072	NP_778242			aprataxin isoform c						cell death|double-strand break repair|regulation of protein stability|response to hydrogen peroxide|single strand break repair	chromatin|nucleolus|nucleoplasm	chromatin binding|damaged DNA binding|DNA 5'-adenosine monophosphate hydrolase activity|double-stranded DNA binding|double-stranded RNA binding|phosphoglycolate phosphatase activity|phosphoprotein binding|polynucleotide 3'-phosphatase activity|protein N-terminus binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)									Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
APTX	54840	broad.mit.edu	37	9	33010718	33010718	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33010718delA	uc003zrz.2	-							NM_175071	NP_778241			aprataxin isoform d						cell death|double-strand break repair|regulation of protein stability|response to hydrogen peroxide|single strand break repair	chromatin|nucleolus|nucleoplasm	chromatin binding|damaged DNA binding|DNA 5'-adenosine monophosphate hydrolase activity|double-stranded DNA binding|double-stranded RNA binding|phosphoglycolate phosphatase activity|phosphoprotein binding|polynucleotide 3'-phosphatase activity|protein N-terminus binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)									Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
SMU1	55234	broad.mit.edu	37	9	33071901	33071901	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33071901delA	uc003zsf.1	-						SMU1_uc010mjo.1_Intron|SMU1_uc010mjp.1_Intron|SMU1_uc011lnu.1_Intron	NM_018225	NP_060695			smu-1 suppressor of mec-8 and unc-52 homolog							cytoplasm|nucleus				ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	34543272	34543272	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34543272delA								ENHO (20235 upstream) : CNTFR (8159 downstream)																																			---	---	---	---
TLN1	7094	broad.mit.edu	37	9	35725917	35725917	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35725917delT	uc003zxt.2	-						TLN1_uc003zxu.3_Intron	NM_006289	NP_006280			talin 1						axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
RECK	8434	broad.mit.edu	37	9	36060651	36060652	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36060651_36060652delTT	uc003zyv.2	+						RECK_uc010mld.2_Intron|RECK_uc003zyu.3_Intron|RECK_uc003zyw.2_Intron|RECK_uc010mle.1_Intron|RECK_uc003zyx.2_Intron	NM_021111	NP_066934			RECK protein precursor							anchored to membrane|peripheral to membrane of membrane fraction|plasma membrane	metalloendopeptidase inhibitor activity|serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)	3			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
RNF38	152006	broad.mit.edu	37	9	36391387	36391387	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36391387delA	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	36600097	36600097	+	Intron	DEL	T	-	-	rs10713474		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36600097delT	uc003zzn.2	+						MELK_uc011lpm.1_Intron|MELK_uc011lpn.1_Intron|MELK_uc011lpo.1_Intron|MELK_uc010mll.2_Intron|MELK_uc011lpp.1_Intron|MELK_uc010mlm.2_Intron|MELK_uc011lpq.1_Intron|MELK_uc011lpr.1_Intron|MELK_uc011lps.1_Intron	NM_014791	NP_055606			maternal embryonic leucine zipper kinase							cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	37055819	37055819	+	IGR	DEL	A	-	-	rs75917621		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37055819delA								PAX5 (21343 upstream) : ZCCHC7 (64650 downstream)																																			---	---	---	---
ZCCHC7	84186	broad.mit.edu	37	9	37164082	37164082	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37164082delT	uc003zzq.2	+						ZCCHC7_uc011lqh.1_Intron|ZCCHC7_uc011lqi.1_Intron|ZCCHC7_uc010mlt.2_Intron|ZCCHC7_uc003zzs.1_Intron	NM_032226	NP_115602			zinc finger, CCHC domain containing 7								nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.0137)														---	---	---	---
TOMM5	401505	broad.mit.edu	37	9	37591693	37591693	+	Intron	DEL	A	-	-	rs111915525		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37591693delA	uc010mlx.2	-						FBXO10_uc004aac.2_5'Flank|FBXO10_uc004aad.2_5'Flank|TOMM5_uc004aae.3_Intron|TOMM5_uc011lql.1_Intron|TOMM5_uc004aaf.2_Intron	NM_001001790	NP_001001790			translocase of outer mitochondrial membrane 5							integral to membrane|mitochondrial outer membrane translocase complex					0																		---	---	---	---
SHB	6461	broad.mit.edu	37	9	38053242	38053242	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38053242delT	uc004aax.2	-							NM_003028	NP_003019			Src homology 2 domain containing adaptor protein						angiogenesis|apoptosis|cell differentiation|signal transduction	cytoplasm|plasma membrane	SH3/SH2 adaptor activity			central_nervous_system(2)|skin(1)	3		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	38225942	38225942	+	IGR	DEL	T	-	-	rs67431254		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38225942delT								SHB (156732 upstream) : ALDH1B1 (166760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	38460457	38460457	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38460457delT								IGFBPL1 (36013 upstream) : C9orf122 (160628 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	38737973	38737973	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38737973delA								C9orf122 (114698 upstream) : CNTNAP3 (334793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	41910778	41910779	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:41910778_41910779delTC								FAM75A5 (583414 upstream) : MGC21881 (37737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	43513065	43513065	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43513065delT								LOC642929 (367581 upstream) : FAM75A6 (111439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	44122397	44122397	+	IGR	DEL	T	-	-	rs117805393		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44122397delT								FAM75A6 (491667 upstream) : FAM27C (867839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66333430	66333430	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66333430delA								FAM74A4 (839044 upstream) : LOC442421 (163040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66456852	66456853	+	Intron	INS	-	AC	AC	rs140941453		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66456852_66456853insAC	uc010mng.1	-						uc004aeb.2_3'UTR|uc004aec.2_5'Flank					Homo sapiens cDNA, FLJ98602.																														---	---	---	---
LOC442421	442421	broad.mit.edu	37	9	66498655	66498655	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66498655delT	uc004aee.1	+						LOC442421_uc004aed.1_Intron					Homo sapiens hypothetical LOC442421, mRNA (cDNA clone IMAGE:40031134).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	66535948	66535948	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66535948delA	uc010mnh.1	-						uc004aef.2_Intron					Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	66803957	66803957	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66803957delT								LOC442421 (300930 upstream) : AQP7P1 (450310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	67300870	67300871	+	IGR	INS	-	TA	TA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67300870_67300871insTA								AQP7P1 (11378 upstream) : FAM27B (492059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	67352540	67352541	+	IGR	INS	-	GATGA	GATGA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67352540_67352541insGATGA								AQP7P1 (63048 upstream) : FAM27B (440389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68408397	68408397	+	5'Flank	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68408397delC	uc004aew.1	+											Homo sapiens cDNA, FLJ98602.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	68426898	68426898	+	IGR	DEL	T	-	-	rs67299135		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68426898delT								FAM27B (632709 upstream) : MIR1299 (575341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68452562	68452563	+	IGR	INS	-	AA	AA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68452562_68452563insAA								FAM27B (658373 upstream) : MIR1299 (549676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68481954	68481956	+	IGR	DEL	AAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68481954_68481956delAAC								FAM27B (687765 upstream) : MIR1299 (520283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68492208	68492208	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68492208delT								FAM27B (698019 upstream) : MIR1299 (510031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68501232	68501232	+	IGR	DEL	C	-	-	rs112144733		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68501232delC								FAM27B (707043 upstream) : MIR1299 (501007 downstream)																																			---	---	---	---
CBWD6	644019	broad.mit.edu	37	9	69205795	69205796	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69205795_69205796insT	uc004afj.3	-						CBWD6_uc004afk.3_Intron|CBWD6_uc011lrf.1_Intron	NM_001085457	NP_001078926			COBW domain containing 6								ATP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	69891586	69891587	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69891586_69891587delTT								LOC100133920 (226637 upstream) : FOXD4L5 (284122 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	71191063	71191063	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71191063delA								C9orf71 (35280 upstream) : PIP5K1B (129553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	71288038	71288038	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71288038delA								C9orf71 (132255 upstream) : PIP5K1B (32578 downstream)																																			---	---	---	---
PIP5K1B	8395	broad.mit.edu	37	9	71572151	71572151	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71572151delA	uc004agu.2	+						PIP5K1B_uc011lrq.1_Intron|PIP5K1B_uc004agv.2_Intron|uc004agx.1_Intron	NM_003558	NP_003549			phosphatidylinositol-4-phosphate 5-kinase, type							endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding			stomach(1)	1				Lung(182;0.133)														---	---	---	---
FXN	2395	broad.mit.edu	37	9	71657156	71657156	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71657156delA	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135			frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0																		---	---	---	---
APBA1	320	broad.mit.edu	37	9	72111880	72111880	+	Intron	DEL	C	-	-	rs142940938		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72111880delC	uc004ahh.2	-							NM_001163	NP_001154			amyloid beta A4 precursor protein-binding,						axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1																		---	---	---	---
APBA1	320	broad.mit.edu	37	9	72266395	72266395	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72266395delT	uc004ahh.2	-							NM_001163	NP_001154			amyloid beta A4 precursor protein-binding,						axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1																		---	---	---	---
MAMDC2	256691	broad.mit.edu	37	9	72759389	72759389	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72759389delT	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	72961329	72961329	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72961329delA	uc004ahr.2	+						SMC5_uc011lry.1_5'Flank	NM_015110	NP_055925			SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TMEM2	23670	broad.mit.edu	37	9	74321157	74321159	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74321157_74321159delAAA	uc011lsa.1	-						TMEM2_uc011lrz.1_5'Flank|TMEM2_uc010mos.2_Intron|TMEM2_uc011lsb.1_Intron	NM_013390	NP_037522			transmembrane protein 2 isoform a							integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)														---	---	---	---
TMEM2	23670	broad.mit.edu	37	9	74331268	74331268	+	Intron	DEL	A	-	-	rs35467741		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74331268delA	uc011lsa.1	-						TMEM2_uc010mos.2_Intron|TMEM2_uc011lsb.1_Intron	NM_013390	NP_037522			transmembrane protein 2 isoform a							integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	74456445	74456446	+	IGR	DEL	TT	-	-	rs77173353		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74456445_74456446delTT								TMEM2 (72645 upstream) : FAM108B1 (20924 downstream)																																			---	---	---	---
GDA	9615	broad.mit.edu	37	9	74765258	74765259	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74765258_74765259delCA	uc004aiq.2	+						GDA_uc011lse.1_Intron|GDA_uc011lsf.1_Intron|GDA_uc004air.2_Intron|GDA_uc010mow.1_Intron|GDA_uc004ais.2_Intron	NM_004293	NP_004284			guanine deaminase						nervous system development|purine base metabolic process|purine nucleotide catabolic process	cytosol	guanine deaminase activity|zinc ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)														---	---	---	---
GDA	9615	broad.mit.edu	37	9	74846481	74846481	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74846481delA	uc004aiq.2	+						GDA_uc011lse.1_Intron|GDA_uc011lsf.1_Intron|GDA_uc004air.2_Intron|GDA_uc010mow.1_Intron|GDA_uc004ais.2_Intron	NM_004293	NP_004284			guanine deaminase						nervous system development|purine base metabolic process|purine nucleotide catabolic process	cytosol	guanine deaminase activity|zinc ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	75499603	75499604	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75499603_75499604delCA								TMC1 (48336 upstream) : ALDH1A1 (15984 downstream)																																			---	---	---	---
ANXA1	301	broad.mit.edu	37	9	75784905	75784905	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75784905delA	uc004ajf.1	+						ANXA1_uc004ajg.1_Intron	NM_000700	NP_000691			annexin I						alpha-beta T cell differentiation|anti-apoptosis|cell surface receptor linked signaling pathway|cellular component movement|inflammatory response|keratinocyte differentiation|lipid metabolic process|peptide cross-linking|positive regulation of vesicle fusion	basolateral plasma membrane|cilium|cornified envelope|cytoplasm|extracellular region|nucleus	calcium ion binding|calcium-dependent phospholipid binding|phospholipase A2 inhibitor activity|protein binding, bridging|receptor binding|structural molecule activity			breast(1)|central_nervous_system(1)	2		all_epithelial(88;2.54e-11)		OV - Ovarian serous cystadenocarcinoma(323;2.82e-06)|GBM - Glioblastoma multiforme(74;0.0325)	Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Clobetasol(DB01013)|Clocortolone(DB00838)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Flumethasone Pivalate(DB00663)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mometasone(DB00764)|Prednicarbate(DB01130)|Prednisone(DB00635)|Rimexolone(DB00896)|Triamcinolone(DB00620)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	75867398	75867398	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75867398delT								ANXA1 (82091 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76659771	76659771	+	IGR	DEL	A	-	-	rs113851564		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76659771delA								ANXA1 (874464 upstream) : RORB (452481 downstream)																																			---	---	---	---
RORB	6096	broad.mit.edu	37	9	77281375	77281376	+	Intron	DEL	AA	-	-	rs71739687		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77281375_77281376delAA	uc004aji.2	+						RORB_uc004ajh.2_Intron	NM_006914	NP_008845			RAR-related orphan receptor B						eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
RPSAP9	653162	broad.mit.edu	37	9	79014570	79014571	+	3'UTR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79014570_79014571delAA	uc011lsj.1	+	1						NR_026890				SubName: Full=Laminin receptor-like protein LAMRL5;												0																		---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79955199	79955199	+	Splice_Site	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79955199delG	uc004akr.2	+	49	7139	c.6879_splice	c.e49+1	p.Q2293_splice	VPS13A_uc004akp.3_Splice_Site_p.Q2293_splice|VPS13A_uc004akq.3_Splice_Site_p.Q2293_splice|VPS13A_uc004aks.2_Splice_Site_p.Q2254_splice	NM_033305	NP_150648			vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
GNA14	9630	broad.mit.edu	37	9	80208251	80208251	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80208251delT	uc004aku.2	-							NM_004297	NP_004288			G alpha 14						activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	81092304	81092304	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81092304delT								PSAT1 (147297 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82988987	82988987	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82988987delA								TLE4 (647330 upstream) : None (None downstream)																																			---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84225192	84225192	+	Frame_Shift_Del	DEL	G	-	-	rs143065311		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84225192delG	uc004aly.2	-	14	1715	c.1274delC	c.(1273-1275)CCTfs	p.P425fs	TLE1_uc004alz.2_Frame_Shift_Del_p.P435fs|TLE1_uc011lsr.1_Frame_Shift_Del_p.P410fs|TLE1_uc004ama.1_Frame_Shift_Del_p.P424fs	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1	425	Pro/Ser-rich.				negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84245052	84245052	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84245052delA	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_Intron|TLE1_uc011lss.1_Intron	NM_005077	NP_005068			transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	84361441	84361441	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84361441delA	uc004amc.2	+						uc004amd.2_Intron					Homo sapiens cDNA clone IMAGE:4813482.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	84420056	84420056	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84420056delT								TLE1 (116460 upstream) : FLJ43950 (108296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84426732	84426733	+	IGR	INS	-	T	T	rs33955301		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84426732_84426733insT								TLE1 (123136 upstream) : FLJ43950 (101619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85382492	85382492	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85382492delT								FLJ46321 (772322 upstream) : RASEF (214825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85783967	85783967	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85783967delT								RASEF (105924 upstream) : FRMD3 (73938 downstream)																																			---	---	---	---
FRMD3	257019	broad.mit.edu	37	9	85959740	85959741	+	Intron	DEL	GT	-	-	rs77054444		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85959740_85959741delGT	uc004ams.1	-						FRMD3_uc004amr.1_Intron	NM_174938	NP_777598			FERM domain containing 3							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
GKAP1	80318	broad.mit.edu	37	9	86430489	86430490	+	Intron	DEL	AC	-	-	rs36048350		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86430489_86430490delAC	uc004amy.2	-						GKAP1_uc004amz.2_Intron|GKAP1_uc011lsu.1_Intron|uc011lsv.1_5'Flank	NM_025211	NP_079487			G kinase anchoring protein 1 isoform a						signal transduction	Golgi apparatus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	87058714	87058715	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87058714_87058715insT								SLC28A3 (75301 upstream) : NTRK2 (224751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87210748	87210750	+	IGR	DEL	AGA	-	-	rs72474033		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87210748_87210750delAGA								SLC28A3 (227335 upstream) : NTRK2 (72716 downstream)																																			---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87320362	87320362	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87320362delT	uc004aoa.1	+						NTRK2_uc004anv.1_Intron|NTRK2_uc004any.1_Intron|NTRK2_uc004anz.1_Intron|NTRK2_uc011lsz.1_Intron|NTRK2_uc011lta.1_Intron|NTRK2_uc004aob.1_Intron|NTRK2_uc011ltb.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	88128170	88128171	+	IGR	INS	-	T	T	rs145647351	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88128170_88128171insT								NTRK2 (489665 upstream) : AGTPBP1 (33284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	88421841	88421841	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88421841delT	uc004aog.1	+						uc004aoh.1_Intron					Homo sapiens cDNA FLJ42532 fis, clone BRACE3003004.																														---	---	---	---
NAA35	60560	broad.mit.edu	37	9	88621085	88621085	+	Intron	DEL	A	-	-	rs34993101		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88621085delA	uc004aoi.3	+						NAA35_uc004aoj.3_Intron	NM_024635	NP_078911			corneal wound healing-related protein						smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3																		---	---	---	---
GOLM1	51280	broad.mit.edu	37	9	88646131	88646131	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88646131delA	uc004aol.2	-						GOLM1_uc004aom.2_Intron	NM_016548	NP_057632			golgi membrane protein 1							Golgi apparatus|integral to plasma membrane					0																		---	---	---	---
DAPK1	1612	broad.mit.edu	37	9	90219825	90219825	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90219825delT	uc004apc.2	+						DAPK1_uc004ape.2_Intron|DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_Intron|DAPK1_uc011lth.1_Intron	NM_004938	NP_004929			death-associated protein kinase 1						apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2														Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	9	90833684	90833684	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90833684delT								CDK20 (244017 upstream) : SPIN1 (169156 downstream)																																			---	---	---	---
SPIN1	10927	broad.mit.edu	37	9	91008203	91008203	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91008203delT	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																		---	---	---	---
SPIN1	10927	broad.mit.edu	37	9	91057604	91057604	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91057604delT	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	91601378	91601379	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91601378_91601379delCA								LOC286238 (334303 upstream) : C9orf47 (4399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91860847	91860847	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91860847delA								SHC3 (67165 upstream) : CKS2 (65266 downstream)																																			---	---	---	---
SECISBP2	79048	broad.mit.edu	37	9	91963300	91963300	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91963300delG	uc004aqj.1	+						SECISBP2_uc011ltk.1_Intron|SECISBP2_uc004aqk.1_Intron|SECISBP2_uc010mqo.1_Intron|SECISBP2_uc011ltl.1_Intron	NM_024077	NP_076982			SECIS binding protein 2						translation	nucleus	mRNA 3'-UTR binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	92993940	92993941	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92993940_92993941insT								LOC100129066 (659266 upstream) : DIRAS2 (378173 downstream)																																			---	---	---	---
DIRAS2	54769	broad.mit.edu	37	9	93405560	93405560	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93405560delT	uc004aqx.1	-							NM_017594	NP_060064			Di-Ras2						small GTPase mediated signal transduction	intracellular|plasma membrane	GTP binding|GTPase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	93837939	93837940	+	5'Flank	INS	-	C	C	rs148583834	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93837939_93837940insC	uc004ard.1	-											Homo sapiens cDNA FLJ46870 fis, clone UTERU3012599.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	94155593	94155596	+	IGR	DEL	ACAC	-	-	rs141722715		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94155593_94155596delACAC								AUH (31387 upstream) : NFIL3 (15733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	94254569	94254569	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94254569delT								NFIL3 (68425 upstream) : ROR2 (70804 downstream)																																			---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94598822	94598825	+	Intron	DEL	AAAA	-	-	rs76649781		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94598822_94598825delAAAA	uc004arj.1	-						ROR2_uc004ari.1_Intron|ROR2_uc004ark.2_Intron	NM_004560	NP_004551			receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20																		---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94624613	94624613	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94624613delA	uc004arj.1	-						ROR2_uc004ari.1_Intron|ROR2_uc004ark.2_Intron	NM_004560	NP_004551			receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	94946730	94946733	+	IGR	DEL	CATC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94946730_94946733delCATC								C9orf44 (24840 upstream) : IARS (25892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	94957414	94957414	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94957414delT								C9orf44 (35524 upstream) : IARS (15211 downstream)																																			---	---	---	---
CENPP	401541	broad.mit.edu	37	9	95124501	95124501	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95124501delA	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																		---	---	---	---
IPPK	64768	broad.mit.edu	37	9	95391161	95391162	+	Intron	INS	-	A	A	rs140414911	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95391161_95391162insA	uc004asl.1	-						IPPK_uc004ask.1_Intron|uc004asn.1_5'Flank	NM_022755	NP_073592			inositol 1,3,4,5,6-pentakisphosphate 2-kinase						inositol or phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol pentakisphosphate 2-kinase activity			ovary(2)	2																		---	---	---	---
IPPK	64768	broad.mit.edu	37	9	95392956	95392956	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95392956delA	uc004asl.1	-						IPPK_uc004ask.1_Intron|uc004asn.1_5'Flank	NM_022755	NP_073592			inositol 1,3,4,5,6-pentakisphosphate 2-kinase						inositol or phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol pentakisphosphate 2-kinase activity			ovary(2)	2																		---	---	---	---
ZNF484	83744	broad.mit.edu	37	9	95609713	95609713	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95609713delT	uc004asu.1	-	5	1505	c.1356delA	c.(1354-1356)AAAfs	p.K452fs	ANKRD19_uc004asr.3_Intron|ZNF484_uc011lub.1_Frame_Shift_Del_p.K454fs|ZNF484_uc010mrb.1_Frame_Shift_Del_p.K416fs|ZNF484_uc004asv.1_Frame_Shift_Del_p.K416fs	NM_031486	NP_113674	Q5JVG2	ZN484_HUMAN	zinc finger protein 484 isoform a	452	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
WNK2	65268	broad.mit.edu	37	9	96068757	96068757	+	Intron	DEL	C	-	-	rs10761207	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96068757delC	uc004ati.1	+						WNK2_uc011lud.1_Intron|WNK2_uc004atj.2_Intron|WNK2_uc004atk.2_Intron	NM_006648	NP_006639			WNK lysine deficient protein kinase 2						intracellular protein kinase cascade		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1)	12																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	96962063	96962063	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96962063delA	uc004auk.2	-											Homo sapiens cDNA clone IMAGE:5265295.																														---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97490521	97490522	+	Intron	INS	-	CA	CA	rs146853147	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97490521_97490522insCA	uc004auy.2	+						C9orf3_uc011lui.1_Intron|C9orf3_uc004aux.1_Intron	NM_032823	NP_116212			aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97550775	97550775	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97550775delT	uc004ava.2	+						C9orf3_uc004aux.1_Intron|C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron	NM_032823	NP_116212			aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
FANCC	2176	broad.mit.edu	37	9	98020496	98020496	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98020496delA	uc004avh.2	-						FANCC_uc004avi.3_Intron|FANCC_uc010mrm.1_Intron|FANCC_uc011lul.1_Intron	NM_000136	NP_000127			Fanconi anemia, complementation group C						protein complex assembly	cytosol|nucleoplasm	protein binding			kidney(1)	1		Acute lymphoblastic leukemia(62;0.138)						D|Mis|N|F|S			AML|leukemia		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
PTCH1	5727	broad.mit.edu	37	9	98238450	98238450	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98238450delA	uc004avk.3	-						PTCH1_uc010mro.2_Intron|PTCH1_uc010mrp.2_Intron|PTCH1_uc010mrq.2_Intron|PTCH1_uc004avl.3_Intron|PTCH1_uc010mrr.2_Intron|PTCH1_uc004avm.3_Intron|PTCH1_uc010mrs.1_Intron	NM_000264	NP_000255			patched isoform L						embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity			skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1)	379		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)												Basal_Cell_Nevus_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	9	98328028	98328028	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98328028delT								PTCH1 (48781 upstream) : C9orf130 (240344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98558636	98558637	+	IGR	DEL	CA	-	-	rs67874420		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98558636_98558637delCA								PTCH1 (279389 upstream) : C9orf130 (9735 downstream)																																			---	---	---	---
C9orf102	375748	broad.mit.edu	37	9	98766792	98766792	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98766792delT	uc004avu.2	+						uc010msa.1_Intron|uc011lun.1_Intron					Homo sapiens cDNA, FLJ97452.						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	98910246	98910246	+	IGR	DEL	A	-	-	rs139074595		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98910246delA								NCRNA00092 (126209 upstream) : HSD17B3 (87343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98973124	98973124	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98973124delG								NCRNA00092 (189087 upstream) : HSD17B3 (24465 downstream)																																			---	---	---	---
SLC35D2	11046	broad.mit.edu	37	9	99083634	99083634	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99083634delA	uc004awc.2	-						SLC35D2_uc010msd.2_Intron|SLC35D2_uc010mse.2_Intron|SLC35D2_uc010msf.2_Intron|SLC35D2_uc004awd.2_Intron	NM_007001	NP_008932			solute carrier family 35, member D2							Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity				0		Acute lymphoblastic leukemia(62;0.0167)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	99201491	99201491	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99201491delA								ZNF367 (20822 upstream) : HABP4 (10923 downstream)																																			---	---	---	---
CTSL2	1515	broad.mit.edu	37	9	99799042	99799042	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99799042delA	uc004awt.2	-						CTSL2_uc010msi.2_Intron|CTSL2_uc004awu.2_Intron|CTSL2_uc010msj.1_Intron|CTSL2_uc010msk.2_Intron	NM_001333	NP_001324			cathepsin L2 preproprotein							lysosome	cysteine-type endopeptidase activity				0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
KIAA1529	57653	broad.mit.edu	37	9	100077590	100077590	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100077590delG	uc011lut.1	+						KIAA1529_uc004axe.1_Intron|KIAA1529_uc004axg.1_Intron|KIAA1529_uc011lus.1_Intron|KIAA1529_uc010msm.1_Intron|KIAA1529_uc004axf.2_Intron|KIAA1529_uc011luv.1_Intron	NM_020893	NP_065944			hypothetical protein LOC57653											ovary(4)|large_intestine(2)|skin(1)	7		Acute lymphoblastic leukemia(62;0.154)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	100548207	100548208	+	IGR	DEL	GT	-	-	rs71993012		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100548207_100548208delGT								XPA (88516 upstream) : FOXE1 (67329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	100564042	100564043	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100564042_100564043delAA								XPA (104351 upstream) : FOXE1 (51494 downstream)																																			---	---	---	---
CORO2A	7464	broad.mit.edu	37	9	100953890	100953890	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100953890delG	uc004aym.2	-						CORO2A_uc004ayn.2_Intron	NM_052820	NP_438171			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	101206955	101206956	+	Intron	INS	-	T	T	rs146302391	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101206955_101206956insT	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)													---	---	---	---
COL15A1	1306	broad.mit.edu	37	9	101811955	101811955	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101811955delT	uc004azb.1	+							NM_001855	NP_001846			alpha 1 type XV collagen precursor						angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	101976841	101976843	+	IGR	DEL	GAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101976841_101976843delGAG								TGFBR1 (60370 upstream) : ALG2 (1865 downstream)																																			---	---	---	---
SEC61B	10952	broad.mit.edu	37	9	101990075	101990075	+	Intron	DEL	T	-	-	rs111986989		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101990075delT	uc004azh.2	+							NM_006808	NP_006799			Sec61 beta subunit						ER-associated protein catabolic process|protein import into nucleus, translocation|retrograde protein transport, ER to cytosol|transmembrane transport	endoplasmic reticulum Sec complex|integral to membrane	epidermal growth factor binding				0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
INVS	27130	broad.mit.edu	37	9	102868606	102868606	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)																---	---	---	---
INVS	27130	broad.mit.edu	37	9	103053354	103053354	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103053354delT	uc004bap.1	+						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	103174318	103174319	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103174318_103174319delTT								TEX10 (59059 upstream) : C9orf30 (15323 downstream)																																			---	---	---	---
TMEFF1	8577	broad.mit.edu	37	9	103279165	103279165	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103279165delT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	103706252	103706252	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103706252delT								MURC (356081 upstream) : LPPR1 (84779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105218708	105218708	+	IGR	DEL	A	-	-	rs12379430	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105218708delA								GRIN3A (717846 upstream) : CYLC2 (538885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	106289526	106289526	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106289526delG								CYLC2 (508756 upstream) : SMC2 (567015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	106539266	106539266	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106539266delT								CYLC2 (758496 upstream) : SMC2 (317275 downstream)																																			---	---	---	---
SMC2	10592	broad.mit.edu	37	9	106885501	106885501	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106885501delA	uc004bbv.2	+	17	2533	c.2245delA	c.(2245-2247)AAAfs	p.K749fs	SMC2_uc004bbu.1_Frame_Shift_Del_p.K749fs|SMC2_uc004bbw.2_Frame_Shift_Del_p.K749fs|SMC2_uc011lvl.1_Frame_Shift_Del_p.K749fs|SMC2_uc004bbx.2_Frame_Shift_Del_p.K749fs	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	749	Potential.				cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	107254231	107254232	+	IGR	DEL	AT	-	-	rs147946238	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107254231_107254232delAT								SMC2 (350538 upstream) : OR13F1 (12312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107366673	107366673	+	IGR	DEL	A	-	-	rs75507694		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107366673delA								OR13C5 (4979 upstream) : OR13C2 (280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107808493	107808495	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107808493_107808495delTTT								ABCA1 (118057 upstream) : SLC44A1 (198434 downstream)																																			---	---	---	---
SLC44A1	23446	broad.mit.edu	37	9	108118459	108118459	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108118459delT	uc004bcn.2	+						SLC44A1_uc010mtk.1_Intron|SLC44A1_uc004bco.1_5'UTR	NM_080546	NP_536856			CDW92 antigen							integral to membrane|mitochondrial outer membrane|plasma membrane	choline transmembrane transporter activity			breast(3)|ovary(1)	4					Choline(DB00122)													---	---	---	---
FKTN	2218	broad.mit.edu	37	9	108320918	108320918	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108320918delA	uc004bcr.2	+						FKTN_uc011lvx.1_Intron|FKTN_uc004bcs.2_Intron|FKTN_uc011lvy.1_Intron	NM_001079802	NP_001073270			fukutin						muscle organ development|negative regulation of cell proliferation|negative regulation of JNK cascade|nervous system development|regulation of protein glycosylation	cis-Golgi network|endoplasmic reticulum|extracellular space|Golgi membrane|integral to membrane|nucleus	transferase activity			breast(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	108538735	108538735	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108538735delT								TMEM38B (1291 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	109063895	109063895	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109063895delT	uc004bcw.2	+											Homo sapiens, clone IMAGE:5538960, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109338065	109338066	+	Intron	INS	-	CA	CA	rs139915293	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109338065_109338066insCA	uc004bcx.2	+											Homo sapiens, clone IMAGE:4246712, mRNA.																														---	---	---	---
RAD23B	5887	broad.mit.edu	37	9	110064252	110064252	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110064252delT	uc004bde.2	+						RAD23B_uc011lwa.1_Intron|RAD23B_uc011lwb.1_Intron	NM_002874	NP_002865			UV excision repair protein RAD23 homolog B						nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleoplasm|proteasome complex|XPC complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			ovary(1)	1													Direct_reversal_of_damage|NER					---	---	---	---
RAD23B	5887	broad.mit.edu	37	9	110069204	110069206	+	Intron	DEL	TTG	-	-	rs71368010		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110069204_110069206delTTG	uc004bde.2	+						RAD23B_uc011lwa.1_Intron|RAD23B_uc011lwb.1_Intron	NM_002874	NP_002865			UV excision repair protein RAD23 homolog B						nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleoplasm|proteasome complex|XPC complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			ovary(1)	1													Direct_reversal_of_damage|NER					---	---	---	---
Unknown	0	broad.mit.edu	37	9	110198099	110198100	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110198099_110198100insT								RAD23B (103630 upstream) : KLF4 (49035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110303571	110303571	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110303571delT								KLF4 (51524 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110404236	110404236	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110404236delT								KLF4 (152189 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110529721	110529721	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110529721delA								KLF4 (277674 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110679182	110679182	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110679182delT								KLF4 (427135 upstream) : ACTL7B (937689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111307034	111307034	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111307034delA								None (None upstream) : ACTL7B (309837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111483362	111483362	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111483362delT								None (None upstream) : ACTL7B (133509 downstream)																																			---	---	---	---
C9orf5	23731	broad.mit.edu	37	9	111795821	111795821	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111795821delA	uc004bdt.3	-						C9orf5_uc004bds.3_Intron|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401			hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)														---	---	---	---
C9orf4	23732	broad.mit.edu	37	9	111899626	111899626	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111899626delT	uc004bdw.1	-	5						NM_014334	NP_055149			hypothetical protein LOC23732							integral to membrane					0																		---	---	---	---
PTPN3	5774	broad.mit.edu	37	9	112153718	112153718	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112153718delG	uc004bed.2	-						PTPN3_uc004beb.2_Intron|PTPN3_uc004bec.2_Intron|PTPN3_uc010mtu.2_Intron|PTPN3_uc011lwg.1_Intron|PTPN3_uc011lwh.1_Intron|PTPN3_uc011lwd.1_Intron|PTPN3_uc011lwe.1_Intron|PTPN3_uc011lwf.1_Intron	NM_002829	NP_002820			protein tyrosine phosphatase, non-receptor type						negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(3)	3																		---	---	---	---
PTPN3	5774	broad.mit.edu	37	9	112238651	112238652	+	Intron	DEL	AA	-	-	rs111446708		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112238651_112238652delAA	uc004bed.2	-						PTPN3_uc011lwg.1_Intron|PTPN3_uc011lwh.1_Intron|PTPN3_uc004bee.3_Intron	NM_002829	NP_002820			protein tyrosine phosphatase, non-receptor type						negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	112272133	112272133	+	IGR	DEL	A	-	-	rs11330633		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112272133delA								PTPN3 (11540 upstream) : PALM2 (130939 downstream)																																			---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112674590	112674591	+	Intron	DEL	AA	-	-	rs80017123		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112674590_112674591delAA	uc004bei.2	+						PALM2_uc004bef.2_Intron|PALM2_uc004beg.2_Intron|PALM2_uc004beh.3_Intron|PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron	NM_001136562	NP_001130034			A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114174440	114174440	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114174440delA	uc004bfe.1	-							NM_001080398	NP_001073867			KIAA0368 protein												0																		---	---	---	---
DNAJC25-GNG10	552891	broad.mit.edu	37	9	114431141	114431141	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114431141delT	uc004bfn.2	+						GNG10_uc011lws.1_Intron|GNG10_uc004bfp.2_Intron	NM_004125	NP_004116			DNAJC25-GNG10 protein						protein folding	integral to membrane	heat shock protein binding|unfolded protein binding				0																		---	---	---	---
C9orf84	158401	broad.mit.edu	37	9	114520479	114520479	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114520479delA	uc004bfr.2	-						C9orf84_uc011lwt.1_Intron|C9orf84_uc004bfs.1_Intron|C9orf84_uc004bfq.2_Intron|C9orf84_uc010mug.2_Intron	NM_173521	NP_775792			hypothetical protein LOC158401 isoform 1											ovary(2)	2																		---	---	---	---
C9orf84	158401	broad.mit.edu	37	9	114526081	114526081	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114526081delA	uc004bfr.2	-						C9orf84_uc011lwt.1_Intron|C9orf84_uc004bfs.1_Intron	NM_173521	NP_775792			hypothetical protein LOC158401 isoform 1											ovary(2)	2																		---	---	---	---
UGCG	7357	broad.mit.edu	37	9	114661070	114661071	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114661070_114661071delTG	uc004bft.2	+							NM_003358	NP_003349			ceramide glucosyltransferase						epidermis development|glucosylceramide biosynthetic process	Golgi membrane|integral to membrane|membrane fraction	ceramide glucosyltransferase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.0433)	Miglustat(DB00419)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	114737126	114737126	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114737126delT								UGCG (41695 upstream) : SUSD1 (65936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	114955663	114955665	+	IGR	DEL	TTT	-	-	rs66947069		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114955663_114955665delTTT								SUSD1 (18107 upstream) : ROD1 (25050 downstream)																																			---	---	---	---
KIAA1958	158405	broad.mit.edu	37	9	115263557	115263558	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115263557_115263558delAA	uc004bgf.1	+						KIAA1958_uc011lwx.1_Intron	NM_133465	NP_597722			hypothetical protein LOC158405											skin(1)	1																		---	---	---	---
SNX30	401548	broad.mit.edu	37	9	115550081	115550082	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115550081_115550082delTT	uc004bgj.3	+							NM_001012994	NP_001013012			sorting nexin family member 30						cell communication|protein transport	cytoplasm	phosphatidylinositol binding				0																		---	---	---	---
WDR31	114987	broad.mit.edu	37	9	116077951	116077951	+	3'UTR	DEL	T	-	-	rs117440141	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116077951delT	uc004bhe.2	-	11					uc004bhb.2_5'Flank|WDR31_uc004bhc.2_3'UTR|WDR31_uc004bhd.2_3'UTR|WDR31_uc004bhf.2_RNA	NM_001012361	NP_001012361			WD repeat domain 31 isoform 1												0																		---	---	---	---
RGS3	5998	broad.mit.edu	37	9	116354778	116354778	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116354778delT	uc004bhq.2	+						RGS3_uc004bhs.2_Intron|RGS3_uc004bht.2_Intron|RGS3_uc010muy.2_Intron|RGS3_uc004bhv.2_Intron|RGS3_uc010muz.1_3'UTR|RGS3_uc004bhw.2_Intron|RGS3_uc011lxh.1_Intron|RGS3_uc004bhx.2_Intron|RGS3_uc004bhy.1_3'UTR|RGS3_uc004bhz.2_Intron|RGS3_uc004bia.2_5'Flank	NM_144488	NP_652759			regulator of G-protein signalling 3 isoform 6						inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
AKNA	80709	broad.mit.edu	37	9	117158957	117158958	+	Intron	INS	-	A	A	rs34723849		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117158957_117158958insA	uc004biw.1	-						AKNA_uc004bis.3_5'Flank|AKNA_uc010mve.2_5'Flank	NM_030767	NP_110394			AT-hook transcription factor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6																		---	---	---	---
C9orf91	203197	broad.mit.edu	37	9	117403924	117403924	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117403924delT	uc004bjd.3	+						C9orf91_uc004bje.3_Intron|C9orf91_uc004bjf.3_Intron	NM_153045	NP_694590			hypothetical protein LOC203197							integral to membrane				pancreas(1)	1																		---	---	---	---
DEC1	50514	broad.mit.edu	37	9	118099999	118099999	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118099999delT	uc004bjk.1	+						DEC1_uc004bjl.1_Intron	NM_017418	NP_059114			deleted in esophageal cancer 1						negative regulation of cell proliferation					ovary(1)	1																		---	---	---	---
DEC1	50514	broad.mit.edu	37	9	118134467	118134467	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118134467delT	uc004bjk.1	+						DEC1_uc004bjl.1_Intron	NM_017418	NP_059114			deleted in esophageal cancer 1						negative regulation of cell proliferation					ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	118224326	118224326	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118224326delT								DEC1 (59403 upstream) : C9orf27 (426220 downstream)																																			---	---	---	---
PAPPA	5069	broad.mit.edu	37	9	118932016	118932016	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118932016delT	uc004bjn.2	+							NM_002581	NP_002572			pregnancy-associated plasma protein A						cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	119170726	119170726	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119170726delA								PAPPA (6127 upstream) : ASTN2 (16781 downstream)																																			---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119485444	119485444	+	Intron	DEL	A	-	-	rs34360377		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119485444delA	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	119748440	119748440	+	Intron	DEL	C	-	-	rs34599827		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119748440delC	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	120051458	120051458	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120051458delG	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	120906194	120906194	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120906194delA								TLR4 (426430 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121480309	121480309	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121480309delT								None (None upstream) : DBC1 (448599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121516290	121516291	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121516290_121516291insT								None (None upstream) : DBC1 (412617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121760656	121760656	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121760656delT								None (None upstream) : DBC1 (168252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121797249	121797251	+	IGR	DEL	ATT	-	-	rs35312936		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121797249_121797251delATT								None (None upstream) : DBC1 (131657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122488410	122488410	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122488410delA								DBC1 (356671 upstream) : MIR147 (518847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122917278	122917281	+	IGR	DEL	GGAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122917278_122917281delGGAG								DBC1 (785539 upstream) : MIR147 (89976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122949788	122949788	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122949788delC								DBC1 (818049 upstream) : MIR147 (57469 downstream)																																			---	---	---	---
CDK5RAP2	55755	broad.mit.edu	37	9	123237810	123237810	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123237810delC	uc004bkf.2	-						CDK5RAP2_uc004bkg.2_Intron|CDK5RAP2_uc011lxw.1_Intron|CDK5RAP2_uc011lxx.1_Intron|CDK5RAP2_uc011lxy.1_Intron|CDK5RAP2_uc011lxz.1_Intron|CDK5RAP2_uc011lya.1_Intron|CDK5RAP2_uc004bkh.1_Intron|CDK5RAP2_uc004bki.2_Intron	NM_018249	NP_060719			CDK5 regulatory subunit associated protein 2						brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
MEGF9	1955	broad.mit.edu	37	9	123407477	123407477	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123407477delA	uc004bkj.1	-						MEGF9_uc011lyb.1_Intron	NM_001080497	NP_001073966			multiple EGF-like-domains 9							integral to membrane	calcium ion binding				0																		---	---	---	---
C5	727	broad.mit.edu	37	9	123752240	123752240	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123752240delA	uc004bkv.2	-							NM_001735	NP_001726			complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)													---	---	---	---
CEP110	11064	broad.mit.edu	37	9	123922664	123922664	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123922664delA	uc004bkx.1	+						CEP110_uc004blb.1_Intron|CEP110_uc010mvp.1_Intron	NM_007018	NP_008949			centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0																		---	---	---	---
TTLL11	158135	broad.mit.edu	37	9	124599591	124599592	+	Intron	INS	-	GTAGTAT	GTAGTAT	rs147662212	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124599591_124599592insGTAGTAT	uc011lyl.1	-						TTLL11_uc004blr.2_Intron	NM_001139442	NP_001132914			tubulin tyrosine ligase-like family, member 11						protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	125108342	125108344	+	IGR	DEL	AAA	-	-	rs111782565		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125108342_125108344delAAA								MRRF (22602 upstream) : PTGS1 (24465 downstream)																																			---	---	---	---
STRBP	55342	broad.mit.edu	37	9	125887690	125887690	+	3'UTR	DEL	T	-	-	rs34536381		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125887690delT	uc004bns.2	-	19					STRBP_uc004bnt.2_3'UTR|STRBP_uc004bnu.2_3'UTR|STRBP_uc004bnv.2_3'UTR|STRBP_uc004bnr.2_3'UTR	NM_018387	NP_060857			spermatid perinuclear RNA binding protein						multicellular organismal development	cytoplasm|nucleus	DNA binding			breast(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	126035618	126035618	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126035618delA								STRBP (4775 upstream) : CRB2 (82830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	126038049	126038049	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126038049delC								STRBP (7206 upstream) : CRB2 (80399 downstream)																																			---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126297183	126297183	+	Intron	DEL	C	-	-	rs12338990	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126297183delC	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126489216	126489216	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126489216delC	uc004bnz.1	-						DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	126735159	126735160	+	IGR	INS	-	GT	GT	rs144177768	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126735159_126735160insGT								DENND1A (42742 upstream) : LHX2 (38729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	127280235	127280235	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127280235delT								NR5A1 (10536 upstream) : NR6A1 (4468 downstream)																																			---	---	---	---
OLFML2A	169611	broad.mit.edu	37	9	127571880	127571880	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127571880delT	uc004bov.2	+						OLFML2A_uc004bow.2_Intron	NM_182487	NP_872293			olfactomedin-like 2A precursor												0																		---	---	---	---
SCAI	286205	broad.mit.edu	37	9	127892960	127892960	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127892960delT	uc004bpe.2	-						SCAI_uc004bpd.2_Intron|SCAI_uc010mwu.2_Intron	NM_001144877	NP_001138349			suppressor of cancer cell invasion isoform 2						negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5																		---	---	---	---
MAPKAP1	79109	broad.mit.edu	37	9	128376081	128376081	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128376081delT	uc004bpv.2	-						MAPKAP1_uc011lzu.1_Intron|MAPKAP1_uc011lzv.1_Intron|MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Intron|MAPKAP1_uc004bpz.2_Intron|MAPKAP1_uc010mxa.2_Intron|MAPKAP1_uc010mxb.1_Intron|MAPKAP1_uc004bqa.2_Intron|MAPKAP1_uc010mxc.1_Intron	NM_001006617	NP_001006618			mitogen-activated protein kinase associated						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|response to stress|T cell costimulation	cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	Ras GTPase binding			ovary(2)|lung(2)	4																		---	---	---	---
MAPKAP1	79109	broad.mit.edu	37	9	128453963	128453963	+	Intron	DEL	A	-	-	rs79557303		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128453963delA	uc004bpv.2	-						MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Intron|MAPKAP1_uc004bpz.2_Intron|MAPKAP1_uc010mxa.2_Intron|MAPKAP1_uc004bqa.2_Intron	NM_001006617	NP_001006618			mitogen-activated protein kinase associated						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|response to stress|T cell costimulation	cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	Ras GTPase binding			ovary(2)|lung(2)	4																		---	---	---	---
PBX3	5090	broad.mit.edu	37	9	128551154	128551154	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128551154delA	uc004bqb.2	+						PBX3_uc004bqc.2_Intron|PBX3_uc004bqd.2_Intron|PBX3_uc011lzw.1_Intron	NM_006195	NP_006186			pre-B-cell leukemia homeobox 3 isoform 1						anterior compartment pattern formation|posterior compartment specification		sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
PBX3	5090	broad.mit.edu	37	9	128598724	128598724	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128598724delA	uc004bqb.2	+						PBX3_uc004bqc.2_Intron|PBX3_uc004bqd.2_Intron|PBX3_uc011lzw.1_Intron	NM_006195	NP_006186			pre-B-cell leukemia homeobox 3 isoform 1						anterior compartment pattern formation|posterior compartment specification		sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	128747472	128747473	+	IGR	INS	-	ACC	ACC	rs139239368		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128747472_128747473insACC								PBX3 (17819 upstream) : FAM125B (341655 downstream)																																			---	---	---	---
LMX1B	4010	broad.mit.edu	37	9	129420498	129420498	+	Intron	DEL	G	-	-	rs117836425	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129420498delG	uc004bqj.2	+						LMX1B_uc004bqi.2_Intron|LMX1B_uc011maa.1_Intron	NM_002316	NP_002307			LIM homeobox transcription factor 1, beta						dorsal/ventral pattern formation|in utero embryonic development	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														Nail-Patella_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	9	129520469	129520469	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129520469delT								LMX1B (57158 upstream) : ZBTB43 (46816 downstream)																																			---	---	---	---
RALGPS1	9649	broad.mit.edu	37	9	129769193	129769193	+	Intron	DEL	T	-	-	rs72091412		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129769193delT	uc004bqo.1	+						RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron	NM_014636	NP_055451			Ral GEF with PH domain and SH3 binding motif 1						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
RALGPS1	9649	broad.mit.edu	37	9	129981171	129981171	+	3'UTR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129981171delG	uc004bqo.1	+	19						NM_014636	NP_055451			Ral GEF with PH domain and SH3 binding motif 1						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
GARNL3	84253	broad.mit.edu	37	9	130138857	130138860	+	Intron	DEL	CTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130138857_130138860delCTTT	uc011mae.1	+						GARNL3_uc011mad.1_Intron|GARNL3_uc010mxi.2_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																		---	---	---	---
ZNF79	7633	broad.mit.edu	37	9	130204681	130204682	+	Intron	DEL	AA	-	-	rs79754795		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130204681_130204682delAA	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																		---	---	---	---
FAM129B	64855	broad.mit.edu	37	9	130325806	130325806	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130325806delT	uc004brh.2	-						FAM129B_uc004bri.2_Intron|FAM129B_uc004brj.3_Intron	NM_022833	NP_073744			hypothetical protein LOC64855 isoform 1								protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	130364054	130364054	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130364054delA								FAM129B (22786 upstream) : STXBP1 (10432 downstream)																																			---	---	---	---
TOR2A	27433	broad.mit.edu	37	9	130498538	130498539	+	5'Flank	DEL	CA	-	-	rs145079558		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130498538_130498539delCA	uc004brs.3	-						TOR2A_uc004brt.3_5'Flank|TOR2A_uc004brw.3_5'Flank|TOR2A_uc011maj.1_5'Flank|TOR2A_uc004bru.3_5'Flank|TOR2A_uc004brv.3_5'Flank|TOR2A_uc004brx.1_5'Flank	NM_001085347	NP_001078816			torsin family 2, member A isoform a						chaperone mediated protein folding requiring cofactor	endoplasmic reticulum|extracellular region	ATP binding|nucleoside-triphosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	130916550	130916555	+	IGR	DEL	TAGGGT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130916550_130916555delTAGGGT								LCN2 (816 upstream) : C9orf16 (5984 downstream)																																			---	---	---	---
DNM1	1759	broad.mit.edu	37	9	131012114	131012114	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131012114delA	uc011mau.1	+						DNM1_uc011mat.1_Intron|DNM1_uc004bub.1_Intron|DNM1_uc004buc.1_Intron|DNM1_uc004bud.3_Intron	NM_004408	NP_004399			dynamin 1 isoform 1						receptor-mediated endocytosis	microtubule	GTP binding|GTPase activity			ovary(2)	2																		---	---	---	---
SPTAN1	6709	broad.mit.edu	37	9	131372839	131372839	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131372839delT	uc004bvl.3	+						SPTAN1_uc004bvm.3_Intron|SPTAN1_uc004bvn.3_Intron	NM_003127	NP_003118			spectrin, alpha, non-erythrocytic 1						actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10																		---	---	---	---
C9orf114	51490	broad.mit.edu	37	9	131588302	131588302	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131588302delT	uc004bwd.2	-	7	664	c.638delA	c.(637-639)AAGfs	p.K213fs	C9orf114_uc004bwe.2_Frame_Shift_Del_p.K213fs|C9orf114_uc010mym.2_RNA	NM_016390	NP_057474	Q5T280	CI114_HUMAN	hypothetical protein LOC51490	213											0																		---	---	---	---
IER5L	389792	broad.mit.edu	37	9	131938053	131938056	+	3'UTR	DEL	AAAC	-	-	rs3831180		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131938053_131938056delAAAC	uc010myt.1	-	1						NM_203434	NP_982258			immediate early response 5-like												0		Ovarian(14;0.0448)|Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)														---	---	---	---
GPR107	57720	broad.mit.edu	37	9	132872635	132872635	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132872635delT	uc004bze.2	+						GPR107_uc004bzb.2_Intron|GPR107_uc004bzc.3_Intron|GPR107_uc011mbx.1_Intron|GPR107_uc004bzd.2_Intron	NM_001136557	NP_001130029			G protein-coupled receptor 107 isoform 1							integral to membrane				upper_aerodigestive_tract(1)	1		Ovarian(14;0.000531)																---	---	---	---
NCS1	23413	broad.mit.edu	37	9	132983173	132983173	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132983173delG	uc004bzi.2	+						NCS1_uc010myz.1_Intron	NM_014286	NP_055101			frequenin homolog isoform 1						negative regulation of calcium ion transport via voltage-gated calcium channel activity|regulation of neuron projection development	cell junction|Golgi cisterna membrane|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	133226294	133226294	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133226294delA								NCS1 (226711 upstream) : ASS1 (93800 downstream)																																			---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134324751	134324751	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134324751delT	uc004can.3	+						BAT2L1_uc010mzj.1_Intron	NM_013318	NP_037450			HLA-B associated transcript 2-like								protein binding				0																		---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134339329	134339332	+	Intron	DEL	TTTT	-	-	rs72463395		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134339329_134339332delTTTT	uc004can.3	+						BAT2L1_uc010mzj.1_Intron	NM_013318	NP_037450			HLA-B associated transcript 2-like								protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	134622717	134622717	+	IGR	DEL	G	-	-	rs66495853		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134622717delG								RAPGEF1 (7500 upstream) : MED27 (112782 downstream)																																			---	---	---	---
SETX	23064	broad.mit.edu	37	9	135171948	135171948	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135171948delA	uc004cbk.2	-						SETX_uc004cbj.2_Intron|SETX_uc010mzt.2_Intron	NM_015046	NP_055861			senataxin						cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)														---	---	---	---
C9orf171	389799	broad.mit.edu	37	9	135357575	135357575	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135357575delT	uc004cbn.2	+						C9orf171_uc004cbo.2_Intron	NM_207417	NP_997300			hypothetical protein LOC389799											ovary(4)|large_intestine(1)	5																		---	---	---	---
C9orf98	158067	broad.mit.edu	37	9	135603109	135603110	+	Intron	DEL	CC	-	-	rs5900989		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135603109_135603110delCC	uc004cbu.1	-						C9orf98_uc010mzx.1_Intron|C9orf98_uc004cbv.1_Intron	NM_152572	NP_689785			putative adenylate kinase-like protein C9orf98							cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;4.89e-06)|Epithelial(140;0.00016)														---	---	---	---
GTF3C5	9328	broad.mit.edu	37	9	135923516	135923516	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135923516delA	uc004cci.3	+						GTF3C5_uc010mzz.2_Intron|GTF3C5_uc004ccj.3_Intron	NM_012087	NP_036219			general transcription factor IIIC, polypeptide 5							transcription factor TFIIIC complex	DNA binding|protein binding				0				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	137396443	137396445	+	IGR	DEL	TTT	-	-	rs111851267		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137396443_137396445delTTT								RXRA (64012 upstream) : COL5A1 (137207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	137792908	137792908	+	IGR	DEL	T	-	-	rs77898783		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137792908delT								FCN2 (13542 upstream) : FCN1 (8528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	137876443	137876443	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137876443delA								FCN1 (66634 upstream) : OLFM1 (90646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	138365235	138365235	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138365235delT	uc004cfp.3	-						uc004cfq.1_Intron					Homo sapiens cDNA clone IMAGE:5295490.																														---	---	---	---
UBAC1	10422	broad.mit.edu	37	9	138818266	138818266	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138818266delA	uc004cgs.1	-							NM_016172	NP_057256			ubiquitin associated domain containing 1							Golgi apparatus|plasma membrane	protein binding			skin(2)	2		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)														---	---	---	---
NACC2	138151	broad.mit.edu	37	9	138974511	138974512	+	Intron	INS	-	A	A	rs144394926	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138974511_138974512insA	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																		---	---	---	---
NACC2	138151	broad.mit.edu	37	9	138988340	138988341	+	5'Flank	DEL	AC	-	-	rs141442569		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138988340_138988341delAC	uc004cgw.2	-						NACC2_uc010nbh.2_5'Flank	NM_144653	NP_653254			BTB (POZ) domain containing 14A						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization	nuclear body					0																		---	---	---	---
QSOX2	169714	broad.mit.edu	37	9	139107235	139107235	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139107235delG	uc010nbi.2	-							NM_181701	NP_859052			quiescin Q6 sulfhydryl oxidase 2 precursor						cell redox homeostasis	extracellular region|integral to membrane|nuclear membrane|plasma membrane	thiol oxidase activity			ovary(1)	1		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)														---	---	---	---
SEC16A	9919	broad.mit.edu	37	9	139368727	139368727	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139368727delG	uc004chx.2	-	3	3650	c.3341delC	c.(3340-3342)CCTfs	p.P1114fs	SEC16A_uc004chv.3_Frame_Shift_Del_p.P504fs|SEC16A_uc004chw.2_Frame_Shift_Del_p.P1114fs|SEC16A_uc010nbn.2_Frame_Shift_Del_p.P1114fs|SEC16A_uc010nbo.1_Frame_Shift_Del_p.P1114fs	NM_014866	NP_055681	O15027	SC16A_HUMAN	SEC16 homolog A	936	Pro-rich.|Required for endoplasmic reticulum localization.				protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane					0		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)														---	---	---	---
ABCA2	20	broad.mit.edu	37	9	139917547	139917548	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139917547_139917548delGA	uc011mem.1	-						ABCA2_uc011mel.1_Intron|ABCA2_uc004ckl.1_Intron|ABCA2_uc004ckm.1_Intron|ABCA2_uc004cko.1_5'Flank|ABCA2_uc010nca.2_5'UTR	NM_001606	NP_001597			ATP-binding cassette, sub-family A, member 2						cholesterol homeostasis|lipid metabolic process|regulation of intracellular cholesterol transport|regulation of transcription from RNA polymerase II promoter|response to drug|response to steroid hormone stimulus	ATP-binding cassette (ABC) transporter complex|cytoplasmic membrane-bounded vesicle|endosome|integral to membrane|microtubule organizing center	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)														---	---	---	---
C9orf167	54863	broad.mit.edu	37	9	140180861	140180861	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140180861delT	uc011mew.1	+											Homo sapiens cDNA FLJ20385 fis, clone KAIA4085.						chaperone mediated protein folding requiring cofactor	integral to membrane	ATP binding|nucleoside-triphosphatase activity			pancreas(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.137)	OV - Ovarian serous cystadenocarcinoma(145;9.07e-05)|Epithelial(140;0.000728)														---	---	---	---
EXD3	54932	broad.mit.edu	37	9	140219891	140219891	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140219891delT	uc004cmp.2	-						C9orf167_uc011mew.1_Intron|EXD3_uc010ncf.1_Intron	NM_017820	NP_060290			exonuclease 3'-5' domain containing 3						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0																		---	---	---	---
WDR85	92715	broad.mit.edu	37	9	140468517	140468517	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140468517delA	uc004cnk.1	-						WDR85_uc004cnl.1_Intron|WDR85_uc004cnm.1_Intron|WDR85_uc004cnn.1_Intron	NM_138778	NP_620133			WD repeat domain 85						peptidyl-diphthamide biosynthetic process from peptidyl-histidine						0	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.00029)|Epithelial(140;0.000509)														---	---	---	---
WDR85	92715	broad.mit.edu	37	9	140472626	140472627	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140472626_140472627insT	uc004cnk.1	-						WDR85_uc004cnl.1_Intron|WDR85_uc004cnm.1_Intron|WDR85_uc004cnn.1_Intron	NM_138778	NP_620133			WD repeat domain 85						peptidyl-diphthamide biosynthetic process from peptidyl-histidine						0	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.00029)|Epithelial(140;0.000509)														---	---	---	---
DIP2C	22982	broad.mit.edu	37	10	383257	383264	+	Intron	DEL	ACGTGTGT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:383257_383264delACGTGTGT	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	933354	933354	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:933354delA	uc001ifs.1	-							NM_015155	NP_055970			La ribonucleoprotein domain family, member 4B								nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	2292497	2292497	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2292497delC								ADARB2 (512779 upstream) : PFKP (817255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	2537087	2537087	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2537087delT								ADARB2 (757369 upstream) : PFKP (572665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	2806592	2806592	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2806592delA								None (None upstream) : PFKP (303160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	2915592	2915594	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2915592_2915594delAAA								None (None upstream) : PFKP (194158 downstream)																																			---	---	---	---
PITRM1	10531	broad.mit.edu	37	10	3182135	3182135	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3182135delC	uc010qah.1	-						PITRM1_uc001igr.1_Intron|PITRM1_uc001igs.1_Intron|PITRM1_uc001igt.1_Intron|PITRM1_uc009xhv.1_Intron|PITRM1_uc001igu.1_Intron|PITRM1_uc010qai.1_Intron|uc001igv.1_5'Flank					SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;						proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	4005467	4005467	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4005467delA								KLF6 (177994 upstream) : LOC100216001 (615977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4264680	4264680	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4264680delA								KLF6 (437207 upstream) : LOC100216001 (356764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4365041	4365041	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4365041delT								KLF6 (537568 upstream) : LOC100216001 (256403 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4487983	4487983	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4487983delT								KLF6 (660510 upstream) : LOC100216001 (133461 downstream)																																			---	---	---	---
GDI2	2665	broad.mit.edu	37	10	5840552	5840553	+	Intron	DEL	AA	-	-	rs76803175		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5840552_5840553delAA	uc001iil.3	-						GDI2_uc001iim.3_Intron|GDI2_uc009xid.2_Intron	NM_001494	NP_001485			GDP dissociation inhibitor 2 isoform 1						protein transport|small GTPase mediated signal transduction	cell surface|cytosol|membrane	protein binding|Rab GDP-dissociation inhibitor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	7031768	7031768	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7031768delA								PRKCQ (409530 upstream) : SFMBT2 (172481 downstream)																																			---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7340732	7340733	+	Intron	INS	-	GT	GT	rs150769738	by1000genomes;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7340732_7340733insGT	uc009xio.1	-						SFMBT2_uc001ijn.1_Intron|SFMBT2_uc010qay.1_Intron|SFMBT2_uc001ijo.1_Intron	NM_001029880	NP_001025051			Scm-like with four mbt domains 2						regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	7549597	7549597	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7549597delA								SFMBT2 (96147 upstream) : ITIH5 (52039 downstream)																																			---	---	---	---
ITIH5	80760	broad.mit.edu	37	10	7622094	7622094	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7622094delT	uc001ijq.2	-						ITIH5_uc001ijp.2_Intron|ITIH5_uc001ijr.1_Intron	NM_030569	NP_085046			inter-alpha trypsin inhibitor heavy chain						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
ITIH2	3698	broad.mit.edu	37	10	7786328	7786328	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7786328delA	uc001ijs.2	+							NM_002216	NP_002207			inter-alpha globulin inhibitor H2 polypeptide						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
KIN	22944	broad.mit.edu	37	10	7816650	7816651	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7816650_7816651insA	uc001ijt.2	-						KIN_uc010qaz.1_Intron|KIN_uc009xip.2_Intron|KIN_uc010qba.1_Intron	NM_012311	NP_036443			HsKin17 protein						DNA recombination|DNA repair|DNA replication|interspecies interaction between organisms|mRNA processing	cytoplasm|nuclear matrix	double-stranded DNA binding|RNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
TAF3	83860	broad.mit.edu	37	10	7929208	7929209	+	Intron	INS	-	G	G	rs11255425	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7929208_7929209insG	uc010qbd.1	+							NM_031923	NP_114129			RNA polymerase II transcription factor TAFII140						maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	8736244	8736244	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8736244delA								GATA3 (619082 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9222858	9222858	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9222858delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9586977	9586977	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9586977delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10455442	10455442	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10455442delC								None (None upstream) : SFTA1P (370960 downstream)																																			---	---	---	---
CELF2	10659	broad.mit.edu	37	10	11098834	11098834	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11098834delC	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron	NM_001025077	NP_001020248			CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	11431669	11431670	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11431669_11431670insC								CELF2 (52999 upstream) : USP6NL (70839 downstream)																																			---	---	---	---
UPF2	26019	broad.mit.edu	37	10	11980643	11980643	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11980643delA	uc001ila.2	-						UPF2_uc001ilb.2_Intron|UPF2_uc001ilc.2_Intron	NM_080599	NP_542166			UPF2 regulator of nonsense transcripts homolog						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)																---	---	---	---
UPF2	26019	broad.mit.edu	37	10	12042038	12042038	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12042038delA	uc001ila.2	-						UPF2_uc001ilb.2_Intron|UPF2_uc001ilc.2_Intron|UPF2_uc009xiz.1_Intron	NM_080599	NP_542166			UPF2 regulator of nonsense transcripts homolog						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)																---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12389256	12389257	+	5'Flank	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12389256_12389257delTT	uc001ilo.2	+						CAMK1D_uc001iln.2_5'Flank	NM_153498	NP_705718			calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)														---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12401524	12401526	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12401524_12401526delTTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	12930501	12930501	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12930501delA								LOC283070 (52957 upstream) : CCDC3 (8124 downstream)																																			---	---	---	---
MCM10	55388	broad.mit.edu	37	10	13206257	13206257	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13206257delT	uc001ima.2	+						MCM10_uc001imb.2_Intron|MCM10_uc001imc.2_Intron	NM_182751	NP_877428			minichromosome maintenance complex component 10						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
BEND7	222389	broad.mit.edu	37	10	13538964	13538964	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13538964delA	uc001imm.2	-						BEND7_uc001imo.3_Intron	NM_152751	NP_689964			BEN domain containing 7 isoform 1								protein binding			ovary(1)|breast(1)	2																		---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	13820598	13820599	+	Intron	INS	-	GT	GT	rs150073571	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13820598_13820599insGT	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imt.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497			FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3																		---	---	---	---
FAM107B	83641	broad.mit.edu	37	10	14668255	14668257	+	Intron	DEL	CTC	-	-	rs72034549		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14668255_14668257delCTC	uc001ina.1	-						FAM107B_uc010qbu.1_Intron	NM_031453	NP_113641			hypothetical protein LOC83641											breast(4)	4																		---	---	---	---
FAM107B	83641	broad.mit.edu	37	10	14715156	14715156	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14715156delC	uc001ina.1	-						FAM107B_uc010qbu.1_Intron	NM_031453	NP_113641			hypothetical protein LOC83641											breast(4)	4																		---	---	---	---
HSPA14	51182	broad.mit.edu	37	10	14890952	14890952	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14890952delA	uc001inf.2	+						HSPA14_uc010qbw.1_Intron	NM_016299	NP_057383			heat shock 70kDa protein 14 isoform 1						'de novo' cotranslational protein folding	cytosol	ATP binding|protein binding			ovary(2)|breast(2)|lung(1)	5																		---	---	---	---
OLAH	55301	broad.mit.edu	37	10	15095716	15095716	+	Intron	DEL	T	-	-	rs114483309	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15095716delT	uc001inu.2	+						ACBD7_uc010qby.1_Intron|OLAH_uc001int.2_Intron	NM_001039702	NP_001034791			oleoyl-ACP hydrolase isoform 2						fatty acid biosynthetic process		myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	15136116	15136117	+	IGR	DEL	AC	-	-	rs36233619		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15136116_15136117delAC								ACBD7 (5341 upstream) : C10orf111 (1268 downstream)																																			---	---	---	---
FAM171A1	221061	broad.mit.edu	37	10	15332215	15332215	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15332215delA	uc001iob.2	-							NM_001010924	NP_001010924			hypothetical protein LOC221061 precursor							integral to membrane				ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	15476363	15476364	+	IGR	DEL	TC	-	-	rs142870851		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15476363_15476364delTC								FAM171A1 (63305 upstream) : ITGA8 (82724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	16209802	16209802	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16209802delA								FAM188A (307283 upstream) : PTER (269165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	16574912	16574913	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16574912_16574913delAA								C1QL3 (10908 upstream) : RSU1 (57706 downstream)																																			---	---	---	---
RSU1	6251	broad.mit.edu	37	10	16841629	16841629	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16841629delA	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	17055411	17055412	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17055411_17055412delCT	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)													---	---	---	---
MRC1	4360	broad.mit.edu	37	10	18198214	18198214	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18198214delT	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																		---	---	---	---
CACNB2	783	broad.mit.edu	37	10	18508702	18508702	+	Intron	DEL	T	-	-	rs10545554		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18508702delT	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc010qcl.1_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron	NM_201596	NP_963890			calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
CACNB2	783	broad.mit.edu	37	10	18565515	18565515	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18565515delT	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc010qcl.1_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron|CACNB2_uc001ipw.2_Intron|CACNB2_uc001ipx.2_Intron	NM_201596	NP_963890			calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
NSUN6	221078	broad.mit.edu	37	10	18924789	18924789	+	Intron	DEL	A	-	-	rs11015255	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18924789delA	uc010qcp.1	-							NM_182543	NP_872349			NOL1/NOP2/Sun domain family, member 6								methyltransferase activity|RNA binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	19229161	19229161	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19229161delT								ARL5B (262221 upstream) : PLXDC2 (876211 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19313304	19313304	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19313304delA								ARL5B (346364 upstream) : PLXDC2 (792068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19322196	19322196	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19322196delT								ARL5B (355256 upstream) : PLXDC2 (783176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19778498	19778499	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19778498_19778499delTT	uc010qcq.1	+											SubName: Full=cDNA FLJ60310;																														---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20253671	20253671	+	Intron	DEL	T	-	-	rs71497298		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20253671delT	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																		---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21148586	21148586	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21148586delA	uc001iqi.2	-						NEBL_uc001iqj.2_Intron|NEBL_uc001iqk.2_Intron	NM_006393	NP_006384			nebulette sarcomeric isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	21594713	21594713	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21594713delT								NEBL (131597 upstream) : C10orf114 (188709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21676490	21676490	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21676490delT								NEBL (213374 upstream) : C10orf114 (106932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21698484	21698485	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21698484_21698485delAA								NEBL (235368 upstream) : C10orf114 (84937 downstream)																																			---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21906184	21906184	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21906184delA	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc001ira.2_Intron|MLLT10_uc001iqz.2_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
DNAJC1	64215	broad.mit.edu	37	10	22291409	22291409	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22291409delA	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	22399520	22399520	+	IGR	DEL	A	-	-	rs10711808		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22399520delA								DNAJC1 (106870 upstream) : COMMD3 (205779 downstream)																																			---	---	---	---
SPAG6	9576	broad.mit.edu	37	10	22676733	22676733	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22676733delT	uc001iri.2	+						SPAG6_uc001irj.2_Intron|SPAG6_uc010qct.1_Intron|SPAG6_uc009xkh.2_Intron	NM_012443	NP_036575			sperm associated antigen 6 isoform 1						cell projection organization|spermatid development	axoneme|cilium|cytoplasm|flagellum|microtubule	binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	23808517	23808517	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23808517delT								OTUD1 (77209 upstream) : KIAA1217 (175158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	23917408	23917409	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23917408_23917409delAA								OTUD1 (186100 upstream) : KIAA1217 (66266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	23949207	23949207	+	IGR	DEL	T	-	-	rs112525756		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23949207delT								OTUD1 (217899 upstream) : KIAA1217 (34468 downstream)																																			---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24159948	24159949	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24159948_24159949delTT	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	24164125	24164127	+	Intron	DEL	TTT	-	-	rs34799226		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24164125_24164127delTTT	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	24624224	24624226	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24624224_24624226delTTT	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																		---	---	---	---
ARHGAP21	57584	broad.mit.edu	37	10	24890792	24890792	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24890792delT	uc001isb.2	-						ARHGAP21_uc010qdb.1_Intron|ARHGAP21_uc009xkl.1_Intron|ARHGAP21_uc010qdc.1_Intron	NM_020824	NP_065875			Rho GTPase activating protein 21						signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	25260035	25260035	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25260035delT								PRTFDC1 (18502 upstream) : ENKUR (10882 downstream)																																			---	---	---	---
ENKUR	219670	broad.mit.edu	37	10	25349646	25349647	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25349646_25349647insT	uc001ish.1	-							NM_145010	NP_659447			enkurin							cilium|flagellum	calmodulin binding|SH3 domain binding				0																		---	---	---	---
GPR158	57512	broad.mit.edu	37	10	25547410	25547410	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25547410delT	uc001isj.2	+							NM_020752	NP_065803			G protein-coupled receptor 158 precursor							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8																		---	---	---	---
GPR158	57512	broad.mit.edu	37	10	25732672	25732672	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25732672delT	uc001isj.2	+							NM_020752	NP_065803			G protein-coupled receptor 158 precursor							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8																		---	---	---	---
MYO3A	53904	broad.mit.edu	37	10	26223696	26223696	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26223696delG	uc001isn.2	+						MYO3A_uc009xko.1_Intron|MYO3A_uc009xkp.1_5'Flank|MYO3A_uc009xkq.1_5'Flank|MYO3A_uc001ism.2_Intron	NM_017433	NP_059129			myosin IIIA						protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	26597349	26597349	+	IGR	DEL	C	-	-	rs913961		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26597349delC								GAD2 (3858 upstream) : APBB1IP (129917 downstream)																																			---	---	---	---
ABI1	10006	broad.mit.edu	37	10	27054256	27054256	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27054256delA	uc001isx.2	-						ABI1_uc001ite.2_Intron|ABI1_uc010qdh.1_Intron|ABI1_uc010qdi.1_Intron|ABI1_uc001isy.2_Intron|ABI1_uc001ita.2_Intron|ABI1_uc001isz.2_Intron|ABI1_uc001itb.2_Intron|ABI1_uc001itc.2_Intron|ABI1_uc010qdj.1_Intron|ABI1_uc001itd.2_Intron|ABI1_uc010qdk.1_Intron|ABI1_uc010qdg.1_Intron	NM_005470	NP_005461			abl-interactor 1 isoform a						actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome	cytoskeletal protein binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	27160112	27160114	+	IGR	DEL	TTT	-	-	rs67729763		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27160112_27160114delTTT								ABI1 (10153 upstream) : NCRNA00202 (60021 downstream)																																			---	---	---	---
MASTL	84930	broad.mit.edu	37	10	27445605	27445605	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27445605delT	uc001itm.2	+						YME1L1_uc001iti.2_5'Flank|YME1L1_uc001itj.2_5'Flank|YME1L1_uc010qdl.1_5'Flank|YME1L1_uc009xkv.2_5'Flank|YME1L1_uc001itk.1_5'Flank|MASTL_uc001itl.2_Intron|MASTL_uc009xkw.1_Intron|MASTL_uc009xkx.1_Intron	NM_032844	NP_116233			microtubule associated serine/threonine						cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus	centrosome|cleavage furrow|nucleus	ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3																		---	---	---	---
MASTL	84930	broad.mit.edu	37	10	27470152	27470152	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27470152delA	uc001itm.2	+						MASTL_uc001itl.2_Intron|MASTL_uc009xkw.1_Intron|MASTL_uc009xkx.1_Intron	NM_032844	NP_116233			microtubule associated serine/threonine						cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus	centrosome|cleavage furrow|nucleus	ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3																		---	---	---	---
ACBD5	91452	broad.mit.edu	37	10	27494275	27494275	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27494275delT	uc010qdp.1	-						ACBD5_uc010qdm.1_Intron|ACBD5_uc010qdn.1_Intron|ACBD5_uc010qdo.1_Intron|ACBD5_uc001ito.2_Intron|ACBD5_uc001itp.2_Intron|ACBD5_uc001itq.2_Intron|ACBD5_uc001itr.1_Intron	NM_145698	NP_663736			acyl-Coenzyme A binding domain containing 5						transport	integral to membrane|peroxisomal membrane	fatty-acyl-CoA binding				0																		---	---	---	---
RAB18	22931	broad.mit.edu	37	10	27822484	27822484	+	Intron	DEL	A	-	-	rs5784015		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27822484delA	uc001itv.2	+						RAB18_uc001itw.2_Intron|RAB18_uc010qdq.1_Intron|RAB18_uc010qdr.1_Intron	NM_021252	NP_067075			RAB18, member RAS oncogene family						endocytosis|protein transport|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction	intracellular|plasma membrane	ATP binding|GTP binding|GTPase activity|transcription factor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	28753504	28753504	+	IGR	DEL	T	-	-	rs75162560		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28753504delT								MPP7 (161509 upstream) : WAC (67923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29303961	29303962	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29303961_29303962insT								BAMBI (332093 upstream) : LYZL1 (274028 downstream)																																			---	---	---	---
SVIL	6840	broad.mit.edu	37	10	29969848	29969848	+	Intron	DEL	A	-	-	rs66861329		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29969848delA	uc001iuu.1	-						SVIL_uc009xld.1_Intron	NM_003174	NP_003165			supervillin isoform 1						cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	30503476	30503477	+	IGR	DEL	CA	-	-	rs71885128		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30503476_30503477delCA								KIAA1462 (99056 upstream) : MTPAP (95254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	30900648	30900652	+	IGR	DEL	AAAGA	-	-	rs137937328		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30900648_30900652delAAAGA								MAP3K8 (149887 upstream) : LYZL2 (57 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	31569099	31569099	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31569099delA								ZNF438 (248233 upstream) : LOC220930 (36359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	31925359	31925359	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31925359delA								ZEB1 (107232 upstream) : ARHGAP12 (169866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	33457141	33457141	+	IGR	DEL	T	-	-	rs79369034		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33457141delT								ITGB1 (209848 upstream) : NRP1 (9279 downstream)																																			---	---	---	---
NRP1	8829	broad.mit.edu	37	10	33529130	33529131	+	Intron	INS	-	AC	AC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33529130_33529131insAC	uc001iwx.3	-						NRP1_uc001iwv.3_Intron|NRP1_uc009xlz.2_Intron|NRP1_uc001iww.3_Intron|NRP1_uc001iwy.3_Intron|NRP1_uc001iwz.2_Intron|NRP1_uc001ixa.2_Intron|NRP1_uc001ixb.1_Intron|NRP1_uc001ixc.1_Intron	NM_003873	NP_003864			neuropilin 1 isoform a						axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	33700216	33700216	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33700216delC								NRP1 (76210 upstream) : PARD3 (699882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34025544	34025544	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34025544delT								NRP1 (401538 upstream) : PARD3 (374554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34180665	34180665	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34180665delG								NRP1 (556659 upstream) : PARD3 (219433 downstream)																																			---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34918382	34918383	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34918382_34918383delCA	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	34964778	34964779	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34964778_34964779delCA	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565			partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	35221124	35221125	+	IGR	DEL	AA	-	-	rs112645965		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35221124_35221125delAA								PARD3 (117201 upstream) : CUL2 (77683 downstream)																																			---	---	---	---
CCNY	219771	broad.mit.edu	37	10	35663997	35663998	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35663997_35663998delTT	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	35956408	35956410	+	IGR	DEL	CAT	-	-	rs150869536		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35956408_35956410delCAT								FZD8 (26046 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36773899	36773899	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36773899delT								FZD8 (843537 upstream) : ANKRD30A (640886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	37872763	37872763	+	IGR	DEL	A	-	-	rs10718865		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37872763delA								ANKRD30A (351268 upstream) : ZNF248 (217684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38368813	38368814	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38368813_38368814delTT								ZNF33A (14787 upstream) : ZNF37A (14461 downstream)																																			---	---	---	---
LOC100129055	100129055	broad.mit.edu	37	10	38474707	38474707	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38474707delA	uc001izn.2	+							NR_024524				Homo sapiens cDNA clone IMAGE:4825074.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	38981874	38981875	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38981874_38981875delAC								LOC399744 (240794 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42610174	42610175	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42610174_42610175delTT								None (None upstream) : LOC441666 (217140 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42650773	42650773	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42650773delG								None (None upstream) : LOC441666 (176542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42668261	42668261	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42668261delA								None (None upstream) : LOC441666 (159054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42695562	42695562	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42695562delA								None (None upstream) : LOC441666 (131753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42712289	42712289	+	IGR	DEL	T	-	-	rs77999482	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42712289delT								None (None upstream) : LOC441666 (115026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42800222	42800226	+	IGR	DEL	TTGGG	-	-	rs147989481		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42800222_42800226delTTGGG								None (None upstream) : LOC441666 (27089 downstream)																																			---	---	---	---
ZNF33B	7582	broad.mit.edu	37	10	43101919	43101919	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43101919delA	uc001jaf.1	-						ZNF33B_uc009xmg.1_Intron|ZNF33B_uc001jae.1_Intron|ZNF33B_uc001jag.1_Intron|ZNF33B_uc001jad.2_Intron	NM_006955	NP_008886			zinc finger protein 33B							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	43354622	43354622	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43354622delC								BMS1 (24239 upstream) : RET (217895 downstream)																																			---	---	---	---
CSGALNACT2	55454	broad.mit.edu	37	10	43653973	43653973	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43653973delT	uc001jan.2	+						CSGALNACT2_uc001jam.1_Intron	NM_018590	NP_061060			chondroitin sulfate						chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process	Golgi cisterna membrane|integral to Golgi membrane	glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	44689891	44689892	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44689891_44689892delGT								HNRNPA3P1 (404026 upstream) : CXCL12 (175715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44804911	44804914	+	IGR	DEL	GAGA	-	-	rs113155204		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44804911_44804914delGAGA								HNRNPA3P1 (519046 upstream) : CXCL12 (60693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44910447	44910447	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44910447delT								CXCL12 (29905 upstream) : TMEM72 (496317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45023900	45023900	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45023900delT								CXCL12 (143358 upstream) : TMEM72 (382864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45363942	45363942	+	Intron	DEL	A	-	-	rs67396686		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45363942delA	uc001jbk.1	-						uc001jbl.2_Intron					Homo sapiens cDNA FLJ31956 fis, clone NT2RP7007359.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	45451594	45451594	+	Intron	DEL	A	-	-	rs113443852		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45451594delA	uc001jbk.1	-						uc001jbl.2_Intron					Homo sapiens cDNA FLJ31956 fis, clone NT2RP7007359.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	45567722	45567724	+	5'Flank	DEL	TTG	-	-	rs111734251		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45567722_45567724delTTG	uc001jbx.1	-											Homo sapiens zinc finger protein 22 (KOX 15), mRNA (cDNA clone IMAGE:4826621).																														---	---	---	---
GPRIN2	9721	broad.mit.edu	37	10	47005612	47005614	+	3'UTR	DEL	AGA	-	-	rs150293212		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47005612_47005614delAGA	uc010qfq.1	+	1						NM_014696	NP_055511			G protein-regulated inducer of neurite outgrowth												0																		---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47083015	47083015	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47083015delT	uc001jed.3	-						PPYR1_uc001jee.2_5'Flank|PPYR1_uc009xna.2_5'Flank					Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3																		---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47109512	47109512	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47109512delG	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-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	47589326	47589327	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47589326_47589327delTG								FAM35B2 (168090 upstream) : ANTXRL (68907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	48375007	48375007	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48375007delT								ZNF488 (1143 upstream) : RBP3 (6482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	49497552	49497552	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49497552delC								FRMPD2 (14835 upstream) : MAPK8 (17138 downstream)																																	OREG0020174	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MAPK8	5599	broad.mit.edu	37	10	49611800	49611801	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49611800_49611801insT	uc009xnz.2	+						MAPK8_uc001jgl.2_Intron|MAPK8_uc001jgm.2_Intron|MAPK8_uc001jgo.2_Intron|MAPK8_uc009xoa.2_Intron|MAPK8_uc001jgn.2_Intron|MAPK8_uc010qgk.1_Intron|MAPK8_uc001jgp.2_Intron|MAPK8_uc001jgq.2_Intron	NM_139047	NP_620635			mitogen-activated protein kinase 8 isoform JNK1						activation of pro-apoptotic gene products|cellular response to mechanical stimulus|induction of apoptosis by intracellular signals|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of apoptosis|negative regulation of protein binding|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of deacetylase activity|regulation of protein localization|regulation of sequence-specific DNA binding transcription factor activity|response to UV|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|histone deacetylase binding|histone deacetylase regulator activity|JUN kinase activity|protein binding			central_nervous_system(3)|lung(2)|stomach(1)|ovary(1)|kidney(1)	8		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)														---	---	---	---
ARHGAP22	58504	broad.mit.edu	37	10	49664955	49664955	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49664955delC	uc001jgt.2	-						ARHGAP22_uc001jgs.2_Intron|ARHGAP22_uc001jgu.2_Intron|ARHGAP22_uc010qgl.1_Intron|ARHGAP22_uc010qgm.1_Intron|ARHGAP22_uc001jgv.2_Intron	NM_021226	NP_067049			Rho GTPase activating protein 2						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity			ovary(1)	1																		---	---	---	---
PARG	8505	broad.mit.edu	37	10	51030270	51030271	+	Intron	INS	-	TG	TG	rs150376140	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51030270_51030271insTG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	52038598	52038598	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52038598delA								ASAH2 (30228 upstream) : SGMS1 (26748 downstream)																																			---	---	---	---
SGMS1	259230	broad.mit.edu	37	10	52144826	52144826	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52144826delT	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																		---	---	---	---
A1CF	29974	broad.mit.edu	37	10	52605552	52605552	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52605552delA	uc001jjj.2	-						A1CF_uc010qhn.1_Intron|A1CF_uc001jji.2_Intron|A1CF_uc001jjh.2_Intron|A1CF_uc010qho.1_Intron|A1CF_uc009xov.2_Intron|A1CF_uc001jjk.1_Intron	NM_138932	NP_620310			apobec-1 complementation factor isoform 2						cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	52710437	52710437	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52710437delA								A1CF (65002 upstream) : PRKG1 (40508 downstream)																																			---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	52808614	52808614	+	Intron	DEL	T	-	-	rs36099501		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52808614delT	uc001jjm.2	+						PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53513116	53513116	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53513116delT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53657628	53657628	+	Intron	DEL	T	-	-	rs111673697		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53657628delT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	54053522	54053522	+	Intron	DEL	A	-	-	rs68171603		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54053522delA	uc001jjm.2	+						PRKG1_uc001jjo.2_Intron|PRKG1_uc009xow.1_Intron|uc001jjq.1_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	54464011	54464013	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54464011_54464013delTTT								DKK1 (386595 upstream) : MBL2 (61128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	54876856	54876856	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54876856delA								MBL2 (345396 upstream) : PCDH15 (685679 downstream)																																			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55913199	55913199	+	Intron	DEL	T	-	-	rs11004101		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55913199delT	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045			protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
Unknown	0	broad.mit.edu	37	10	57682339	57682339	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57682339delG								PCDH15 (294637 upstream) : ZWINT (434860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58084521	58084521	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58084521delA								PCDH15 (696819 upstream) : ZWINT (32678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58330626	58330626	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58330626delA								ZWINT (209592 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58624285	58624285	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58624285delA								ZWINT (503251 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59944151	59944151	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59944151delA								None (None upstream) : IPMK (11467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	60058910	60058911	+	IGR	DEL	AA	-	-	rs112577286		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60058910_60058911delAA								CISD1 (9892 upstream) : UBE2D1 (35828 downstream)																																			---	---	---	---
BICC1	80114	broad.mit.edu	37	10	60548865	60548865	+	Intron	DEL	A	-	-	rs75442527		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60548865delA	uc001jki.1	+							NM_001080512	NP_001073981			bicaudal C homolog 1						multicellular organismal development		RNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
FAM13C	220965	broad.mit.edu	37	10	61019830	61019830	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61019830delT	uc001jkn.2	-						FAM13C_uc001jko.2_Intron|FAM13C_uc010qid.1_Intron|FAM13C_uc010qie.1_Intron|FAM13C_uc010qif.1_Intron|FAM13C_uc001jkp.2_Intron	NM_198215	NP_937858			hypothetical protein LOC220965 isoform 1											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	61513095	61513095	+	Intron	DEL	A	-	-	rs112492086		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61513095delA	uc001jkr.2	-											Homo sapiens mRNA of muscle specific gene M1.																														---	---	---	---
ANK3	288	broad.mit.edu	37	10	61900370	61900370	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61900370delA	uc001jky.2	-						ANK3_uc001jkw.2_5'UTR|ANK3_uc009xpa.2_5'UTR|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron|ANK3_uc001jlc.1_Intron	NM_020987	NP_066267			ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
TMEM26	219623	broad.mit.edu	37	10	63196084	63196084	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63196084delA	uc001jlo.2	-						TMEM26_uc010qij.1_Intron|TMEM26_uc001jlq.2_Intron	NM_178505	NP_848600			transmembrane protein 26							integral to membrane					0	Prostate(12;0.0112)																	---	---	---	---
ZNF365	22891	broad.mit.edu	37	10	64216604	64216605	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64216604_64216605delCA	uc001jmc.2	+						ZNF365_uc001jmb.3_Intron	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	64286200	64286200	+	Intron	DEL	A	-	-	rs143270002		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64286200delA	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	64451567	64451568	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64451567_64451568delAA								ZNF365 (19796 upstream) : ADO (112948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	64813199	64813200	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64813199_64813200insC								EGR2 (234272 upstream) : NRBF2 (79807 downstream)																																			---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64949281	64949281	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64949281delT	uc001jmn.2	-						JMJD1C_uc001jml.2_Intron|JMJD1C_uc001jmm.2_Intron|JMJD1C_uc010qiq.1_Intron|JMJD1C_uc009xpi.2_Intron|JMJD1C_uc009xpj.1_Intron|JMJD1C_uc001jmo.2_Intron	NM_032776	NP_116165			jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	66037843	66037843	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66037843delT								REEP3 (655872 upstream) : ANXA2P3 (547442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66106050	66106050	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66106050delT								REEP3 (724079 upstream) : ANXA2P3 (479235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66401571	66401572	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66401571_66401572delTT								None (None upstream) : ANXA2P3 (183713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66700624	66700624	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66700624delT								ANXA2P3 (113990 upstream) : CTNNA3 (979101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66714475	66714475	+	IGR	DEL	T	-	-	rs76798913		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66714475delT								ANXA2P3 (127841 upstream) : CTNNA3 (965250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66729697	66729697	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66729697delA								ANXA2P3 (143063 upstream) : CTNNA3 (950028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66810375	66810376	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66810375_66810376delTT								ANXA2P3 (223741 upstream) : CTNNA3 (869349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	67074862	67074862	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67074862delT								ANXA2P3 (488228 upstream) : CTNNA3 (604863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	67636178	67636178	+	IGR	DEL	A	-	-	rs77443205		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67636178delA								None (None upstream) : CTNNA3 (43547 downstream)																																			---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	67735136	67735136	+	Intron	DEL	T	-	-	rs7084117	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67735136delT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	67948192	67948192	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67948192delT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68307676	68307677	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68307676_68307677delTT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68526199	68526199	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68526199delT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68979700	68979700	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68979700delT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|CTNNA3_uc001jna.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
PBLD	64081	broad.mit.edu	37	10	70068579	70068580	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70068579_70068580insC	uc001jns.1	-						PBLD_uc001jnt.1_Intron|PBLD_uc001jnu.1_Intron|PBLD_uc001jnv.1_5'Flank	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	70150526	70150527	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70150526_70150527delTT	uc001job.2	-						RUFY2_uc001jnz.1_Intron|RUFY2_uc001joc.2_Intron|RUFY2_uc010qiw.1_Intron|RUFY2_uc001jod.1_Intron|RUFY2_uc009xpv.1_Intron	NM_017987	NP_060457			RUN and FYVE domain-containing 2 isoform a							nucleus	metal ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70553919	70553919	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70553919delA								CCAR1 (2612 upstream) : STOX1 (33375 downstream)																																			---	---	---	---
DDX50	79009	broad.mit.edu	37	10	70674143	70674143	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70674143delA	uc001jou.2	+						DDX50_uc001jot.2_3'UTR|DDX50_uc010qjc.1_Intron	NM_024045	NP_076950			nucleolar protein GU2							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1																		---	---	---	---
KIAA1279	26128	broad.mit.edu	37	10	70770499	70770500	+	Intron	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70770499_70770500insG	uc001joy.2	+							NM_015634	NP_056449			KIF1 binding protein						cell differentiation|mitochondrial transport|nervous system development	mitochondrion	kinesin binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70791316	70791316	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70791316delT								KIAA1279 (14582 upstream) : SRGN (56512 downstream)																																			---	---	---	---
HK1	3098	broad.mit.edu	37	10	71030342	71030344	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71030342_71030344delAAA	uc001jpj.3	+						HK1_uc009xqc.1_Intron|HK1_uc001jpg.3_Intron|HK1_uc001jph.3_Intron|HK1_uc001jpi.3_Intron	NM_033500	NP_277035			hexokinase 1 isoform HKI-td						glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71054024	71054024	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71054024delA	uc001jpj.3	+						HK1_uc009xqc.1_Intron|HK1_uc001jpg.3_Intron|HK1_uc001jph.3_Intron|HK1_uc001jpi.3_Intron	NM_033500	NP_277035			hexokinase 1 isoform HKI-td						glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71106800	71106800	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71106800delT	uc001jpl.3	+						HK1_uc001jpg.3_Intron|HK1_uc001jph.3_Intron|HK1_uc001jpi.3_Intron|HK1_uc001jpj.3_Intron|HK1_uc001jpk.3_Intron|HK1_uc009xqd.2_Intron	NM_000188	NP_000179			hexokinase 1 isoform HKI						glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
TSPAN15	23555	broad.mit.edu	37	10	71241825	71241825	+	Intron	DEL	A	-	-	rs71717997		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71241825delA	uc001jpo.1	+							NM_012339	NP_036471			transmembrane 4 superfamily member 15							integral to plasma membrane|membrane fraction					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	72043218	72043219	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72043218_72043219delCA								NPFFR1 (17070 upstream) : LRRC20 (15510 downstream)																																			---	---	---	---
KIAA1274	27143	broad.mit.edu	37	10	72245160	72245160	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72245160delT	uc001jrd.3	+							NM_014431	NP_055246			KIAA1274											ovary(2)|central_nervous_system(1)	3																		---	---	---	---
KIAA1274	27143	broad.mit.edu	37	10	72249280	72249280	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72249280delG	uc001jrd.3	+							NM_014431	NP_055246			KIAA1274											ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ADAMTS14	140766	broad.mit.edu	37	10	72521914	72521914	+	3'UTR	DEL	A	-	-	rs3832690		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72521914delA	uc001jrh.2	+	22					ADAMTS14_uc001jrg.2_3'UTR	NM_080722	NP_542453			ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	72553863	72553863	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72553863delT								C10orf27 (8706 upstream) : SGPL1 (21841 downstream)																																			---	---	---	---
PCBD1	5092	broad.mit.edu	37	10	72644720	72644720	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73533998	73534001	+	Intron	DEL	CCCT	-	-	rs67157291		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73533998_73534001delCCCT	uc001jrx.3	+						C10orf54_uc001jsd.2_5'Flank|C10orf54_uc001jse.2_5'Flank|C10orf54_uc009xqm.2_5'Flank|C10orf54_uc001jsf.1_5'Flank	NM_022124	NP_071407			cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73931190	73931190	+	Intron	DEL	T	-	-	rs113830754		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73931190delT	uc001jst.1	-						ASCC1_uc001jsr.1_Intron|ASCC1_uc001jss.1_Intron|ASCC1_uc001jsu.1_Intron|ASCC1_uc010qju.1_Intron					RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0																		---	---	---	---
OIT3	170392	broad.mit.edu	37	10	74653469	74653469	+	5'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74653469delA	uc001jte.1	+	1					OIT3_uc009xqs.1_RNA	NM_152635	NP_689848			oncoprotein-induced transcript 3 precursor							nuclear envelope	calcium ion binding			ovary(2)	2	Prostate(51;0.0198)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	74739774	74739774	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74739774delT								PLA2G12B (25264 upstream) : P4HA1 (27208 downstream)																																			---	---	---	---
P4HA1	5033	broad.mit.edu	37	10	74790296	74790296	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74790296delT	uc010qka.1	-						P4HA1_uc001jtg.2_Intron|P4HA1_uc001jth.2_Intron|P4HA1_uc010qkb.1_Intron|P4HA1_uc001jti.2_Intron	NM_001142595	NP_001136067			prolyl 4-hydroxylase, alpha I subunit isoform 2							endoplasmic reticulum lumen|mitochondrion	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity			ovary(1)	1	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
TTC18	118491	broad.mit.edu	37	10	75119654	75119654	+	5'Flank	DEL	A	-	-	rs112418911		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75119654delA	uc009xrc.2	-						TTC18_uc001jty.2_5'Flank|TTC18_uc009xrd.1_5'Flank	NM_145170	NP_660153			tetratricopeptide repeat domain 18								binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)																	---	---	---	---
USP54	159195	broad.mit.edu	37	10	75335437	75335437	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75335437delA	uc001juo.2	-						USP54_uc001jup.2_Intron|USP54_uc010qkl.1_Intron	NM_152586	NP_689799			ubiquitin specific peptidase 54						ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(3)|lung(2)|kidney(1)	6	Prostate(51;0.0112)																	---	---	---	---
CAMK2G	818	broad.mit.edu	37	10	75575128	75575128	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75575128delC	uc001jvm.1	-						CAMK2G_uc001jvo.1_Intron|CAMK2G_uc001jvq.1_Intron|CAMK2G_uc001jvr.1_Intron|CAMK2G_uc001jvp.1_Intron|CAMK2G_uc001jvs.1_Intron|CAMK2G_uc001jvt.1_Intron|CAMK2G_uc001jvu.1_Intron|CAMK2G_uc009xrp.1_Intron	NM_172171	NP_751911			calcium/calmodulin-dependent protein kinase II						insulin secretion|interferon-gamma-mediated signaling pathway|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding|calmodulin-dependent protein kinase activity			lung(1)|stomach(1)	2	Prostate(51;0.0112)																	---	---	---	---
VCL	7414	broad.mit.edu	37	10	75803110	75803110	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75803110delT	uc001jwd.2	+						VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Intron|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706			vinculin isoform meta-VCL						adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)																	---	---	---	---
VCL	7414	broad.mit.edu	37	10	75831726	75831726	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75831726delA	uc001jwd.2	+						VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Intron|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706			vinculin isoform meta-VCL						adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)																	---	---	---	---
AP3M1	26985	broad.mit.edu	37	10	75896701	75896701	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75896701delA	uc001jwf.2	-						AP3M1_uc001jwg.2_Intron|AP3M1_uc001jwh.2_Intron|AP3M1_uc010qla.1_Intron	NM_207012	NP_996895			adaptor-related protein complex 3, mu 1 subunit						protein targeting to lysosome|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus|lysosome	protein binding				0	Prostate(51;0.0112)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	76578244	76578244	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76578244delA								ADK (109185 upstream) : MYST4 (8135 downstream)																																			---	---	---	---
VDAC2	7417	broad.mit.edu	37	10	76975480	76975480	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76975480delT	uc001jwz.2	+						VDAC2_uc010qld.1_Intron|VDAC2_uc001jxa.2_Intron|VDAC2_uc010qle.1_Intron	NM_003375	NP_003366			voltage-dependent anion channel 2							mitochondrial nucleoid|mitochondrial outer membrane|pore complex	nucleotide binding|porin activity|protein binding|voltage-gated anion channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)				Dihydroxyaluminium(DB01375)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	77015815	77015815	+	IGR	DEL	T	-	-	rs75192001		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77015815delT								COMTD1 (20045 upstream) : ZNF503 (141790 downstream)																																			---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	77873234	77873234	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77873234delA	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	79319455	79319455	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79319455delA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron|uc001jxr.1_RNA	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	79544629	79544629	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79544629delA								KCNMA1 (147052 upstream) : DLG5 (5922 downstream)																																			---	---	---	---
DLG5	9231	broad.mit.edu	37	10	79677282	79677282	+	Intron	DEL	A	-	-	rs35757354		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79677282delA	uc001jzk.2	-							NM_004747	NP_004738			discs large homolog 5						cell-cell adhesion|intracellular signal transduction|negative regulation of cell proliferation|regulation of apoptosis	cell junction|cytoplasm	beta-catenin binding|cytoskeletal protein binding|receptor signaling complex scaffold activity			ovary(5)|breast(3)	8	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)															---	---	---	---
POLR3A	11128	broad.mit.edu	37	10	79768608	79768608	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79768608delA	uc001jzn.2	-							NM_007055	NP_008986			polymerase (RNA) III (DNA directed) polypeptide						innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity|ribonucleoside binding|zinc ion binding				0	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	79819555	79819556	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79819555_79819556delCA								RPS24 (2985 upstream) : LOC283050 (883528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	80529021	80529022	+	IGR	INS	-	TG	TG	rs138526740	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80529021_80529022insTG								RPS24 (712451 upstream) : LOC283050 (174062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	80546613	80546613	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80546613delA								RPS24 (730043 upstream) : LOC283050 (156471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	81455957	81455957	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81455957delG	uc001kat.2	-											full-length cDNA clone CS0DC003YI17 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
C10orf57	80195	broad.mit.edu	37	10	81841422	81841422	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81841422delA	uc001kbl.2	+						LOC219347_uc001kbk.2_5'Flank|LOC219347_uc001kbi.3_5'Flank|LOC219347_uc009xsk.2_5'Flank|LOC219347_uc009xsl.2_5'Flank|LOC219347_uc009xsm.2_5'Flank|LOC219347_uc001kbj.3_5'Flank|C10orf57_uc009xsn.2_Frame_Shift_Del_p.S38fs|C10orf57_uc010qlv.1_Intron|C10orf57_uc010qlw.1_Intron|C10orf57_uc001kbn.3_RNA|C10orf57_uc009xsp.2_RNA|C10orf57_uc001kbo.3_Intron	NM_025125	NP_079401			hypothetical protein LOC80195							integral to membrane					0	Prostate(51;0.0095)|all_epithelial(25;0.175)		Epithelial(14;0.0793)|Colorectal(32;0.109)|all cancers(16;0.154)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	82057637	82057637	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82057637delT								MAT1A (8203 upstream) : DYDC1 (38227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82835952	82835952	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82835952delT								SH2D4B (429636 upstream) : NRG3 (799118 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82974761	82974761	+	IGR	DEL	T	-	-	rs112125896		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82974761delT								SH2D4B (568445 upstream) : NRG3 (660309 downstream)																																			---	---	---	---
NRG3	10718	broad.mit.edu	37	10	83826578	83826578	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83826578delT	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848			neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)														---	---	---	---
NRG3	10718	broad.mit.edu	37	10	84054191	84054194	+	Intron	DEL	GTGT	-	-	rs112576898		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84054191_84054194delGTGT	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848			neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)														---	---	---	---
NRG3	10718	broad.mit.edu	37	10	84702730	84702730	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84702730delA	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron|NRG3_uc001kcr.2_Intron	NM_001010848	NP_001010848			neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	84751410	84751410	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84751410delT								NRG3 (4475 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85631224	85631224	+	IGR	DEL	A	-	-	rs77388451		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85631224delA								NRG3 (884289 upstream) : GHITM (267961 downstream)																																	OREG0020331	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	10	85885378	85885378	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85885378delT								None (None upstream) : GHITM (13807 downstream)																																			---	---	---	---
GHITM	27069	broad.mit.edu	37	10	85901203	85901203	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85901203delT	uc001kcs.1	+						GHITM_uc010qma.1_Intron|GHITM_uc010qmb.1_5'Flank	NM_014394	NP_055209			growth hormone inducible transmembrane protein						apoptosis	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
GHITM	27069	broad.mit.edu	37	10	85910380	85910380	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85910380delT	uc001kcs.1	+						GHITM_uc010qma.1_Intron|GHITM_uc010qmb.1_Intron	NM_014394	NP_055209			growth hormone inducible transmembrane protein						apoptosis	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
GHITM	27069	broad.mit.edu	37	10	85910432	85910432	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85910432delA	uc001kcs.1	+						GHITM_uc010qma.1_Intron|GHITM_uc010qmb.1_Intron	NM_014394	NP_055209			growth hormone inducible transmembrane protein						apoptosis	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	86056853	86056854	+	IGR	DEL	TT	-	-	rs67286102		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86056853_86056854delTT								RGR (37909 upstream) : FAM190B (31556 downstream)																																			---	---	---	---
FAM190B	54462	broad.mit.edu	37	10	86147290	86147290	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86147290delT	uc001kdh.1	+						FAM190B_uc010qmd.1_Intron	NM_018999	NP_061872			granule cell antiserum positive 14											ovary(3)|skin(1)	4																		---	---	---	---
FAM190B	54462	broad.mit.edu	37	10	86193529	86193529	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86193529delT	uc001kdh.1	+						FAM190B_uc010qmd.1_Intron|FAM190B_uc001kdi.1_Intron|FAM190B_uc010qme.1_Intron	NM_018999	NP_061872			granule cell antiserum positive 14											ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	86759674	86759675	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86759674_86759675delAC								FAM190B (481398 upstream) : GRID1 (599637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	86996471	86996471	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86996471delA								FAM190B (718195 upstream) : GRID1 (362841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	87092598	87092599	+	IGR	INS	-	GT	GT	rs71473701		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87092598_87092599insGT								FAM190B (814322 upstream) : GRID1 (266713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	88383735	88383735	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88383735delA								WAPAL (102194 upstream) : OPN4 (30579 downstream)																																			---	---	---	---
BMPR1A	657	broad.mit.edu	37	10	88574535	88574536	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88574535_88574536insT	uc001kdy.2	+							NM_004329	NP_004320			bone morphogenetic protein receptor, type IA						BMP signaling pathway|immune response|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	integral to membrane|plasma membrane	ATP binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta receptor activity			lung(3)|large_intestine(1)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	8								Mis|N|F			gastrointestinal polyps			Hereditary_Mixed_Polyposis_syndrome_type_2|Juvenile_Polyposis				---	---	---	---
BMPR1A	657	broad.mit.edu	37	10	88673875	88673875	+	Intron	DEL	A	-	-	rs78241517		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88673875delA	uc001kdy.2	+							NM_004329	NP_004320			bone morphogenetic protein receptor, type IA						BMP signaling pathway|immune response|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	integral to membrane|plasma membrane	ATP binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta receptor activity			lung(3)|large_intestine(1)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	8								Mis|N|F			gastrointestinal polyps			Hereditary_Mixed_Polyposis_syndrome_type_2|Juvenile_Polyposis				---	---	---	---
MINPP1	9562	broad.mit.edu	37	10	89272866	89272866	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89272866delT	uc001keu.2	+						MINPP1_uc009xtf.1_Intron|MINPP1_uc001kev.2_Intron	NM_004897	NP_004888			multiple inositol polyphosphate histidine						bone mineralization|polyphosphate metabolic process	endoplasmic reticulum lumen	acid phosphatase activity|bisphosphoglycerate 3-phosphatase activity|multiple inositol-polyphosphate phosphatase activity|phosphohistidine phosphatase activity			urinary_tract(1)	1		Colorectal(252;0.122)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00123)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	89362426	89362426	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89362426delA								MINPP1 (49258 upstream) : PAPSS2 (57050 downstream)																																			---	---	---	---
PAPSS2	9060	broad.mit.edu	37	10	89472722	89472723	+	Intron	DEL	TT	-	-	rs148721342		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89472722_89472723delTT	uc001kex.2	+						PAPSS2_uc001kew.2_Intron|PAPSS2_uc009xtg.1_Intron	NM_004670	NP_004661			3'-phosphoadenosine 5'-phosphosulfate synthase 2						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|protein binding|sulfate adenylyltransferase (ATP) activity			central_nervous_system(1)|skin(1)	2		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)														---	---	---	---
ATAD1	84896	broad.mit.edu	37	10	89514658	89514658	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89514658delA	uc001key.1	-						ATAD1_uc010qmr.1_Intron|ATAD1_uc009xth.1_Intron|ATAD1_uc001kez.1_Intron	NM_032810	NP_116199			ATPase family, AAA domain containing 1							peroxisome	ATP binding|nucleoside-triphosphatase activity			large_intestine(1)|ovary(1)	2		all_cancers(4;6.78e-12)|Prostate(4;3.56e-12)|all_epithelial(4;5.58e-09)|Melanoma(5;0.0273)|Breast(4;0.0424)|all_hematologic(4;0.0846)|Colorectal(252;0.207)|Glioma(4;0.217)|all_neural(4;0.224)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00131)|GBM - Glioblastoma multiforme(1;1.1e-32)|Lung(2;1.4e-05)|LUSC - Lung squamous cell carcinoma(2;2.69e-05)|Colorectal(12;7.09e-05)|COAD - Colon adenocarcinoma(12;0.000261)|STAD - Stomach adenocarcinoma(243;0.235)														---	---	---	---
PTEN	5728	broad.mit.edu	37	10	89725294	89725294	+	3'UTR	DEL	T	-	-	rs1044487		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89725294delT	uc001kfb.2	+	10						NM_000314	NP_000305			phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)			31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			---	---	---	---
RNLS	55328	broad.mit.edu	37	10	90265028	90265028	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90265028delA	uc001kfe.2	-						RNLS_uc010qms.1_Intron|RNLS_uc001kfd.2_Intron|RNLS_uc009xtj.2_Intron	NM_001031709	NP_001026879			renalase isoform 1							extracellular region	oxidoreductase activity			ovary(1)	1																		---	---	---	---
ANKRD22	118932	broad.mit.edu	37	10	90594708	90594708	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90594708delA	uc001kfj.3	-							NM_144590	NP_653191			ankyrin repeat domain 22												0		Colorectal(252;0.0163)		Colorectal(12;6.29e-05)|COAD - Colon adenocarcinoma(12;7.69e-05)														---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90681950	90681950	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90681950delA	uc001kfk.2	+						STAMBPL1_uc010qmx.1_Intron|STAMBPL1_uc009xto.2_Intron|STAMBPL1_uc001kfl.2_Intron|STAMBPL1_uc001kfn.2_Intron	NM_020799	NP_065850			STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
SLC16A12	387700	broad.mit.edu	37	10	91239948	91239948	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91239948delA	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-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	91923375	91923375	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91923375delA								KIF20B (388675 upstream) : HTR7 (577203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	92295687	92295688	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92295687_92295688insA								KIF20B (760987 upstream) : HTR7 (204890 downstream)																																			---	---	---	---
ANKRD1	27063	broad.mit.edu	37	10	92680929	92680929	+	5'UTR	DEL	A	-	-	rs10881855	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92680929delA	uc001khe.1	-	1						NM_014391	NP_055206			cardiac ankyrin repeat protein						cellular lipid metabolic process|defense response|signal transduction		DNA binding				0		Colorectal(252;0.0475)																---	---	---	---
HECTD2	143279	broad.mit.edu	37	10	93218207	93218207	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93218207delA	uc001khl.2	+						LOC100188947_uc010qnl.1_Intron|HECTD2_uc001khk.2_Intron|HECTD2_uc010qnm.1_Intron|HECTD2_uc001khm.2_Intron	NM_182765	NP_877497			HECT domain containing 2 isoform a						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			skin(1)	1																		---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93722539	93722539	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93722539delT	uc001khr.2	+						BTAF1_uc001khs.1_Intron	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93783442	93783442	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93783442delA	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)																---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93787238	93787238	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93787238delT	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)																---	---	---	---
IDE	3416	broad.mit.edu	37	10	94275943	94275943	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94275943delA	uc001kia.2	-							NM_004969	NP_004960			insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
IDE	3416	broad.mit.edu	37	10	94276526	94276526	+	Intron	DEL	A	-	-	rs7895832	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94276526delA	uc001kia.2	-							NM_004969	NP_004960			insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
IDE	3416	broad.mit.edu	37	10	94300007	94300010	+	Intron	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94300007_94300010delAAAA	uc001kia.2	-							NM_004969	NP_004960			insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
KIF11	3832	broad.mit.edu	37	10	94388745	94388746	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94388745_94388746delTT	uc001kic.2	+						KIF11_uc010qnq.1_Intron	NM_004523	NP_004514			kinesin family member 11						blood coagulation|cell division|microtubule-based movement|spindle assembly involved in mitosis	chromatin remodeling complex|cytosol|kinesin complex|microtubule|spindle pole	ATP binding|microtubule motor activity|protein kinase binding			skin(1)	1																		---	---	---	---
EXOC6	54536	broad.mit.edu	37	10	94600425	94600425	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94600425delT	uc010qnr.1	+						EXOC6_uc001kie.2_Intron	NM_001013848	NP_001013870			SEC15-like 1 isoform b						protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)																---	---	---	---
EXOC6	54536	broad.mit.edu	37	10	94661838	94661839	+	Intron	INS	-	AC	AC	rs144352636	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94661838_94661839insAC	uc001kig.2	+						EXOC6_uc010qnr.1_Intron|EXOC6_uc001kie.2_Intron|EXOC6_uc009xub.2_Intron|EXOC6_uc009xuc.2_Intron	NM_019053	NP_061926			SEC15-like 1 isoform a						protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)																---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95142663	95142663	+	Intron	DEL	T	-	-	rs143460456		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95142663delT	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_5'Flank	NM_013451	NP_038479			myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95154538	95154539	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95154538_95154539delTT	uc001kin.2	-						MYOF_uc001kio.2_Intron	NM_013451	NP_038479			myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
LGI1	9211	broad.mit.edu	37	10	95538103	95538112	+	Intron	DEL	CACACACACA	-	-	rs111285656		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95538103_95538112delCACACACACA	uc001kjc.3	+						LGI1_uc010qnv.1_Intron|LGI1_uc001kjd.3_Intron|LGI1_uc009xui.2_Intron|LGI1_uc001kje.2_Intron	NM_005097	NP_005088			leucine-rich, glioma inactivated 1 precursor						axon guidance|cell proliferation|positive regulation of cell growth|positive regulation of synaptic transmission	cell junction|extracellular space|synapse	receptor binding			ovary(2)|central_nervous_system(1)|skin(1)	4		Colorectal(252;0.124)																---	---	---	---
PLCE1	51196	broad.mit.edu	37	10	95916620	95916620	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95916620delA	uc001kjk.2	+						PLCE1_uc010qnx.1_Intron|PLCE1_uc001kjm.2_Intron	NM_016341	NP_057425			phospholipase C, epsilon 1 isoform 1						activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)																---	---	---	---
HELLS	3070	broad.mit.edu	37	10	96313731	96313731	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	96672556	96672556	+	IGR	DEL	A	-	-	rs149042821		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96672556delA								CYP2C19 (59886 upstream) : CYP2C9 (25859 downstream)																																			---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97133365	97133365	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97133365delA	uc001kkp.2	-						SORBS1_uc001kkk.2_Intron|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97206918	97206918	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97206918delA	uc001kkw.2	-						SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron|SORBS1_uc001kkx.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
ALDH18A1	5832	broad.mit.edu	37	10	97383329	97383329	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97383329delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	98046752	98046752	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98046752delT								BLNK (15419 upstream) : DNTT (17333 downstream)																																			---	---	---	---
MMS19	64210	broad.mit.edu	37	10	99221731	99221731	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99221731delA	uc001kns.3	-						MMS19_uc001knq.2_5'Flank|MMS19_uc009xvs.2_Intron|MMS19_uc009xvt.2_Intron|MMS19_uc001knr.2_Intron|MMS19_uc010qox.1_Intron|MMS19_uc001knt.2_Intron|MMS19_uc001knu.1_Intron	NM_022362	NP_071757			MMS19 nucleotide excision repair homolog						chromosome segregation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent|two-component signal transduction system (phosphorelay)	cytoplasm|holo TFIIH complex|MMXD complex	estrogen receptor binding|protein binding, bridging|receptor signaling complex scaffold activity|transcription coactivator activity				0		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)									Direct_reversal_of_damage|NER					---	---	---	---
PI4K2A	55361	broad.mit.edu	37	10	99413674	99413675	+	Intron	DEL	AA	-	-	rs78918098		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99413674_99413675delAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	99469900	99469900	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99469900delT								AVPI1 (22885 upstream) : MARVELD1 (3581 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	99849786	99849788	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99849786_99849788delTTT								CRTAC1 (59201 upstream) : C10orf28 (44593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	100043401	100043401	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100043401delT								LOXL4 (15394 upstream) : PYROXD2 (99922 downstream)																																			---	---	---	---
HPSE2	60495	broad.mit.edu	37	10	100357431	100357432	+	Intron	DEL	AA	-	-	rs146875691		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100357431_100357432delAA	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600			heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)														---	---	---	---
HPSE2	60495	broad.mit.edu	37	10	100443114	100443114	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100443114delA	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600			heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	101277242	101277242	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101277242delT								GOT1 (86712 upstream) : NKX2-3 (15448 downstream)																																			---	---	---	---
COX15	1355	broad.mit.edu	37	10	101478984	101478984	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101478984delT	uc001kqb.3	-						COX15_uc001kqc.3_Intron|COX15_uc010qpj.1_Intron	NM_078470	NP_510870			COX15 homolog isoform 1						heme a biosynthetic process|respiratory chain complex IV assembly|respiratory gaseous exchange	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)														---	---	---	---
BLOC1S2	282991	broad.mit.edu	37	10	102034426	102034426	+	3'UTR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102034426delC	uc001kqw.1	-	5					BLOC1S2_uc001kqv.1_3'UTR	NM_173809	NP_776170			biogenesis of lysosome-related organelles						melanosome organization|microtubule nucleation|platelet dense granule organization|positive regulation of cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of apoptosis	BLOC-1 complex|centrosome|gamma-tubulin complex|nucleus	gamma-tubulin binding|identical protein binding|protein C-terminus binding			ovary(1)	1		Colorectal(252;0.117)		Epithelial(162;2.44e-10)|all cancers(201;1.97e-08)														---	---	---	---
PKD2L1	9033	broad.mit.edu	37	10	102060153	102060153	+	Intron	DEL	A	-	-	rs67126182		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102060153delA	uc001kqx.1	-						PKD2L1_uc009xwm.1_Intron	NM_016112	NP_057196			polycystic kidney disease 2-like 1						signal transduction	integral to membrane	calcium activated cation channel activity|calcium ion binding|cytoskeletal protein binding			ovary(4)	4		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)														---	---	---	---
C10orf75	90271	broad.mit.edu	37	10	102136361	102136362	+	Intron	DEL	AA	-	-	rs78452484		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102136361_102136362delAA	uc001kqz.3	+						C10orf75_uc001kra.3_Intron	NR_026762				Homo sapiens cDNA FLJ12974 fis, clone NT2RP2006103.												0																		---	---	---	---
HIF1AN	55662	broad.mit.edu	37	10	102305592	102305592	+	Intron	DEL	T	-	-	rs11817143	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102305592delT	uc001krj.3	+							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	102628452	102628453	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102628452_102628453insC								PAX2 (38755 upstream) : FAM178A (43873 downstream)																																			---	---	---	---
BTRC	8945	broad.mit.edu	37	10	103164755	103164758	+	Intron	DEL	AAAA	-	-	rs34206285		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103164755_103164758delAAAA	uc001kta.2	+						BTRC_uc001ksz.1_Intron|BTRC_uc001ktb.2_Intron|BTRC_uc001ktc.2_Intron	NM_033637	NP_378663			beta-transducin repeat containing protein						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway	cytosol|nucleus|SCF ubiquitin ligase complex				ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)														---	---	---	---
FBXW4	6468	broad.mit.edu	37	10	103378650	103378650	+	Intron	DEL	A	-	-	rs75454639		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103378650delA	uc001kto.2	-							NM_022039	NP_071322			F-box and WD repeat domain containing 4						ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	ubiquitin ligase complex				skin(1)	1		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	103585338	103585339	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103585338_103585339delAA								MGEA5 (6638 upstream) : KCNIP2 (393 downstream)																																			---	---	---	---
GBF1	8729	broad.mit.edu	37	10	104022099	104022099	+	Intron	DEL	T	-	-	rs72044354		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104022099delT	uc001kux.1	+						GBF1_uc001kuw.2_Intron|GBF1_uc001kuy.1_Intron|GBF1_uc001kuz.1_Intron	NM_004193	NP_004184			golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)														---	---	---	---
GBF1	8729	broad.mit.edu	37	10	104134960	104134960	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104134960delA	uc001kux.1	+						GBF1_uc001kuy.1_Intron|GBF1_uc001kuz.1_Intron	NM_004193	NP_004184			golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)														---	---	---	---
GBF1	8729	broad.mit.edu	37	10	104140752	104140753	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104140752_104140753delAA	uc001kux.1	+						GBF1_uc001kuy.1_Intron|GBF1_uc001kuz.1_Intron	NM_004193	NP_004184			golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)														---	---	---	---
NT5C2	22978	broad.mit.edu	37	10	104879856	104879856	+	Intron	DEL	A	-	-	rs2148199		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104879856delA	uc001kwo.2	-						NT5C2_uc010qqp.1_Intron|NT5C2_uc001kwq.2_Intron|NT5C2_uc001kwp.2_Intron	NM_012229	NP_036361			5'-nucleotidase, cytosolic II						purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding				0		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)													---	---	---	---
PDCD11	22984	broad.mit.edu	37	10	105179557	105179557	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105179557delT	uc001kwy.1	+							NM_014976	NP_055791			programmed cell death 11						mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)														---	---	---	---
NEURL	9148	broad.mit.edu	37	10	105351810	105351810	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105351810delT	uc001kxh.2	+	6					SH3PXD2A_uc010qqr.1_Intron	NM_004210	NP_004201			neuralized-like						nervous system development	perinuclear region of cytoplasm	zinc ion binding				0				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)														---	---	---	---
C10orf79	80217	broad.mit.edu	37	10	105939743	105939743	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105939743delT	uc001kxw.2	-						C10orf79_uc009xxq.2_Intron|C10orf79_uc001kxx.3_Intron	NM_025145	NP_079421			hypothetical protein LOC80217												0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)														---	---	---	---
C10orf79	80217	broad.mit.edu	37	10	105958963	105958963	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105958963delA	uc001kxw.2	-						C10orf79_uc001kxx.3_Intron|C10orf79_uc001kxy.1_Intron	NM_025145	NP_079421			hypothetical protein LOC80217												0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)														---	---	---	---
CCDC147	159686	broad.mit.edu	37	10	106182313	106182313	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106182313delT	uc001kyh.2	+							NM_001008723	NP_001008723			coiled-coil domain containing 147											ovary(2)|central_nervous_system(2)|skin(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)														---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106655209	106655209	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106655209delA	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	106759712	106759712	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106759712delG	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	106947738	106947740	+	Intron	DEL	TGG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106947738_106947740delTGG	uc001kyi.1	+						SORCS3_uc010qqz.1_Intron	NM_014978	NP_055793			VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)														---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106992344	106992345	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106992344_106992345insT	uc001kyi.1	+						SORCS3_uc010qqz.1_Intron	NM_014978	NP_055793			VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	107058815	107058815	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107058815delA								SORCS3 (33822 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107167323	107167323	+	IGR	DEL	T	-	-	rs77865595		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107167323delT								SORCS3 (142330 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	108238117	108238118	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108238117_108238118delAA								None (None upstream) : SORCS1 (95304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	108275952	108275953	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108275952_108275953delAA								None (None upstream) : SORCS1 (57469 downstream)																																			---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108355889	108355889	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108355889delA	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108379952	108379952	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108379952delA	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108414613	108414613	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108414613delT	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108480835	108480836	+	Intron	DEL	AA	-	-	rs147432157		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108480835_108480836delAA	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108748303	108748303	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108748303delT	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	110701661	110701661	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110701661delA								None (None upstream) : XPNPEP1 (922863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111232843	111232844	+	IGR	DEL	TT	-	-	rs67236426		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111232843_111232844delTT								None (None upstream) : XPNPEP1 (391680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111697766	111697766	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111697766delT								XPNPEP1 (14564 upstream) : ADD3 (58342 downstream)																																			---	---	---	---
ADD3	120	broad.mit.edu	37	10	111893350	111893350	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111893350delA	uc001kyt.3	+	16	2409	c.2095delA	c.(2095-2097)AAAfs	p.K699fs	ADD3_uc001kys.3_Frame_Shift_Del_p.K667fs|ADD3_uc001kyu.2_Frame_Shift_Del_p.K699fs|ADD3_uc001kyv.2_Frame_Shift_Del_p.K699fs|ADD3_uc001kyw.2_Frame_Shift_Del_p.K667fs|ADD3_uc001kyx.2_Frame_Shift_Del_p.K272fs	NM_016824	NP_058432	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma) isoform a	699	Interaction with calmodulin (Potential).					cytoskeleton	actin binding|calmodulin binding|metal ion binding|structural constituent of cytoskeleton			ovary(2)|skin(2)|large_intestine(1)	5		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)														---	---	---	---
MXI1	4601	broad.mit.edu	37	10	111973725	111973725	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111973725delC	uc001kyy.2	+						MXI1_uc001kyz.2_Intron	NM_130439	NP_569157			MAX interactor 1 isoform b						cytoplasmic sequestering of transcription factor|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription corepressor activity				0		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;1.33e-05)|all cancers(201;0.000277)|BRCA - Breast invasive adenocarcinoma(275;0.127)														---	---	---	---
MXI1	4601	broad.mit.edu	37	10	112017068	112017069	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112017068_112017069delTG	uc001kza.2	+						MXI1_uc001kyy.2_Intron|MXI1_uc001kyz.2_Intron|MXI1_uc010qrc.1_Intron|MXI1_uc009xxu.2_Intron|MXI1_uc009xxv.2_Intron	NM_005962	NP_005953			MAX interactor 1 isoform a						cytoplasmic sequestering of transcription factor|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription corepressor activity				0		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;1.33e-05)|all cancers(201;0.000277)|BRCA - Breast invasive adenocarcinoma(275;0.127)														---	---	---	---
SMNDC1	10285	broad.mit.edu	37	10	112062785	112062785	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112062785delA	uc001kzc.3	-							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	112587166	112587166	+	Intron	DEL	A	-	-	rs111267955		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112587166delA	uc001kzf.2	+							NM_001134363	NP_001127835			RNA binding motif protein 20							nucleus	nucleotide binding|RNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	113094106	113094106	+	IGR	DEL	T	-	-	rs79791540		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113094106delT								ADRA2A (253446 upstream) : GPAM (815516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113220000	113220001	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113220000_113220001insA								ADRA2A (379340 upstream) : GPAM (689621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113645491	113645491	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113645491delT								ADRA2A (804831 upstream) : GPAM (264131 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113724303	113724303	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113724303delA								ADRA2A (883643 upstream) : GPAM (185319 downstream)																																			---	---	---	---
GUCY2GP	390003	broad.mit.edu	37	10	114093053	114093053	+	Intron	DEL	T	-	-	rs144952286	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114093053delT	uc010qri.1	-							NR_028134				Homo sapiens guanylate cyclase 2G homolog (mouse) pseudogene (GUCY2G), non-coding RNA, 611.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	114123666	114123669	+	IGR	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114123666_114123669delAAAA								GUCY2GP (7313 upstream) : ACSL5 (10247 downstream)																																			---	---	---	---
VTI1A	143187	broad.mit.edu	37	10	114297946	114297946	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114297946delA	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)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114823653	114823656	+	Intron	DEL	GTGT	-	-	rs150845819		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114823653_114823656delGTGT	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron|TCF7L2_uc010qru.1_Intron	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114844670	114844670	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114844670delA	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron|TCF7L2_uc010qru.1_Intron	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114922769	114922770	+	Intron	DEL	AA	-	-	rs113088460		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114922769_114922770delAA	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron|TCF7L2_uc010qru.1_Intron|TCF7L2_uc010qrv.1_Intron|TCF7L2_uc010qrw.1_Intron|TCF7L2_uc010qrx.1_Intron	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114924806	114924807	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114924806_114924807delAC	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron|TCF7L2_uc010qru.1_Intron|TCF7L2_uc010qrv.1_Intron|TCF7L2_uc010qrw.1_Intron|TCF7L2_uc010qrx.1_Intron	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	114945282	114945282	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114945282delA								TCF7L2 (17848 upstream) : HABP2 (367496 downstream)																																			---	---	---	---
NHLRC2	374354	broad.mit.edu	37	10	115618199	115618199	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115618199delA	uc001lax.1	+							NM_198514	NP_940916			NHL repeat containing 2						cell redox homeostasis					ovary(1)	1				Epithelial(162;0.017)|all cancers(201;0.0187)														---	---	---	---
NHLRC2	374354	broad.mit.edu	37	10	115634806	115634806	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115634806delT	uc001lax.1	+							NM_198514	NP_940916			NHL repeat containing 2						cell redox homeostasis					ovary(1)	1				Epithelial(162;0.017)|all cancers(201;0.0187)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	115816008	115816009	+	IGR	DEL	AA	-	-	rs11308940		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115816008_115816009delAA								ADRB1 (9343 upstream) : C10orf118 (65965 downstream)																																			---	---	---	---
TDRD1	56165	broad.mit.edu	37	10	115981072	115981073	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115981072_115981073insT	uc001lbg.1	+						TDRD1_uc001lbf.2_Intron|TDRD1_uc001lbh.1_Intron|TDRD1_uc001lbi.1_Intron|TDRD1_uc010qsc.1_Intron|TDRD1_uc001lbj.2_Intron	NM_198795	NP_942090			tudor domain containing 1						DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	116168505	116168505	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116168505delT								AFAP1L2 (3990 upstream) : ABLIM1 (22365 downstream)																																			---	---	---	---
ABLIM1	3983	broad.mit.edu	37	10	116450448	116450448	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116450448delT	uc001lbz.1	-											Homo sapiens cDNA FLJ25105 fis, clone CBR01442.						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)														---	---	---	---
ABLIM1	3983	broad.mit.edu	37	10	116467693	116467693	+	Intron	DEL	C	-	-	rs56877526		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116467693delC	uc001lbz.1	-											Homo sapiens cDNA FLJ25105 fis, clone CBR01442.						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)														---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117496946	117496946	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117496946delA	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)														---	---	---	---
KIAA1598	57698	broad.mit.edu	37	10	118776202	118776203	+	Intron	INS	-	CCAT	CCAT	rs149771536	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118776202_118776203insCCAT	uc010qsq.1	-							NM_018330	NP_060800			shootin1 isoform b						axon guidance	axon					0				all cancers(201;0.00494)														---	---	---	---
RAB11FIP2	22841	broad.mit.edu	37	10	119800089	119800089	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119800089delA	uc001ldj.1	-						RAB11FIP2_uc009xyz.1_Intron	NM_014904	NP_055719			RAB11 family interacting protein 2						protein transport	plasma membrane|recycling endosome membrane	protein homodimerization activity				0		Colorectal(252;0.235)		all cancers(201;0.0238)														---	---	---	---
C10orf46	143384	broad.mit.edu	37	10	120467214	120467214	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120467214delA	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	120602651	120602652	+	IGR	INS	-	A	A	rs139172326	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120602651_120602652insA								C10orf46 (87893 upstream) : NANOS1 (186576 downstream)																																			---	---	---	---
SFXN4	119559	broad.mit.edu	37	10	120902895	120902895	+	Intron	DEL	C	-	-	rs11198802		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120902895delC	uc001leb.2	-						SFXN4_uc001ldy.2_Intron|SFXN4_uc001ldz.2_Intron|SFXN4_uc001lea.2_Intron	NM_213649	NP_998814			sideroflexin 4						iron ion homeostasis	integral to membrane|mitochondrial membrane	cation transmembrane transporter activity			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)														---	---	---	---
GRK5	2869	broad.mit.edu	37	10	120969000	120969013	+	Intron	DEL	TTTTTTTTTTTTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120969000_120969013delTTTTTTTTTTTTTT	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299			G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)												OREG0020575	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GRK5	2869	broad.mit.edu	37	10	121054294	121054295	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121054294_121054295insT	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299			G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)														---	---	---	---
SEC23IP	11196	broad.mit.edu	37	10	121651189	121651189	+	5'Flank	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121651189delC	uc001leu.1	+						SEC23IP_uc010qtc.1_5'Flank	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	121991203	121991204	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121991203_121991204insT								SEC23IP (289958 upstream) : PPAPDC1A (225262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	122484436	122484436	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122484436delA								PPAPDC1A (135069 upstream) : WDR11 (126259 downstream)																																			---	---	---	---
WDR11	55717	broad.mit.edu	37	10	122627975	122627975	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122627975delA	uc010qtf.1	+						WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron	NM_018117	NP_060587			bromodomain and WD repeat domain containing 2							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	123133676	123133677	+	IGR	INS	-	GTGC	GTGC	rs141357889	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123133676_123133677insGTGC								WDR11 (464641 upstream) : FGFR2 (104168 downstream)																																			---	---	---	---
FGFR2	2263	broad.mit.edu	37	10	123310734	123310734	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123310734delA	uc010qtk.1	-						FGFR2_uc010qtg.1_Intron|FGFR2_uc010qth.1_Intron|FGFR2_uc010qti.1_Intron|FGFR2_uc010qtj.1_Intron|FGFR2_uc010qtl.1_Intron|FGFR2_uc010qtm.1_Intron|FGFR2_uc001lfl.3_Intron|FGFR2_uc001lfm.2_Intron|FGFR2_uc001lfn.3_Intron|FGFR2_uc010qtn.1_Intron|FGFR2_uc010qto.1_Intron|FGFR2_uc001lfo.1_Intron|FGFR2_uc010qtp.1_Intron|FGFR2_uc010qtq.1_Intron	NM_000141	NP_000132			fibroblast growth factor receptor 2 isoform 1						angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123975000	123975000	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123975000delC	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|TACC2_uc001lgb.2_Intron|TACC2_uc010qtw.1_Intron	NM_206862	NP_996744			transforming, acidic coiled-coil containing							microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	125928230	125928231	+	IGR	INS	-	GT	GT	rs146304542	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125928230_125928231insGT								CHST15 (75024 upstream) : OAT (157641 downstream)																																			---	---	---	---
FAM175B	23172	broad.mit.edu	37	10	126505229	126505229	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126505229delA	uc001lib.3	+							NM_032182	NP_115558			hypothetical protein LOC23172							BRISC complex	polyubiquitin binding				0																		---	---	---	---
CTBP2	1488	broad.mit.edu	37	10	126780405	126780405	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126780405delA	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320			C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)														---	---	---	---
CTBP2	1488	broad.mit.edu	37	10	126791255	126791256	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126791255_126791256insT	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320			C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)														---	---	---	---
CTBP2	1488	broad.mit.edu	37	10	126836471	126836471	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126836471delA	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320			C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	126999469	126999469	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126999469delA								CTBP2 (149845 upstream) : LOC100169752 (263471 downstream)																																			---	---	---	---
C10orf122	387718	broad.mit.edu	37	10	127356880	127356880	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127356880delT	uc001lik.3	-						C10orf122_uc001lij.2_Intron	NM_001128202	NP_001121674			hypothetical protein LOC387718												0																		---	---	---	---
ADAM12	8038	broad.mit.edu	37	10	127853745	127853745	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127853745delT	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)														---	---	---	---
ADAM12	8038	broad.mit.edu	37	10	127885679	127885681	+	Intron	DEL	GAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127885679_127885681delGAC	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	128255309	128255309	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128255309delA	uc010qum.1	-						C10orf90_uc009yao.2_Intron	NM_001004298	NP_001004298			hypothetical protein LOC118611											ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128818832	128818832	+	Intron	DEL	A	-	-	rs34630387		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128818832delA	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	129016231	129016232	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129016231_129016232insT	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	129059069	129059070	+	Intron	INS	-	TG	TG	rs150388896	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129059069_129059070insTG	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	129126645	129126645	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129126645delT	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	129141792	129141793	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129141792_129141793delTT	uc001ljt.2	+						DOCK1_uc010qun.1_Intron|DOCK1_uc009yaq.2_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	129343080	129343081	+	IGR	INS	-	TC	TC	rs145456578	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129343080_129343081insTC								DOCK1 (92299 upstream) : NPS (4532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130014338	130014338	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130014338delG	uc001lkg.1	+											Homo sapiens cDNA FLJ42232 fis, clone THYMU3000224.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	130053090	130053090	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130053090delT	uc001lkg.1	+											Homo sapiens cDNA FLJ42232 fis, clone THYMU3000224.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	130352908	130352909	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130352908_130352909insT								MKI67 (428440 upstream) : MGMT (912545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	131201282	131201282	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131201282delA								None (None upstream) : MGMT (64172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	131233805	131233805	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131233805delT								None (None upstream) : MGMT (31649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	131800691	131800691	+	IGR	DEL	T	-	-	rs113226679		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131800691delT								EBF3 (38600 upstream) : GLRX3 (133972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132008015	132008016	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132008015_132008016insA								GLRX3 (25231 upstream) : TCERG1L (882640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132749839	132749839	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132749839delT								GLRX3 (767055 upstream) : TCERG1L (140817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132762237	132762240	+	5'Flank	DEL	AGGG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132762237_132762240delAGGG	hsa-mir-378c|MI0015825	-																																									---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	132982018	132982019	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132982018_132982019delGA	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597			transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	133031721	133031722	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133031721_133031722delAC	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597			transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	133052001	133052001	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133052001delA	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597			transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	133845245	133845245	+	IGR	DEL	T	-	-	rs77448309		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133845245delT								BNIP3 (49810 upstream) : JAKMIP3 (73068 downstream)																																			---	---	---	---
STK32C	282974	broad.mit.edu	37	10	134073575	134073575	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134073575delA	uc001lle.1	-						STK32C_uc001lld.1_Intron|STK32C_uc010quu.1_Intron|STK32C_uc009ybc.1_Intron|STK32C_uc009ybd.1_Intron	NM_173575	NP_775846			serine/threonine kinase 32C								ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)														---	---	---	---
STK32C	282974	broad.mit.edu	37	10	134081159	134081160	+	Intron	DEL	AT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134081159_134081160delAT	uc001lle.1	-						STK32C_uc001lld.1_Intron|STK32C_uc010quu.1_Intron|STK32C_uc009ybc.1_Intron|STK32C_uc009ybd.1_Intron	NM_173575	NP_775846			serine/threonine kinase 32C								ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)														---	---	---	---
LRRC27	80313	broad.mit.edu	37	10	134188696	134188696	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134188696delT	uc010quw.1	+	11	1738	c.1543delT	c.(1543-1545)TTTfs	p.F515fs	LRRC27_uc001llg.2_RNA|LRRC27_uc001lli.2_Frame_Shift_Del_p.F515fs|LRRC27_uc001llj.2_Frame_Shift_Del_p.F453fs	NM_030626	NP_085129	Q9C0I9	LRC27_HUMAN	leucine rich repeat containing 27 isoform a	515										ovary(1)	1		all_cancers(35;6.28e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;9.12e-05)|Epithelial(32;0.000116)|all cancers(32;0.000145)|BRCA - Breast invasive adenocarcinoma(275;0.218)														---	---	---	---
INPP5A	3632	broad.mit.edu	37	10	134406065	134406065	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134406065delG	uc001llp.2	+						INPP5A_uc001llo.1_Intron	NM_005539	NP_005530			inositol polyphosphate-5-phosphatase A						cell communication	membrane	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|PH domain binding			skin(1)	1		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	135474720	135474721	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	11	357189	357190	+	IGR	INS	-	ACAA	ACAA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:357189_357190insACAA								IFITM3 (36275 upstream) : B4GALNT4 (12605 downstream)																																			---	---	---	---
PHRF1	57661	broad.mit.edu	37	11	581844	581845	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:581844_581845insA	uc001lqe.2	+						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																		---	---	---	---
DEAF1	10522	broad.mit.edu	37	11	649421	649421	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:649421delA	uc001lqq.1	-						DEAF1_uc009ycf.1_Intron	NM_021008	NP_066288			deformed epidermal autoregulatory factor 1						embryonic skeletal system development|germ cell development|neural tube closure|regulation of mammary gland epithelial cell proliferation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|cytoplasm|extracellular region|nucleus	protein binding|zinc ion binding				0		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	743105	743105	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:743105delT								EPS8L2 (15379 upstream) : TALDO1 (4327 downstream)																																			---	---	---	---
AP2A2	161	broad.mit.edu	37	11	950628	950628	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:950628delA	uc001lss.2	+						AP2A2_uc001lst.1_Intron|AP2A2_uc009yco.1_Intron	NM_012305	NP_036437			adaptor-related protein complex 2, alpha 2						axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|cytosol	lipid binding|protein transporter activity				0		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	1044516	1044517	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1044516_1044517delCT								MUC6 (7810 upstream) : MUC2 (30358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	1924511	1924511	+	IGR	DEL	T	-	-	rs76507065		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1924511delT								LSP1 (11019 upstream) : TNNT3 (16288 downstream)																																			---	---	---	---
TSPAN32	10077	broad.mit.edu	37	11	2328201	2328205	+	Intron	DEL	AAGAG	-	-	rs143581324		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2328201_2328205delAAGAG	uc001lvy.1	+						TSPAN32_uc001lvx.1_Intron|TSPAN32_uc009ydk.1_Intron|TSPAN32_uc010qxk.1_Intron|TSPAN32_uc009ydl.1_Intron|TSPAN32_uc001lvz.1_Intron|TSPAN32_uc001lwb.1_Intron|TSPAN32_uc001lwc.1_Intron	NM_139022	NP_620591			tumor-suppressing subtransferable candidate 6						cell-cell signaling	integral to membrane				central_nervous_system(1)	1		all_epithelial(84;4.89e-05)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.00791)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000533)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)														---	---	---	---
KCNQ1	3784	broad.mit.edu	37	11	2836859	2836859	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2836859delG	uc001lwn.2	+						KCNQ1_uc001lwo.2_Intron	NM_000218	NP_000209			potassium voltage-gated channel, KQT-like						blood circulation|membrane depolarization|muscle contraction|sensory perception of sound		delayed rectifier potassium channel activity|protein binding			ovary(1)	1		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)													---	---	---	---
NAP1L4	4676	broad.mit.edu	37	11	2985356	2985356	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2985356delT	uc001lxc.2	-						NAP1L4_uc010qxm.1_Intron|NAP1L4_uc010qxn.1_Intron|SNORA54_uc001lxd.1_5'Flank	NM_005969	NP_005960			nucleosome assembly protein 1-like 4						nucleosome assembly	chromatin assembly complex|cytoplasm	unfolded protein binding			ovary(1)	1		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)														---	---	---	---
ZNF195	7748	broad.mit.edu	37	11	3399173	3399173	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3399173delA	uc001lxt.2	-						ZNF195_uc001lxv.2_Intron|ZNF195_uc001lxs.2_Intron|ZNF195_uc010qxr.1_Intron|ZNF195_uc009ydz.2_Intron|ZNF195_uc001lxu.2_Intron	NM_001130520	NP_001123992			zinc finger protein 195 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	3590656	3590657	+	IGR	INS	-	C	C	rs142804195	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3590656_3590657insC								LOC650368 (160278 upstream) : TRPC2 (47805 downstream)																																			---	---	---	---
ART1	417	broad.mit.edu	37	11	3681478	3681478	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3681478delC	uc001lye.1	+	3	830	c.729delC	c.(727-729)ATCfs	p.I243fs	ART1_uc009yeb.1_Frame_Shift_Del_p.I243fs	NM_004314	NP_004305	P52961	NAR1_HUMAN	ADP-ribosyltransferase 1 precursor	243					protein ADP-ribosylation	anchored to membrane|integral to plasma membrane|sarcoplasmic reticulum membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity				0		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0351)|LUSC - Lung squamous cell carcinoma(625;0.195)	Becaplermin(DB00102)													---	---	---	---
STIM1	6786	broad.mit.edu	37	11	3936145	3936145	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3936145delT	uc001lyv.2	+						STIM1_uc009yef.2_Intron	NM_003156	NP_003147			stromal interaction molecule 1 precursor						activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	4233105	4233105	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4233105delT								RRM1 (9346 upstream) : OR52B4 (155478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	4700783	4700783	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4700783delA								OR51E1 (24069 upstream) : OR51E2 (618 downstream)																																			---	---	---	---
OR51B5	282763	broad.mit.edu	37	11	5459254	5459254	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5459254delT	uc001maq.1	-						HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron	NM_001005567	NP_001005567			olfactory receptor, family 51, subfamily B,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
TRIM6-TRIM34	445372	broad.mit.edu	37	11	5629928	5629929	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5629928_5629929insA	uc001mbf.2	+						HBG2_uc001mak.1_Intron|TRIM6_uc009yeo.1_Intron|TRIM6_uc010qzj.1_Intron|TRIM6_uc001mbc.1_Intron|TRIM6_uc001mbe.2_Intron|TRIM6_uc010qzk.1_Intron|TRIM6_uc010qzl.1_Intron|TRIM6_uc001mbd.2_Intron|TRIM6_uc001mbg.1_Intron|TRIM6_uc009yep.1_Intron	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	117854	broad.mit.edu	37	11	5633122	5633122	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5633122delT	uc001mbc.1	+	8					HBG2_uc001mak.1_Intron|TRIM6-TRIM34_uc001mbf.2_Intron|TRIM6_uc009yeo.1_3'UTR|TRIM6_uc010qzj.1_3'UTR|TRIM6_uc001mbe.2_3'UTR|TRIM6_uc010qzk.1_3'UTR|TRIM6_uc010qzl.1_3'UTR|TRIM6_uc001mbd.2_3'UTR|TRIM6_uc001mbg.1_3'UTR|TRIM6_uc009yep.1_3'UTR	NM_058166	NP_477514			tripartite motif-containing 6 isoform 2						protein trimerization	cytoplasm	zinc ion binding				0		Lung NSC(207;2.23e-07)|all_lung(207;1.81e-06)|Medulloblastoma(188;0.00225)|Breast(177;0.0101)|all_neural(188;0.0212)		Epithelial(150;1.12e-45)|BRCA - Breast invasive adenocarcinoma(625;0.00101)|LUSC - Lung squamous cell carcinoma(625;0.192)														---	---	---	---
TRIM5	85363	broad.mit.edu	37	11	5856032	5856033	+	Intron	INS	-	AC	AC	rs144844373	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5856032_5856033insAC	uc001mbq.1	-							NM_033093	NP_149084			tripartite motif protein TRIM5 isoform delta						interspecies interaction between organisms|protein trimerization|response to virus	cytoplasm|cytoplasmic mRNA processing body	ligase activity|protein binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	6067831	6067831	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6067831delG								OR56A1 (18897 upstream) : OR56B4 (61178 downstream)																																			---	---	---	---
TRIM3	10612	broad.mit.edu	37	11	6472757	6472757	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6472757delC	uc001mdh.2	-						TRIM3_uc001mdi.2_Intron|TRIM3_uc010raj.1_Intron|TRIM3_uc009yfd.2_Intron|TRIM3_uc010rak.1_Intron	NM_006458	NP_006449			tripartite motif-containing 3						nervous system development|protein transport	early endosome	protein C-terminus binding|zinc ion binding			central_nervous_system(2)|large_intestine(1)|ovary(1)|skin(1)	5		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	6688275	6688275	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6688275delT								DCHS1 (11201 upstream) : MRPL17 (13341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	6688657	6688658	+	IGR	INS	-	T	T	rs3074185		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6688657_6688658insT								DCHS1 (11583 upstream) : MRPL17 (12958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	6826149	6826149	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6826149delA								OR6A2 (9010 upstream) : OR10A5 (40765 downstream)																																			---	---	---	---
ZNF215	7762	broad.mit.edu	37	11	6996704	6996704	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6996704delT	uc001mez.1	+							NM_013250	NP_037382			zinc finger protein 215						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)														---	---	---	---
SYT9	143425	broad.mit.edu	37	11	7312923	7312924	+	Intron	DEL	AA	-	-	rs67506487		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7312923_7312924delAA	uc001mfe.2	+						SYT9_uc001mfd.2_Intron|SYT9_uc009yfi.2_Intron	NM_175733	NP_783860			synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)														---	---	---	---
SYT9	143425	broad.mit.edu	37	11	7335203	7335203	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7335203delG	uc001mfe.2	+						SYT9_uc001mfd.2_Intron|SYT9_uc009yfi.2_Intron	NM_175733	NP_783860			synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)														---	---	---	---
SYT9	143425	broad.mit.edu	37	11	7407407	7407407	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7407407delA	uc001mfe.2	+						SYT9_uc001mfd.2_Intron|SYT9_uc009yfi.2_Intron	NM_175733	NP_783860			synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)														---	---	---	---
SYT9	143425	broad.mit.edu	37	11	7487999	7487999	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7487999delT	uc001mfe.2	+						SYT9_uc009yfi.2_Intron|uc001mff.1_Intron|uc001mfg.2_5'Flank	NM_175733	NP_783860			synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	7491007	7491007	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7491007delA	uc001mff.1	-											Homo sapiens cDNA FLJ46728 fis, clone TRACH3019142.																														---	---	---	---
OLFML1	283298	broad.mit.edu	37	11	7514520	7514521	+	Intron	DEL	TA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7514520_7514521delTA	uc001mfi.2	+						uc001mff.1_Intron|OLFML1_uc010raz.1_Intron|OLFML1_uc010rba.1_Intron	NM_198474	NP_940876			olfactomedin-like 1 precursor							extracellular region				ovary(2)	2				Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	7707198	7707198	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7707198delA								CYB5R2 (12204 upstream) : OVCH2 (5247 downstream)																																			---	---	---	---
TUB	7275	broad.mit.edu	37	11	8118863	8118863	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8118863delC	uc001mga.2	+	7	925	c.776delC	c.(775-777)GCCfs	p.A259fs	TUB_uc010rbk.1_Frame_Shift_Del_p.A265fs|TUB_uc001mfy.2_Frame_Shift_Del_p.A314fs	NM_177972	NP_813977	P50607	TUB_HUMAN	tubby isoform b	259					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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	8618786	8618786	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8618786delT								STK33 (3011 upstream) : TRIM66 (14800 downstream)																																			---	---	---	---
TRIM66	9866	broad.mit.edu	37	11	8635431	8635431	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8635431delA	uc010rbo.1	-	20						NM_014818	NP_055633			tripartite motif-containing 66							aggresome|nucleus	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	9145248	9145248	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9145248delA								FLJ46111 (27511 upstream) : DENND5A (15129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	9381244	9381245	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9381244_9381245delAC								TMEM41B (44948 upstream) : IPO7 (24924 downstream)																																			---	---	---	---
ZNF143	7702	broad.mit.edu	37	11	9528749	9528750	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9528749_9528750delCA	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)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	9817705	9817706	+	Intron	DEL	TT	-	-	rs72243966		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9817705_9817706delTT	uc001mib.2	-						uc001mhz.1_Intron|SBF2_uc001mid.2_Intron	NM_030962	NP_112224			SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	10275933	10275933	+	Intron	DEL	A	-	-	rs78715254		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10275933delA	uc001mib.2	-							NM_030962	NP_112224			SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
LYVE1	10894	broad.mit.edu	37	11	10587361	10587362	+	Intron	INS	-	T	T	rs10709248		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10587361_10587362insT	uc001miv.2	-						uc001miu.2_Intron|LYVE1_uc010rca.1_Intron	NM_006691	NP_006682			lymphatic vessel endothelial hyaluronan receptor						anatomical structure morphogenesis|cell-matrix adhesion|cellular component movement|response to wounding|transport	integral to plasma membrane|membrane fraction				central_nervous_system(1)|skin(1)	2				all cancers(16;7.22e-08)|Epithelial(150;1.03e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0609)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	10742761	10742761	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10742761delA								MRVI1 (27226 upstream) : CTR9 (30050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	11105832	11105832	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11105832delT								ZBED5 (226212 upstream) : GALNTL4 (186589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	11126480	11126480	+	IGR	DEL	A	-	-	rs144233791		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11126480delA								ZBED5 (246860 upstream) : GALNTL4 (165941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	12551933	12551933	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12551933delA								PARVA (523 upstream) : TEAD1 (144036 downstream)																																			---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12899207	12899207	+	Intron	DEL	A	-	-	rs112123980		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12899207delA	uc001mkj.3	+						TEAD1_uc001mkk.3_5'Flank|TEAD1_uc009ygl.2_5'Flank	NM_021961	NP_068780			TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	13189527	13189528	+	IGR	DEL	TT	-	-	rs67527870		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13189527_13189528delTT								RASSF10 (156880 upstream) : ARNTL (109797 downstream)																																			---	---	---	---
SPON1	10418	broad.mit.edu	37	11	14283394	14283394	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14283394delA	uc001mle.2	+							NM_006108	NP_006099			spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)														---	---	---	---
COPB1	1315	broad.mit.edu	37	11	14492586	14492586	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14492586delA	uc001mli.2	-						COPB1_uc001mlg.2_Intron|COPB1_uc001mlh.2_Intron	NM_016451	NP_057535			coatomer protein complex, subunit beta 1						COPI coating of Golgi vesicle|interspecies interaction between organisms|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|ER-Golgi intermediate compartment|plasma membrane	protein binding|structural molecule activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
INSC	387755	broad.mit.edu	37	11	15257912	15257912	+	Intron	DEL	A	-	-	rs112956879		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15257912delA	uc001mly.2	+						INSC_uc001mlz.2_Intron|INSC_uc001mma.2_Intron|INSC_uc010rcs.1_Intron|INSC_uc001mmb.2_Intron|INSC_uc001mmc.2_Intron	NM_001031853	NP_001027024			inscuteable isoform a						cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	15330723	15330724	+	IGR	INS	-	CT	CT	rs147013678	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15330723_15330724insCT								INSC (61971 upstream) : SOX6 (657272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15384523	15384523	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15384523delT								INSC (115771 upstream) : SOX6 (603473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15633650	15633650	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15633650delA								INSC (364898 upstream) : SOX6 (354346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15895003	15895004	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15895003_15895004insA								INSC (626251 upstream) : SOX6 (92992 downstream)																																			---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16119182	16119184	+	In_Frame_Del	DEL	AGC	-	-	rs150961105		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16119182_16119184delAGC	uc001mme.2	-	8	1021_1023	c.988_990delGCT	c.(988-990)GCTdel	p.A330del	SOX6_uc001mmd.2_In_Frame_Del_p.A320del|SOX6_uc001mmf.2_In_Frame_Del_p.A317del|SOX6_uc001mmg.2_In_Frame_Del_p.A317del	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4	317	Poly-Ala.				muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16486002	16486002	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16486002delA	uc001mmg.2	-						SOX6_uc001mmh.1_Intron|SOX6_uc001mmi.3_Intron|SOX6_uc001mmj.2_Intron	NM_033326	NP_201583			SRY (sex determining region Y)-box 6 isoform 2						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16583442	16583443	+	Intron	INS	-	T	T	rs147535830		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16583442_16583443insT	uc001mmi.3	-						SOX6_uc001mmh.1_Intron|SOX6_uc001mmj.2_Intron					Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
PLEKHA7	144100	broad.mit.edu	37	11	17001261	17001261	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17001261delA	uc001mmo.2	-						PLEKHA7_uc010rcu.1_Intron	NM_175058	NP_778228			pleckstrin homology domain containing, family A						epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	17248852	17248852	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17248852delA								PIK3C2A (19322 upstream) : NUCB2 (33035 downstream)																																			---	---	---	---
HPS5	11234	broad.mit.edu	37	11	18316379	18316379	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18316379delA	uc001mod.1	-						HPS5_uc001moe.1_Intron|HPS5_uc001mof.1_Intron	NM_181507	NP_852608			Hermansky-Pudlak syndrome 5 isoform a							cytosol				ovary(1)|pancreas(1)|skin(1)	3														Hermansky-Pudlak_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	11	18659313	18659316	+	IGR	DEL	AGTT	-	-	rs145158655		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18659313_18659316delAGTT								SPTY2D1 (3293 upstream) : TMEM86A (61035 downstream)																																			---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19904821	19904821	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19904821delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	20197011	20197012	+	IGR	INS	-	T	T	rs116120272	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20197011_20197012insT								DBX1 (15141 upstream) : HTATIP2 (188219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	20338061	20338061	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20338061delA								DBX1 (156191 upstream) : HTATIP2 (47170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	20676873	20676874	+	IGR	DEL	TT	-	-	rs75574799		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20676873_20676874delTT								SLC6A5 (265 upstream) : NELL1 (14243 downstream)																																			---	---	---	---
NELL1	4745	broad.mit.edu	37	11	20786708	20786708	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20786708delA	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	21108934	21108934	+	Intron	DEL	A	-	-	rs67175878		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21108934delA	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																		---	---	---	---
ANO5	203859	broad.mit.edu	37	11	22261301	22261301	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22261301delT	uc001mqi.2	+						ANO5_uc001mqj.2_Intron	NM_213599	NP_998764			anoctamin 5 isoform a							chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
GAS2	2620	broad.mit.edu	37	11	22813519	22813520	+	Intron	DEL	GG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22813519_22813520delGG	uc009yie.2	+						GAS2_uc001mqm.2_Intron|GAS2_uc001mqn.2_Intron|GAS2_uc001mqo.2_Intron	NM_001143830	NP_001137302			growth arrest-specific 2						cell cycle arrest|cellular component disassembly involved in apoptosis|regulation of cell shape	actin filament|cytosol|membrane				ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	22853439	22853442	+	Intron	DEL	AATT	-	-	rs79117348		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22853439_22853442delAATT	uc001mqq.1	+						SVIP_uc001mqp.3_5'Flank					full-length cDNA clone CS0DJ011YO21 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	23121162	23121162	+	IGR	DEL	G	-	-	rs7483126	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23121162delG								SVIP (269780 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23168960	23168960	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23168960delA								SVIP (317578 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23444053	23444054	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23444053_23444054delTG								SVIP (592671 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23584327	23584327	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23584327delT								SVIP (732945 upstream) : LUZP2 (934229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23589296	23589297	+	IGR	DEL	AA	-	-	rs112190544		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23589296_23589297delAA								SVIP (737914 upstream) : LUZP2 (929259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23636396	23636396	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23636396delT								SVIP (785014 upstream) : LUZP2 (882160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23865671	23865672	+	IGR	INS	-	TG	TG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23865671_23865672insTG								None (None upstream) : LUZP2 (652884 downstream)																																			---	---	---	---
LUZP2	338645	broad.mit.edu	37	11	24959447	24959448	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24959447_24959448delAA	uc001mqs.2	+						LUZP2_uc009yif.2_Intron|LUZP2_uc009yig.2_Intron	NM_001009909	NP_001009909			leucine zipper protein 2 precursor							extracellular region				ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	25319244	25319244	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25319244delT								LUZP2 (215062 upstream) : ANO3 (891585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	25780888	25780888	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25780888delA								LUZP2 (676706 upstream) : ANO3 (429941 downstream)																																			---	---	---	---
SLC5A12	159963	broad.mit.edu	37	11	26705575	26705576	+	Intron	INS	-	TGTG	TGTG	rs145705590	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26705575_26705576insTGTG	uc001mra.2	-						SLC5A12_uc001mrb.2_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	26759726	26759727	+	IGR	DEL	GC	-	-	rs145916350		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26759726_26759727delGC								SLC5A12 (14752 upstream) : FIBIN (255901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	27257515	27257516	+	IGR	INS	-	GAAG	GAAG	rs7929850		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27257515_27257516insGAAG								BBOX1 (108161 upstream) : CCDC34 (102545 downstream)																																			---	---	---	---
BDNFOS	497258	broad.mit.edu	37	11	27566051	27566052	+	Intron	DEL	TT	-	-	rs75852992		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27566051_27566052delTT	uc001mrm.2	+						BDNFOS_uc009yij.2_Intron|BDNFOS_uc009yik.2_Intron|BDNFOS_uc009yil.2_Intron|BDNFOS_uc001mrp.2_Intron|BDNFOS_uc009yim.2_Intron|BDNFOS_uc009yin.2_Intron|BDNFOS_uc009yio.2_Intron|BDNFOS_uc009yip.2_Intron|BDNFOS_uc001mrn.2_Intron|BDNFOS_uc009yiq.2_Intron|BDNFOS_uc001mro.2_Intron|BDNFOS_uc009yir.2_Intron|BDNFOS_uc009yis.2_Intron|BDNFOS_uc009yit.2_Intron|BDNFOS_uc009yiu.2_Intron|BDNFOS_uc009yiv.2_Intron|BDNFOS_uc009yiw.2_Intron|BDNFOS_uc009yix.2_Intron|BDNFOS_uc009yiy.2_Intron|BDNFOS_uc009yiz.2_Intron|BDNFOS_uc001mrq.3_Intron|BDNFOS_uc001mrr.3_Intron|BDNFOS_uc009yja.2_Intron|BDNFOS_uc009yjb.2_Intron	NR_002832				Homo sapiens non-coding transcript BT2C (BDNF) mRNA, complete sequence; alternatively spliced.												0																		---	---	---	---
METT5D1	196074	broad.mit.edu	37	11	28255011	28255011	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28255011delT	uc001msh.2	+						METT5D1_uc001msg.2_Intron|METT5D1_uc001mse.2_Intron	NM_001113528	NP_001107000			methyltransferase 5 domain containing 1 isoform								methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	29776225	29776225	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29776225delA								None (None upstream) : KCNA4 (255541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30024686	30024686	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30024686delA								None (None upstream) : KCNA4 (7080 downstream)																																			---	---	---	---
C11orf46	120534	broad.mit.edu	37	11	30352754	30352754	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30352754delA	uc001mso.1	+	2	423	c.259delA	c.(259-261)AAAfs	p.K87fs		NM_152316	NP_689529	Q8N8R7	CK046_HUMAN	hypothetical protein LOC120534	87											0																		---	---	---	---
C11orf46	120534	broad.mit.edu	37	11	30358034	30358035	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30358034_30358035delTT	uc001mso.1	+						C11orf46_uc001msp.2_5'Flank	NM_152316	NP_689529			hypothetical protein LOC120534												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	31082998	31082999	+	Intron	INS	-	TG	TG	rs147625273	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31082998_31082999insTG	uc009yjk.1	-						uc009yjl.1_Intron|DCDC1_uc001msu.1_Intron					RecName: Full=Doublecortin domain-containing protein 5;																														---	---	---	---
ELP4	26610	broad.mit.edu	37	11	31608910	31608910	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31608910delA	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	31785302	31785303	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31785302_31785303delTT	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	32018108	32018108	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32018108delT	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	32121862	32121865	+	Intron	DEL	CTTG	-	-	rs3830870		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32121862_32121865delCTTG	uc010reb.1	+						RCN1_uc010rea.1_Intron|RCN1_uc001mtk.2_Intron	NM_002901	NP_002892			reticulocalbin 1 precursor							endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)																	---	---	---	---
TCP11L1	55346	broad.mit.edu	37	11	33081527	33081527	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33081527delT	uc001mud.2	+						TCP11L1_uc009yju.2_Intron|TCP11L1_uc010rei.1_Intron|TCP11L1_uc001mue.2_Intron|TCP11L1_uc001muf.1_Intron	NM_018393	NP_060863			t-complex 11 (mouse) like 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	33429550	33429550	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33429550delT								HIPK3 (53611 upstream) : C11orf41 (134327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	33544001	33544001	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33544001delA								HIPK3 (168062 upstream) : C11orf41 (19876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	33868931	33868931	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33868931delC								FBXO3 (72860 upstream) : LMO2 (11194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	34005429	34005429	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34005429delT								LMO2 (91593 upstream) : CAPRIN1 (67801 downstream)																																			---	---	---	---
NAT10	55226	broad.mit.edu	37	11	34145709	34145710	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34145709_34145710insA	uc001mvk.2	+						NAT10_uc010ren.1_Intron	NM_024662	NP_078938			N-acetyltransferase 10 isoform a							nucleolus	ATP binding|N-acetyltransferase activity|protein binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)																---	---	---	---
CAT	847	broad.mit.edu	37	11	34482505	34482505	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34482505delA	uc001mvm.2	+						CAT_uc009ykc.1_Intron|CAT_uc001mvn.2_5'Flank	NM_001752	NP_001743			catalase						hydrogen peroxide catabolic process|negative regulation of apoptosis|positive regulation of cell division|protein tetramerization|purine base metabolic process|purine nucleotide catabolic process|UV protection	peroxisomal matrix|peroxisomal membrane	catalase activity|heme binding|NADP binding|protein homodimerization activity			ovary(2)|pancreas(1)	3		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	34828529	34828529	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34828529delT								EHF (145448 upstream) : APIP (68185 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	35056968	35056969	+	IGR	DEL	CA	-	-	rs72390887		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35056968_35056969delCA								PDHX (39294 upstream) : CD44 (103448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	35141568	35141568	+	IGR	DEL	A	-	-	rs66583846		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35141568delA								PDHX (123894 upstream) : CD44 (18849 downstream)																																			---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35462851	35462851	+	Intron	DEL	A	-	-	rs79736526		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35462851delA	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991			regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35513670	35513670	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35513670delC	uc001mwg.2	-	3	345	c.302delG	c.(301-303)GGTfs	p.G101fs	PAMR1_uc001mwf.2_Frame_Shift_Del_p.G101fs|PAMR1_uc010rew.1_Frame_Shift_Del_p.G101fs|PAMR1_uc010rex.1_Frame_Shift_Del_p.G61fs	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform	101					proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
TRAF6	7189	broad.mit.edu	37	11	36522666	36522666	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36522666delT	uc001mwr.1	-						TRAF6_uc001mws.1_Intron	NM_145803	NP_665802			TNF receptor-associated factor 6						activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|ossification|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of osteoclast differentiation|positive regulation of T cell cytokine production|protein autoubiquitination|protein K63-linked ubiquitination|response to interleukin-1|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cell cortex|cytosol|endosome membrane|internal side of plasma membrane|nuclear membrane	histone deacetylase binding|mitogen-activated protein kinase kinase kinase binding|protein kinase B binding|protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1	all_lung(20;0.211)	all_hematologic(20;0.107)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	37307798	37307798	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37307798delT								C11orf74 (611408 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38157087	38157088	+	IGR	DEL	AA	-	-	rs112467251		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38157087_38157088delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38390607	38390607	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38390607delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38465321	38465322	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38465321_38465322delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39077272	39077272	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39077272delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39096528	39096529	+	IGR	INS	-	TC	TC	rs150527951	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39096528_39096529insTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39492767	39492767	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39492767delT								None (None upstream) : LRRC4C (642986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39772734	39772734	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39772734delT								None (None upstream) : LRRC4C (363019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39807913	39807914	+	IGR	INS	-	G	G	rs139217614	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39807913_39807914insG								None (None upstream) : LRRC4C (327839 downstream)																																			---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40453740	40453740	+	Intron	DEL	T	-	-	rs75877762		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40453740delT	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	41258125	41258125	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41258125delA	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	41467417	41467418	+	Intron	DEL	TG	-	-	rs67175251		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41467417_41467418delTG	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	42082667	42082667	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42082667delA								LRRC4C (601344 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42138312	42138312	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42138312delT								LRRC4C (656989 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42372236	42372237	+	IGR	DEL	TG	-	-	rs72008796		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42372236_42372237delTG								LRRC4C (890913 upstream) : API5 (961268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42554869	42554870	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42554869_42554870delGT								None (None upstream) : API5 (778635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42788573	42788573	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42788573delT								None (None upstream) : API5 (544932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43222142	43222142	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43222142delA								None (None upstream) : API5 (111363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43278538	43278538	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43278538delA								None (None upstream) : API5 (54967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43515494	43515494	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43515494delA								TTC17 (1 upstream) : MIR670 (65712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44083017	44083018	+	IGR	INS	-	TTG	TTG	rs148930240	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44083017_44083018insTTG								ACCSL (1490 upstream) : ACCS (4457 downstream)																																			---	---	---	---
TSPAN18	90139	broad.mit.edu	37	11	44933580	44933580	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44933580delT	uc001mye.3	+						TP53I11_uc001myf.1_Intron|TSPAN18_uc001myg.2_Intron	NM_130783	NP_570139			tetraspanin 18 isoform 2							integral to membrane					0																		---	---	---	---
TP53I11	9537	broad.mit.edu	37	11	44958276	44958276	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44958276delC	uc001myi.2	-						TP53I11_uc001myf.1_Intron|TP53I11_uc001myj.2_Intron|TP53I11_uc001myk.2_Intron|TP53I11_uc001myl.2_Intron|TP53I11_uc001mym.2_Intron	NM_006034	NP_006025			p53-induced protein						negative regulation of cell proliferation|response to stress	integral to membrane				ovary(1)	1																OREG0020923	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PRDM11	56981	broad.mit.edu	37	11	45191894	45191894	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45191894delA	uc001myo.2	+							NM_020229	NP_064614			PR domain containing 11											upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	45367151	45367151	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45367151delG								SYT13 (59267 upstream) : CHST1 (303276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45418693	45418695	+	IGR	DEL	AGA	-	-	rs149588979		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45418693_45418695delAGA								SYT13 (110809 upstream) : CHST1 (251732 downstream)																																			---	---	---	---
PHF21A	51317	broad.mit.edu	37	11	46008802	46008803	+	Intron	INS	-	ATGT	ATGT	rs57573859		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46008802_46008803insATGT	uc001ncc.3	-						PHF21A_uc001ncb.3_Intron|PHF21A_uc009ykx.2_Intron|PHF21A_uc001nce.2_Intron	NM_001101802	NP_001095272			BRAF35/HDAC2 complex isoform a						blood coagulation|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|transcription, DNA-dependent	histone deacetylase complex	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
PHF21A	51317	broad.mit.edu	37	11	46055773	46055773	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46055773delC	uc001ncc.3	-						PHF21A_uc001ncb.3_Intron|PHF21A_uc009ykx.2_Intron|PHF21A_uc001nce.2_Intron	NM_001101802	NP_001095272			BRAF35/HDAC2 complex isoform a						blood coagulation|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|transcription, DNA-dependent	histone deacetylase complex	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	46254749	46254749	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46254749delA								PHF21A (111764 upstream) : CREB3L1 (44479 downstream)																																			---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46536192	46536192	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46536192delT	uc010rgu.1	-						AMBRA1_uc010rgt.1_Intron|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219			activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46593850	46593850	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46593850delA	uc010rgu.1	-						AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219			activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
F2	2147	broad.mit.edu	37	11	46741233	46741233	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46741233delC	uc001ndf.3	+						F2_uc001ndg.3_Intron	NM_000506	NP_000497			coagulation factor II preproprotein						activation of caspase activity|acute-phase response|blood coagulation, intrinsic pathway|cell surface receptor linked signaling pathway|cytosolic calcium ion homeostasis|fibrinolysis|leukocyte migration|negative regulation of astrocyte differentiation|negative regulation of fibrinolysis|negative regulation of platelet activation|negative regulation of proteolysis|peptidyl-glutamic acid carboxylation|platelet activation|positive regulation of collagen biosynthetic process|positive regulation of protein phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of release of sequestered calcium ion into cytosol|post-translational protein modification|proteolysis|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	cytosol|endoplasmic reticulum lumen|extracellular space|Golgi lumen|plasma membrane|soluble fraction	calcium ion binding|growth factor activity|serine-type endopeptidase activity|thrombospondin receptor activity			ovary(3)	3		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)|Enoxaparin(DB01225)|Heparin(DB01109)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Simvastatin(DB00641)|Suramin(DB04786)|Warfarin(DB00682)|Ximelagatran(DB04898)													---	---	---	---
F2	2147	broad.mit.edu	37	11	46747850	46747850	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46747850delG	uc001ndf.3	+						F2_uc001ndg.3_Intron	NM_000506	NP_000497			coagulation factor II preproprotein						activation of caspase activity|acute-phase response|blood coagulation, intrinsic pathway|cell surface receptor linked signaling pathway|cytosolic calcium ion homeostasis|fibrinolysis|leukocyte migration|negative regulation of astrocyte differentiation|negative regulation of fibrinolysis|negative regulation of platelet activation|negative regulation of proteolysis|peptidyl-glutamic acid carboxylation|platelet activation|positive regulation of collagen biosynthetic process|positive regulation of protein phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of release of sequestered calcium ion into cytosol|post-translational protein modification|proteolysis|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	cytosol|endoplasmic reticulum lumen|extracellular space|Golgi lumen|plasma membrane|soluble fraction	calcium ion binding|growth factor activity|serine-type endopeptidase activity|thrombospondin receptor activity			ovary(3)	3		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)|Enoxaparin(DB01225)|Heparin(DB01109)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Simvastatin(DB00641)|Suramin(DB04786)|Warfarin(DB00682)|Ximelagatran(DB04898)													---	---	---	---
F2	2147	broad.mit.edu	37	11	46748556	46748556	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46748556delT	uc001ndf.3	+						F2_uc001ndg.3_Intron	NM_000506	NP_000497			coagulation factor II preproprotein						activation of caspase activity|acute-phase response|blood coagulation, intrinsic pathway|cell surface receptor linked signaling pathway|cytosolic calcium ion homeostasis|fibrinolysis|leukocyte migration|negative regulation of astrocyte differentiation|negative regulation of fibrinolysis|negative regulation of platelet activation|negative regulation of proteolysis|peptidyl-glutamic acid carboxylation|platelet activation|positive regulation of collagen biosynthetic process|positive regulation of protein phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of release of sequestered calcium ion into cytosol|post-translational protein modification|proteolysis|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	cytosol|endoplasmic reticulum lumen|extracellular space|Golgi lumen|plasma membrane|soluble fraction	calcium ion binding|growth factor activity|serine-type endopeptidase activity|thrombospondin receptor activity			ovary(3)	3		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)|Enoxaparin(DB01225)|Heparin(DB01109)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Simvastatin(DB00641)|Suramin(DB04786)|Warfarin(DB00682)|Ximelagatran(DB04898)													---	---	---	---
F2	2147	broad.mit.edu	37	11	46753942	46753942	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46753942delT	uc001ndf.3	+						F2_uc001ndg.3_Intron	NM_000506	NP_000497			coagulation factor II preproprotein						activation of caspase activity|acute-phase response|blood coagulation, intrinsic pathway|cell surface receptor linked signaling pathway|cytosolic calcium ion homeostasis|fibrinolysis|leukocyte migration|negative regulation of astrocyte differentiation|negative regulation of fibrinolysis|negative regulation of platelet activation|negative regulation of proteolysis|peptidyl-glutamic acid carboxylation|platelet activation|positive regulation of collagen biosynthetic process|positive regulation of protein phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of release of sequestered calcium ion into cytosol|post-translational protein modification|proteolysis|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	cytosol|endoplasmic reticulum lumen|extracellular space|Golgi lumen|plasma membrane|soluble fraction	calcium ion binding|growth factor activity|serine-type endopeptidase activity|thrombospondin receptor activity			ovary(3)	3		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)|Enoxaparin(DB01225)|Heparin(DB01109)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Simvastatin(DB00641)|Suramin(DB04786)|Warfarin(DB00682)|Ximelagatran(DB04898)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	46763330	46763330	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46763330delA								F2 (2275 upstream) : CKAP5 (1754 downstream)																																			---	---	---	---
CKAP5	9793	broad.mit.edu	37	11	46789347	46789347	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46789347delT	uc001ndi.1	-						CKAP5_uc009ylg.1_Intron|CKAP5_uc001ndj.1_Intron|CKAP5_uc001ndh.1_Intron	NM_001008938	NP_001008938			colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
CKAP5	9793	broad.mit.edu	37	11	46842546	46842546	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46842546delA	uc001ndi.1	-						CKAP5_uc009ylg.1_5'Flank|CKAP5_uc001ndj.1_Intron	NM_001008938	NP_001008938			colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	46944130	46944130	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46944130delT								LRP4 (4054 upstream) : C11orf49 (14121 downstream)																																			---	---	---	---
C11orf49	79096	broad.mit.edu	37	11	46985841	46985843	+	Intron	DEL	TTT	-	-	rs75975634		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46985841_46985843delTTT	uc001ndp.2	+						C11orf49_uc001nds.2_Intron|C11orf49_uc001ndq.2_Intron|C11orf49_uc001ndr.2_Intron|C11orf49_uc010rgx.1_Intron|C11orf49_uc010rgy.1_Intron|C11orf49_uc010rgz.1_Intron	NM_024113	NP_077018			hypothetical protein LOC79096 isoform 3												0																		---	---	---	---
C11orf49	79096	broad.mit.edu	37	11	47094886	47094886	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47094886delA	uc001ndp.2	+						C11orf49_uc001nds.2_Intron|C11orf49_uc001ndq.2_Intron|C11orf49_uc001ndr.2_Intron|C11orf49_uc010rgx.1_Intron|C11orf49_uc010rgy.1_Intron|C11orf49_uc010rgz.1_Intron	NM_024113	NP_077018			hypothetical protein LOC79096 isoform 3												0																		---	---	---	---
C11orf49	79096	broad.mit.edu	37	11	47179895	47179895	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47179895delA	uc001ndp.2	+						C11orf49_uc001nds.2_Intron|C11orf49_uc001ndq.2_Intron|C11orf49_uc001ndr.2_Intron|C11orf49_uc010rgx.1_Intron|C11orf49_uc010rgy.1_Intron|C11orf49_uc010rgz.1_Intron	NM_024113	NP_077018			hypothetical protein LOC79096 isoform 3												0																		---	---	---	---
MADD	8567	broad.mit.edu	37	11	47336750	47336750	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47336750delA	uc001ner.1	+						MADD_uc001neq.2_Intron|MADD_uc001nev.1_Intron|MADD_uc001nes.1_Intron|MADD_uc001net.1_Intron|MADD_uc009yln.1_Intron|MADD_uc001neu.1_Intron|MADD_uc001nex.2_Intron|MADD_uc001nez.2_Intron|MADD_uc001new.2_Intron|MADD_uc009ylo.2_Intron	NM_003682	NP_003673			MAP-kinase activating death domain-containing						activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)														---	---	---	---
NDUFS3	4722	broad.mit.edu	37	11	47602712	47602712	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47602712delT	uc001nga.2	+						NDUFS3_uc001nft.3_Intron|KBTBD4_uc001nfw.1_5'Flank|KBTBD4_uc001nfx.2_5'Flank|KBTBD4_uc001nfz.2_5'Flank|KBTBD4_uc001nfy.2_5'Flank|NDUFS3_uc010rhn.1_3'UTR	NM_004551	NP_004542			NADH dehydrogenase (ubiquinone) Fe-S protein 3						induction of apoptosis|mitochondrial electron transport, NADH to ubiquinone|negative regulation of cell growth|reactive oxygen species metabolic process|transport	mitochondrial respiratory chain complex I	electron carrier activity|NADH dehydrogenase (ubiquinone) activity|protein binding				0					NADH(DB00157)													---	---	---	---
AGBL2	79841	broad.mit.edu	37	11	47693082	47693085	+	Intron	DEL	AAAC	-	-	rs72375237		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47693082_47693085delAAAC	uc001ngg.2	-						AGBL2_uc001ngf.2_Intron|AGBL2_uc010rhq.1_Intron|AGBL2_uc001ngh.1_Intron	NM_024783	NP_079059			carboxypeptidase 2, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
AGBL2	79841	broad.mit.edu	37	11	47711399	47711400	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47711399_47711400delCT	uc001ngg.2	-						AGBL2_uc001ngf.2_Intron|AGBL2_uc010rhq.1_Intron|AGBL2_uc001ngh.1_Intron	NM_024783	NP_079059			carboxypeptidase 2, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
NUP160	23279	broad.mit.edu	37	11	47804929	47804929	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47804929delA	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																		---	---	---	---
NUP160	23279	broad.mit.edu	37	11	47849248	47849248	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47849248delA	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																		---	---	---	---
PTPRJ	5795	broad.mit.edu	37	11	48188450	48188450	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48188450delT	uc001ngp.3	+							NM_002843	NP_002834			protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	48599746	48599747	+	IGR	DEL	TT	-	-	rs79743761		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48599746_48599747delTT								OR4A47 (88474 upstream) : FOLH1 (568441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48750881	48750881	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48750881delT								OR4A47 (239609 upstream) : FOLH1 (417307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49077937	49077938	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49077937_49077938insA								OR4A47 (566665 upstream) : FOLH1 (90250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49144970	49144970	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49144970delT								OR4A47 (633698 upstream) : FOLH1 (23218 downstream)																																			---	---	---	---
LOC440040	440040	broad.mit.edu	37	11	49831959	49831959	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49831959delA	uc010rhy.1	+	7					LOC440040_uc009ymb.2_3'UTR	NR_027044				SubName: Full=cDNA FLJ60249, highly similar to Metabotropic glutamate receptor 5;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	50735411	50735411	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50735411delA								LOC646813 (355608 upstream) : OR4A5 (676037 downstream)																																			---	---	---	---
OR4C11	219429	broad.mit.edu	37	11	55373687	55373688	+	5'Flank	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55373687_55373688delCA	uc010rii.1	-							NM_001004700	NP_001004700			olfactory receptor, family 4, subfamily C,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	56268035	56268035	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56268035delA								OR5M8 (9189 upstream) : OR5M11 (41782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	56408816	56408817	+	IGR	DEL	TA	-	-	rs117992140	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56408816_56408817delTA								OR5M1 (27838 upstream) : OR5AP2 (148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	57203142	57203142	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57203142delT								SLC43A3 (8089 upstream) : RTN4RL2 (25197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	57394152	57394152	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57394152delT								SERPING1 (11826 upstream) : MIR130A (14519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	57395672	57395672	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57395672delA								SERPING1 (13346 upstream) : MIR130A (12999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	58164684	58164685	+	IGR	INS	-	AAG	AAG	rs149385388	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58164684_58164685insAAG								OR5B17 (38142 upstream) : OR5B3 (5255 downstream)																																			---	---	---	---
PATL1	219988	broad.mit.edu	37	11	59409225	59409226	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59409225_59409226delAA	uc001noe.3	-							NM_152716	NP_689929			protein associated with topoisomerase II homolog						cytoplasmic mRNA processing body assembly|deadenylation-dependent decapping of nuclear-transcribed mRNA	cytoplasmic mRNA processing body	protein binding|RNA binding			ovary(1)	1																		---	---	---	---
MRPL16	54948	broad.mit.edu	37	11	59574982	59574982	+	Intron	DEL	A	-	-	rs113228199		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59574982delA	uc001noh.2	-							NM_017840	NP_060310			mitochondrial ribosomal protein L16 precursor								rRNA binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	59591727	59591727	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59591727delT								MRPL16 (13382 upstream) : GIF (5021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59880027	59880027	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59880027delT								MS4A2 (14013 upstream) : MS4A6A (59054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59990524	59990524	+	Intron	DEL	A	-	-	rs113391522		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59990524delA	uc001nov.2	-						uc001now.2_Intron|uc001nox.2_Intron|uc001noy.2_Intron|uc009ymw.2_Intron					Homo sapiens mRNA for hypothetical protein, partial cds, clone:Hsa11-digit17-05-01-R.																														---	---	---	---
MS4A1	931	broad.mit.edu	37	11	60234644	60234644	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60234644delA	uc001npp.2	+						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)													---	---	---	---
MS4A1	931	broad.mit.edu	37	11	60236247	60236247	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60236247delT	uc001npp.2	+	8					MS4A1_uc001npq.2_3'UTR|MS4A1_uc009yna.2_3'UTR|MS4A1_uc009ymz.2_3'UTR|MS4A1_uc010rlc.1_3'UTR	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	60513910	60513910	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60513910delA								MS4A8B (30628 upstream) : MS4A15 (10430 downstream)																																			---	---	---	---
CD6	923	broad.mit.edu	37	11	60762627	60762628	+	Intron	DEL	TC	-	-	rs3016177		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60762627_60762628delTC	uc001nqq.2	+						CD6_uc009yni.2_Intron|CD6_uc009ynj.2_Intron|CD6_uc001nqp.2_Intron|CD6_uc001nqr.2_Intron|CD6_uc001nqs.2_Intron|CD6_uc001nqt.2_Intron	NM_006725	NP_006716			CD6 molecule precursor						cell adhesion	cell surface|integral to plasma membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
CD6	923	broad.mit.edu	37	11	60783054	60783054	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60783054delA	uc001nqq.2	+						CD6_uc001nqp.2_Intron|CD6_uc001nqr.2_Intron|CD6_uc001nqs.2_Intron|CD6_uc001nqt.2_Intron	NM_006725	NP_006716			CD6 molecule precursor						cell adhesion	cell surface|integral to plasma membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	60956960	60956960	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60956960delA								VPS37C (28044 upstream) : PGA3 (14024 downstream)																																			---	---	---	---
CPSF7	79869	broad.mit.edu	37	11	61183087	61183087	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61183087delA	uc001nrq.2	-						CPSF7_uc001nro.2_Intron|CPSF7_uc001nrp.2_Intron|CPSF7_uc001nrr.2_Intron	NM_001136040	NP_001129512			pre-mRNA cleavage factor I, 59 kDa subunit						mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription	mRNA cleavage factor complex	nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1																		---	---	---	---
CPSF7	79869	broad.mit.edu	37	11	61187728	61187728	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61187728delT	uc001nrq.2	-						CPSF7_uc001nro.2_Intron|CPSF7_uc001nrp.2_Intron|CPSF7_uc001nrr.2_Intron|CPSF7_uc001nrs.1_Intron	NM_001136040	NP_001129512			pre-mRNA cleavage factor I, 59 kDa subunit						mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription	mRNA cleavage factor complex	nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	61434879	61434879	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61434879delT								RPLP0P2 (27958 upstream) : DAGLA (13031 downstream)																																			---	---	---	---
FADS2	9415	broad.mit.edu	37	11	61616380	61616380	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61616380delT	uc001nsl.1	+						FADS2_uc001nsj.2_Intron|FADS2_uc010rlo.1_Intron|FADS2_uc001nsk.2_Intron	NM_004265	NP_004256			fatty acid desaturase 2						electron transport chain|transport|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	heme binding			ovary(1)|pancreas(1)	2					Alpha-Linolenic Acid(DB00132)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	61796498	61796500	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61796498_61796500delTTT								FTH1 (61366 upstream) : INCENP (94945 downstream)																																			---	---	---	---
INCENP	3619	broad.mit.edu	37	11	61917391	61917392	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	61947445	61947448	+	IGR	DEL	TTTG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61947445_61947448delTTTG								INCENP (26810 upstream) : SCGB1D1 (10262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	62166689	62166689	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62166689delA								ASRGL1 (5804 upstream) : SCGB1A1 (19834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	62317926	62317926	+	IGR	DEL	T	-	-	rs71458417		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62317926delT								AHNAK (3594 upstream) : EEF1G (9147 downstream)																																			---	---	---	---
ROM1	6094	broad.mit.edu	37	11	62382265	62382265	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62382265delC	uc001ntv.2	+	3	1551	c.1010delC	c.(1009-1011)GCCfs	p.A337fs	EML3_uc001ntt.1_5'Flank|EML3_uc001ntu.1_5'Flank|EML3_uc010rly.1_5'Flank	NM_000327	NP_000318	Q03395	ROM1_HUMAN	retinal outer segment membrane protein 1	337	Cytoplasmic (Potential).				cell adhesion|visual perception	integral to plasma membrane				ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
GANAB	23193	broad.mit.edu	37	11	62413383	62413383	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62413383delT	uc001nub.2	-						GANAB_uc001nua.2_Intron|GANAB_uc001nuc.2_Intron|GANAB_uc010rma.1_Intron|GANAB_uc010rmb.1_Intron	NM_198334	NP_938148			neutral alpha-glucosidase AB isoform 2						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|Golgi apparatus|melanosome	carbohydrate binding|glucan 1,3-alpha-glucosidase activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
HRASLS5	117245	broad.mit.edu	37	11	63260407	63260408	+	5'Flank	DEL	TC	-	-	rs61092049		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63260407_63260408delTC	uc001nwy.2	-						HRASLS5_uc001nwz.2_5'Flank|HRASLS5_uc010rmq.1_5'Flank|HRASLS5_uc009yos.2_5'Flank	NM_054108	NP_473449			HRAS-like suppressor family, member 5 isoform 1											ovary(1)	1																		---	---	---	---
RTN3	10313	broad.mit.edu	37	11	63450315	63450315	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63450315delA	uc001nxq.2	+						RTN3_uc001nxo.2_Intron|RTN3_uc001nxm.2_Intron|RTN3_uc001nxn.2_Intron|RTN3_uc001nxp.2_Intron|RTN3_uc009yov.2_Intron|RTN3_uc010rmt.1_Intron|RTN3_uc010rmu.1_Intron	NM_201428	NP_958831			reticulon 3 isoform b						apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
RTN3	10313	broad.mit.edu	37	11	63507760	63507760	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63507760delT	uc001nxq.2	+						RTN3_uc001nxo.2_Intron|RTN3_uc001nxm.2_Intron|RTN3_uc001nxn.2_Intron|RTN3_uc001nxp.2_Intron|RTN3_uc009yov.2_Intron|RTN3_uc010rmt.1_Intron|RTN3_uc010rmu.1_Intron	NM_201428	NP_958831			reticulon 3 isoform b						apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
OTUB1	55611	broad.mit.edu	37	11	63765136	63765136	+	3'UTR	DEL	C	-	-	rs35556442		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63765136delC	uc001nyf.1	+	7					OTUB1_uc001nyg.1_3'UTR|OTUB1_uc010rmz.1_3'UTR|OTUB1_uc010rna.1_3'UTR|OTUB1_uc009ypa.2_3'UTR|OTUB1_uc009ypb.1_3'UTR	NM_017670	NP_060140			otubain 1						protein K48-linked deubiquitination	cytoplasm	NEDD8-specific protease activity|omega peptidase activity|ubiquitin binding|ubiquitin-specific protease activity			breast(1)	1																		---	---	---	---
MACROD1	28992	broad.mit.edu	37	11	63888156	63888156	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63888156delA	uc001nyh.2	-							NM_014067	NP_054786			MACRO domain containing 1												0																		---	---	---	---
STIP1	10963	broad.mit.edu	37	11	63965695	63965695	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63965695delT	uc001nyk.1	+						STIP1_uc010rnb.1_Intron	NM_006819	NP_006810			stress-induced-phosphoprotein 1						axon guidance|response to stress	Golgi apparatus|nucleus				ovary(2)|liver(1)	3																		---	---	---	---
GPR137	56834	broad.mit.edu	37	11	64038530	64038531	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64038530_64038531delCT	uc009ypj.1	+						BAD_uc001nzd.2_Intron|BAD_uc001nzc.2_Intron	NM_020155	NP_064540			G protein-coupled receptor 137							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	64943328	64943328	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64943328delT								SPDYC (2641 upstream) : CAPN1 (5444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	66862369	66862369	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66862369delA								RHOD (22882 upstream) : KDM2A (24371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	66874951	66874952	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66874951_66874952delCA								RHOD (35464 upstream) : KDM2A (11788 downstream)																																			---	---	---	---
CARNS1	57571	broad.mit.edu	37	11	67189366	67189367	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67189366_67189367delTT	uc009yrp.2	+						PPP1CA_uc001okx.1_5'Flank|CARNS1_uc001olc.3_Intron	NM_020811	NP_065862			ATP-grasp domain containing 1						carnosine biosynthetic process		ATP binding|carnosine synthase activity|metal ion binding				0																		---	---	---	---
CORO1B	57175	broad.mit.edu	37	11	67209168	67209168	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67209168delG	uc001olj.1	-						CORO1B_uc009yrs.1_Intron|CORO1B_uc001olk.1_Intron|CORO1B_uc009yrt.1_Intron|CORO1B_uc009yru.1_Intron|CORO1B_uc001oll.1_Intron|CORO1B_uc010rps.1_Intron|CORO1B_uc009yrv.1_Frame_Shift_Del_p.H164fs	NM_020441	NP_065174			coronin, actin binding protein, 1B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm	actin filament binding			large_intestine(1)|ovary(1)	2			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	67711334	67711334	+	IGR	DEL	A	-	-	rs112830151		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67711334delA								LOC645332 (138527 upstream) : UNC93B1 (47241 downstream)																																			---	---	---	---
CHKA	1119	broad.mit.edu	37	11	67829387	67829387	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67829387delA	uc001onj.2	-						CHKA_uc001onk.2_Intron|uc001onl.1_5'Flank	NM_001277	NP_001268			choline kinase alpha isoform a						lipid transport|phosphatidylethanolamine biosynthetic process	cytoplasm	ATP binding|choline kinase activity|drug binding|ethanolamine kinase activity|signal transducer activity			ovary(1)|central_nervous_system(1)	2					Choline(DB00122)													---	---	---	---
SUV420H1	51111	broad.mit.edu	37	11	67939864	67939865	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67939864_67939865delTT	uc001onm.1	-						SUV420H1_uc009yse.1_Intron|SUV420H1_uc001onn.1_Intron|SUV420H1_uc009ysf.2_Intron|SUV420H1_uc001ono.1_Intron|SUV420H1_uc001onp.2_Intron|SUV420H1_uc010rqa.1_Intron|SUV420H1_uc001onq.2_Intron	NM_017635	NP_060105			suppressor of variegation 4-20 homolog 1 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			ovary(2)|kidney(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	68014183	68014184	+	IGR	DEL	AA	-	-	rs79299369		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68014183_68014184delAA								SUV420H1 (33115 upstream) : C11orf24 (14621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	69261685	69261685	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69261685delT								MYEOV (105236 upstream) : CCND1 (194188 downstream)																																			---	---	---	---
FGF4	2249	broad.mit.edu	37	11	69590393	69590393	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69590393delT	uc001opg.1	-						FGF4_uc010rqj.1_5'Flank	NM_002007	NP_001998			fibroblast growth factor 4 precursor						cell-cell signaling|chondroblast differentiation|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|mesenchymal cell proliferation|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of ERK1 and ERK2 cascade	extracellular region	growth factor activity|heparin binding				0	Melanoma(5;1.89e-05)		LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)		Pentosan Polysulfate(DB00686)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	69823278	69823278	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69823278delC								FGF3 (189086 upstream) : ANO1 (101130 downstream)																																			---	---	---	---
ANO1	55107	broad.mit.edu	37	11	69949371	69949371	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69949371delA	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron	NM_018043	NP_060513			anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2																		---	---	---	---
ANO1	55107	broad.mit.edu	37	11	70028923	70028923	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70028923delA	uc001opj.2	+						ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron|ANO1_uc010rql.1_Intron	NM_018043	NP_060513			anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	70056170	70056170	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70056170delC								FADD (2662 upstream) : PPFIA1 (60653 downstream)																																			---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70371576	70371576	+	Intron	DEL	T	-	-	rs76247353		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70371576delT	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)															---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70796172	70796172	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70796172delT	uc001oqc.2	-							NM_012309	NP_036441			SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	72192427	72192427	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72192427delT								CLPB (46743 upstream) : PDE2A (94759 downstream)																																			---	---	---	---
ARAP1	116985	broad.mit.edu	37	11	72421119	72421120	+	Intron	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72421119_72421120insG	uc001osu.2	-						ARAP1_uc001osv.2_Intron|ARAP1_uc001osr.2_Intron|ARAP1_uc001oss.2_Intron|ARAP1_uc009yth.2_Intron|ARAP1_uc010rre.1_Intron	NM_001040118	NP_001035207			ArfGAP with RhoGAP domain, ankyrin repeat and PH						actin filament reorganization involved in cell cycle|negative regulation of stress fiber assembly|positive regulation of Cdc42 GTPase activity|positive regulation of filopodium assembly|regulation of ARF GTPase activity|regulation of cell shape|regulation of cellular component movement|small GTPase mediated signal transduction	cytosol|Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|Rho GTPase activator activity|zinc ion binding			skin(1)	1																		---	---	---	---
ARAP1	116985	broad.mit.edu	37	11	72477161	72477161	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72477161delA	uc001osv.2	-						STARD10_uc001osy.2_Intron|STARD10_uc001osz.3_Intron|STARD10_uc001ota.2_Intron|STARD10_uc001otb.2_Intron	NM_001040118	NP_001035207			ArfGAP with RhoGAP domain, ankyrin repeat and PH						actin filament reorganization involved in cell cycle|negative regulation of stress fiber assembly|positive regulation of Cdc42 GTPase activity|positive regulation of filopodium assembly|regulation of ARF GTPase activity|regulation of cell shape|regulation of cellular component movement|small GTPase mediated signal transduction	cytosol|Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|Rho GTPase activator activity|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	72891180	72891180	+	IGR	DEL	A	-	-	rs72090326		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72891180delA								FCHSD2 (38037 upstream) : P2RY2 (38164 downstream)																																			---	---	---	---
FAM168A	23201	broad.mit.edu	37	11	73271279	73271279	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73271279delT	uc001otz.1	-						FAM168A_uc001oty.1_Intron|FAM168A_uc009ytp.1_Intron	NM_015159	NP_055974			hypothetical protein LOC23201												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	73323711	73323711	+	IGR	DEL	A	-	-	rs72428297		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73323711delA								FAM168A (14483 upstream) : PLEKHB1 (33512 downstream)																																			---	---	---	---
RAB6A	5870	broad.mit.edu	37	11	73429959	73429959	+	Intron	DEL	A	-	-	rs34792668		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73429959delA	uc001oue.2	-						RAB6A_uc001ouf.2_Intron|RAB6A_uc009yts.2_Intron	NM_002869	NP_002860			RAB6A, member RAS oncogene family isoform a						minus-end-directed organelle transport along microtubule|peptidyl-cysteine methylation|protein targeting to Golgi|retrograde vesicle-mediated transport, Golgi to ER|small GTPase mediated signal transduction	cytoplasmic vesicle|cytosol|Golgi membrane|trans-Golgi network	GTP binding|GTPase activity|protein domain specific binding				0																		---	---	---	---
MRPL48	51642	broad.mit.edu	37	11	73536692	73536693	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73536692_73536693insA	uc001ouh.3	+						MRPL48_uc009ytt.2_Intron|MRPL48_uc010rri.1_Intron|MRPL48_uc009ytu.2_Intron	NM_016055	NP_057139			mitochondrial ribosomal protein L48 precursor						translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0																		---	---	---	---
PAAF1	80227	broad.mit.edu	37	11	73615680	73615680	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73615680delT	uc001ouk.1	+						PAAF1_uc001oul.1_Intron|PAAF1_uc009ytx.1_Intron|PAAF1_uc001oum.1_Intron	NM_025155	NP_079431			proteasomal ATPase-associated factor 1						interspecies interaction between organisms	proteasome complex	protein binding			ovary(1)|skin(1)	2	Breast(11;7.42e-05)																	---	---	---	---
C2CD3	26005	broad.mit.edu	37	11	73864256	73864260	+	Intron	DEL	AAAAC	-	-	rs151096789		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73864256_73864260delAAAAC	uc001ouu.2	-						C2CD3_uc001ouv.2_Intron	NM_015531	NP_056346			C2 calcium-dependent domain containing 3							centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)																	---	---	---	---
PGM2L1	283209	broad.mit.edu	37	11	74082034	74082034	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74082034delA	uc001ovb.1	-							NM_173582	NP_775853			phosphoglucomutase 2-like 1						glucose 1-phosphate metabolic process	cytosol	glucose-1,6-bisphosphate synthase activity|phosphoglucomutase activity			ovary(1)	1	Breast(11;3.32e-06)																	---	---	---	---
PGM2L1	283209	broad.mit.edu	37	11	74107451	74107451	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74107451delT	uc001ovb.1	-							NM_173582	NP_775853			phosphoglucomutase 2-like 1						glucose 1-phosphate metabolic process	cytosol	glucose-1,6-bisphosphate synthase activity|phosphoglucomutase activity			ovary(1)	1	Breast(11;3.32e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	74137730	74137730	+	IGR	DEL	T	-	-	rs112060305		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74137730delT								PGM2L1 (28228 upstream) : KCNE3 (28158 downstream)																																			---	---	---	---
POLD3	10714	broad.mit.edu	37	11	74347711	74347711	+	Intron	DEL	T	-	-	rs75919585		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74347711delT	uc001ovf.1	+						POLD3_uc009yua.1_Intron	NM_006591	NP_006582			DNA-directed DNA polymerase delta 3						base-excision repair|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|mismatch repair|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	delta DNA polymerase complex|nucleoplasm	DNA-directed DNA polymerase activity|protein binding			kidney(2)|ovary(1)	3	Breast(11;3.21e-06)																	---	---	---	---
SLCO2B1	11309	broad.mit.edu	37	11	74869534	74869534	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74869534delT	uc001owb.2	+						SLCO2B1_uc010rrp.1_Intron|SLCO2B1_uc010rrq.1_Intron|SLCO2B1_uc010rrr.1_Intron|SLCO2B1_uc010rrs.1_Intron|SLCO2B1_uc001owc.2_Intron|SLCO2B1_uc001owd.2_5'Flank	NM_007256	NP_009187			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|breast(1)	2					Ergoloid mesylate(DB01049)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	74928431	74928434	+	IGR	DEL	TCTC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74928431_74928434delTCTC								SLCO2B1 (10987 upstream) : ARRB1 (48048 downstream)																																			---	---	---	---
GDPD5	81544	broad.mit.edu	37	11	75191373	75191373	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75191373delA	uc001owo.3	-						GDPD5_uc001owp.3_Intron|GDPD5_uc009yuc.2_5'Flank|GDPD5_uc009yud.2_Intron	NM_030792	NP_110419			glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	75289711	75289711	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75289711delT								SERPINH1 (5867 upstream) : MAP6 (8253 downstream)																																			---	---	---	---
MOGAT2	80168	broad.mit.edu	37	11	75433540	75433540	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75433540delA	uc010rru.1	+						MOGAT2_uc001oww.1_Intron|MOGAT2_uc010rrv.1_Intron	NM_025098	NP_079374			monoacylglycerol O-acyltransferase 2						glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			ovary(2)	2	Ovarian(111;0.103)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	75456392	75456392	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75456392delA								MOGAT2 (14062 upstream) : DGAT2 (23386 downstream)																																			---	---	---	---
UVRAG	7405	broad.mit.edu	37	11	75559242	75559244	+	Intron	DEL	AAA	-	-	rs72400531		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75559242_75559244delAAA	uc001oxc.2	+						UVRAG_uc010rrw.1_Intron	NM_003369	NP_003360			UV radiation resistance associated						DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6																		---	---	---	---
UVRAG	7405	broad.mit.edu	37	11	75672911	75672911	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75672911delA	uc001oxc.2	+						UVRAG_uc010rrw.1_Intron|UVRAG_uc009yuh.1_Intron	NM_003369	NP_003360			UV radiation resistance associated						DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6																		---	---	---	---
ACER3	55331	broad.mit.edu	37	11	76672596	76672596	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76672596delA	uc009yum.1	+						ACER3_uc010rsg.1_Intron|ACER3_uc009yul.1_Intron|ACER3_uc001oxu.2_Intron|ACER3_uc009yun.1_Intron|ACER3_uc009yuo.1_Intron|ACER3_uc010rsh.1_Intron|ACER3_uc010rsi.1_Intron|ACER3_uc010rsj.1_Intron	NM_018367	NP_060837			phytoceramidase, alkaline						ceramide metabolic process|phytosphingosine biosynthetic process|positive regulation of cell proliferation|sphingosine biosynthetic process	integral to endoplasmic reticulum membrane|integral to Golgi membrane	phytoceramidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	76773933	76773934	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76773933_76773934insA								B3GNT6 (20930 upstream) : CAPN5 (4058 downstream)																																			---	---	---	---
PAK1	5058	broad.mit.edu	37	11	77145979	77145979	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77145979delT	uc001oyh.3	-						PAK1_uc001oyg.3_Intron	NM_002576	NP_002567			p21-activated kinase 1 isoform 2						apoptosis|axon guidance|cytoskeleton organization|ER-nucleus signaling pathway|positive regulation of JUN kinase activity|positive regulation of peptidyl-serine phosphorylation|protein autophosphorylation|T cell costimulation|T cell receptor signaling pathway	cytosol|focal adhesion|Golgi apparatus	ATP binding|collagen binding|protein binding|protein serine/threonine kinase activity			skin(2)|stomach(1)|lung(1)	4	all_cancers(14;1.75e-18)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	77209527	77209528	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77209527_77209528delAC								PAK1 (24419 upstream) : AQP11 (90908 downstream)																																			---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77436580	77436580	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)															---	---	---	---
INTS4	92105	broad.mit.edu	37	11	77689786	77689787	+	Intron	INS	-	A	A	rs148185606	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77689786_77689787insA	uc001oys.2	-						INTS4_uc001oyt.2_Intron|INTS4_uc001oyu.1_Intron|INTS4_uc001oyv.1_RNA	NM_033547	NP_291025			integrator complex subunit 4						snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)															---	---	---	---
INTS4	92105	broad.mit.edu	37	11	77702604	77702604	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77702604delT	uc001oys.2	-						INTS4_uc001oyt.2_Intron|INTS4_uc001oyu.1_Intron|INTS4_uc001oyv.1_Intron	NM_033547	NP_291025			integrator complex subunit 4						snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)															---	---	---	---
USP35	57558	broad.mit.edu	37	11	77916627	77916627	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77916627delT	uc009yva.1	+						USP35_uc001oze.2_Intron|USP35_uc001ozc.2_Intron|USP35_uc010rsp.1_Intron|USP35_uc001ozd.2_Intron|USP35_uc001ozf.2_Intron	NM_020798	NP_065849			ubiquitin specific protease 35						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)	3	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)															---	---	---	---
GAB2	9846	broad.mit.edu	37	11	77960895	77960895	+	Intron	DEL	T	-	-	rs67790560		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77960895delT	uc001ozh.2	-						GAB2_uc001ozg.2_Intron	NM_080491	NP_536739			GRB2-associated binding protein 2 isoform a						osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity			ovary(5)|lung(1)	6	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)															---	---	---	---
GAB2	9846	broad.mit.edu	37	11	78032918	78032919	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78032918_78032919delAA	uc001ozh.2	-						GAB2_uc001ozg.2_Intron	NM_080491	NP_536739			GRB2-associated binding protein 2 isoform a						osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity			ovary(5)|lung(1)	6	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)															---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78555685	78555685	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78555685delA	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	78994024	78994025	+	Intron	INS	-	TGT	TGT	rs142981655	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78994024_78994025insTGT	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	79029518	79029518	+	Intron	DEL	A	-	-	rs35793375		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79029518delA	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	79210167	79210167	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79210167delT								ODZ4 (58472 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	79240148	79240148	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79240148delA								ODZ4 (88453 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80132826	80132826	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80132826delA								ODZ4 (981131 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80681334	80681334	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80681334delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80728546	80728546	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80728546delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80769595	80769596	+	IGR	INS	-	TT	TT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80769595_80769596insTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81225248	81225248	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81225248delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81727315	81727315	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81727315delA	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	82038622	82038624	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82038622_82038624delAAA	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	82241345	82241346	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82241345_82241346delGT								None (None upstream) : FAM181B (201707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	82331111	82331111	+	IGR	DEL	A	-	-	rs80058342		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82331111delA								None (None upstream) : FAM181B (111942 downstream)																																			---	---	---	---
RAB30	27314	broad.mit.edu	37	11	82752238	82752239	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82752238_82752239delAA	uc001ozu.2	-						RAB30_uc010rst.1_Intron|RAB30_uc001ozv.2_Intron	NM_014488	NP_055303			RAB30, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi stack|plasma membrane	GTP binding|GTPase activity				0																		---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83167698	83167698	+	3'UTR	DEL	A	-	-	rs35990465		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83167698delA	uc001paj.2	-	23					DLG2_uc001pai.2_3'UTR|DLG2_uc010rsy.1_3'UTR|DLG2_uc010rsz.1_3'UTR|DLG2_uc010rta.1_3'UTR|DLG2_uc001pak.2_3'UTR|DLG2_uc010rsw.1_3'UTR|DLG2_uc010rsx.1_3'UTR	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83168709	83168709	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83168709delT	uc001paj.2	-	23					DLG2_uc001pai.2_3'UTR|DLG2_uc010rsy.1_3'UTR|DLG2_uc010rsz.1_3'UTR|DLG2_uc010rta.1_3'UTR|DLG2_uc001pak.2_3'UTR|DLG2_uc010rsw.1_3'UTR|DLG2_uc010rsx.1_3'UTR	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84128804	84128805	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84128804_84128805delTT	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84297194	84297197	+	Intron	DEL	AAAA	-	-	rs138188482		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84297194_84297197delAAAA	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84302358	84302358	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84302358delT	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84542106	84542106	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84542106delA	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	85313432	85313432	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85313432delT	uc001pak.2	-							NM_001142699	NP_001136171			chapsyn-110 isoform 1							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
SYTL2	54843	broad.mit.edu	37	11	85437306	85437306	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85437306delT	uc010rth.1	-						SYTL2_uc010rtg.1_Intron|SYTL2_uc010rti.1_Intron|SYTL2_uc010rtj.1_Intron|SYTL2_uc009yvj.2_RNA|SYTL2_uc001pbd.2_Frame_Shift_Del_p.N65fs|SYTL2_uc001pbb.2_Frame_Shift_Del_p.N65fs|SYTL2_uc001pbc.2_Frame_Shift_Del_p.N65fs|SYTL2_uc010rtf.1_Intron	NM_001162951	NP_001156423			synaptotagmin-like 2 isoform g						intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)														---	---	---	---
SYTL2	54843	broad.mit.edu	37	11	85524734	85524737	+	5'Flank	DEL	CCTC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85524734_85524737delCCTC	uc010rti.1	-						SYTL2_uc010rtj.1_5'Flank	NM_032943	NP_116561			synaptotagmin-like 2 isoform a						intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)														---	---	---	---
PICALM	8301	broad.mit.edu	37	11	85715557	85715557	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85715557delT	uc001pbm.2	-						PICALM_uc001pbl.2_Intron|PICALM_uc001pbn.2_Intron|PICALM_uc010rtl.1_Intron|PICALM_uc010rtk.1_5'Flank|PICALM_uc001pbo.1_Intron	NM_007166	NP_009097			phosphatidylinositol-binding clathrin assembly						clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)						T	MLLT10|MLL	TALL|AML|								---	---	---	---
Unknown	0	broad.mit.edu	37	11	86057362	86057362	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86057362delT								C11orf73 (378 upstream) : CCDC81 (28416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	86413976	86413976	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86413976delT								ME3 (30298 upstream) : PRSS23 (97515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	86438611	86438611	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86438611delA								ME3 (54933 upstream) : PRSS23 (72880 downstream)																																			---	---	---	---
PRSS23	11098	broad.mit.edu	37	11	86646803	86646803	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86646803delG	uc001pcc.1	+						uc001pcd.2_RNA					Homo sapiens serine protease mRNA, complete cds.						proteolysis	extracellular region|nucleus	serine-type endopeptidase activity			central_nervous_system(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
TMEM135	65084	broad.mit.edu	37	11	87019546	87019546	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87019546delT	uc001pch.2	+						TMEM135_uc010rtt.1_Intron|TMEM135_uc001pci.2_Intron	NM_022918	NP_075069			transmembrane protein 135							integral to membrane					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	87036545	87036546	+	IGR	INS	-	CT	CT	rs142700961	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87036545_87036546insCT								TMEM135 (1977 upstream) : RAB38 (809885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87278169	87278169	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87278169delA								TMEM135 (243601 upstream) : RAB38 (568262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87405863	87405864	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87405863_87405864insT								TMEM135 (371295 upstream) : RAB38 (440567 downstream)																																			---	---	---	---
TYR	7299	broad.mit.edu	37	11	88938268	88938268	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88938268delA	uc001pcs.2	+							NM_000372	NP_000363			tyrosinase precursor						eye pigment biosynthetic process|melanin biosynthetic process from tyrosine|visual perception	Golgi-associated vesicle|integral to membrane|lysosome|melanosome membrane|perinuclear region of cytoplasm	copper ion binding|monophenol monooxygenase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|NADH(DB00157)									Oculocutaneous_Albinism				---	---	---	---
TYR	7299	broad.mit.edu	37	11	89027212	89027212	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89027212delT	uc001pcs.2	+							NM_000372	NP_000363			tyrosinase precursor						eye pigment biosynthetic process|melanin biosynthetic process from tyrosine|visual perception	Golgi-associated vesicle|integral to membrane|lysosome|melanosome membrane|perinuclear region of cytoplasm	copper ion binding|monophenol monooxygenase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|NADH(DB00157)									Oculocutaneous_Albinism				---	---	---	---
TRIM49	57093	broad.mit.edu	37	11	89534160	89534161	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89534160_89534161delAA	uc001pdb.2	-							NM_020358	NP_065091			ring finger protein 18							intracellular	zinc ion binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	89606416	89606416	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89606416delT								TRIM53 (22274 upstream) : TRIM49L (38165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91373750	91373750	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91373750delA								MIR1261 (771380 upstream) : FAT3 (711512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91698441	91698441	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91698441delA								None (None upstream) : FAT3 (386821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91812806	91812806	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91812806delA								None (None upstream) : FAT3 (272456 downstream)																																			---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92180389	92180390	+	Intron	DEL	GT	-	-	rs34833885		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92180389_92180390delGT	uc001pdj.3	+							NM_001008781	NP_001008781			FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
Unknown	0	broad.mit.edu	37	11	93032699	93032699	+	IGR	DEL	T	-	-	rs35883917		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93032699delT								SLC36A4 (101604 upstream) : CCDC67 (30457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	93306781	93306781	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93306781delA								C11orf75 (30235 upstream) : KIAA1731 (88035 downstream)																																			---	---	---	---
KIAA1731	85459	broad.mit.edu	37	11	93433593	93433595	+	Intron	DEL	TTT	-	-	rs150231786		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93433593_93433595delTTT	uc009ywb.1	+						KIAA1731_uc001pdu.1_Intron	NM_033395	NP_203753			hypothetical protein LOC85459							centrosome					0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
MED17	9440	broad.mit.edu	37	11	93540286	93540286	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93540286delT	uc001pem.3	+							NM_004268	NP_004259			mediator complex subunit 17						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
C11orf90	387804	broad.mit.edu	37	11	93576256	93576256	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93576256delA	uc010ruc.1	-							NM_001144871	NP_001138343			hypothetical protein LOC387804 precursor							integral to membrane					0																		---	---	---	---
PANX1	24145	broad.mit.edu	37	11	93871093	93871093	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93871093delT	uc001per.2	+						PANX1_uc001peq.2_Intron	NM_015368	NP_056183			pannexin 1						positive regulation of interleukin-1 beta secretion|protein hexamerization|synaptic transmission	bleb|endoplasmic reticulum membrane|gap junction|integral to membrane	calcium channel activity|gap junction hemi-channel activity|leak channel activity|receptor binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
MRE11A	4361	broad.mit.edu	37	11	94203462	94203462	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94203462delA	uc001peu.2	-						MRE11A_uc001pev.2_Intron|MRE11A_uc009ywj.2_Intron	NM_005591	NP_005582			meiotic recombination 11 homolog A isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase	Mre11 complex|nucleoplasm	3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity			breast(4)|lung(1)	5		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)											Homologous_recombination	Ataxia-Telangiectasia-Like_Disorder				---	---	---	---
Unknown	0	broad.mit.edu	37	11	94733328	94733328	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94733328delA								KDM4D (654 upstream) : KDM4DL (25094 downstream)																																			---	---	---	---
ENDOD1	23052	broad.mit.edu	37	11	94860021	94860021	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94860021delT	uc001pfh.2	+							NM_015036	NP_055851			endonuclease domain containing 1 precursor							extracellular region	endonuclease activity|metal ion binding|nucleic acid binding				0		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	95183819	95183819	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95183819delT								SESN3 (218114 upstream) : FAM76B (318287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	95378953	95378953	+	IGR	DEL	A	-	-	rs79959341		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95378953delA								SESN3 (413248 upstream) : FAM76B (123153 downstream)																																			---	---	---	---
CEP57	9702	broad.mit.edu	37	11	95551111	95551111	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95551111delT	uc001pfp.1	+						CEP57_uc001pfo.1_Intron|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				---	---	---	---
Unknown	0	broad.mit.edu	37	11	96681603	96681604	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96681603_96681604insA								JRKL (554876 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	97420715	97420715	+	IGR	DEL	A	-	-	rs2852899		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97420715delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98506150	98506151	+	IGR	DEL	GT	-	-	rs3018596		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98506150_98506151delGT								None (None upstream) : CNTN5 (385720 downstream)																																			---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99607077	99607077	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99607077delT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
ARHGAP42	143872	broad.mit.edu	37	11	100649401	100649401	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100649401delA	uc001pge.2	+							NM_152432	NP_689645			Rho-type GTPase-activating protein FLJ32810						filopodium assembly|signal transduction	intracellular	cytoskeletal adaptor activity|GTPase activator activity|SH3 domain binding				0																		---	---	---	---
ARHGAP42	143872	broad.mit.edu	37	11	100780073	100780074	+	Intron	DEL	TT	-	-	rs150503256		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100780073_100780074delTT	uc001pge.2	+							NM_152432	NP_689645			Rho-type GTPase-activating protein FLJ32810						filopodium assembly|signal transduction	intracellular	cytoskeletal adaptor activity|GTPase activator activity|SH3 domain binding				0																		---	---	---	---
TRPC6	7225	broad.mit.edu	37	11	101339637	101339637	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101339637delA	uc001pgk.3	-						TRPC6_uc009ywy.2_Intron|TRPC6_uc009ywz.1_Intron	NM_004621	NP_004612			transient receptor potential cation channel,						axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)														---	---	---	---
C11orf70	85016	broad.mit.edu	37	11	101920583	101920583	+	Intron	DEL	A	-	-	rs10716793		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101920583delA	uc001pgp.2	+						C11orf70_uc001pgo.2_Intron|C11orf70_uc001pgq.2_Intron	NM_032930	NP_116319			hypothetical protein LOC85016											skin(1)	1	all_epithelial(12;0.0137)	Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.0137)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0335)														---	---	---	---
YAP1	10413	broad.mit.edu	37	11	102088429	102088429	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102088429delT	uc001pgt.2	+						YAP1_uc001pgs.2_Intron|YAP1_uc001pgu.2_Intron|YAP1_uc001pgv.2_Intron|YAP1_uc010ruo.1_Intron|YAP1_uc001pgw.2_Intron|YAP1_uc010rup.1_Intron	NM_001130145	NP_001123617			Yes-associated protein 1, 65kDa isoform 1						cell proliferation|cellular response to gamma radiation|contact inhibition|hippo signaling cascade|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)														---	---	---	---
BIRC2	329	broad.mit.edu	37	11	102248668	102248668	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102248668delT	uc001pgy.2	+						BIRC2_uc010ruq.1_Intron|BIRC2_uc010rur.1_Intron	NM_001166	NP_001157			baculoviral IAP repeat-containing protein 2						cell surface receptor linked signaling pathway|cellular component disassembly involved in apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination	CD40 receptor complex|cytosol|internal side of plasma membrane	protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	102437897	102437899	+	IGR	DEL	AGA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102437897_102437899delAGA								MMP7 (36419 upstream) : MMP20 (9668 downstream)																																			---	---	---	---
MMP12	4321	broad.mit.edu	37	11	102737945	102737945	+	Intron	DEL	A	-	-	rs28381681		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102737945delA	uc001phk.2	-							NM_002426	NP_002417			matrix metalloproteinase 12 preproprotein						positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)													---	---	---	---
DCUN1D5	84259	broad.mit.edu	37	11	102936353	102936353	+	Intron	DEL	A	-	-	rs2514009		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102936353delA	uc001phm.2	-						DCUN1D5_uc010ruw.1_Intron	NM_032299	NP_115675			DCN1, defective in cullin neddylation 1, domain												0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.00032)|Epithelial(105;0.0689)|all cancers(92;0.186)														---	---	---	---
DCUN1D5	84259	broad.mit.edu	37	11	102937497	102937497	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102937497delA	uc001phm.2	-						DCUN1D5_uc010ruw.1_Intron	NM_032299	NP_115675			DCN1, defective in cullin neddylation 1, domain												0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.00032)|Epithelial(105;0.0689)|all cancers(92;0.186)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103162888	103162889	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103162888_103162889delTT	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932			dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	104536023	104536023	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104536023delT								PDGFD (500996 upstream) : CASP12 (220419 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	105360544	105360544	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105360544delT								CARD18 (350738 upstream) : GRIA4 (120256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	105377420	105377420	+	IGR	DEL	A	-	-	rs111289837		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105377420delA								CARD18 (367614 upstream) : GRIA4 (103380 downstream)																																			---	---	---	---
GRIA4	2893	broad.mit.edu	37	11	105781021	105781021	+	Intron	DEL	T	-	-	rs113570660		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105781021delT	uc001pix.2	+						GRIA4_uc001piu.1_Intron|GRIA4_uc001piw.2_Intron|GRIA4_uc009yxk.1_Intron	NM_000829	NP_000820			glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	106167219	106167219	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106167219delA								AASDHPPT (197800 upstream) : GUCY1A2 (390691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	106319777	106319777	+	IGR	DEL	T	-	-	rs35057176		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106319777delT								AASDHPPT (350358 upstream) : GUCY1A2 (238133 downstream)																																			---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106612914	106612914	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106612914delT	uc001pjg.1	-						GUCY1A2_uc010rvo.1_Intron|GUCY1A2_uc009yxn.1_Intron	NM_000855	NP_000846			guanylate cyclase 1, soluble, alpha 2						intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)														---	---	---	---
CWF19L2	143884	broad.mit.edu	37	11	107207381	107207381	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107207381delA	uc010rvp.1	-	15	2291	c.2261delT	c.(2260-2262)TTGfs	p.L754fs	CWF19L2_uc001pjh.3_RNA|CWF19L2_uc009yxo.2_RNA	NM_152434	NP_689647	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control	754							catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	107350339	107350339	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107350339delT								CWF19L2 (21767 upstream) : ALKBH8 (23115 downstream)																																			---	---	---	---
SLC35F2	54733	broad.mit.edu	37	11	107686994	107686995	+	Intron	DEL	GT	-	-	rs72121896		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107686994_107686995delGT	uc001pjq.2	-						SLC35F2_uc010rvu.1_Intron|SLC35F2_uc001pjs.2_Intron	NM_017515	NP_059985			solute carrier family 35, member F2						transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	107856266	107856266	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107856266delA								RAB39 (22060 upstream) : CUL5 (23142 downstream)																																			---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107959943	107959943	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107959943delT	uc001pjv.2	+						CUL5_uc001pju.2_Intron	NM_003478	NP_003469			Vasopressin-activated calcium-mobilizing						cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)														---	---	---	---
NPAT	4863	broad.mit.edu	37	11	108031565	108031565	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108031565delA	uc001pjz.3	-						NPAT_uc010rvv.1_Intron	NM_002519	NP_002510			nuclear protein,  ataxia-telangiectasia locus						positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)														---	---	---	---
ATM	472	broad.mit.edu	37	11	108172779	108172779	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108172779delT	uc001pkb.1	+						ATM_uc009yxr.1_Intron|ATM_uc001pke.1_Intron|ATM_uc001pkg.1_Intron|ATM_uc009yxt.1_5'Flank	NM_000051	NP_000042			ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)				D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			---	---	---	---
ATM	472	broad.mit.edu	37	11	108206006	108206006	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108206006delT	uc001pkb.1	+						ATM_uc009yxr.1_Intron|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_RNA|ATM_uc001pke.1_Intron	NM_000051	NP_000042			ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)				D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			---	---	---	---
C11orf65	160140	broad.mit.edu	37	11	108263819	108263819	+	Intron	DEL	T	-	-	rs7948591	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108263819delT	uc001pkh.2	-						C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron	NM_152587	NP_689800			hypothetical protein LOC160140											ovary(1)	1		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;8.21e-06)|BRCA - Breast invasive adenocarcinoma(274;1.01e-05)|all cancers(92;0.000189)|Colorectal(284;0.114)|OV - Ovarian serous cystadenocarcinoma(223;0.144)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	109119102	109119103	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109119102_109119103insT								DDX10 (307456 upstream) : C11orf87 (173772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109250719	109250719	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109250719delT								DDX10 (439073 upstream) : C11orf87 (42156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109489436	109489436	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109489436delG								C11orf87 (189598 upstream) : ZC3H12C (474490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109629432	109629432	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109629432delT								C11orf87 (329594 upstream) : ZC3H12C (334494 downstream)																																			---	---	---	---
RDX	5962	broad.mit.edu	37	11	110150303	110150303	+	Intron	DEL	T	-	-	rs55863897		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110150303delT	uc001pku.2	-						RDX_uc009yxx.1_Intron|RDX_uc009yxy.2_Intron|RDX_uc009yxz.2_Intron|RDX_uc009yya.2_Intron|RDX_uc010rwe.1_Intron	NM_002906	NP_002897			radixin						actin filament capping	cleavage furrow|cytoskeleton|extrinsic to membrane|Golgi apparatus|nucleolus|plasma membrane	actin binding				0		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	110225699	110225699	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110225699delT	uc001pkv.1	+						uc001pkw.1_5'Flank					Homo sapiens cDNA FLJ36798 fis, clone ADRGL2007283.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	110266558	110266559	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110266558_110266559delTT	uc001pkv.1	+						uc001pkw.1_Intron					Homo sapiens cDNA FLJ36798 fis, clone ADRGL2007283.																														---	---	---	---
ARHGAP20	57569	broad.mit.edu	37	11	110528616	110528616	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110528616delA	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	110885071	110885071	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110885071delG								ARHGAP20 (301159 upstream) : C11orf53 (241636 downstream)																																			---	---	---	---
C11orf53	341032	broad.mit.edu	37	11	111145266	111145267	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111145266_111145267delTG	uc001plc.2	+							NM_198498	NP_940900			hypothetical protein LOC341032												0		all_cancers(61;2.05e-09)|Melanoma(852;4.04e-05)|all_epithelial(67;6.15e-05)|all_hematologic(158;0.000826)|Acute lymphoblastic leukemia(157;0.000966)|all_neural(223;0.0332)|Medulloblastoma(222;0.0425)|Breast(348;0.147)		Epithelial(105;1.7e-06)|BRCA - Breast invasive adenocarcinoma(274;3.16e-06)|all cancers(92;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0507)														---	---	---	---
BTG4	54766	broad.mit.edu	37	11	111381363	111381363	+	Intron	DEL	T	-	-	rs113662105		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111381363delT	uc001plj.2	-						BTG4_uc001plk.2_Intron|uc001pll.2_RNA|uc001plm.2_5'Flank|MIR34B_hsa-mir-34b|MI0000742_5'Flank|MIR34C_hsa-mir-34c|MI0000743_5'Flank	NM_017589	NP_060059			B-cell translocation gene 4						cell cycle arrest|negative regulation of cell proliferation|neuron differentiation						0		all_cancers(61;3.78e-13)|all_epithelial(67;5.29e-08)|Melanoma(852;3.15e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0204)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.22e-06)|BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|all cancers(92;2.18e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0509)														---	---	---	---
C11orf57	55216	broad.mit.edu	37	11	111953144	111953144	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111953144delT	uc001pmr.3	+						C11orf57_uc001pmu.2_3'UTR|C11orf57_uc001pmw.3_Intron|C11orf57_uc001pmt.3_Intron|C11orf57_uc001pmv.3_Intron|C11orf57_uc001pms.3_Intron	NM_001082970	NP_001076439			hypothetical protein LOC55216 isoform b											breast(2)|ovary(1)	3		all_cancers(61;9.8e-15)|all_epithelial(67;6.57e-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;3.6e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;7.01e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0521)														---	---	---	---
PTS	5805	broad.mit.edu	37	11	112097784	112097786	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112097784_112097786delAAA	uc001pnj.3	+						PTS_uc009yyo.2_Intron	NM_000317	NP_000308			6-pyruvoyltetrahydropterin synthase						cellular amino acid metabolic process|central nervous system development|tetrahydrobiopterin biosynthetic process	mitochondrion	6-pyruvoyltetrahydropterin synthase activity|metal ion binding				0		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	112208014	112208017	+	IGR	DEL	CAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112208014_112208017delCAAA								PTS (67337 upstream) : NCAM1 (623978 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	112752836	112752839	+	IGR	DEL	CCCA	-	-	rs71795676		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112752836_112752839delCCCA								PTS (612159 upstream) : NCAM1 (79156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	112788786	112788787	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112788786_112788787delAG								PTS (648109 upstream) : NCAM1 (43208 downstream)																																			---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	112904998	112904998	+	Intron	DEL	T	-	-	rs148642032		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112904998delT	uc009yyq.1	+						NCAM1_uc001pno.2_Intron	NM_001076682	NP_001070150			neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)														---	---	---	---
TTC12	54970	broad.mit.edu	37	11	113231132	113231132	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113231132delA	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)														---	---	---	---
TTC12	54970	broad.mit.edu	37	11	113238943	113238944	+	RNA	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113238943_113238944delAG	uc001pnw.2	+	22		c.2182_2183delAG				NM_017868				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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	113593033	113593033	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113593033delA								TMPRSS5 (15965 upstream) : ZW10 (10878 downstream)																																			---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	113984398	113984398	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113984398delA	uc001pop.2	+						ZBTB16_uc001poo.1_Intron|ZBTB16_uc001poq.2_Intron	NM_006006	NP_005997			promyelocytic leukemia zinc finger protein						apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)														---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	114045035	114045036	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114045035_114045036delTT	uc001pop.2	+						ZBTB16_uc001poo.1_Intron|ZBTB16_uc001poq.2_Intron	NM_006006	NP_005997			promyelocytic leukemia zinc finger protein						apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	114195917	114195917	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114195917delT								NNMT (12679 upstream) : C11orf71 (66253 downstream)																																			---	---	---	---
FAM55A	120400	broad.mit.edu	37	11	114393231	114393231	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114393231delA	uc001ppa.2	-						FAM55A_uc010rxd.1_Intron	NM_152315	NP_689528			hypothetical protein LOC120400							extracellular region					0		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;3.02e-06)|Epithelial(105;0.000144)|all cancers(92;0.00106)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	114947272	114947272	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114947272delA								FAM55B (369620 upstream) : CADM1 (92681 downstream)																																			---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115061219	115061220	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115061219_115061220delTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	116192599	116192599	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116192599delA								CADM1 (817358 upstream) : BUD13 (426289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116332238	116332238	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116332238delA								CADM1 (956997 upstream) : BUD13 (286650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116577585	116577586	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116577585_116577586delAA								None (None upstream) : BUD13 (41302 downstream)																																			---	---	---	---
APOC3	345	broad.mit.edu	37	11	116698848	116698849	+	5'Flank	INS	-	TC	TC	rs142122586		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116698848_116698849insTC	uc001ppt.1	+							NM_000040	NP_000031			apolipoprotein C-III precursor						Cdc42 protein signal transduction|cholesterol efflux|cholesterol homeostasis|chylomicron remnant clearance|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle remodeling|lipoprotein metabolic process|negative regulation of cholesterol import|negative regulation of fatty acid biosynthetic process|negative regulation of high-density lipoprotein particle clearance|negative regulation of lipoprotein lipase activity|negative regulation of low-density lipoprotein particle clearance|negative regulation of receptor-mediated endocytosis|negative regulation of triglyceride catabolic process|negative regulation of very-low-density lipoprotein particle clearance|negative regulation of very-low-density lipoprotein particle remodeling|phospholipid efflux|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle assembly	chylomicron|intermediate-density lipoprotein particle|spherical high-density lipoprotein particle|very-low-density lipoprotein particle	high-density lipoprotein particle receptor binding|lipase inhibitor activity|phospholipid binding				0	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)														---	---	---	---
PCSK7	9159	broad.mit.edu	37	11	117080564	117080564	+	Intron	DEL	A	-	-	rs74878497		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117080564delA	uc001pqr.2	-						PCSK7_uc001pqs.1_5'Flank	NM_004716	NP_004707			proprotein convertase subtilisin/kexin type 7						peptide hormone processing	integral to Golgi membrane	serine-type endopeptidase activity				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)				T	IGH@	MLCLS								---	---	---	---
RNF214	257160	broad.mit.edu	37	11	117148206	117148207	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117148206_117148207delAC	uc001pqt.2	+						RNF214_uc001pqu.2_Intron|RNF214_uc010rxf.1_Intron	NM_207343	NP_997226			ring finger protein 214								zinc ion binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)														---	---	---	---
RNF214	257160	broad.mit.edu	37	11	117155670	117155670	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117155670delA	uc001pqt.2	+						RNF214_uc001pqu.2_Intron|RNF214_uc010rxf.1_Intron	NM_207343	NP_997226			ring finger protein 214								zinc ion binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)														---	---	---	---
CEP164	22897	broad.mit.edu	37	11	117242511	117242512	+	Intron	INS	-	T	T	rs34338708		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117242511_117242512insT	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)														---	---	---	---
MLL	4297	broad.mit.edu	37	11	118338723	118338724	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118338723_118338724delTT	uc001pta.2	+						MLL_uc001ptb.2_Intron|MLL_uc001psz.1_Intron|MLL_uc001ptd.1_5'Flank	NM_005933	NP_005924			myeloid/lymphoid or mixed-lineage leukemia						apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)				T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								---	---	---	---
TMEM25	84866	broad.mit.edu	37	11	118402088	118402089	+	Intron	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118402088_118402089insG	uc010rye.1	+						TMEM25_uc010ryd.1_Intron|TMEM25_uc001ptk.3_Intron|TMEM25_uc001pth.2_Intron|TMEM25_uc009zad.2_Intron|TMEM25_uc001pti.2_Intron|TMEM25_uc010ryf.1_Intron|TMEM25_uc001ptl.2_Intron|TMEM25_uc001ptm.2_Intron|TMEM25_uc001ptn.2_5'Flank	NM_032780	NP_116169			transmembrane protein 25 isoform 1							extracellular region|integral to membrane|plasma membrane					0	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	118737919	118737919	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118737919delA								DDX6 (75947 upstream) : CXCR5 (16622 downstream)																																			---	---	---	---
CXCR5	643	broad.mit.edu	37	11	118763377	118763377	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118763377delG	uc001pue.3	+						CXCR5_uc001puf.2_5'Flank	NM_001716	NP_001707			Burkitt lymphoma receptor 1 isoform 1						B cell activation|cellular component movement	integral to plasma membrane	C-X-C chemokine receptor activity			breast(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)														---	---	---	---
BCL9L	283149	broad.mit.edu	37	11	118769560	118769560	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118769560delG	uc001pug.2	-	8	5029	c.4064delC	c.(4063-4065)CCTfs	p.P1355fs	BCL9L_uc009zal.2_Frame_Shift_Del_p.P1350fs	NM_182557	NP_872363	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	1355	Pro-rich.				negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		transcription coactivator activity			ovary(1)|pancreas(1)	2	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	118797228	118797229	+	IGR	DEL	CA	-	-	rs56391556		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118797228_118797229delCA								BCL9L (15615 upstream) : UPK2 (29797 downstream)																																			---	---	---	---
CCDC84	338657	broad.mit.edu	37	11	118871605	118871605	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118871605delT	uc001pul.2	+						CCDC84_uc010ryk.1_Intron|CCDC84_uc010ryl.1_Intron|CCDC84_uc010rym.1_Intron	NM_198489	NP_940891			coiled-coil domain containing 84											ovary(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)														---	---	---	---
RPS25	6230	broad.mit.edu	37	11	118888382	118888388	+	Intron	DEL	AAAAACA	-	-	rs55689620		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118888382_118888388delAAAAACA	uc001pun.2	-						TRAPPC4_uc010ryn.1_5'Flank|TRAPPC4_uc010ryo.1_5'Flank|TRAPPC4_uc010ryp.1_5'Flank|TRAPPC4_uc001pup.2_5'Flank|TRAPPC4_uc010ryq.1_5'Flank	NM_001028	NP_001019			ribosomal protein S25						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)														---	---	---	---
TRAPPC4	51399	broad.mit.edu	37	11	118891139	118891140	+	Intron	INS	-	T	T	rs142545556	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118891139_118891140insT	uc010ryo.1	+						RPS25_uc001pun.2_5'Flank|TRAPPC4_uc010ryn.1_3'UTR|TRAPPC4_uc010ryp.1_Intron|TRAPPC4_uc001pup.2_Intron|TRAPPC4_uc010ryq.1_Intron	NM_016146	NP_057230			trafficking protein particle complex 4						dendrite development|ER to Golgi vesicle-mediated transport	cis-Golgi network|dendrite|endoplasmic reticulum|Golgi stack|synaptic vesicle	protein binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	119036173	119036173	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119036173delT								ABCG4 (2801 upstream) : NLRX1 (3264 downstream)																																			---	---	---	---
CBL	867	broad.mit.edu	37	11	119091615	119091615	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119091615delT	uc001pwe.2	+							NM_005188	NP_005179			Cas-Br-M (murine) ecotropic retroviral						epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1)	149		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)										CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome				---	---	---	---
PVRL1	5818	broad.mit.edu	37	11	119549105	119549105	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119549105delG	uc001pwv.2	-						PVRL1_uc001pwu.1_Intron|PVRL1_uc001pww.2_Intron	NM_002855	NP_002846			poliovirus receptor-related 1 isoform 1						adherens junction organization|cell junction assembly|entry of virus into host cell|heterophilic cell-cell adhesion|homophilic cell adhesion|immune response	cell-cell adherens junction|extracellular region|integral to membrane	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity				0		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)														---	---	---	---
POU2F3	25833	broad.mit.edu	37	11	120157531	120157531	+	Intron	DEL	T	-	-	rs138754962		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120157531delT	uc001pxc.2	+						POU2F3_uc010rzk.1_Intron|POU2F3_uc010rzl.1_Intron	NM_014352	NP_055167			POU transcription factor						negative regulation by host of viral transcription	cytoplasm	sequence-specific DNA binding			ovary(1)|skin(1)	2		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)														---	---	---	---
POU2F3	25833	broad.mit.edu	37	11	120168487	120168487	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120168487delT	uc001pxc.2	+						POU2F3_uc010rzk.1_Intron|POU2F3_uc010rzl.1_Intron	NM_014352	NP_055167			POU transcription factor						negative regulation by host of viral transcription	cytoplasm	sequence-specific DNA binding			ovary(1)|skin(1)	2		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)														---	---	---	---
POU2F3	25833	broad.mit.edu	37	11	120171475	120171475	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120171475delA	uc001pxc.2	+						POU2F3_uc010rzk.1_Intron|POU2F3_uc010rzl.1_Intron	NM_014352	NP_055167			POU transcription factor						negative regulation by host of viral transcription	cytoplasm	sequence-specific DNA binding			ovary(1)|skin(1)	2		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)														---	---	---	---
TMEM136	219902	broad.mit.edu	37	11	120199552	120199553	+	Intron	DEL	GT	-	-	rs12803536		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120199552_120199553delGT	uc001pxh.1	+						TMEM136_uc001pxg.2_Intron|TMEM136_uc010rzm.1_Intron|TMEM136_uc001pxj.2_Intron|TMEM136_uc009zas.1_Intron|TMEM136_uc001pxi.1_Intron	NM_174926	NP_777586			transmembrane protein 136							integral to membrane				ovary(1)	1		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Hepatocellular(160;0.206)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.07e-06)														---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120335722	120335722	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120335722delA	uc001pxl.1	+						ARHGEF12_uc009zat.2_Intron|ARHGEF12_uc010rzn.1_Intron|ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128			Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120346024	120346024	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120346024delT	uc001pxl.1	+						ARHGEF12_uc009zat.2_Intron|ARHGEF12_uc010rzn.1_Intron|ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128			Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120405454	120405454	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120405454delG	uc001pxn.2	+							NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120807746	120807746	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120807746delT	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120827332	120827332	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120827332delT	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	121295715	121295716	+	IGR	DEL	AA	-	-	rs36005566		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121295715_121295716delAA								SC5DL (111598 upstream) : SORL1 (27245 downstream)																																			---	---	---	---
SORL1	6653	broad.mit.edu	37	11	121468104	121468104	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121468104delT	uc001pxx.2	+						SORL1_uc010rzp.1_Intron|SORL1_uc010rzq.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	121552837	121552837	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121552837delT								SORL1 (48366 upstream) : LOC399959 (406974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	121566039	121566039	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121566039delT								SORL1 (61568 upstream) : LOC399959 (393772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	121583990	121584006	+	IGR	DEL	AAACAAACAAACAAACA	-	-	rs56929600		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121583990_121584006delAAACAAACAAACAAACA								SORL1 (79519 upstream) : LOC399959 (375805 downstream)																																			---	---	---	---
LOC399959	399959	broad.mit.edu	37	11	122030470	122030471	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122030470_122030471delTG	uc009zba.2	-							NR_024430				Homo sapiens cDNA FLJ34394 fis, clone HCHON2000676.												0																		---	---	---	---
UBASH3B	84959	broad.mit.edu	37	11	122579000	122579000	+	Intron	DEL	T	-	-	rs35377710		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122579000delT	uc001pyi.3	+							NM_032873	NP_116262			ubiquitin associated and SH3 domain containing,							cytoplasm|nucleus	protein tyrosine phosphatase activity			central_nervous_system(1)	1		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)														---	---	---	---
ASAM	79827	broad.mit.edu	37	11	122982286	122982286	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122982286delG	uc001pyt.2	-							NM_024769	NP_079045			adipocyte-specific adhesion molecule precursor							integral to membrane|tight junction					0		Breast(109;0.0025)|Lung NSC(97;0.0179)|all_lung(97;0.0182)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.73e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)												OREG0021444	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	123080051	123080051	+	IGR	DEL	T	-	-	rs11339104		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123080051delT								ASAM (14044 upstream) : GRAMD1B (316477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	123205950	123205950	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123205950delA								ASAM (139943 upstream) : GRAMD1B (190578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	123297294	123297296	+	IGR	DEL	CCG	-	-	rs55991480		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123297294_123297296delCCG								ASAM (231287 upstream) : GRAMD1B (99232 downstream)																																			---	---	---	---
GRAMD1B	57476	broad.mit.edu	37	11	123489375	123489375	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123489375delT	uc001pyx.2	+						GRAMD1B_uc001pyw.2_Intron|GRAMD1B_uc010rzw.1_Intron|GRAMD1B_uc010rzx.1_Intron|GRAMD1B_uc001pyy.2_Intron	NM_020716	NP_065767			GRAM domain containing 1B							integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	123616939	123616939	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123616939delT								ZNF202 (4576 upstream) : OR6X1 (7351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	123703687	123703687	+	IGR	DEL	A	-	-	rs113947966		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123703687delA								OR6M1 (26630 upstream) : TMEM225 (49948 downstream)																																			---	---	---	---
OR4D5	219875	broad.mit.edu	37	11	123808313	123808313	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123808313delA	uc001pzk.1	+							NM_001001965	NP_001001965			olfactory receptor, family 4, subfamily D,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)														---	---	---	---
OR10G8	219869	broad.mit.edu	37	11	123899495	123899495	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123899495delT	uc001pzp.1	+							NM_001004464	NP_001004464			olfactory receptor, family 10, subfamily G,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)														---	---	---	---
SIAE	54414	broad.mit.edu	37	11	124519316	124519316	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124519316delT	uc001qan.2	-							NM_170601	NP_733746			sialate O-acetylesterase precursor							extracellular region|lysosome	carboxylesterase activity|sialate O-acetylesterase activity				0	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)														---	---	---	---
C11orf61	79684	broad.mit.edu	37	11	124669346	124669346	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124669346delC	uc001qba.1	-						C11orf61_uc001qaz.1_Intron|C11orf61_uc010sap.1_Intron|uc001qbb.2_5'Flank	NM_024631	NP_078907			hypothetical protein LOC79684												0	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0079)														---	---	---	---
CCDC15	80071	broad.mit.edu	37	11	124862880	124862880	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124862880delT	uc001qbm.3	+							NM_025004	NP_079280			coiled-coil domain containing 15							centrosome				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)														---	---	---	---
CCDC15	80071	broad.mit.edu	37	11	124909949	124909949	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124909949delT	uc001qbm.3	+							NM_025004	NP_079280			coiled-coil domain containing 15							centrosome				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)														---	---	---	---
PKNOX2	63876	broad.mit.edu	37	11	125137660	125137661	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125137660_125137661delTG	uc001qbu.2	+						PKNOX2_uc010saz.1_Intron|PKNOX2_uc010sba.1_Intron|PKNOX2_uc010sbb.1_Intron	NM_022062	NP_071345			PBX/knotted 1 homeobox 2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)														---	---	---	---
EI24	9538	broad.mit.edu	37	11	125452395	125452395	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125452395delA	uc001qca.2	+						EI24_uc001qcb.2_Intron|EI24_uc010sbd.1_Intron|EI24_uc009zbl.2_Intron|EI24_uc001qcc.2_Intron|EI24_uc010sbe.1_Intron|EI24_uc010sbf.1_Intron	NM_004879	NP_004870			etoposide induced 2.4 isoform 1						apoptosis|autophagy|induction of apoptosis|negative regulation of cell growth	endoplasmic reticulum membrane|integral to membrane|nuclear membrane				ovary(1)	1	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)														---	---	---	---
STT3A	3703	broad.mit.edu	37	11	125467144	125467144	+	Intron	DEL	C	-	-	rs513209	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125467144delC	uc001qcd.2	+						STT3A_uc009zbm.2_Intron|STT3A_uc001qce.2_Intron|STT3A_uc010sbg.1_Intron	NM_152713	NP_689926			integral membrane protein 1						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity				0	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)														---	---	---	---
PUS3	83480	broad.mit.edu	37	11	125764947	125764947	+	Intron	DEL	T	-	-	rs144232833		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125764947delT	uc001qcy.2	-						HYLS1_uc009zbv.2_Intron|HYLS1_uc001qcx.3_Intron	NM_031307	NP_112597			pseudouridylate synthase 3							nucleus	RNA binding			ovary(1)	1	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)														---	---	---	---
DCPS	28960	broad.mit.edu	37	11	126191583	126191584	+	Intron	INS	-	GAAGG	GAAGG	rs140653662	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126191583_126191584insGAAGG	uc001qdp.2	+							NM_014026	NP_054745			mRNA decapping enzyme						deadenylation-dependent decapping of nuclear-transcribed mRNA|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	exoribonuclease activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	127052128	127052128	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127052128delA								KIRREL3 (178773 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	127220248	127220248	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127220248delG								KIRREL3 (346893 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	127366393	127366393	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127366393delA								KIRREL3 (493038 upstream) : ETS1 (962263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	127824297	127824297	+	IGR	DEL	A	-	-	rs35154048		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127824297delA								KIRREL3 (950942 upstream) : ETS1 (504359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	127908998	127908998	+	IGR	DEL	A	-	-	rs948250	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127908998delA								None (None upstream) : ETS1 (419658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	128484738	128484739	+	IGR	INS	-	TT	TT	rs138070098	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128484738_128484739insTT								ETS1 (27285 upstream) : FLI1 (71691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	129455251	129455252	+	IGR	INS	-	T	T	rs111437942		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129455251_129455252insT								BARX2 (133078 upstream) : TMEM45B (230489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	129549295	129549295	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129549295delG								BARX2 (227122 upstream) : TMEM45B (136446 downstream)																																			---	---	---	---
ADAMTS15	170689	broad.mit.edu	37	11	130331725	130331726	+	Intron	INS	-	CT	CT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130331725_130331726insCT	uc010scd.1	+							NM_139055	NP_620686			a disintegrin-like and metalloprotease						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	130458685	130458685	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130458685delC								ADAMTS15 (114970 upstream) : SNX19 (287082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	130506605	130506605	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130506605delC								ADAMTS15 (162890 upstream) : SNX19 (239162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	130580988	130580989	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130580988_130580989insG								ADAMTS15 (237273 upstream) : SNX19 (164778 downstream)																																			---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132345586	132345586	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132345586delA	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132452050	132452051	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132452050_132452051delAG	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132500422	132500423	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132500422_132500423delTG	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132519164	132519164	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132519164delT	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
GLB1L3	112937	broad.mit.edu	37	11	134171460	134171460	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134171460delT	uc009zdf.2	+						GLB1L3_uc010scs.1_Intron|GLB1L3_uc010sct.1_Intron|GLB1L3_uc010scu.1_Intron	NM_001080407	NP_001073876			galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)														---	---	---	---
GLB1L3	112937	broad.mit.edu	37	11	134178448	134178450	+	Intron	DEL	CAT	-	-	rs140914654	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134178448_134178450delCAT	uc009zdf.2	+						GLB1L3_uc010scu.1_Intron|GLB1L3_uc001qho.3_Intron	NM_001080407	NP_001073876			galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	134685791	134685792	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134685791_134685792delTT								B3GAT1 (403979 upstream) : None (None downstream)																																			---	---	---	---
WNK1	65125	broad.mit.edu	37	12	878375	878376	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:878375_878376delTT	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	968799	968800	+	Intron	DEL	TT	-	-	rs112501353	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:968799_968800delTT	uc001qio.3	+						WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_5'Flank	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	996697	996697	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:996697delT	uc001qio.3	+						WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_018979	NP_061852			WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1307103	1307103	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1307103delT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc009zdp.2_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884			RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1453016	1453018	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1453016_1453018delTTT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884			RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1502744	1502744	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1502744delT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884			RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1581821	1581821	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1581821delA	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884			RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
ADIPOR2	79602	broad.mit.edu	37	12	1837025	1837025	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1837025delA	uc001qjm.2	+						ADIPOR2_uc001qjn.2_Intron	NM_024551	NP_078827			adiponectin receptor 2						fatty acid oxidation|hormone-mediated signaling pathway	integral to membrane	hormone binding|receptor activity				0	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)															---	---	---	---
ADIPOR2	79602	broad.mit.edu	37	12	1863751	1863751	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1863751delA	uc001qjm.2	+						ADIPOR2_uc001qjn.2_Intron	NM_024551	NP_078827			adiponectin receptor 2						fatty acid oxidation|hormone-mediated signaling pathway	integral to membrane	hormone binding|receptor activity				0	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)															---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2381059	2381059	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2381059delA	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630			calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2521822	2521822	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2521822delT	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630			calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2719649	2719649	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2719649delC	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630			calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2743051	2743051	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2743051delA	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_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630			calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	2900343	2900344	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2900343_2900344insT								CACNA1C (93228 upstream) : FKBP4 (3764 downstream)																																			---	---	---	---
TULP3	7289	broad.mit.edu	37	12	3042824	3042824	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3042824delA	uc010seh.1	+						TULP3_uc010sef.1_Intron|TULP3_uc009zec.1_Intron|TULP3_uc010seg.1_Intron|TULP3_uc001qlj.2_Intron|TULP3_uc010sei.1_Intron	NM_003324	NP_003315			tubby like protein 3 isoform 1						G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
TSPAN9	10867	broad.mit.edu	37	12	3234740	3234741	+	Intron	INS	-	CT	CT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3234740_3234741insCT	uc001qlp.2	+							NM_006675	NP_006666			tetraspanin 9							integral to plasma membrane|membrane fraction				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)															---	---	---	---
EFCAB4B	84766	broad.mit.edu	37	12	3843795	3843796	+	Intron	INS	-	TG	TG	rs141431490	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3843795_3843796insTG	uc001qmj.2	-						EFCAB4B_uc010sen.1_Intron|EFCAB4B_uc010seo.1_Intron	NM_032680	NP_116069			EF-hand calcium binding domain 4B isoform c						activation of store-operated calcium channel activity|store-operated calcium entry	cytoplasm	calcium ion binding|protein binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	3869132	3869133	+	IGR	DEL	TC	-	-	rs149311969	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3869132_3869133delTC								EFCAB4B (6766 upstream) : PARP11 (48894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	4058767	4058768	+	IGR	INS	-	GA	GA	rs143686434	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4058767_4058768insGA								PARP11 (76159 upstream) : CCND2 (324134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	4186433	4186434	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4186433_4186434delAC								PARP11 (203825 upstream) : CCND2 (196468 downstream)																																			---	---	---	---
KCNA6	3742	broad.mit.edu	37	12	4930585	4930602	+	Intron	DEL	TGTGTGTGTGTGTGTGTG	-	-	rs71953017		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4930585_4930602delTGTGTGTGTGTGTGTGTG	uc001qng.2	+							NM_002235	NP_002226			potassium voltage-gated channel, shaker-related							voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(2)|ovary(1)	3															HNSCC(72;0.22)			---	---	---	---
Unknown	0	broad.mit.edu	37	12	5066866	5066866	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5066866delT								KCNA1 (39446 upstream) : KCNA5 (86219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	5123486	5123487	+	IGR	DEL	AC	-	-	rs146650714		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5123486_5123487delAC								KCNA1 (96066 upstream) : KCNA5 (29598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	5180707	5180708	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5180707_5180708delAG								KCNA5 (24759 upstream) : NTF3 (360572 downstream)																																			---	---	---	---
ANO2	57101	broad.mit.edu	37	12	5835303	5835304	+	Intron	DEL	AA	-	-	rs80154417		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5835303_5835304delAA	uc001qnm.2	-							NM_020373	NP_065106			anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7																		---	---	---	---
VWF	7450	broad.mit.edu	37	12	6058813	6058813	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6058813delA	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	6229014	6229017	+	Intron	DEL	AAAT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6229014_6229017delAAAT	uc001qnn.1	-						VWF_uc010set.1_Intron|VWF_uc001qno.1_Intron	NM_000552	NP_000543			von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
VWF	7450	broad.mit.edu	37	12	6236537	6236537	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6236537delA	uc001qnn.1	-						VWF_uc010set.1_5'Flank|VWF_uc001qno.1_5'Flank	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)													---	---	---	---
CD9	928	broad.mit.edu	37	12	6343637	6343638	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6343637_6343638delAA	uc001qnp.1	+						CD9_uc010sev.1_Intron|CD9_uc001qnq.1_Intron	NM_001769	NP_001760			CD9 antigen						cell adhesion|cellular component movement|fusion of sperm to egg plasma membrane|paranodal junction assembly|platelet activation|platelet degranulation	integral to plasma membrane|platelet alpha granule membrane				ovary(1)	1																		---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6699370	6699371	+	Intron	INS	-	A	A	rs142768189	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6699370_6699371insA	uc001qpo.2	-						CHD4_uc001qpn.2_Intron|CHD4_uc001qpp.2_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																		---	---	---	---
ING4	51147	broad.mit.edu	37	12	6770272	6770272	+	Intron	DEL	T	-	-	rs62688161		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6770272delT	uc001qpw.3	-						ING4_uc001qpv.3_Intron|ING4_uc001qpy.3_Intron|ING4_uc001qpx.3_Intron|ING4_uc009zes.2_Intron|ING4_uc009zet.2_Intron|ING4_uc009zeu.2_Intron|ING4_uc009zev.2_Intron	NM_001127582	NP_001121054			inhibitor of growth family, member 4 isoform 9						apoptosis|cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation|negative regulation of cell proliferation|negative regulation of growth|negative regulation of transcription, DNA-dependent|positive regulation of apoptosis	histone acetyltransferase complex	protein binding|transcription coactivator activity|zinc ion binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
CD4	920	broad.mit.edu	37	12	6911486	6911486	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6911486delT	uc001qqv.1	+						CD4_uc009zez.1_Intron|CD4_uc009zfa.1_Intron|CD4_uc009zfb.1_Intron|CD4_uc010sfj.1_Intron|CD4_uc009zfc.1_Intron|CD4_uc010sfk.1_Intron|CD4_uc010sfl.1_Intron	NM_000616	NP_000607			CD4 antigen precursor						cell adhesion|entry into host cell|immune response|induction by virus of host cell-cell fusion|initiation of viral infection|maintenance of protein location in cell|positive regulation of interleukin-2 biosynthetic process|positive regulation of protein kinase activity|protein palmitoleylation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|T cell selection|transmembrane receptor protein tyrosine kinase signaling pathway	early endosome|endoplasmic reticulum membrane|integral to membrane|T cell receptor complex	coreceptor activity|extracellular matrix structural constituent|glycoprotein binding|MHC class II protein binding|protein homodimerization activity|protein kinase binding|transmembrane receptor activity|zinc ion binding				0		Myeloproliferative disorder(1001;0.0122)																---	---	---	---
ATN1	1822	broad.mit.edu	37	12	7045189	7045189	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7045189delC	uc001qrw.1	+	5	996	c.759delC	c.(757-759)CACfs	p.H253fs	ATN1_uc001qrx.1_Frame_Shift_Del_p.H253fs|ATN1_uc001qry.1_Frame_Shift_Del_p.H252fs	NM_001007026	NP_001007027	P54259	ATN1_HUMAN	atrophin-1	253					cell death|central nervous system development	cytoplasm|nucleus	protein domain specific binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																		---	---	---	---
C1S	716	broad.mit.edu	37	12	7166833	7166834	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7166833_7166834insA	uc001qsj.2	+						C1S_uc001qsk.2_5'Flank|C1S_uc001qsl.2_5'Flank|C1S_uc009zfr.2_5'Flank|C1S_uc009zfs.2_5'Flank	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	7338794	7338794	+	IGR	DEL	G	-	-	rs113717305		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7338794delG								CLSTN3 (27266 upstream) : PEX5 (2965 downstream)																																			---	---	---	---
MFAP5	8076	broad.mit.edu	37	12	8808303	8808303	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8808303delT	uc001qut.1	-						MFAP5_uc001qus.2_Intron|MFAP5_uc009zge.1_Intron	NM_003480	NP_003471			microfibrillar associated protein 5 precursor							microfibril	extracellular matrix structural constituent			breast(1)	1	Lung SC(5;0.184)																	---	---	---	---
RIMKLB	57494	broad.mit.edu	37	12	8837106	8837106	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8837106delT	uc001quu.2	+						RIMKLB_uc009zgf.1_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	9171276	9171276	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9171276delA								KLRG1 (7938 upstream) : LOC144571 (46497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	9431039	9431039	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9431039delA								MIR1244 (38892 upstream) : LOC642846 (5214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	9520667	9520667	+	RNA	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9520667delG	uc009zgp.2	+	1		c.608delG								Homo sapiens cDNA clone IMAGE:4838157.																														---	---	---	---
CLECL1	160365	broad.mit.edu	37	12	9882173	9882175	+	Intron	DEL	TAC	-	-	rs148742345		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9882173_9882175delTAC	uc001qwj.2	-							NM_172004	NP_742001			type II transmembrane protein DCAL1							integral to membrane|plasma membrane	sugar binding				0																		---	---	---	---
OLR1	4973	broad.mit.edu	37	12	10316530	10316530	+	Intron	DEL	A	-	-	rs75825237		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10316530delA	uc001qxo.1	-						OLR1_uc010sgz.1_Intron|OLR1_uc010sha.1_Intron	NM_002543	NP_002534			oxidized low density lipoprotein (lectin-like)						blood circulation|blood coagulation|inflammatory response|leukocyte migration|proteolysis	extracellular region|integral to plasma membrane|membrane fraction	sugar binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	10359779	10359779	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10359779delA								C12orf59 (15377 upstream) : GABARAPL1 (5710 downstream)																																			---	---	---	---
PRB4	5545	broad.mit.edu	37	12	11224321	11224321	+	Intron	DEL	T	-	-	rs111710751		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11224321delT	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)			---	---	---	---
LRP6	4040	broad.mit.edu	37	12	12282496	12282496	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12282496delT	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)																---	---	---	---
DDX47	51202	broad.mit.edu	37	12	12886257	12886257	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12886257delA	uc001rav.2	+						APOLD1_uc001rau.3_Intron	NM_016355	NP_057439			DEAD (Asp-Glu-Ala-Asp) box polypeptide 47							nucleolus|nucleolus	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding				0		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	12998530	12998530	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12998530delT								DDX47 (15621 upstream) : RPL13AP20 (29881 downstream)																																			---	---	---	---
HTR7P1	93164	broad.mit.edu	37	12	13183918	13183918	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13183918delA	uc001rbh.2	+											Homo sapiens cDNA FLJ43688 fis, clone TBAES2003492.												0																		---	---	---	---
GSG1	83445	broad.mit.edu	37	12	13250025	13250025	+	Intron	DEL	A	-	-	rs35978682		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13250025delA	uc001rbn.2	-						GSG1_uc001rbj.2_5'Flank|GSG1_uc001rbk.2_5'Flank|GSG1_uc001rbl.2_5'Flank|GSG1_uc001rbm.2_5'Flank|GSG1_uc001rbo.2_Intron|GSG1_uc001rbp.2_Intron|GSG1_uc001rbq.1_Intron	NM_001080555	NP_001074024			germ cell associated 1 isoform 4							endoplasmic reticulum membrane|integral to membrane					0		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	13431196	13431196	+	IGR	DEL	T	-	-	rs11830349	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13431196delT								EMP1 (61489 upstream) : C12orf36 (92827 downstream)																																	OREG0021689	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	12	13508021	13508022	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13508021_13508022insA								EMP1 (138314 upstream) : C12orf36 (16001 downstream)																																			---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13724942	13724943	+	Intron	DEL	GA	-	-	rs1024840		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13724942_13724943delGA	uc001rbt.2	-							NM_000834	NP_000825			N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13843250	13843253	+	Intron	DEL	CATG	-	-	rs151062998	by1000genomes;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13843250_13843253delCATG	uc001rbt.2	-							NM_000834	NP_000825			N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	14083886	14083886	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14083886delA	uc001rbt.2	-							NM_000834	NP_000825			N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	14133591	14133591	+	5'Flank	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14133591delG	uc001rbt.2	-							NM_000834	NP_000825			N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	14406356	14406356	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14406356delA								GRIN2B (273334 upstream) : ATF7IP (112255 downstream)																																			---	---	---	---
ATF7IP	55729	broad.mit.edu	37	12	14610235	14610235	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14610235delT	uc001rbw.2	+						ATF7IP_uc010shs.1_Intron|ATF7IP_uc001rbu.2_Intron|ATF7IP_uc001rbv.1_Intron|ATF7IP_uc001rbx.2_Intron|ATF7IP_uc010sht.1_Intron|ATF7IP_uc001rby.3_Intron|ATF7IP_uc001rca.2_Intron	NM_018179	NP_060649			activating transcription factor 7 interacting						DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5																		---	---	---	---
PLBD1	79887	broad.mit.edu	37	12	14671874	14671874	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14671874delA	uc001rcc.1	-							NM_024829	NP_079105			phospholipase B domain containing 1						lipid catabolic process	extracellular region	hydrolase activity				0																		---	---	---	---
ERP27	121506	broad.mit.edu	37	12	15086007	15086008	+	Intron	INS	-	ATTC	ATTC	rs145855574	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15086007_15086008insATTC	uc001rco.2	-							NM_152321	NP_689534			endoplasmic reticulum protein 27 kDa precursor							endoplasmic reticulum lumen				breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	16938492	16938492	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16938492delT								LMO3 (175734 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	17259583	17259583	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17259583delT								LMO3 (496825 upstream) : RERGL (974221 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	18134117	18134117	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18134117delT								None (None upstream) : RERGL (99687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	19551733	19551733	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19551733delC								PLEKHA5 (22402 upstream) : AEBP2 (40875 downstream)																																			---	---	---	---
SLCO1B3	28234	broad.mit.edu	37	12	21029772	21029772	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21029772delT	uc001rek.2	+						SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron|SLCO1B3_uc001reo.2_Intron	NM_019844	NP_062818			solute carrier organic anion transporter family,						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)																	---	---	---	---
PYROXD1	79912	broad.mit.edu	37	12	21614917	21614917	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21614917delT	uc001rew.2	+						PYROXD1_uc009ziq.2_Intron|PYROXD1_uc009zir.2_Intron	NM_024854	NP_079130			pyridine nucleotide-disulphide oxidoreductase								oxidoreductase activity			ovary(1)	1																		---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	22068696	22068696	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22068696delT	uc001rfi.1	-	5	742	c.722delA	c.(721-723)AAGfs	p.K241fs	ABCC9_uc001rfh.2_Frame_Shift_Del_p.K241fs|ABCC9_uc001rfj.1_Frame_Shift_Del_p.K241fs	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	241	Cytoplasmic (Potential).				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
CMAS	55907	broad.mit.edu	37	12	22198174	22198174	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22198174delA	uc001rfm.2	+						CMAS_uc001rfn.2_5'Flank	NM_018686	NP_061156			cytidine monophospho-N-acetylneuraminic acid						lipopolysaccharide biosynthetic process	nucleus	N-acylneuraminate cytidylyltransferase activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	22251901	22251902	+	IGR	INS	-	TA	TA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22251901_22251902insTA								CMAS (33300 upstream) : ST8SIA1 (94424 downstream)																																			---	---	---	---
KIAA0528	9847	broad.mit.edu	37	12	22625136	22625136	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22625136delA	uc001rfq.2	-						KIAA0528_uc010sir.1_Intron|KIAA0528_uc010sis.1_Intron|KIAA0528_uc010sit.1_Intron|KIAA0528_uc010siu.1_Intron|KIAA0528_uc001rfr.2_Intron	NM_014802	NP_055617			hypothetical protein LOC9847								protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	23038747	23038748	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23038747_23038748insT								ETNK1 (195140 upstream) : SOX5 (646484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	23296769	23296770	+	Intron	DEL	TT	-	-	rs140867735		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23296769_23296770delTT	uc001rfu.1	+											Homo sapiens cDNA FLJ37414 fis, clone BRAWH1000157.																														---	---	---	---
SOX5	6660	broad.mit.edu	37	12	24659341	24659342	+	Intron	DEL	AA	-	-	rs35651729		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24659341_24659342delAA	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																		---	---	---	---
BCAT1	586	broad.mit.edu	37	12	25031692	25031693	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25031692_25031693insA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	25118756	25118758	+	IGR	DEL	TTT	-	-	rs71448097		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25118756_25118758delTTT								BCAT1 (16448 upstream) : C12orf77 (27612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	25470481	25470481	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25470481delG								KRAS (66618 upstream) : IFLTD1 (158535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	26342529	26342529	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26342529delA								BHLHE41 (64526 upstream) : SSPN (5740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	26456522	26456522	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26456522delT								SSPN (50669 upstream) : ITPR2 (31765 downstream)																																			---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26596618	26596618	+	Intron	DEL	C	-	-	rs2220406	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26596618delC	uc001rhg.2	-						ITPR2_uc009zjg.1_Intron	NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26617050	26617050	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26617050delT	uc001rhg.2	-						ITPR2_uc009zjg.1_Intron	NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26713205	26713205	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26713205delC	uc001rhg.2	-							NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26783380	26783380	+	Intron	DEL	A	-	-	rs67839691	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26783380delA	uc001rhg.2	-							NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
TM7SF3	51768	broad.mit.edu	37	12	27152717	27152717	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27152717delA	uc010sjl.1	-							NM_016551	NP_057635			transmembrane 7 superfamily member 3 precursor							integral to membrane|plasma membrane				upper_aerodigestive_tract(2)	2	Colorectal(261;0.0847)																	---	---	---	---
STK38L	23012	broad.mit.edu	37	12	27416461	27416461	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27416461delG	uc001rhr.2	+						STK38L_uc001rhs.2_Intron|STK38L_uc010sjm.1_Intron	NM_015000	NP_055815			serine/threonine kinase 38 like						intracellular protein kinase cascade|regulation of cellular component organization	actin cytoskeleton|cytoplasm	actin binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|kidney(1)	5	Colorectal(261;0.0847)																	---	---	---	---
STK38L	23012	broad.mit.edu	37	12	27467937	27467937	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27467937delT	uc001rhr.2	+						STK38L_uc001rhs.2_Intron|STK38L_uc010sjm.1_Intron|STK38L_uc010sjn.1_Intron|STK38L_uc010sjo.1_5'Flank	NM_015000	NP_055815			serine/threonine kinase 38 like						intracellular protein kinase cascade|regulation of cellular component organization	actin cytoskeleton|cytoplasm	actin binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|kidney(1)	5	Colorectal(261;0.0847)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	28015228	28015228	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28015228delA								KLHDC5 (59256 upstream) : PTHLH (95790 downstream)																																			---	---	---	---
CCDC91	55297	broad.mit.edu	37	12	28546313	28546313	+	Intron	DEL	T	-	-	rs79816596		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28546313delT	uc001riq.2	+						CCDC91_uc001rio.2_Intron|CCDC91_uc009zjk.2_Intron|CCDC91_uc001rip.1_Intron|CCDC91_uc001rir.2_Intron|CCDC91_uc009zjl.2_Intron	NM_018318	NP_060788			GGA binding partner						protein transport	Golgi apparatus|membrane				central_nervous_system(1)	1	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	28703639	28703639	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28703639delG								CCDC91 (541 upstream) : FAR2 (598593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	29244586	29244586	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29244586delA								CCDC91 (541488 upstream) : FAR2 (57646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	29264163	29264164	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29264163_29264164delTT								CCDC91 (561065 upstream) : FAR2 (38068 downstream)																																			---	---	---	---
FAR2	55711	broad.mit.edu	37	12	29306272	29306272	+	Intron	DEL	A	-	-	rs35811111		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29306272delA	uc001ris.3	+							NM_018099	NP_060569			fatty acyl CoA reductase 2						ether lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	29985413	29985413	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29985413delT								TMTC1 (47721 upstream) : IPO8 (796510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30397548	30397549	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30397548_30397549delAC								TMTC1 (459856 upstream) : IPO8 (384374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30535731	30535731	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30535731delA								TMTC1 (598039 upstream) : IPO8 (246192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	31164621	31164621	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31164621delA								TSPAN11 (15085 upstream) : DDX11 (62158 downstream)																																			---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31559081	31559081	+	Intron	DEL	T	-	-	rs79912456		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31559081delT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	31957590	31957590	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31957590delT								H3F3C (12415 upstream) : C12orf35 (154763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	32089333	32089334	+	IGR	INS	-	C	C	rs145121392	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32089333_32089334insC								H3F3C (144158 upstream) : C12orf35 (23019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	32228548	32228548	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32228548delT								C12orf35 (82517 upstream) : BICD1 (31637 downstream)																																			---	---	---	---
BICD1	636	broad.mit.edu	37	12	32363057	32363057	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32363057delT	uc001rku.2	+						BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron	NM_001714	NP_001705			bicaudal D homolog 1 isoform 1						anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)															---	---	---	---
BICD1	636	broad.mit.edu	37	12	32453041	32453041	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32453041delT	uc001rku.2	+						BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron	NM_001714	NP_001705			bicaudal D homolog 1 isoform 1						anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)															---	---	---	---
FGD4	121512	broad.mit.edu	37	12	32681331	32681331	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32681331delT	uc001rkz.2	+						FGD4_uc001rlc.2_Intron|FGD4_uc001rky.2_Intron|FGD4_uc001rla.2_Intron|FGD4_uc001rkx.3_Intron	NM_139241	NP_640334			FYVE, RhoGEF and PH domain containing 4						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	33181052	33181053	+	IGR	INS	-	TC	TC	rs149874252	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33181052_33181053insTC								PKP2 (131272 upstream) : SYT10 (347295 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34656193	34656193	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34656193delG								ALG10 (474959 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	37880402	37880402	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:37880402delG								None (None upstream) : ALG10B (830155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	37998330	37998330	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:37998330delT								None (None upstream) : ALG10B (712227 downstream)																																			---	---	---	---
CPNE8	144402	broad.mit.edu	37	12	39061595	39061595	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39061595delT	uc001rls.1	-						CPNE8_uc001rlr.1_Intron	NM_153634	NP_705898			copine VIII											pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	39444654	39444654	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39444654delT								CPNE8 (145234 upstream) : KIF21A (242377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	39673206	39673206	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39673206delA								CPNE8 (373786 upstream) : KIF21A (13825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	39901948	39901948	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39901948delT								KIF21A (65030 upstream) : ABCD2 (43074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	40857190	40857190	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40857190delT								LRRK2 (94106 upstream) : CNTN1 (229168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	40954133	40954134	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40954133_40954134delAA	uc001rmk.1	+						uc009zjx.1_Intron					Homo sapiens cDNA FLJ35746 fis, clone TESTI2004399, moderately similar to APOMUCIN.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	40990431	40990431	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40990431delT								LRRK2 (227347 upstream) : CNTN1 (95927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	41076430	41076430	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41076430delT								LRRK2 (313346 upstream) : CNTN1 (9928 downstream)																																			---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41641768	41641772	+	Intron	DEL	GACGT	-	-	rs143805440		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41641768_41641772delGACGT	uc010skn.1	+							NM_013377	NP_037509			PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41792199	41792199	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41792199delA	uc010skn.1	+							NM_013377	NP_037509			PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	42098234	42098235	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42098234_42098235insT								PDZRN4 (129850 upstream) : GXYLT1 (377415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	42424334	42424334	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42424334delT								PDZRN4 (455950 upstream) : GXYLT1 (51316 downstream)																																			---	---	---	---
GXYLT1	283464	broad.mit.edu	37	12	42524350	42524350	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42524350delA	uc001rms.3	-						GXYLT1_uc001rmt.3_Intron	NM_173601	NP_775872			glycosyltransferase 8 domain containing 3						O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0																		---	---	---	---
YAF2	10138	broad.mit.edu	37	12	42572689	42572689	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42572689delA	uc001rmv.2	-						YAF2_uc001rmw.2_Intron|YAF2_uc010sko.1_Intron|YAF2_uc010skp.1_Intron	NM_005748	NP_005739			YY1 associated factor 2						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription coactivator activity|transcription corepressor activity|zinc ion binding				0	all_cancers(12;0.000425)	Lung NSC(34;0.0402)|all_lung(34;0.057)		GBM - Glioblastoma multiforme(48;0.0514)														---	---	---	---
PPHLN1	51535	broad.mit.edu	37	12	42796471	42796471	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42796471delT	uc001rng.1	+						PPHLN1_uc001rmy.2_Intron|PPHLN1_uc001rne.2_Intron|PPHLN1_uc001rnb.2_Intron|PPHLN1_uc001rnd.2_Intron|PPHLN1_uc001rnc.2_Intron|PPHLN1_uc001rnf.2_Intron|PPHLN1_uc010skq.1_Intron|PPHLN1_uc010skr.1_Intron|PPHLN1_uc010sks.1_Intron|PPHLN1_uc010skt.1_Intron|PPHLN1_uc001rni.1_Intron|PPHLN1_uc001rnh.1_Intron|PPHLN1_uc010sku.1_Intron	NM_016488	NP_057572			periphilin 1 isoform 1						keratinization	cytoplasm|nucleus				ovary(1)|breast(1)	2	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)														---	---	---	---
PRICKLE1	144165	broad.mit.edu	37	12	42884604	42884605	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42884604_42884605insT	uc001rnm.2	-						PRICKLE1_uc009zka.2_Intron	NM_153026	NP_694571			prickle homolog 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)														---	---	---	---
PRICKLE1	144165	broad.mit.edu	37	12	42979282	42979282	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42979282delC	uc001rnm.2	-						PRICKLE1_uc009zka.2_Intron	NM_153026	NP_694571			prickle homolog 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	43059838	43059838	+	IGR	DEL	T	-	-	rs34403302		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43059838delT								PRICKLE1 (76266 upstream) : ADAMTS20 (688175 downstream)																																			---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43752840	43752841	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43752840_43752841delCT	uc010skx.1	-							NM_025003	NP_079279			a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)														---	---	---	---
ANO6	196527	broad.mit.edu	37	12	45825315	45825315	+	3'UTR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45825315delG	uc001roo.2	+	20					ANO6_uc010sld.1_Intron|ANO6_uc010sle.1_Intron|ANO6_uc010slf.1_3'UTR|ANO6_uc010slg.1_3'UTR	NM_001025356	NP_001020527			anoctamin 6 isoform a						activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	46043235	46043235	+	IGR	DEL	A	-	-	rs80354258		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46043235delA								ANO6 (209048 upstream) : LOC400027 (76575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	46404796	46404796	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46404796delT								SFRS2IP (18893 upstream) : SLC38A1 (172047 downstream)																																			---	---	---	---
SLC38A1	81539	broad.mit.edu	37	12	46591290	46591290	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46591290delA	uc001rpa.2	-						SLC38A1_uc001rpb.2_Intron|SLC38A1_uc001rpc.2_Intron|SLC38A1_uc001rpd.2_Intron|SLC38A1_uc001rpe.2_Intron|SLC38A1_uc009zkj.1_Intron	NM_030674	NP_109599			amino acid transporter system A1						cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)															---	---	---	---
SLC38A1	81539	broad.mit.edu	37	12	46623311	46623311	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46623311delA	uc001rpa.2	-						SLC38A1_uc001rpb.2_Intron|SLC38A1_uc001rpc.2_Intron|SLC38A1_uc001rpd.2_Intron|SLC38A1_uc001rpe.2_Intron|SLC38A1_uc010slh.1_Intron|SLC38A1_uc009zkj.1_Intron	NM_030674	NP_109599			amino acid transporter system A1						cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	46844809	46844810	+	IGR	INS	-	TCCC	TCCC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46844809_46844810insTCCC								SLC38A2 (78164 upstream) : SLC38A4 (313734 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47343414	47343414	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47343414delT								SLC38A4 (123634 upstream) : AMIGO2 (126077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47395461	47395461	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47395461delA								SLC38A4 (175681 upstream) : AMIGO2 (74030 downstream)																																			---	---	---	---
FAM113B	91523	broad.mit.edu	37	12	47597493	47597493	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47597493delT	uc001rpn.2	+							NM_138371	NP_612380			hypothetical protein LOC91523								hydrolase activity			skin(3)|ovary(2)	5	Renal(347;0.138)|Lung SC(27;0.192)																	---	---	---	---
FAM113B	91523	broad.mit.edu	37	12	47601815	47601815	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47601815delT	uc001rpn.2	+						uc001rpo.1_5'Flank	NM_138371	NP_612380			hypothetical protein LOC91523								hydrolase activity			skin(3)|ovary(2)	5	Renal(347;0.138)|Lung SC(27;0.192)																	---	---	---	---
HDAC7	51564	broad.mit.edu	37	12	48181527	48181527	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48181527delG	uc010slo.1	-	21	2616	c.2421delC	c.(2419-2421)CCCfs	p.P807fs	HDAC7_uc009zku.2_RNA|HDAC7_uc001rqe.2_Frame_Shift_Del_p.P241fs|HDAC7_uc001rqj.3_Frame_Shift_Del_p.P770fs|HDAC7_uc001rqk.3_Frame_Shift_Del_p.P790fs|HDAC7_uc010slp.1_Frame_Shift_Del_p.P51fs	NM_015401	NP_056216	Q8WUI4	HDAC7_HUMAN	histone deacetylase 7 isoform a	768	Histone deacetylase.				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)														---	---	---	---
ZNF641	121274	broad.mit.edu	37	12	48738938	48738938	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48738938delT	uc001rrn.1	-						ZNF641_uc001rro.1_Intron|ZNF641_uc010sls.1_Intron	NM_152320	NP_689533			zinc finger protein 641						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
C12orf54	121273	broad.mit.edu	37	12	48882264	48882265	+	Intron	INS	-	A	A	rs71439447		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48882264_48882265insA	uc001rrr.2	+						C12orf54_uc009zky.1_Intron	NM_152319	NP_689532			hypothetical protein LOC121273												0																		---	---	---	---
DDX23	9416	broad.mit.edu	37	12	49235170	49235170	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49235170delA	uc001rsm.2	-							NM_004818	NP_004809			DEAD (Asp-Glu-Ala-Asp) box polypeptide 23							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent RNA helicase activity|nucleic acid binding|protein binding			kidney(3)|ovary(1)|lung(1)|skin(1)	6																		---	---	---	---
SPATS2	65244	broad.mit.edu	37	12	49861939	49861939	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49861939delT	uc001rud.2	+						SPATS2_uc001rue.2_Intron|SPATS2_uc009zli.1_Intron|SPATS2_uc001ruf.2_Intron|SPATS2_uc001rug.2_Intron	NM_023071	NP_075559			spermatogenesis associated, serine-rich 2							cytoplasm				breast(1)	1																		---	---	---	---
SPATS2	65244	broad.mit.edu	37	12	49888986	49888986	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49888986delT	uc001rud.2	+						SPATS2_uc001rue.2_Intron|SPATS2_uc009zli.1_Intron|SPATS2_uc001ruf.2_Intron|SPATS2_uc001rug.2_Intron	NM_023071	NP_075559			spermatogenesis associated, serine-rich 2							cytoplasm				breast(1)	1																		---	---	---	---
GPD1	2819	broad.mit.edu	37	12	50501749	50501749	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50501749delC	uc001rvz.2	+						GPD1_uc001rwa.2_Intron	NM_005276	NP_005267			glycerol-3-phosphate dehydrogenase 1 (soluble)						glycerol-3-phosphate catabolic process|triglyceride biosynthetic process	cytosol|glycerol-3-phosphate dehydrogenase complex	glycerol-3-phosphate dehydrogenase|protein homodimerization activity				0					NADH(DB00157)													---	---	---	---
LASS5	91012	broad.mit.edu	37	12	50527855	50527856	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50527855_50527856delAA	uc001rwd.3	-						LASS5_uc001rwc.2_Intron|LASS5_uc001rwe.3_Intron|LASS5_uc001rwf.3_Intron	NM_147190	NP_671723			LAG1 homolog, ceramide synthase 5						ceramide biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity				0																		---	---	---	---
MIR1293	100302220	broad.mit.edu	37	12	50627995	50627996	+	RNA	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50627995_50627996delTT	hsa-mir-1293|MI0006355	-						LIMA1_uc001rwj.3_Intron|LIMA1_uc001rwk.3_Intron|LIMA1_uc010smr.1_Intron|LIMA1_uc010sms.1_Intron																	0																		---	---	---	---
LARP4	113251	broad.mit.edu	37	12	50824444	50824444	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50824444delT	uc001rwp.1	+						LARP4_uc001rwo.1_Intron|LARP4_uc001rwq.1_Intron|LARP4_uc001rwr.1_Intron|LARP4_uc001rws.1_Intron|LARP4_uc001rwm.2_Intron|LARP4_uc001rwn.2_Intron	NM_052879	NP_443111			c-Mpl binding protein isoform a								nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	50922014	50922014	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50922014delT	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	50937061	50937061	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50937061delT	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	51080676	51080676	+	Intron	DEL	A	-	-	rs62672860		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51080676delA	uc001rwv.2	+						DIP2B_uc009zlt.2_Intron	NM_173602	NP_775873			DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6																		---	---	---	---
SLC11A2	4891	broad.mit.edu	37	12	51380553	51380554	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51380553_51380554insA	uc001rxe.3	-						SLC11A2_uc001rxd.3_Intron|SLC11A2_uc001rxc.3_Intron|SLC11A2_uc001rxf.2_Intron|SLC11A2_uc001rxg.1_3'UTR|SLC11A2_uc010smx.1_3'UTR|SLC11A2_uc001rxh.1_3'UTR|SLC11A2_uc001rxj.1_3'UTR|SLC11A2_uc001rxi.2_3'UTR|SLC11A2_uc001rxk.1_3'UTR	NM_000617	NP_000608			solute carrier family 11 (proton-coupled						activation of caspase activity|cellular iron ion homeostasis|cellular response to oxidative stress|detection of oxygen|ferrous iron import|multicellular organismal iron ion homeostasis|response to hypoxia|response to iron ion	apical plasma membrane|basal part of cell|cell surface|cytoplasmic vesicle|early endosome|late endosome|late endosome membrane|lysosomal membrane|lysosome|nucleus|paraferritin complex|perinuclear region of cytoplasm|perinuclear region of cytoplasm|plasma membrane|recycling endosome|trans-Golgi network	cadmium ion transmembrane transporter activity|cadmium ion transmembrane transporter activity|cobalt ion transmembrane transporter activity|copper ion transmembrane transporter activity|ferrous iron transmembrane transporter activity|ferrous iron transmembrane transporter activity|lead ion transmembrane transporter activity|lead ion transmembrane transporter activity|manganese ion transmembrane transporter activity|manganese ion transmembrane transporter activity|nickel ion transmembrane transporter activity|protein binding|solute:hydrogen symporter activity|vanadium ion transmembrane transporter activity|zinc ion transmembrane transporter activity			large_intestine(1)	1																		---	---	---	---
CSRNP2	81566	broad.mit.edu	37	12	51463464	51463464	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51463464delT	uc001rxu.1	-							NM_030809	NP_110436			TGF-beta induced apoptosis protein 12						apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
SMAGP	57228	broad.mit.edu	37	12	51649565	51649566	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51649565_51649566insT	uc001ryc.1	-						SMAGP_uc001ryd.1_Intron|SMAGP_uc001rye.1_Intron|SMAGP_uc001ryf.1_Intron	NM_001033873	NP_001029045			small trans-membrane and glycosylated protein							cytoplasmic vesicle membrane|integral to membrane|plasma membrane					0																		---	---	---	---
BIN2	51411	broad.mit.edu	37	12	51715189	51715189	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51715189delT	uc001ryg.2	-						BIN2_uc009zlz.2_Intron|BIN2_uc001ryh.2_Intron|BIN2_uc010sng.1_Intron	NM_016293	NP_057377			bridging integrator 2							cytoplasm	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	52268981	52268981	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52268981delA								FIGNL2 (52773 upstream) : ANKRD33 (12812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	52297731	52297732	+	IGR	INS	-	AC	AC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52297731_52297732insAC								ANKRD33 (12227 upstream) : ACVRL1 (3470 downstream)																																			---	---	---	---
ACVRL1	94	broad.mit.edu	37	12	52311966	52311966	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52311966delG	uc001rzj.2	+						ACVRL1_uc001rzk.2_Intron|ACVRL1_uc010snm.1_Intron	NM_000020	NP_000011			activin A receptor type II-like 1 precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|blood vessel maturation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of endothelial cell migration|negative regulation of focal adhesion assembly|positive regulation of BMP signaling pathway|positive regulation of transcription, DNA-dependent|regulation of blood pressure|regulation of blood vessel endothelial cell migration|regulation of DNA replication|regulation of endothelial cell proliferation|transforming growth factor beta receptor signaling pathway|wound healing, spreading of epidermal cells	cell surface|integral to plasma membrane	activin binding|activin receptor activity, type I|ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			lung(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)									Hereditary_Hemorrhagic_Telangiectasia				---	---	---	---
Unknown	0	broad.mit.edu	37	12	52333348	52333349	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52333348_52333349delTT								ACVRL1 (16204 upstream) : ACVR1B (12137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	52501562	52501562	+	RNA	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52501562delT	uc009zme.1	+	3		c.961delT								Homo sapiens olfactory receptor, family 7, subfamily E, member 47 pseudogene, mRNA (cDNA clone IMAGE:5590288).																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	52526038	52526039	+	IGR	INS	-	G	G	rs114702286	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52526038_52526039insG								C12orf44 (54760 upstream) : KRT80 (36742 downstream)																																			---	---	---	---
KRT77	374454	broad.mit.edu	37	12	53099679	53099679	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53099679delA	uc001saw.2	-						KRT77_uc009zmi.2_5'Flank	NM_175078	NP_778253			keratin 77							keratin filament	structural molecule activity			ovary(1)	1																		---	---	---	---
KRT79	338785	broad.mit.edu	37	12	53223675	53223675	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53223675delA	uc001sbb.2	-						KRT79_uc001sba.2_Intron	NM_175834	NP_787028			keratin 6L							keratin filament	structural molecule activity			ovary(2)|skin(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	53265114	53265114	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53265114delA								KRT78 (22336 upstream) : KRT8 (25857 downstream)																																			---	---	---	---
SPRYD3	84926	broad.mit.edu	37	12	53475414	53475414	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53475414delT	uc001sbt.1	-						SPRYD3_uc010snw.1_5'Flank	NM_032840	NP_116229			SPRY domain containing 3											central_nervous_system(1)	1																		---	---	---	---
SP7	121340	broad.mit.edu	37	12	53729815	53729815	+	5'Flank	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53729815delG	uc001sct.2	-						SP7_uc001scu.2_Intron|SP7_uc001scv.2_Intron	NM_152860	NP_690599			osterix						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	53742697	53742697	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53742697delT								SP7 (12531 upstream) : SP1 (31282 downstream)																																			---	---	---	---
SP1	6667	broad.mit.edu	37	12	53782762	53782762	+	Intron	DEL	A	-	-	rs72249045		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53782762delA	uc001scw.2	+						SP1_uc010sog.1_Intron	NM_138473	NP_612482			Sp1 transcription factor isoform a						positive regulation by host of viral transcription|positive regulation of transcription from RNA polymerase II promoter	cytoplasm	double-stranded DNA binding|histone deacetylase binding|HMG box domain binding|protein C-terminus binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(357;0.00527)														---	---	---	---
SP1	6667	broad.mit.edu	37	12	53790059	53790060	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53790059_53790060delAA	uc001scw.2	+						SP1_uc010sog.1_Intron	NM_138473	NP_612482			Sp1 transcription factor isoform a						positive regulation by host of viral transcription|positive regulation of transcription from RNA polymerase II promoter	cytoplasm	double-stranded DNA binding|histone deacetylase binding|HMG box domain binding|protein C-terminus binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(357;0.00527)														---	---	---	---
MAP3K12	7786	broad.mit.edu	37	12	53887499	53887500	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53887499_53887500insT	uc001sdm.1	-						MAP3K12_uc001sdn.1_Intron	NM_006301	NP_006292			mitogen-activated protein kinase kinase kinase						histone phosphorylation|JNK cascade|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation	cytosol|membrane fraction|plasma membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			lung(2)|ovary(1)|breast(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	54099446	54099446	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54099446delT								ATP5G2 (28934 upstream) : CALCOCO1 (5457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	54128755	54128756	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54128755_54128756insG								CALCOCO1 (7448 upstream) : HOXC13 (203820 downstream)																																			---	---	---	---
HNRNPA1	3178	broad.mit.edu	37	12	54676166	54676166	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54676166delT	uc001sfl.2	+						CBX5_uc001sfk.3_5'Flank|CBX5_uc001sfi.3_5'Flank|HNRNPA1_uc001sfm.2_Intron|HNRNPA1_uc009zng.2_Intron|HNRNPA1_uc009znh.2_Intron|HNRNPA1_uc009zni.2_Intron|HNRNPA1_uc001sfn.2_Intron|HNRNPA1_uc001sfo.3_Intron|HNRNPA1_uc001sfp.1_Intron|HNRNPA1_uc009znj.1_Intron	NM_031157	NP_112420			heterogeneous nuclear ribonucleoprotein A1						interspecies interaction between organisms|mRNA transport|nuclear import	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	nucleotide binding|protein binding|single-stranded DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
COPZ1	22818	broad.mit.edu	37	12	54744007	54744008	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54744007_54744008delTT	uc001sfs.1	+						COPZ1_uc001sft.2_Intron|COPZ1_uc009znm.1_Intron|COPZ1_uc010sot.1_Intron	NM_016057	NP_057141			coatomer protein complex, subunit zeta 1						COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	55047068	55047069	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55047068_55047069delGT								DCD (4919 upstream) : MUCL1 (201230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55328230	55328230	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55328230delA								MUCL1 (76058 upstream) : KIAA0748 (15635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55481224	55481224	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55481224delT								NEUROD4 (57424 upstream) : OR9K2 (42329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55535852	55535852	+	IGR	DEL	A	-	-	rs112459891		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55535852delA								OR9K2 (11293 upstream) : OR10A7 (78957 downstream)																																			---	---	---	---
STAT2	6773	broad.mit.edu	37	12	56736218	56736219	+	3'UTR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56736218_56736219delAA	uc001slc.2	-	24					STAT2_uc001slb.2_3'UTR|STAT2_uc001sld.2_3'UTR	NM_005419	NP_005410			signal transducer and activator of transcription						interspecies interaction between organisms|JAK-STAT cascade|regulation of transcription from RNA polymerase II promoter|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	cytosol|nucleoplasm|plasma membrane	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3																		---	---	---	---
RBMS2	5939	broad.mit.edu	37	12	56913909	56913909	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56913909delA	uc001sln.2	+						RBMS2_uc010sqp.1_5'Flank|RBMS2_uc010sqq.1_5'Flank|RBMS2_uc009zou.2_5'Flank	NM_002898	NP_002889			RNA binding motif, single stranded interacting						RNA processing	nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
RBMS2	5939	broad.mit.edu	37	12	56952971	56952971	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56952971delT	uc001sln.2	+						RBMS2_uc010sqp.1_Intron|RBMS2_uc010sqq.1_Intron|RBMS2_uc009zou.2_Intron	NM_002898	NP_002889			RNA binding motif, single stranded interacting						RNA processing	nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
ATP5B	506	broad.mit.edu	37	12	57038363	57038363	+	Intron	DEL	A	-	-	rs71642550		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57038363delA	uc001slr.2	-						SNORD59B_uc001sls.1_5'Flank	NM_001686	NP_001677			mitochondrial ATP synthase beta subunit						angiogenesis|ATP hydrolysis coupled proton transport|regulation of intracellular pH|respiratory electron transport chain	cell surface|mitochondrial nucleoid|mitochondrial proton-transporting ATP synthase, catalytic core|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|hydrogen-exporting ATPase activity, phosphorylative mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)	1																		---	---	---	---
TMEM194A	23306	broad.mit.edu	37	12	57458047	57458047	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57458047delT	uc001smy.2	-						TMEM194A_uc001smx.2_Intron|TMEM194A_uc010sra.1_Intron	NM_001130963	NP_001124435			transmembrane protein 194A isoform a							integral to membrane					0																		---	---	---	---
TMEM194A	23306	broad.mit.edu	37	12	57466469	57466469	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
NXPH4	11247	broad.mit.edu	37	12	57609692	57609693	+	5'Flank	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57609692_57609693delGA	uc010srf.1	+						NXPH4_uc009zpj.2_5'Flank	NM_007224	NP_009155			neurexophilin 4 precursor						neuropeptide signaling pathway	extracellular region					0																		---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57672278	57672278	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57672278delA	uc009zpm.1	-						R3HDM2_uc010srn.1_Intron|R3HDM2_uc001snu.2_Intron|R3HDM2_uc001snr.2_Intron|R3HDM2_uc001sns.2_Intron|R3HDM2_uc001snt.2_Intron|R3HDM2_uc009zpn.1_Intron	NM_014925	NP_055740			R3H domain containing 2							nucleus	nucleic acid binding			ovary(2)	2																		---	---	---	---
CTDSP2	10106	broad.mit.edu	37	12	58228907	58228908	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58228907_58228908delAA	uc001sqm.2	-						CTDSP2_uc009zqf.2_Intron|CTDSP2_uc009zqg.2_Intron	NM_005730	NP_005721			nuclear LIM interactor-interacting factor 2						protein dephosphorylation	nucleus|soluble fraction	CTD phosphatase activity|metal ion binding			central_nervous_system(1)	1	all_neural(12;0.00559)|Glioma(12;0.0143)|Melanoma(17;0.122)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	59583151	59583152	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59583151_59583152delTT								LRIG3 (268889 upstream) : SLC16A7 (406696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	60305961	60305961	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60305961delA								SLC16A7 (130554 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	60456892	60456892	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60456892delA								SLC16A7 (281485 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	60935419	60935420	+	IGR	INS	-	ACAC	ACAC	rs142621114	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60935419_60935420insACAC								SLC16A7 (760012 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61420273	61420273	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61420273delT								None (None upstream) : FAM19A2 (681770 downstream)																																			---	---	---	---
PPM1H	57460	broad.mit.edu	37	12	63142310	63142315	+	Intron	DEL	ACACAC	-	-	rs150410425		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63142310_63142315delACACAC	uc001srk.3	-							NM_020700	NP_065751			protein phosphatase 1H (PP2C domain containing)								phosphoprotein phosphatase activity			lung(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	63355428	63355429	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63355428_63355429delTT								PPM1H (26513 upstream) : AVPR1A (184787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	63779368	63779369	+	IGR	DEL	TA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63779368_63779369delTA								AVPR1A (232778 upstream) : DPY19L2 (173324 downstream)																																			---	---	---	---
DPY19L2	283417	broad.mit.edu	37	12	63992649	63992649	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63992649delT	uc001srp.1	-						DPY19L2_uc009zqk.1_Intron	NM_173812	NP_776173			dpy-19-like 2						multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	64562519	64562519	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64562519delA								SRGAP1 (20906 upstream) : C12orf66 (23901 downstream)																																			---	---	---	---
C12orf56	115749	broad.mit.edu	37	12	64746925	64746925	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64746925delT	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)														---	---	---	---
RASSF3	283349	broad.mit.edu	37	12	65019524	65019525	+	Intron	INS	-	GCC	GCC	rs150264333	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65019524_65019525insGCC	uc001ssd.2	+						RASSF3_uc009zqn.2_Intron	NM_178169	NP_835463			Ras association (RalGDS/AF-6) domain family						signal transduction	cytoplasm|microtubule	identical protein binding				0			Lung(2;0.00133)|LUAD - Lung adenocarcinoma(6;0.0665)|LUSC - Lung squamous cell carcinoma(43;0.132)	GBM - Glioblastoma multiforme(28;0.0611)														---	---	---	---
LEMD3	23592	broad.mit.edu	37	12	65576398	65576398	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65576398delT	uc001ssl.1	+						LEMD3_uc009zqo.1_Intron	NM_014319	NP_055134			LEM domain containing 3						negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway	integral to nuclear inner membrane|membrane fraction	DNA binding|nucleotide binding|protein binding			central_nervous_system(3)|ovary(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	65875871	65875871	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65875871delT								MSRB3 (15191 upstream) : RPSAP52 (275932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	66078670	66078670	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66078670delA								MSRB3 (217990 upstream) : RPSAP52 (73133 downstream)																																			---	---	---	---
HMGA2	8091	broad.mit.edu	37	12	66221759	66221759	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66221759delT	uc001ssx.2	+						RPSAP52_uc001sso.2_5'Flank|HMGA2_uc001ssw.1_Intron|HMGA2_uc001ssp.1_Intron|HMGA2_uc010ssv.1_Intron|HMGA2_uc001sss.1_Intron|HMGA2_uc001sst.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								---	---	---	---
HELB	92797	broad.mit.edu	37	12	66716672	66716672	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66716672delT	uc001sti.2	+						HELB_uc010ssz.1_Intron|HELB_uc009zqt.1_Intron	NM_033647	NP_387467			helicase (DNA) B						DNA replication, synthesis of RNA primer		ATP binding|ATP-dependent 5'-3' DNA helicase activity|single-stranded DNA-dependent ATP-dependent DNA helicase activity			central_nervous_system(1)|pancreas(1)	2			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	67384758	67384761	+	IGR	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67384758_67384761delAAAA								GRIP1 (186864 upstream) : CAND1 (278300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	67579767	67579768	+	IGR	INS	-	T	T	rs61919011	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67579767_67579768insT								GRIP1 (381873 upstream) : CAND1 (83293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	67816882	67816883	+	IGR	DEL	TT	-	-	rs35205377		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67816882_67816883delTT								CAND1 (108494 upstream) : DYRK2 (225629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68039472	68039472	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68039472delA								CAND1 (331084 upstream) : DYRK2 (3040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68057800	68057802	+	IGR	DEL	TTT	-	-	rs72279868		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68057800_68057802delTTT								DYRK2 (1357 upstream) : IFNG (490748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68368111	68368111	+	IGR	DEL	T	-	-	rs141619924	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68368111delT								DYRK2 (311668 upstream) : IFNG (180439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68585452	68585452	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68585452delT								IFNG (31931 upstream) : IL26 (9677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	69552695	69552696	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69552695_69552696delTT								CPM (195675 upstream) : CPSF6 (80621 downstream)																																			---	---	---	---
CPSF6	11052	broad.mit.edu	37	12	69646940	69646940	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69646940delT	uc001sut.3	+						CPSF6_uc001suu.3_Intron	NM_007007	NP_008938			cleavage and polyadenylation specific factor 6,						mRNA polyadenylation|protein tetramerization	mRNA cleavage factor complex|paraspeckles|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding				0	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)															---	---	---	---
FRS2	10818	broad.mit.edu	37	12	69958024	69958025	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69958024_69958025delTT	uc001suy.2	+						FRS2_uc001suz.2_Intron|FRS2_uc009zrj.2_Intron|FRS2_uc009zrk.2_Intron	NM_006654	NP_006645			fibroblast growth factor receptor substrate 2						activation of MAPKK activity|activation of phospholipase C activity|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|transmembrane receptor protein tyrosine phosphatase signaling pathway	endomembrane system|endosome|integral to plasma membrane|membrane fraction	fibroblast growth factor receptor binding|insulin receptor binding|phosphatase activator activity|transmembrane receptor protein tyrosine kinase adaptor activity			prostate(1)|kidney(1)	2	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	70031922	70031922	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70031922delA								LRRC10 (26980 upstream) : BEST3 (5218 downstream)																																			---	---	---	---
BEST3	144453	broad.mit.edu	37	12	70049361	70049362	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70049361_70049362insG	uc001svg.2	-	10	1559_1560	c.1332_1333insC	c.(1330-1335)CCCAGGfs	p.P444fs	BEST3_uc001svd.1_Intron|BEST3_uc001sve.1_Intron|BEST3_uc001svf.2_Frame_Shift_Ins_p.P231fs|BEST3_uc010stm.1_Frame_Shift_Ins_p.P338fs	NM_032735	NP_116124	Q8N1M1	BEST3_HUMAN	vitelliform macular dystrophy 2-like 3 isoform	444_445	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	chloride channel activity				0	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)															---	---	---	---
ZFC3H1	196441	broad.mit.edu	37	12	72009100	72009100	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72009100delA	uc001swo.2	-							NM_144982	NP_659419			proline/serine-rich coiled-coil 2						RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	72592713	72592714	+	IGR	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72592713_72592714delGA								TPH2 (166492 upstream) : LOC283392 (63614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74743472	74743473	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74743472_74743473delTC								None (None upstream) : ATXN7L3B (188078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74758138	74758138	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74758138delA								None (None upstream) : ATXN7L3B (173413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	75092382	75092383	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75092382_75092383delTC								ATXN7L3B (157159 upstream) : KCNC2 (341514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	75249017	75249017	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75249017delT								ATXN7L3B (313794 upstream) : KCNC2 (184880 downstream)																																			---	---	---	---
KCNC2	3747	broad.mit.edu	37	12	75435987	75435987	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75435987delT	uc009zry.2	-						KCNC2_uc001sxe.2_Intron|KCNC2_uc001sxf.2_Intron	NM_139136	NP_631874			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																		---	---	---	---
CAPS2	84698	broad.mit.edu	37	12	75693815	75693815	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75693815delA	uc001sxk.3	-						CAPS2_uc001sxm.3_Intron|CAPS2_uc009zsa.2_Intron|CAPS2_uc001sxi.3_Intron|CAPS2_uc001sxj.3_Intron|CAPS2_uc001sxl.3_Intron	NM_032606	NP_115995			calcyphosine 2								calcium ion binding			ovary(2)	2																		---	---	---	---
CAPS2	84698	broad.mit.edu	37	12	75752385	75752385	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75752385delA	uc001sxm.3	-						CAPS2_uc009zsa.2_Intron|GLIPR1L1_uc001sxn.2_Intron|GLIPR1L1_uc001sxo.2_Intron					RecName: Full=Calcyphosin-2; AltName: Full=Calcyphosine-2;								calcium ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	76175446	76175446	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76175446delA								KRR1 (270028 upstream) : PHLDA1 (243782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76186801	76186801	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76186801delC								KRR1 (281383 upstream) : PHLDA1 (232427 downstream)																																			---	---	---	---
OSBPL8	114882	broad.mit.edu	37	12	76804022	76804022	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76804022delT	uc001sye.1	-						OSBPL8_uc001syf.1_Intron|OSBPL8_uc001syg.1_Intron|OSBPL8_uc001syh.1_Intron	NM_020841	NP_065892			oxysterol-binding protein-like protein 8 isoform						lipid transport		lipid binding			ovary(1)	1																		---	---	---	---
E2F7	144455	broad.mit.edu	37	12	77448016	77448016	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77448016delA	uc001sym.3	-						E2F7_uc001syn.2_Intron	NM_203394	NP_976328			E2F transcription factor 7						cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	77645130	77645130	+	IGR	DEL	T	-	-	rs66976964		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77645130delT								E2F7 (185770 upstream) : NAV3 (579939 downstream)																																			---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78334655	78334655	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78334655delT	uc001syp.2	+						NAV3_uc001syo.2_Intron	NM_014903	NP_055718			neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17															HNSCC(70;0.22)			---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78478362	78478363	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78478362_78478363delCT	uc001syp.2	+						NAV3_uc001syo.2_Intron|NAV3_uc010sub.1_Intron	NM_014903	NP_055718			neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17															HNSCC(70;0.22)			---	---	---	---
Unknown	0	broad.mit.edu	37	12	78611250	78611250	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78611250delT								NAV3 (4462 upstream) : SYT1 (646523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	79029158	79029158	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79029158delA								NAV3 (422370 upstream) : SYT1 (228615 downstream)																																			---	---	---	---
PPP1R12A	4659	broad.mit.edu	37	12	80169698	80169698	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80169698delT	uc001syz.2	-	25					PPP1R12A_uc010suc.1_3'UTR|PPP1R12A_uc001sza.2_3'UTR|PPP1R12A_uc010sud.1_3'UTR|PPP1R12A_uc001szb.2_3'UTR|PPP1R12A_uc001syy.2_RNA	NM_002480	NP_002471			protein phosphatase 1, regulatory (inhibitor)							contractile fiber	protein binding|signal transducer activity			ovary(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	80597110	80597110	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80597110delT								PPP1R12A (267875 upstream) : PTPRQ (241016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	80633100	80633100	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80633100delT								PPP1R12A (303865 upstream) : PTPRQ (205026 downstream)																																			---	---	---	---
PTPRQ	374462	broad.mit.edu	37	12	81063246	81063246	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81063246delA	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	81080540	81080543	+	IGR	DEL	ACAC	-	-	rs71867751		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81080540_81080543delACAC								PTPRQ (6572 upstream) : MYF6 (20903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	81107212	81107212	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81107212delA								MYF6 (3961 upstream) : MYF5 (3496 downstream)																																			---	---	---	---
PPFIA2	8499	broad.mit.edu	37	12	82012033	82012034	+	Intron	DEL	TG	-	-	rs35408377		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82012033_82012034delTG	uc001szo.1	-						PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron	NM_003625	NP_003616			PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6																		---	---	---	---
SLC6A15	55117	broad.mit.edu	37	12	85255161	85255161	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85255161delA	uc001szv.2	-	12					SLC6A15_uc010sul.1_3'UTR|SLC6A15_uc001szw.1_3'UTR	NM_182767	NP_877499			solute carrier family 6, member 15 isoform 1						cellular nitrogen compound metabolic process|leucine transport|proline transport	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			pancreas(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	85335285	85335285	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85335285delA								SLC6A15 (28679 upstream) : TSPAN19 (72810 downstream)																																			---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85510663	85510663	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85510663delT	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-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85554294delT	uc001tac.2	+							NM_001079910	NP_001073379			leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	85964828	85964829	+	IGR	INS	-	T	T	rs147840454	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85964828_85964829insT								ALX1 (269269 upstream) : RASSF9 (233502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	86156400	86156400	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86156400delT								ALX1 (460841 upstream) : RASSF9 (41931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	86169095	86169095	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86169095delT								ALX1 (473536 upstream) : RASSF9 (29236 downstream)																																			---	---	---	---
MGAT4C	25834	broad.mit.edu	37	12	86486636	86486636	+	Intron	DEL	T	-	-	rs139660970	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86486636delT	uc001tai.3	-						MGAT4C_uc001tal.3_Intron|MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron|MGAT4C_uc010sum.1_Intron|MGAT4C_uc001tah.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	87138385	87138385	+	Intron	DEL	A	-	-	rs66908213		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87138385delA	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	87826193	87826193	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87826193delA								MGAT4C (593512 upstream) : C12orf50 (547623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	88340140	88340140	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88340140delA								None (None upstream) : C12orf50 (33676 downstream)																																			---	---	---	---
C12orf29	91298	broad.mit.edu	37	12	88436703	88436703	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88436703delT	uc001tao.2	+						C12orf29_uc001tap.2_Intron|C12orf29_uc009zsk.2_Intron	NM_001009894	NP_001009894			hypothetical protein LOC91298												0																		---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88512305	88512305	+	Frame_Shift_Del	DEL	T	-	-	rs77980773		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88512305delT	uc001tar.2	-	17	2010	c.1666delA	c.(1666-1668)ATTfs	p.I556fs	CEP290_uc001tat.2_Frame_Shift_Del_p.I318fs|CEP290_uc009zsl.1_RNA	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	556	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7																		---	---	---	---
TMTC3	160418	broad.mit.edu	37	12	88542053	88542053	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88542053delT	uc001tau.2	+						TMTC3_uc009zsm.2_Intron	NM_181783	NP_861448			transmembrane and tetratricopeptide repeat							integral to membrane	binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	88830386	88830386	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88830386delA								TMTC3 (236723 upstream) : KITLG (56183 downstream)																																			---	---	---	---
KITLG	4254	broad.mit.edu	37	12	88926063	88926063	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88926063delA	uc001tav.2	-						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				---	---	---	---
Unknown	0	broad.mit.edu	37	12	89426298	89426298	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89426298delA								KITLG (452060 upstream) : DUSP6 (315541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89772738	89772738	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89772738delT								DUSP6 (26442 upstream) : POC1B (40763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89943555	89943558	+	IGR	DEL	TTTT	-	-	rs71911586		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89943555_89943558delTTTT								POC1B (23778 upstream) : ATP2B1 (38270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	90081371	90081371	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90081371delT								ATP2B1 (31527 upstream) : LOC338758 (21361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	90282527	90282527	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90282527delA								LOC338758 (176799 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91646468	91646468	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91646468delT								DCN (69662 upstream) : BTG1 (732398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	92113595	92113626	+	IGR	DEL	GAAGGAAGGAAAGAAAGAAGGAAGGAAGGAAA	-	-	rs12830115		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92113595_92113626delGAAGGAAGGAAAGAAAGAAGGAAGGAAGGAAA								DCN (536789 upstream) : BTG1 (265240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	92201409	92201410	+	IGR	DEL	AA	-	-	rs113449300		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92201409_92201410delAA								DCN (624603 upstream) : BTG1 (177456 downstream)																																			---	---	---	---
BTG1	694	broad.mit.edu	37	12	92459508	92459508	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92459508delA	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	92630413	92630414	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92630413_92630414delTT								BTG1 (90740 upstream) : CLLU1OS (183456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93006704	93006706	+	IGR	DEL	TGA	-	-	rs140223958		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93006704_93006706delTGA								CLLU1 (129248 upstream) : C12orf74 (90134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93373581	93373581	+	IGR	DEL	A	-	-	rs145543062		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93373581delA								EEA1 (50474 upstream) : NUDT4 (398120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93377482	93377482	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93377482delT								EEA1 (54375 upstream) : NUDT4 (394219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93475692	93475692	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93475692delT								EEA1 (152585 upstream) : NUDT4 (296009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93477467	93477467	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93477467delA								EEA1 (154360 upstream) : NUDT4 (294234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93714874	93714875	+	IGR	DEL	TT	-	-	rs76923498		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93714874_93714875delTT								EEA1 (391767 upstream) : NUDT4 (56826 downstream)																																			---	---	---	---
MRPL42	28977	broad.mit.edu	37	12	93873154	93873154	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93873154delT	uc001tcr.2	+						MRPL42_uc001tcq.2_Intron|MRPL42_uc001tcs.2_Intron|MRPL42_uc001tct.2_Intron	NM_172177	NP_751917			mitochondrial ribosomal protein L42 isoform a						translation	mitochondrial small ribosomal subunit	structural constituent of ribosome			ovary(2)	2																		---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94703662	94703662	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94703662delT	uc001tdd.2	-						CCDC41_uc001tde.2_Intron	NM_016122	NP_057206			NY-REN-58 antigen												0																		---	---	---	---
TMCC3	57458	broad.mit.edu	37	12	95028194	95028194	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95028194delA	uc001tdj.2	-							NM_020698	NP_065749			transmembrane and coiled-coil domain family 3							integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	95169777	95169778	+	IGR	INS	-	GTGT	GTGT	rs139726229	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95169777_95169778insGTGT								TMCC3 (125453 upstream) : MIR492 (58396 downstream)																																			---	---	---	---
NDUFA12	55967	broad.mit.edu	37	12	95388068	95388068	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95388068delT	uc001tdl.2	-							NM_018838	NP_061326			13kDa differentiation-associated protein						respiratory electron transport chain|respiratory gaseous exchange|response to oxidative stress|transport	mitochondrial respiratory chain complex I	electron carrier activity|NADH dehydrogenase (ubiquinone) activity				0					NADH(DB00157)													---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95445724	95445724	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95445724delA	uc001tdm.3	-						NR2C1_uc010suu.1_Intron|NR2C1_uc001tdo.3_Intron|NR2C1_uc001tdn.3_Intron	NM_003297	NP_003288			nuclear receptor subfamily 2, group C, member 1						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	PML body	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
FGD6	55785	broad.mit.edu	37	12	95493394	95493394	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95493394delT	uc001tdp.3	-						FGD6_uc009zsx.2_Intron|FGD6_uc001tdq.1_Intron	NM_018351	NP_060821			FYVE, RhoGEF and PH domain containing 6						actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3																		---	---	---	---
VEZT	55591	broad.mit.edu	37	12	95639906	95639906	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95639906delT	uc001tdz.2	+						VEZT_uc009zsy.1_Intron|VEZT_uc001tdr.2_Intron|VEZT_uc001tds.2_Intron|VEZT_uc001tdt.2_Intron|VEZT_uc009zsz.1_Intron|VEZT_uc001tdv.2_Intron|VEZT_uc001tdw.1_Intron|VEZT_uc009zta.1_Intron	NM_017599	NP_060069			vezatin, adherens junctions transmembrane							acrosomal vesicle|adherens junction|integral to membrane|nucleus				ovary(1)	1																		---	---	---	---
VEZT	55591	broad.mit.edu	37	12	95644524	95644527	+	Intron	DEL	TTTT	-	-	rs63079862		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95644524_95644527delTTTT	uc001tdz.2	+						VEZT_uc009zsy.1_Intron|VEZT_uc001tdr.2_Intron|VEZT_uc001tds.2_Intron|VEZT_uc001tdt.2_Intron|VEZT_uc009zsz.1_Intron|VEZT_uc001tdv.2_Intron|VEZT_uc001tdw.1_Intron|VEZT_uc009zta.1_Intron	NM_017599	NP_060069			vezatin, adherens junctions transmembrane							acrosomal vesicle|adherens junction|integral to membrane|nucleus				ovary(1)	1																		---	---	---	---
LTA4H	4048	broad.mit.edu	37	12	96410678	96410678	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96410678delA	uc001ten.1	-						LTA4H_uc010suy.1_Intron|LTA4H_uc010suz.1_Intron|LTA4H_uc010sva.1_Intron|LTA4H_uc009ztj.2_5'Flank	NM_000895	NP_000886			leukotriene A4 hydrolase						hormone biosynthetic process|inflammatory response|leukotriene biosynthetic process|peptide catabolic process|prostanoid metabolic process|proteolysis	cytosol|nucleus	aminopeptidase activity|epoxide hydrolase activity|leukotriene-A4 hydrolase activity|metallopeptidase activity|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(1)	1																		---	---	---	---
C12orf63	374467	broad.mit.edu	37	12	97082670	97082670	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97082670delT	uc001tet.1	+							NM_198520	NP_940922			hypothetical protein LOC374467											skin(6)|ovary(1)	7																		---	---	---	---
C12orf63	374467	broad.mit.edu	37	12	97082938	97082938	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	97810987	97810987	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97810987delC								NEDD1 (463526 upstream) : RMST (47812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	97996429	97996429	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97996429delA								RMST (37636 upstream) : LOC100128191 (910324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98091938	98091938	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98091938delT								RMST (133145 upstream) : LOC100128191 (814815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98389953	98389953	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98389953delT	hsa-mir-4303|MI0015834	-																																									---	---	---	---
SLC25A3	5250	broad.mit.edu	37	12	98989068	98989068	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98989068delT	uc001tfo.2	+						SLC25A3_uc001tfm.2_Intron|SLC25A3_uc001tfn.2_Intron|SLC25A3_uc001tfp.2_Intron|SLC25A3_uc001tfq.2_Intron|SLC25A3_uc001tfr.2_Intron|SLC25A3_uc001tfs.2_5'UTR|SLC25A3_uc009ztn.2_Intron|SLC25A3_uc001tft.2_Intron	NM_005888	NP_005879			solute carrier family 25 member 3 isoform a						generation of precursor metabolites and energy	integral to plasma membrane|mitochondrial inner membrane	phosphate carrier activity|symporter activity				0		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)														---	---	---	---
IKBIP	121457	broad.mit.edu	37	12	99034551	99034551	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99034551delT	uc001tfv.2	-						IKBIP_uc001tfw.2_Intron|IKBIP_uc001tfx.2_Intron	NM_201612	NP_963906			IKK interacting protein isoform 2						induction of apoptosis|response to X-ray	endoplasmic reticulum membrane|integral to membrane	protein binding				0																		---	---	---	---
APAF1	317	broad.mit.edu	37	12	99115575	99115575	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99115575delA	uc001tfz.2	+						APAF1_uc001tfy.2_Intron|APAF1_uc001tga.2_Intron|APAF1_uc001tgb.2_Intron|APAF1_uc001tgc.2_Intron|APAF1_uc009zto.2_Intron	NM_181861	NP_863651			apoptotic peptidase activating factor 1 isoform						activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)													---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	100175880	100175880	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100175880delA	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)														---	---	---	---
SLC17A8	246213	broad.mit.edu	37	12	100789403	100789404	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100789403_100789404delTT	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480			solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3																		---	---	---	---
SLC17A8	246213	broad.mit.edu	37	12	100808940	100808940	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100808940delT	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480			solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	100838265	100838269	+	IGR	DEL	TTTTT	-	-	rs34251459		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100838265_100838269delTTTTT								SLC17A8 (22429 upstream) : NR1H4 (29410 downstream)																																			---	---	---	---
SLC5A8	160728	broad.mit.edu	37	12	101566546	101566546	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101566546delC	uc001thz.3	-							NM_145913	NP_666018			solute carrier family 5 (iodide transporter),						apoptosis|sodium ion transport	apical plasma membrane|integral to membrane	monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity				0																OREG0022060	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101689237	101689237	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101689237delT	uc001tia.1	+							NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101700103	101700104	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101700103_101700104delTT	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	101846201	101846201	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101846201delC								ARL1 (44629 upstream) : SPIC (22998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	101956172	101956172	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101956172delA								SPIC (75398 upstream) : MYBPC1 (32575 downstream)																																			---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102053726	102053726	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102053726delT	uc001tii.2	+						MYBPC1_uc001tig.2_Intron|MYBPC1_uc010svq.1_Intron|MYBPC1_uc001tih.2_Intron|MYBPC1_uc001tij.2_Intron|MYBPC1_uc010svr.1_Intron|MYBPC1_uc010svs.1_Intron|MYBPC1_uc010svt.1_Intron|MYBPC1_uc010svu.1_Intron|MYBPC1_uc001tik.2_Intron	NM_206820	NP_996556			myosin binding protein C, slow type isoform 3						cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102072935	102072936	+	Intron	INS	-	G	G	rs146386238		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102072935_102072936insG	uc001tii.2	+						MYBPC1_uc001tig.2_Intron|MYBPC1_uc010svq.1_Intron|MYBPC1_uc001tih.2_Intron|MYBPC1_uc001tij.2_Intron|MYBPC1_uc010svr.1_Intron|MYBPC1_uc010svs.1_Intron|MYBPC1_uc010svt.1_Intron|MYBPC1_uc010svu.1_Intron|MYBPC1_uc001tik.2_Intron|MYBPC1_uc001til.2_Intron|MYBPC1_uc001tim.2_Intron	NM_206820	NP_996556			myosin binding protein C, slow type isoform 3						cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
NUP37	79023	broad.mit.edu	37	12	102492806	102492806	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102492806delT	uc001tjc.2	-						NUP37_uc009zub.1_Intron	NM_024057	NP_076962			nucleoporin 37kDa						carbohydrate metabolic process|cell division|chromosome segregation|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	102643654	102643654	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102643654delT								PMCH (52040 upstream) : IGF1 (145991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	103937666	103937669	+	IGR	DEL	TTTG	-	-	rs56023569	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103937666_103937669delTTTG								C12orf42 (47917 upstream) : STAB2 (43400 downstream)																																			---	---	---	---
TXNRD1	7296	broad.mit.edu	37	12	104725255	104725255	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104725255delT	uc010swk.1	+						TXNRD1_uc010swl.1_Intron|TXNRD1_uc010swm.1_Intron|TXNRD1_uc010swn.1_Intron|TXNRD1_uc010swo.1_Intron|TXNRD1_uc010swp.1_Intron|TXNRD1_uc010swq.1_Intron|TXNRD1_uc001tku.2_Intron|TXNRD1_uc009zun.2_Intron	NM_001093771	NP_001087240			thioredoxin reductase 1 isoform 3						cell redox homeostasis|cellular lipid metabolic process|electron transport chain|nucleobase, nucleoside and nucleotide interconversion|signal transduction|transport	cytosol|nucleolus	electron carrier activity|flavin adenine dinucleotide binding|NADP binding|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity				0																		---	---	---	---
CHST11	50515	broad.mit.edu	37	12	105046758	105046758	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105046758delT	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	106279083	106279083	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106279083delA								C12orf75 (513788 upstream) : NUAK1 (178042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106394895	106394895	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106394895delA								C12orf75 (629600 upstream) : NUAK1 (62230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106650085	106650085	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106650085delA								CKAP4 (8372 upstream) : TCP11L2 (46496 downstream)																																			---	---	---	---
POLR3B	55703	broad.mit.edu	37	12	106755895	106755895	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106755895delT	uc001tlp.2	+						POLR3B_uc001tlq.2_Intron	NM_018082	NP_060552			DNA-directed RNA polymerase III B isoform 1						innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
RFX4	5992	broad.mit.edu	37	12	106976983	106976984	+	5'Flank	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106976983_106976984delTC	uc001tlr.2	+							NM_213594	NP_998759			regulatory factor X4 isoform c						transcription, DNA-dependent	nucleus	DNA binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	107328193	107328193	+	IGR	DEL	A	-	-	rs35755084		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107328193delA								RIC8B (45101 upstream) : C12orf23 (21351 downstream)																																			---	---	---	---
CRY1	1407	broad.mit.edu	37	12	107393932	107393932	+	Intron	DEL	T	-	-	rs80347092		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107393932delT	uc001tmi.3	-							NM_004075	NP_004066			cryptochrome 1 (photolyase-like)						DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	blue light photoreceptor activity|DNA photolyase activity|double-stranded DNA binding|nucleotide binding|protein binding			ovary(3)	3																		---	---	---	---
CRY1	1407	broad.mit.edu	37	12	107418975	107418975	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107418975delT	uc001tmi.3	-							NM_004075	NP_004066			cryptochrome 1 (photolyase-like)						DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	blue light photoreceptor activity|DNA photolyase activity|double-stranded DNA binding|nucleotide binding|protein binding			ovary(3)	3																		---	---	---	---
CRY1	1407	broad.mit.edu	37	12	107439016	107439016	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107439016delA	uc001tmi.3	-							NM_004075	NP_004066			cryptochrome 1 (photolyase-like)						DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	blue light photoreceptor activity|DNA photolyase activity|double-stranded DNA binding|nucleotide binding|protein binding			ovary(3)	3																		---	---	---	---
PRDM4	11108	broad.mit.edu	37	12	108127165	108127167	+	3'UTR	DEL	ATT	-	-	rs35721831		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108127165_108127167delATT	uc001tmp.2	-	12					PRDM4_uc010sww.1_3'UTR|PRDM4_uc001tmq.2_RNA	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																		---	---	---	---
PRDM4	11108	broad.mit.edu	37	12	108135043	108135043	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108135043delA	uc001tmp.2	-						PRDM4_uc010sww.1_Intron|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																		---	---	---	---
WSCD2	9671	broad.mit.edu	37	12	108545426	108545426	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108545426delC	uc001tms.2	+						WSCD2_uc001tmt.2_Intron	NM_014653	NP_055468			WSC domain containing 2							integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	109783232	109783232	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109783232delT								FOXN4 (36207 upstream) : MYO1H (43292 downstream)																																			---	---	---	---
MYO1H	283446	broad.mit.edu	37	12	109844455	109844455	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109844455delA	uc010sxn.1	+							NM_001101421	NP_001094891			myosin 1H							myosin complex	motor activity				0																		---	---	---	---
MYO1H	283446	broad.mit.edu	37	12	109845512	109845512	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109845512delT	uc010sxn.1	+							NM_001101421	NP_001094891			myosin 1H							myosin complex	motor activity				0																		---	---	---	---
MYO1H	283446	broad.mit.edu	37	12	109881706	109881707	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109881706_109881707insA	uc010sxo.1	+						MYO1H_uc010sxn.1_Intron					SubName: Full=cDNA FLJ54829, moderately similar to Myosin Ic; SubName: Full=Myosin IH, isoform CRA_a;							myosin complex	motor activity				0																		---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110580531	110580532	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110580531_110580532insA	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	110618215	110618215	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110618215delT	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																		---	---	---	---
VPS29	51699	broad.mit.edu	37	12	110937446	110937446	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110937446delA	uc001tqy.2	-						VPS29_uc001tqw.2_5'Flank|VPS29_uc001tqx.2_Intron|VPS29_uc001tqz.2_Intron|RAD9B_uc001trc.1_5'Flank|RAD9B_uc001trf.3_5'Flank|RAD9B_uc001trg.3_5'Flank|RAD9B_uc010sya.1_5'Flank|RAD9B_uc001tre.3_5'Flank|RAD9B_uc001trd.3_5'Flank	NM_016226	NP_057310			vacuolar protein sorting 29 isoform 1						protein transport	endosome membrane	metal ion binding|phosphoserine phosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	111034577	111034577	+	IGR	DEL	T	-	-	rs76650769		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111034577delT								PPTC7 (13513 upstream) : TCTN1 (17303 downstream)																																			---	---	---	---
TCTN1	79600	broad.mit.edu	37	12	111072441	111072441	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111072441delT	uc009zvs.2	+						TCTN1_uc009zvr.1_Intron|TCTN1_uc001trl.2_Intron|TCTN1_uc001trm.2_Intron|TCTN1_uc010syc.1_Intron|TCTN1_uc001tro.2_Intron|TCTN1_uc001trp.3_Intron|TCTN1_uc001trn.3_Intron|TCTN1_uc001trj.1_Intron|TCTN1_uc001trk.3_Intron|HVCN1_uc001trq.1_Intron	NM_001082537	NP_001076006			tectonic family member 1 isoform 2						multicellular organismal development	extracellular region					0																		---	---	---	---
HVCN1	84329	broad.mit.edu	37	12	111120769	111120770	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111120769_111120770insA	uc001trs.1	-						HVCN1_uc001trq.1_Intron|HVCN1_uc001trt.1_Intron|HVCN1_uc010syd.1_Intron	NM_032369	NP_115745			hydrogen voltage-gated channel 1						response to pH|response to zinc ion	integral to membrane	voltage-gated proton channel activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	111249221	111249222	+	IGR	DEL	TG	-	-	rs71750470		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111249221_111249222delTG								PPP1CC (68464 upstream) : CCDC63 (35589 downstream)																																			---	---	---	---
MYL2	4633	broad.mit.edu	37	12	111356183	111356183	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111356183delA	uc001try.3	-						MYL2_uc001trx.3_Intron	NM_000432	NP_000423			slow cardiac myosin regulatory light chain 2						cardiac myofibril assembly|heart contraction|muscle filament sliding|negative regulation of cell growth|regulation of striated muscle contraction|ventricular cardiac muscle tissue morphogenesis	cytosol|myosin complex|sarcomere	actin monomer binding|calcium ion binding|myosin heavy chain binding|structural constituent of muscle			ovary(1)	1																		---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111550365	111550366	+	Intron	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111550365_111550366insG	uc001tsa.1	+						CUX2_uc001tsb.1_Intron	NM_015267	NP_056082			cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6																		---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111580052	111580052	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111580052delA	uc001tsa.1	+						CUX2_uc001tsb.1_Intron	NM_015267	NP_056082			cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6																		---	---	---	---
FAM109A	144717	broad.mit.edu	37	12	111802568	111802570	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111802568_111802570delAAA	uc001tsd.3	-						FAM109A_uc009zvu.2_Intron|FAM109A_uc001tsc.2_5'Flank	NM_144671	NP_653272			hypothetical protein LOC144717						endosome organization|receptor recycling|retrograde transport, endosome to Golgi	clathrin-coated vesicle|early endosome|recycling endosome|trans-Golgi network	protein homodimerization activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	111821658	111821658	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111821658delT								FAM109A (14733 upstream) : SH2B3 (22094 downstream)																																			---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	111914265	111914266	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111914265_111914266delAA	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron|ATXN2_uc001tsg.2_Intron	NM_002973	NP_002964			ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2																		---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	112032147	112032149	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112032147_112032149delTTT	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																		---	---	---	---
ACAD10	80724	broad.mit.edu	37	12	112146127	112146127	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112146127delC	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																		---	---	---	---
ACAD10	80724	broad.mit.edu	37	12	112156925	112156925	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112156925delA	uc001tsq.2	+						ACAD10_uc001tso.3_Intron|ACAD10_uc001tsp.2_Intron|ACAD10_uc009zvx.2_Intron|ACAD10_uc001tsr.2_Intron|ACAD10_uc001tss.1_Intron	NM_025247	NP_079523			acyl-Coenzyme A dehydrogenase family, member 10								acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2																		---	---	---	---
ACAD10	80724	broad.mit.edu	37	12	112175646	112175647	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112175646_112175647delGT	uc001tsq.2	+						ACAD10_uc001tsp.2_Intron|ACAD10_uc009zvx.2_Intron|ACAD10_uc001tss.1_Intron	NM_025247	NP_079523			acyl-Coenzyme A dehydrogenase family, member 10								acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2																		---	---	---	---
ERP29	10961	broad.mit.edu	37	12	112455939	112455939	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112455939delT	uc001ttk.1	+						ERP29_uc001ttl.1_Intron	NM_006817	NP_006808			endoplasmic reticulum protein 29 isoform 1						intracellular protein transport|protein folding|protein secretion	endoplasmic reticulum lumen|melanosome	protein disulfide isomerase activity				0																		---	---	---	---
NAA25	80018	broad.mit.edu	37	12	112512338	112512338	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112512338delA	uc001ttm.2	-						NAA25_uc001ttn.3_Intron|NAA25_uc009zvz.1_Intron|NAA25_uc009zwa.1_Intron	NM_024953	NP_079229			mitochondrial distribution and morphology 20							cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
C12orf51	283450	broad.mit.edu	37	12	112690936	112690936	+	Intron	DEL	T	-	-	rs74455713		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112690936delT	uc009zwc.2	-						C12orf51_uc010syk.1_Intron|C12orf51_uc001tts.2_Intron|C12orf51_uc001ttt.3_Intron	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	112759728	112759728	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112759728delA								C12orf51 (15690 upstream) : RPL6 (83267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	112787444	112787444	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112787444delA								C12orf51 (43406 upstream) : RPL6 (55551 downstream)																																			---	---	---	---
PTPN11	5781	broad.mit.edu	37	12	112930867	112930867	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112930867delT	uc001ttx.2	+							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				---	---	---	---
OAS1	4938	broad.mit.edu	37	12	113345089	113345090	+	Intron	DEL	GA	-	-	rs61096170	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113345089_113345090delGA	uc001tud.2	+						OAS1_uc010syn.1_Intron|OAS1_uc010syo.1_Intron|OAS1_uc001tub.2_Intron|OAS1_uc001tuc.2_Intron|OAS1_uc009zwf.2_Intron	NM_016816	NP_058132			2',5'-oligoadenylate synthetase 1 isoform 1						interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	endoplasmic reticulum|microsome|mitochondrion|nucleus	ATP binding|nucleotidyltransferase activity|RNA binding			ovary(2)	2																		---	---	---	---
OAS1	4938	broad.mit.edu	37	12	113365571	113365571	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113365571delT	uc009zwf.2	+							NM_002534	NP_002525			2',5'-oligoadenylate synthetase 1 isoform 2						interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	endoplasmic reticulum|microsome|mitochondrion|nucleus	ATP binding|nucleotidyltransferase activity|RNA binding			ovary(2)	2																		---	---	---	---
CCDC42B	387885	broad.mit.edu	37	12	113593482	113593482	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113593482delA	uc010sys.1	+							NM_001144872	NP_001138344			coiled-coil domain containing 42B												0																		---	---	---	---
IQCD	115811	broad.mit.edu	37	12	113645153	113645153	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113645153delA	uc001tuv.1	-						IQCD_uc001tuu.2_Intron	NM_138451	NP_612460			IQ motif containing D											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	113847546	113847548	+	IGR	DEL	TCA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113847546_113847548delTCA								SDS (5854 upstream) : SDSL (12668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114791704	114791704	+	IGR	DEL	A	-	-	rs145772162		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114791704delA								RBM19 (387528 upstream) : TBX5 (32 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114921705	114921707	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114921705_114921707delAAA								TBX5 (75458 upstream) : TBX3 (186352 downstream)																																			---	---	---	---
TBX3	6926	broad.mit.edu	37	12	115110242	115110242	+	Intron	DEL	T	-	-	rs112710097		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115110242delT	uc001tvt.1	-						TBX3_uc001tvu.1_Intron	NM_016569	NP_057653			T-box 3 protein isoform 2						anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding			ovary(2)|skin(1)	3	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	115769911	115769912	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115769911_115769912delAC								TBX3 (647942 upstream) : MED13L (626471 downstream)																																			---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116406919	116406919	+	Intron	DEL	A	-	-	rs35517594		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116406919delA	uc001tvw.2	-							NM_015335	NP_056150			mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	117128089	117128090	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117128089_117128090insG								MAP1LC3B2 (113664 upstream) : C12orf49 (25506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	117297444	117297444	+	IGR	DEL	T	-	-	rs34429362		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117297444delT								RNFT2 (6010 upstream) : HRK (1584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	117563877	117563879	+	IGR	DEL	ATC	-	-	rs144400052		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117563877_117563879delATC								TESC (26626 upstream) : FBXO21 (17707 downstream)																																			---	---	---	---
KSR2	283455	broad.mit.edu	37	12	117908878	117908878	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117908878delT	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	118083748	118083748	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118083748delT	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)																	---	---	---	---
TAOK3	51347	broad.mit.edu	37	12	118615305	118615305	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118615305delA	uc001twx.2	-						TAOK3_uc001twv.2_Intron|TAOK3_uc001tww.2_Intron|TAOK3_uc001twy.3_Intron	NM_016281	NP_057365			TAO kinase 3						MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	118859775	118859776	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118859775_118859776delAC								SUDS3 (3936 upstream) : SRRM4 (559620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	119123135	119123136	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119123135_119123136delAG								SUDS3 (267296 upstream) : SRRM4 (296260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	119289362	119289362	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119289362delT								SUDS3 (433523 upstream) : SRRM4 (130034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	119345783	119345783	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119345783delA								SUDS3 (489944 upstream) : SRRM4 (73613 downstream)																																			---	---	---	---
CCDC60	160777	broad.mit.edu	37	12	119937143	119937143	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119937143delA	uc001txe.2	+						uc001txf.2_Intron	NM_178499	NP_848594			coiled-coil domain containing 60											ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)														---	---	---	---
CIT	11113	broad.mit.edu	37	12	120147253	120147253	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120147253delA	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	120150675	120150675	+	Intron	DEL	A	-	-	rs113783917		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	120171871	120171872	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120171871_120171872delCA	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	120179028	120179028	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120179028delA	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	120256111	120256111	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120256111delA	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)														---	---	---	---
CCDC64	92558	broad.mit.edu	37	12	120458795	120458795	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120458795delA	uc001txl.1	+						CCDC64_uc001txk.2_Intron|CCDC64_uc009zwv.1_Intron	NM_207311	NP_997194			coiled-coil domain containing 64						Golgi to secretory granule transport|neuron projection development	centrosome	dynactin binding|Rab GTPase binding			ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
CCDC64	92558	broad.mit.edu	37	12	120462264	120462265	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120462264_120462265insA	uc001txl.1	+						CCDC64_uc001txk.2_Intron|CCDC64_uc009zwv.1_Intron	NM_207311	NP_997194			coiled-coil domain containing 64						Golgi to secretory granule transport|neuron projection development	centrosome	dynactin binding|Rab GTPase binding			ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
RPLP0	6175	broad.mit.edu	37	12	120638265	120638265	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120638265delA	uc001txp.2	-						RPLP0_uc001txq.2_Intron|RPLP0_uc001txr.2_Intron|uc001txs.1_5'Flank	NM_053275	NP_444505			ribosomal protein P0						endocrine pancreas development|interspecies interaction between organisms|ribosome biogenesis|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	120706717	120706717	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120706717delA								PXN (3154 upstream) : NME2P1 (13223 downstream)																																			---	---	---	---
SIRT4	23409	broad.mit.edu	37	12	120738104	120738104	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120738104delA	uc001tyc.2	+							NM_012240	NP_036372			sirtuin 4						chromatin silencing|negative regulation of insulin secretion|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
COQ5	84274	broad.mit.edu	37	12	120968611	120968612	+	5'Flank	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120968611_120968612insT	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)																	---	---	---	---
P2RX4	5025	broad.mit.edu	37	12	121660168	121660168	+	Intron	DEL	T	-	-	rs72191683		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121660168delT	uc001tzr.2	+						P2RX4_uc010szr.1_Intron|P2RX4_uc010szs.1_Intron|P2RX4_uc009zxc.2_Intron|P2RX4_uc001tzs.2_Intron|P2RX4_uc009zxb.2_Intron|P2RX4_uc010szt.1_Intron	NM_002560	NP_002551			purinergic receptor P2X4						endothelial cell activation|negative regulation of cardiac muscle hypertrophy|positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin secretion|regulation of apoptosis|regulation of blood pressure|regulation of sodium ion transport|relaxation of cardiac muscle|response to ATP|response to fluid shear stress|sensory perception of pain|tissue homeostasis	cell junction|perinuclear region of cytoplasm	cadherin binding|copper ion binding|extracellular ATP-gated cation channel activity|protein homodimerization activity|purinergic nucleotide receptor activity|receptor binding|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
CAMKK2	10645	broad.mit.edu	37	12	121700315	121700315	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121700315delA	uc001tzu.2	-						CAMKK2_uc001tzt.2_Intron|CAMKK2_uc001tzv.2_Intron|CAMKK2_uc001tzw.2_Intron|CAMKK2_uc001tzx.2_Intron|CAMKK2_uc001tzy.2_Intron|CAMKK2_uc001tzz.1_5'Flank|CAMKK2_uc001uaa.1_Intron|CAMKK2_uc001uab.2_Intron|CAMKK2_uc001uac.2_Intron	NM_006549	NP_006540			calcium/calmodulin-dependent protein kinase						calcium-mediated signaling|MAPKKK cascade|positive regulation of transcription, DNA-dependent|protein autophosphorylation|regulation of protein kinase activity	cytoplasm	ATP binding|calcium ion binding|calmodulin binding|calmodulin-dependent protein kinase activity|protein tyrosine kinase activity			lung(1)|large_intestine(1)|stomach(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
ANAPC5	51433	broad.mit.edu	37	12	121768573	121768573	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121768573delA	uc001uag.2	-						ANAPC5_uc010szu.1_5'UTR|ANAPC5_uc001uae.2_Intron|ANAPC5_uc010szv.1_Intron|ANAPC5_uc001uaf.2_Intron|ANAPC5_uc001uah.2_Intron|ANAPC5_uc001uai.1_Intron	NM_016237	NP_057321			anaphase-promoting complex subunit 5 isoform a						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity			skin(3)|breast(2)|kidney(1)	6	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
WDR66	144406	broad.mit.edu	37	12	122362025	122362026	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122362025_122362026delTT	uc009zxk.2	+							NM_144668	NP_653269			WD repeat domain 66								calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)														---	---	---	---
DIABLO	56616	broad.mit.edu	37	12	122692666	122692666	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122692666delA	uc010tab.1	-	7					DIABLO_uc010taa.1_3'UTR|DIABLO_uc010tac.1_RNA|DIABLO_uc010tad.1_3'UTR|VPS33A_uc001ucc.2_RNA	NM_019887	NP_063940			diablo isoform 1 precursor						activation of caspase activity by cytochrome c|induction of apoptosis via death domain receptors	CD40 receptor complex|cytosol|internal side of plasma membrane|mitochondrial intermembrane space	protein binding				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000302)|Epithelial(86;0.00051)|BRCA - Breast invasive adenocarcinoma(302;0.223)														---	---	---	---
CLIP1	6249	broad.mit.edu	37	12	122819988	122819988	+	Intron	DEL	A	-	-	rs35684124		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122819988delA	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	122849800	122849800	+	Intron	DEL	A	-	-	rs114387181	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122849800delA	uc001ucg.1	-						CLIP1_uc001uch.1_Intron|CLIP1_uc001uci.1_Intron|CLIP1_uc001ucj.1_5'Flank|CLIP1_uc010tae.1_Intron	NM_002956	NP_002947			restin isoform a						mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)														---	---	---	---
GPR81	27198	broad.mit.edu	37	12	123172354	123172354	+	Intron	DEL	A	-	-	rs34886675		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123172354delA	uc001ucw.1	-							NM_032554				G protein-coupled receptor 81						response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)														---	---	---	---
DENR	8562	broad.mit.edu	37	12	123252222	123252223	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123252222_123252223delTC	uc001uda.2	+						DENR_uc010tag.1_Intron|DENR_uc001udb.2_Intron	NM_003677	NP_003668			density-regulated protein								protein binding|translation initiation factor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.28e-05)|Epithelial(86;6.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.199)														---	---	---	---
CDK2AP1	8099	broad.mit.edu	37	12	123757199	123757200	+	5'Flank	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123757199_123757200delTT	uc001ueq.2	-						CDK2AP1_uc001uep.2_5'Flank	NM_004642	NP_004633			CDK2-associated protein  1						DNA-dependent DNA replication|protein phosphorylation|S phase of mitotic cell cycle	cytoplasm|nucleus	DNA binding|protein binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000554)|Epithelial(86;0.00178)														---	---	---	---
SBNO1	55206	broad.mit.edu	37	12	123794283	123794283	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123794283delT	uc010tap.1	-	25	3416	c.3416delA	c.(3415-3417)AATfs	p.N1139fs	SBNO1_uc009zxv.2_RNA|SBNO1_uc010tao.1_Frame_Shift_Del_p.N1138fs|SBNO1_uc010taq.1_Frame_Shift_Del_p.N90fs|SBNO1_uc001ues.1_Frame_Shift_Del_p.N90fs	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1	1139							ATP binding|DNA binding|hydrolase activity			breast(5)|skin(2)|ovary(1)|kidney(1)	9	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)														---	---	---	---
DDX55	57696	broad.mit.edu	37	12	124103201	124103202	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124103201_124103202delTG	uc001ufi.2	+						DDX55_uc001ufh.2_Intron|DDX55_uc001ufk.2_Intron|DDX55_uc001ufl.2_Translation_Start_Site	NM_020936	NP_065987			DEAD (Asp-Glu-Ala-Asp) box polypeptide 55								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)												OREG0022230	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GTF2H3	2967	broad.mit.edu	37	12	124126075	124126075	+	Intron	DEL	T	-	-	rs112546170		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124126075delT	uc001ufo.1	+						GTF2H3_uc010tau.1_Intron	NM_001516	NP_001507			general transcription factor IIH, polypeptide 3,						mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of viral transcription|protein phosphorylation|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	core TFIIH complex|holo TFIIH complex	damaged DNA binding|metal ion binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|translation factor activity, nucleic acid binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.1e-05)|Epithelial(86;0.000388)|all cancers(50;0.00362)									NER					---	---	---	---
CCDC92	80212	broad.mit.edu	37	12	124446706	124446706	+	Intron	DEL	A	-	-	rs35510464		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124446706delA	uc001ufw.1	-						CCDC92_uc001ufx.1_Intron|CCDC92_uc001ufy.1_Intron	NM_025140	NP_079416			coiled-coil domain containing 92												0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.0002)|OV - Ovarian serous cystadenocarcinoma(86;0.000222)|all cancers(50;0.00129)|BRCA - Breast invasive adenocarcinoma(302;0.242)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124868080	124868080	+	Intron	DEL	A	-	-	rs148277001		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124868080delA	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron	NM_001077261	NP_001070729			nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124894231	124894231	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124894231delT	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron	NM_001077261	NP_001070729			nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124923424	124923425	+	Intron	INS	-	AC	AC	rs138222196		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124923424_124923425insAC	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729			nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124956729	124956729	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124956729delA	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729			nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	125026057	125026057	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125026057delG	uc001ugj.1	-							NM_006312	NP_006303			nuclear receptor co-repressor 2 isoform 1						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	125361706	125361706	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125361706delA								SCARB1 (13187 upstream) : UBC (34488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	125651632	125651633	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125651632_125651633delAC								AACS (23760 upstream) : TMEM132B (159529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126191539	126191539	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126191539delT								TMEM132B (47950 upstream) : LOC100128554 (735488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126585145	126585145	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126585145delT								TMEM132B (441556 upstream) : LOC100128554 (341882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127064620	127064620	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127064620delA								LOC100128554 (107290 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127274146	127274147	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127274146_127274147delAA								LOC100128554 (316816 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127485205	127485205	+	Intron	DEL	A	-	-	rs63163561		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127485205delA	uc001uho.2	-											Homo sapiens cDNA clone IMAGE:4829480.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	127720073	127720074	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127720073_127720074delAA								LOC100128554 (762743 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128318547	128318547	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128318547delC								None (None upstream) : TMEM132C (580744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128674118	128674119	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128674118_128674119delGT								None (None upstream) : TMEM132C (225172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128888009	128888009	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128888009delT								None (None upstream) : TMEM132C (11282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	129259403	129259403	+	IGR	DEL	T	-	-	rs112929999		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129259403delT								TMEM132C (66940 upstream) : SLC15A4 (18336 downstream)																																			---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	129802201	129802201	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129802201delT	uc009zyl.1	-							NM_133448	NP_597705			transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	130623256	130623256	+	IGR	DEL	G	-	-	rs68074923		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130623256delG								LOC100190940 (96369 upstream) : FZD10 (23776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	130714579	130714579	+	IGR	DEL	T	-	-	rs76917333		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130714579delT								FZD10 (64295 upstream) : PIWIL1 (108035 downstream)																																			---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	130919596	130919596	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130919596delT	uc001uil.2	-						RIMBP2_uc001uim.2_Intron|RIMBP2_uc001uin.1_Intron	NM_015347	NP_056162			RIM-binding protein 2							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	130995023	130995023	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130995023delT	uc001uil.2	-						RIMBP2_uc001uim.2_Intron	NM_015347	NP_056162			RIM-binding protein 2							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	131123310	131123310	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131123310delA	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)														---	---	---	---
LOC116437	116437	broad.mit.edu	37	12	131682618	131682619	+	Intron	INS	-	T	T	rs143708916	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131682618_131682619insT	uc001uiw.2	+							NR_026670				Homo sapiens mRNA; cDNA DKFZp434L2430 (from clone DKFZp434L2430).												0																		---	---	---	---
ULK1	8408	broad.mit.edu	37	12	132388457	132388457	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132388457delG	uc001uje.2	+							NM_003565	NP_003556			Unc-51-like kinase 1						autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	133040656	133040657	+	IGR	INS	-	CAC	CAC	rs145584553	by1000genomes;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133040656_133040657insCAC								GALNT9 (134751 upstream) : FBRSL1 (26500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	19565928	19565929	+	IGR	INS	-	A	A	rs150976558	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19565928_19565929insA								LOC284232 (119819 upstream) : LOC348021 (16470 downstream)																																			---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19642787	19642788	+	Intron	INS	-	TCG	TCG	rs113422088		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19642787_19642788insTCG	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19643738	19643738	+	Intron	DEL	A	-	-	rs112391429		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19643738delA	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19644140	19644141	+	Intron	DEL	AT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19644140_19644141delAT	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	19802369	19802370	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19802369_19802370insT								TUBA3C (46433 upstream) : LOC100101938 (34571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	19943478	19943478	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19943478delA								LOC100101938 (24365 upstream) : TPTE2 (53543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	20184463	20184463	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20184463delT								TPTE2 (48749 upstream) : MPHOSPH8 (23417 downstream)																																			---	---	---	---
PSPC1	55269	broad.mit.edu	37	13	20321481	20321481	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20321481delT	uc001uml.2	-						PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron	NM_001042414	NP_001035879			paraspeckle protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	20360580	20360580	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20360580delA								PSPC1 (3497 upstream) : ZMYM5 (37044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	20367995	20367996	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20367995_20367996insC								PSPC1 (10912 upstream) : ZMYM5 (29628 downstream)																																			---	---	---	---
ZMYM5	9205	broad.mit.edu	37	13	20409967	20409967	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20409967delT	uc010tcn.1	-						ZMYM5_uc001umm.1_Intron	NM_001142684	NP_001136156			zinc finger protein 237 isoform 3							nucleus	zinc ion binding				0		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	20690063	20690063	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20690063delA								ZMYM2 (29125 upstream) : GJA3 (22332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	20778653	20778653	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20778653delT								GJB2 (11539 upstream) : GJB6 (17449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	21136684	21136684	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21136684delT								CRYL1 (36672 upstream) : IFT88 (4524 downstream)																																			---	---	---	---
IFT88	8100	broad.mit.edu	37	13	21143712	21143713	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21143712_21143713delAA	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	21236442	21236442	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21236442delA	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)														---	---	---	---
XPO4	64328	broad.mit.edu	37	13	21358785	21358785	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21358785delA	uc001unq.3	-							NM_022459	NP_071904			exportin 4						protein transport	cytoplasm|nucleus	protein binding			large_intestine(1)|ovary(1)|kidney(1)	3		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	21529973	21529973	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21529973delT								XPO4 (53060 upstream) : LATS2 (17205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	21541085	21541086	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21541085_21541086delAA								XPO4 (64172 upstream) : LATS2 (6092 downstream)																																			---	---	---	---
LATS2	26524	broad.mit.edu	37	13	21592801	21592801	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21592801delT	uc009zzs.2	-						LATS2_uc001unr.3_Intron	NM_014572	NP_055387			LATS, large tumor suppressor, homolog 2						cell division|G1/S transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|intracellular protein kinase cascade|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity	microtubule organizing center|nucleus|spindle pole	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(3)|ovary(2)|breast(1)|pancreas(1)	10		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)														---	---	---	---
SKA3	221150	broad.mit.edu	37	13	21742058	21742058	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21742058delA	uc001unt.2	-						SKA3_uc001unv.2_Intron|SKA3_uc001unu.2_Intron	NM_145061	NP_659498			SKA3						cell division|chromosome segregation|mitosis|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytoplasm|spindle microtubule	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	21766036	21766036	+	IGR	DEL	G	-	-	rs9506630	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21766036delG								MRP63 (12818 upstream) : ZDHHC20 (184474 downstream)																																			---	---	---	---
ZDHHC20	253832	broad.mit.edu	37	13	21959102	21959102	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21959102delA	uc001uob.2	-						ZDHHC20_uc001uod.2_Intron|ZDHHC20_uc001uoc.2_Intron|ZDHHC20_uc001uoe.2_Intron|ZDHHC20_uc010tcs.1_Intron	NM_153251	NP_694983			zinc finger, DHHC-type containing 20							integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)														---	---	---	---
ZDHHC20	253832	broad.mit.edu	37	13	21964106	21964106	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21964106delA	uc001uob.2	-						ZDHHC20_uc001uod.2_Intron|ZDHHC20_uc001uoc.2_Intron|ZDHHC20_uc001uoe.2_Intron|ZDHHC20_uc010tcs.1_Intron	NM_153251	NP_694983			zinc finger, DHHC-type containing 20							integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)														---	---	---	---
ZDHHC20	253832	broad.mit.edu	37	13	21988036	21988036	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21988036delA	uc001uob.2	-						ZDHHC20_uc001uod.2_Intron|ZDHHC20_uc001uoc.2_Intron|ZDHHC20_uc001uoe.2_Intron|ZDHHC20_uc010tcs.1_Intron	NM_153251	NP_694983			zinc finger, DHHC-type containing 20							integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	22296482	22296482	+	IGR	DEL	T	-	-	rs68144774		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22296482delT								FGF9 (17842 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22323026	22323026	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22323026delT								FGF9 (44386 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22344574	22344575	+	IGR	DEL	TT	-	-	rs67882052		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22344574_22344575delTT								FGF9 (65934 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22545524	22545525	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22545524_22545525delTG								FGF9 (266884 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22679852	22679852	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22679852delT	uc001uoi.2	+											Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	23253536	23253538	+	IGR	DEL	CTT	-	-	rs113089800		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23253536_23253538delCTT								FGF9 (974896 upstream) : SGCG (501522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23397958	23397958	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23397958delA								None (None upstream) : SGCG (357102 downstream)																																			---	---	---	---
SGCG	6445	broad.mit.edu	37	13	23891334	23891334	+	Intron	DEL	A	-	-	rs76170240		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23891334delA	uc001uom.2	+						SGCG_uc009zzv.2_Intron|SGCG_uc009zzw.2_Intron	NM_000231	NP_000222			gamma sarcoglycan						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)														---	---	---	---
SACS	26278	broad.mit.edu	37	13	24007892	24007892	+	5'Flank	DEL	T	-	-	rs79531295		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24007892delT	uc001uon.2	-							NM_014363	NP_055178			sacsin						cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	24025410	24025410	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24025410delC								SACS (17569 upstream) : TNFRSF19 (119313 downstream)																																			---	---	---	---
TNFRSF19	55504	broad.mit.edu	37	13	24167428	24167428	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24167428delA	uc001uov.1	+						TNFRSF19_uc001uot.2_Intron|TNFRSF19_uc010tcu.1_Intron|TNFRSF19_uc001uow.2_Intron|TNFRSF19_uc001uou.2_Intron	NM_018647	NP_061117			tumor necrosis factor receptor superfamily,						apoptosis|induction of apoptosis|JNK cascade	integral to membrane|mitochondrion	tumor necrosis factor receptor activity			kidney(1)|skin(1)	2		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)														---	---	---	---
TNFRSF19	55504	broad.mit.edu	37	13	24185288	24185291	+	Intron	DEL	CACT	-	-	rs145953294	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24185288_24185291delCACT	uc001uov.1	+						TNFRSF19_uc001uot.2_Intron|TNFRSF19_uc010tcu.1_Intron|TNFRSF19_uc001uow.2_Intron	NM_018647	NP_061117			tumor necrosis factor receptor superfamily,						apoptosis|induction of apoptosis|JNK cascade	integral to membrane|mitochondrion	tumor necrosis factor receptor activity			kidney(1)|skin(1)	2		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)														---	---	---	---
SPATA13	221178	broad.mit.edu	37	13	24679584	24679584	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24679584delT	uc001upd.1	+						C1QTNF9_uc001upe.2_Intron	NM_153023	NP_694568			spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)														---	---	---	---
SPATA13	221178	broad.mit.edu	37	13	24690909	24690910	+	Intron	DEL	CC	-	-	rs68080717		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24690909_24690910delCC	uc001upd.1	+						C1QTNF9_uc001upe.2_Intron	NM_153023	NP_694568			spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	24930023	24930024	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24930023_24930024delCA								C1QTNF9 (33358 upstream) : PARP4 (65051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	24989737	24989738	+	IGR	DEL	GT	-	-	rs3082324		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24989737_24989738delGT								C1QTNF9 (93072 upstream) : PARP4 (5337 downstream)																																			---	---	---	---
PARP4	143	broad.mit.edu	37	13	25000864	25000864	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25000864delA	uc001upl.2	-							NM_006437	NP_006428			poly (ADP-ribose) polymerase family, member 4						cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity			ovary(3)|skin(1)	4		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)														---	---	---	---
RNF17	56163	broad.mit.edu	37	13	25349247	25349247	+	Intron	DEL	A	-	-	rs34394824		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25349247delA	uc001upr.2	+						RNF17_uc010tdd.1_Intron|RNF17_uc010aab.2_Intron|RNF17_uc010tde.1_Intron|RNF17_uc001ups.2_Intron|RNF17_uc001upq.1_Intron	NM_031277	NP_112567			ring finger protein 17						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)														---	---	---	---
RNF17	56163	broad.mit.edu	37	13	25363467	25363467	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25363467delT	uc001upr.2	+						RNF17_uc010tdd.1_Intron|RNF17_uc010aab.2_Intron|RNF17_uc010tde.1_Intron|RNF17_uc001ups.2_Intron|RNF17_uc001upq.1_Intron	NM_031277	NP_112567			ring finger protein 17						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	25705164	25705164	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25705164delA								PABPC3 (32462 upstream) : FAM123A (37509 downstream)																																			---	---	---	---
MTMR6	9107	broad.mit.edu	37	13	25818967	25818970	+	Intron	DEL	CAAA	-	-	rs142798727	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25818967_25818970delCAAA	uc001uqe.1	-							NM_004685	NP_004676			myotubularin related protein 6							cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)|skin(2)	4		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26006803	26006803	+	Intron	DEL	T	-	-	rs71186884		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26006803delT	uc001uqk.2	+							NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26264528	26264528	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26264528delT	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron|ATP8A2_uc010aaj.1_Intron	NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26420324	26420324	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26420324delA	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron|ATP8A2_uc010aaj.1_Intron	NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26553078	26553078	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26553078delA	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron	NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
CDK8	1024	broad.mit.edu	37	13	26936360	26936363	+	Intron	DEL	GATG	-	-	rs66479948		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26936360_26936363delGATG	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	27402983	27402983	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27402983delT								GPR12 (68061 upstream) : USP12 (239455 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	27463302	27463302	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27463302delA								GPR12 (128380 upstream) : USP12 (179136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	27531468	27531479	+	IGR	DEL	GGACAGTCTTCA	-	-	rs67745169		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27531468_27531479delGGACAGTCTTCA								GPR12 (196546 upstream) : USP12 (110959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	27851077	27851077	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27851077delA								RASL11A (3250 upstream) : GTF3A (147604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	27922234	27922235	+	IGR	INS	-	GTGTGTGT	GTGTGTGT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27922234_27922235insGTGTGTGT								RASL11A (74407 upstream) : GTF3A (76446 downstream)																																			---	---	---	---
MTIF3	219402	broad.mit.edu	37	13	28012936	28012937	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28012936_28012937delTT	uc001urh.2	-						MTIF3_uc001uri.2_Intron|MTIF3_uc001urj.2_Intron|MTIF3_uc001urk.2_Intron	NM_152912	NP_690876			mitochondrial translational initiation factor 3						regulation of translational initiation|ribosome disassembly	mitochondrion	ribosomal small subunit binding|translation initiation factor activity			ovary(1)|skin(1)	2		Lung SC(185;0.0161)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.108)|OV - Ovarian serous cystadenocarcinoma(117;0.157)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	28264469	28264469	+	IGR	DEL	T	-	-	rs76242626	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28264469delT								POLR1D (22922 upstream) : GSX1 (102311 downstream)																																			---	---	---	---
FLT3	2322	broad.mit.edu	37	13	28635910	28635910	+	Intron	DEL	A	-	-	rs78564726		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28635910delA	uc001urw.2	-						FLT3_uc010aao.2_Intron|FLT3_uc010tdn.1_Intron	NM_004119	NP_004110			fms-related tyrosine kinase 3 precursor						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)			Mis|O		AML|ALL								---	---	---	---
FLT3	2322	broad.mit.edu	37	13	28656640	28656640	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28656640delT	uc001urw.2	-						FLT3_uc010aao.2_Intron|FLT3_uc010tdn.1_Intron	NM_004119	NP_004110			fms-related tyrosine kinase 3 precursor						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)			Mis|O		AML|ALL								---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28874659	28874668	+	3'UTR	DEL	CACACACACA	-	-	rs58634271		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28874659_28874668delCACACACACA	uc001usb.3	-	30					FLT1_uc010aap.2_3'UTR|FLT1_uc010aaq.2_3'UTR|FLT1_uc001usa.3_3'UTR	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	29482791	29482791	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29482791delC								SLC46A3 (189641 upstream) : MTUS2 (115957 downstream)																																			---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	30021437	30021438	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30021437_30021438insA	uc001usl.3	+						MTUS2_uc001usm.3_Intron|MTUS2_uc010aau.2_Intron	NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	30065680	30065681	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30065680_30065681delGT	uc001usl.3	+						MTUS2_uc001usm.3_Intron|MTUS2_uc010aau.2_Intron	NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
HMGB1	3146	broad.mit.edu	37	13	31055979	31055979	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31055979delT	uc001usz.2	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	31365482	31365482	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31365482delA								ALOX5AP (26926 upstream) : C13orf33 (114830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31442404	31442404	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31442404delT								ALOX5AP (103848 upstream) : C13orf33 (37908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31572532	31572532	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31572532delA								C13orf26 (23381 upstream) : HSPH1 (138233 downstream)																																			---	---	---	---
HSPH1	10808	broad.mit.edu	37	13	31721829	31721830	+	Intron	DEL	AT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31721829_31721830delAT	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)														---	---	---	---
HSPH1	10808	broad.mit.edu	37	13	31730145	31730145	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31730145delT	uc001utj.2	-						HSPH1_uc001utk.2_Intron|HSPH1_uc010aaw.2_Intron|HSPH1_uc001utl.2_Intron|HSPH1_uc010tds.1_Intron|HSPH1_uc010tdt.1_Intron|HSPH1_uc010aax.1_Intron|HSPH1_uc010aay.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	32309633	32309633	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32309633delT								B3GALTL (403224 upstream) : RXFP2 (4046 downstream)																																			---	---	---	---
RXFP2	122042	broad.mit.edu	37	13	32313942	32313942	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32313942delA	uc001utt.2	+						RXFP2_uc010aba.2_Intron	NM_130806	NP_570718			relaxin/insulin-like family peptide receptor 2							integral to membrane|plasma membrane					0		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32712283	32712283	+	Intron	DEL	T	-	-	rs33953205		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32712283delT	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32807143	32807143	+	Intron	DEL	A	-	-	rs113731882		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32807143delA	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32821607	32821607	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32821607delA	uc001utx.2	+	48	7472	c.6976delA	c.(6976-6978)AAAfs	p.K2326fs	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	2326					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
BRCA2	675	broad.mit.edu	37	13	32946015	32946015	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32946015delA	uc001uub.1	+							NM_000059	NP_000050			breast cancer 2, early onset						cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)				D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33337568	33337568	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33337568delT	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847			PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	33376748	33376749	+	IGR	INS	-	G	G	rs148851732	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33376748_33376749insG								PDS5B (24593 upstream) : KL (213452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	33654546	33654546	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33654546delT								KL (14265 upstream) : STARD13 (22727 downstream)																																			---	---	---	---
STARD13	90627	broad.mit.edu	37	13	33829629	33829629	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33829629delC	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	33855544	33855547	+	Intron	DEL	TGTG	-	-	rs67265721		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33855544_33855547delTGTG	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	33869842	33869842	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33869842delG	uc001uux.2	-						STARD13_uc010abh.1_Intron	NM_052851	NP_443083			StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)														---	---	---	---
STARD13	90627	broad.mit.edu	37	13	34038975	34038975	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34038975delA	uc001uux.2	-							NM_052851	NP_443083			StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)														---	---	---	---
RFC3	5983	broad.mit.edu	37	13	34421722	34421722	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34421722delA	uc001uva.2	+							NM_181558	NP_853536			replication factor C 3 isoform 2						cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|nucleotide-excision repair, DNA gap filling|response to organophosphorus|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding				0		Hepatocellular(188;0.0191)|Lung SC(185;0.0548)		all cancers(112;5.09e-06)|Epithelial(112;6.52e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00107)|OV - Ovarian serous cystadenocarcinoma(117;0.0285)|GBM - Glioblastoma multiforme(144;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	34678609	34678609	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34678609delA								RFC3 (137915 upstream) : NBEA (837847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	34730928	34730928	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34730928delT								RFC3 (190234 upstream) : NBEA (785528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	34938036	34938036	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34938036delA								RFC3 (397342 upstream) : NBEA (578420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	35113579	35113579	+	IGR	DEL	A	-	-	rs9571838	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35113579delA								RFC3 (572885 upstream) : NBEA (402877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	35144255	35144255	+	IGR	DEL	C	-	-	rs79325841		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35144255delC								RFC3 (603561 upstream) : NBEA (372201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	35309758	35309758	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35309758delT								RFC3 (769064 upstream) : NBEA (206698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	35314136	35314146	+	IGR	DEL	AGAAACATAGT	-	-	rs112256027		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35314136_35314146delAGAAACATAGT								RFC3 (773442 upstream) : NBEA (202310 downstream)																																			---	---	---	---
NBEA	26960	broad.mit.edu	37	13	35683682	35683682	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35683682delT	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	36087154	36087154	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36087154delT	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)														---	---	---	---
DCLK1	9201	broad.mit.edu	37	13	36479929	36479929	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36479929delA	uc001uvf.2	-							NM_004734	NP_004725			doublecortin-like kinase 1						cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	37039911	37039911	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37039911delT								CCNA1 (22893 upstream) : C13orf36 (208138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37041458	37041459	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37041458_37041459insT								CCNA1 (24440 upstream) : C13orf36 (206590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37144266	37144269	+	IGR	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37144266_37144269delAAAA								CCNA1 (127248 upstream) : C13orf36 (103780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37317451	37317451	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37317451delT								C13orf36 (45478 upstream) : RFXAP (75888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37747806	37747809	+	IGR	DEL	TTTT	-	-	rs5802861		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37747806_37747809delTTTT								CSNK1A1L (68005 upstream) : POSTN (388911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37767845	37767852	+	IGR	DEL	AAGAATGA	-	-	rs11279937		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37767845_37767852delAAGAATGA								CSNK1A1L (88044 upstream) : POSTN (368868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37867659	37867659	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37867659delT								CSNK1A1L (187858 upstream) : POSTN (269061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37920961	37920961	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37920961delT								CSNK1A1L (241160 upstream) : POSTN (215759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	38070502	38070502	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38070502delA								CSNK1A1L (390701 upstream) : POSTN (66218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	38546743	38546745	+	IGR	DEL	GTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38546743_38546745delGTT								TRPC4 (102804 upstream) : UFM1 (377197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	38693133	38693133	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38693133delT								TRPC4 (249194 upstream) : UFM1 (230809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	38698676	38698676	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38698676delA								TRPC4 (254737 upstream) : UFM1 (225266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	38804287	38804287	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38804287delA								TRPC4 (360348 upstream) : UFM1 (119655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	38976616	38976616	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38976616delA								UFM1 (39474 upstream) : FREM2 (284557 downstream)																																			---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39433124	39433124	+	Intron	DEL	C	-	-	rs7982078	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39433124delC	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)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39441021	39441021	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39441021delT	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)														---	---	---	---
LHFP	10186	broad.mit.edu	37	13	39988794	39988794	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39988794delT	uc001uxf.2	-							NM_005780	NP_005771			lipoma HMGIC fusion partner precursor							integral to membrane	DNA binding		HMGA2/LHFP(2)	soft_tissue(2)|lung(1)|breast(1)	4		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)				T	HMGA2	lipoma								---	---	---	---
COG6	57511	broad.mit.edu	37	13	40360790	40360790	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40360790delT	uc010acb.2	+							NM_001145079	NP_001138551			component of oligomeric golgi complex 6 isoform						protein transport	Golgi membrane|Golgi transport complex				kidney(1)|skin(1)	2		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	40593298	40593298	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40593298delA								COG6 (227496 upstream) : LOC646982 (327975 downstream)																																			---	---	---	---
LOC646982	646982	broad.mit.edu	37	13	40993525	40993526	+	Intron	DEL	AG	-	-	rs9315775	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40993525_40993526delAG	uc010tfa.1	-						LOC646982_uc001uxj.3_Intron	NR_024507				Homo sapiens cDNA, FLJ17553.												0																		---	---	---	---
LOC646982	646982	broad.mit.edu	37	13	40993526	40993526	+	Intron	DEL	G	-	-	rs9315775	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40993526delG	uc010tfa.1	-						LOC646982_uc001uxj.3_Intron	NR_024507				Homo sapiens cDNA, FLJ17553.												0																		---	---	---	---
FOXO1	2308	broad.mit.edu	37	13	41106471	41106471	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41106471delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	41250932	41250932	+	IGR	DEL	T	-	-	rs11302175		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41250932delT								FOXO1 (10198 upstream) : MIR320D-1 (51032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	41268848	41268849	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41268848_41268849delTT								FOXO1 (28114 upstream) : MIR320D-1 (33115 downstream)																																			---	---	---	---
SUGT1L1	283507	broad.mit.edu	37	13	41468017	41468017	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41468017delA	uc001uxp.1	-							NR_003365				Homo sapiens cDNA FLJ35913 fis, clone TESTI2010239.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	41673329	41673329	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41673329delT								WBP4 (15192 upstream) : KBTBD6 (28380 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	41685653	41685653	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41685653delA								WBP4 (27516 upstream) : KBTBD6 (16056 downstream)																																			---	---	---	---
MTRF1	9617	broad.mit.edu	37	13	41826024	41826024	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41826024delT	uc001uxx.2	-						MTRF1_uc001uxy.2_Intron|MTRF1_uc001uxz.2_Intron|MTRF1_uc010tff.1_Intron|MTRF1_uc001uyc.1_Intron	NM_004294	NP_004285			mitochondrial translational release factor 1						regulation of translational termination	mitochondrion	translation release factor activity, codon specific				0		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)														---	---	---	---
MTRF1	9617	broad.mit.edu	37	13	41828987	41828987	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41828987delT	uc001uxx.2	-						MTRF1_uc001uxy.2_Intron|MTRF1_uc001uxz.2_Intron|MTRF1_uc010tff.1_Intron|MTRF1_uc001uyc.1_Intron	NM_004294	NP_004285			mitochondrial translational release factor 1						regulation of translational termination	mitochondrion	translation release factor activity, codon specific				0		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	41880519	41880520	+	IGR	INS	-	A	A	rs80026940		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41880519_41880520insA								MTRF1 (42777 upstream) : NAA16 (4821 downstream)																																			---	---	---	---
NAA16	79612	broad.mit.edu	37	13	41915973	41915974	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41915973_41915974delTT	uc001uyf.2	+						NAA16_uc010tfg.1_Intron|NAA16_uc001uye.3_Intron|NAA16_uc001uyd.3_Intron	NM_024561	NP_078837			NMDA receptor regulated 1-like protein isoform						N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent	cytoplasm|transcription factor complex	binding			central_nervous_system(1)	1																		---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42143782	42143783	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42143782_42143783delTT	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	42162694	42162694	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42162694delA	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	42303361	42303362	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42303361_42303362insC	uc001uyj.2	-						KIAA0564_uc001uyk.2_Intron	NM_015058	NP_055873			hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)														---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42458816	42458816	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42458816delT	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	42563137	42563138	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42563137_42563138delAA								KIAA0564 (27916 upstream) : DGKH (51034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	42599967	42599967	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42599967delT								KIAA0564 (64746 upstream) : DGKH (14205 downstream)																																			---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42686046	42686046	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42686046delT	uc001uyl.1	+						DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_Intron	NM_178009	NP_821077			diacylglycerol kinase, eta isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42824114	42824115	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42824114_42824115delTT	uc001uyp.2	+											Homo sapiens DGKH-1 mRNA for diacylglycerol kinase eta1, complete cds.						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	43047387	43047387	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43047387delT								AKAP11 (149985 upstream) : TNFSF11 (89485 downstream)																																			---	---	---	---
TNFSF11	8600	broad.mit.edu	37	13	43140217	43140217	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43140217delT	uc001uyt.2	+							NM_033012	NP_143026			tumor necrosis factor ligand superfamily, member						immune response|monocyte chemotaxis|osteoclast differentiation|positive regulation of bone resorption|positive regulation of corticotropin-releasing hormone secretion|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling|positive regulation of fever generation by positive regulation of prostaglandin secretion|positive regulation of homotypic cell-cell adhesion|positive regulation of NF-kappaB transcription factor activity|positive regulation of osteoclast differentiation|positive regulation of T cell activation	cytoplasm|extracellular space|integral to plasma membrane	cytokine activity|receptor activity|tumor necrosis factor receptor binding				0		Lung NSC(96;1.11e-05)|Breast(139;0.00868)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000249)|GBM - Glioblastoma multiforme(144;0.00119)|BRCA - Breast invasive adenocarcinoma(63;0.073)														---	---	---	---
TNFSF11	8600	broad.mit.edu	37	13	43151977	43151977	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43151977delA	uc001uyu.2	+						TNFSF11_uc001uyt.2_Intron	NM_003701	NP_003692			tumor necrosis factor ligand superfamily, member						immune response|monocyte chemotaxis|osteoclast differentiation|positive regulation of bone resorption|positive regulation of corticotropin-releasing hormone secretion|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling|positive regulation of fever generation by positive regulation of prostaglandin secretion|positive regulation of homotypic cell-cell adhesion|positive regulation of NF-kappaB transcription factor activity|positive regulation of osteoclast differentiation|positive regulation of T cell activation	cytoplasm|extracellular space|integral to plasma membrane	cytokine activity|receptor activity|tumor necrosis factor receptor binding				0		Lung NSC(96;1.11e-05)|Breast(139;0.00868)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000249)|GBM - Glioblastoma multiforme(144;0.00119)|BRCA - Breast invasive adenocarcinoma(63;0.073)														---	---	---	---
C13orf30	144809	broad.mit.edu	37	13	43357576	43357576	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43357576delT	uc010tfk.1	+						C13orf30_uc010tfl.1_Intron	NM_182508	NP_872314			hypothetical protein LOC144809												0		Lung NSC(96;0.000369)|Prostate(109;0.0305)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.000512)|OV - Ovarian serous cystadenocarcinoma(117;0.000563)|BRCA - Breast invasive adenocarcinoma(63;0.0677)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	43412557	43412558	+	IGR	INS	-	AG	AG	rs143639135		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43412557_43412558insAG								C13orf30 (46874 upstream) : EPSTI1 (49564 downstream)																																			---	---	---	---
DNAJC15	29103	broad.mit.edu	37	13	43629378	43629378	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43629378delA	uc001uyy.2	+							NM_013238	NP_037370			DNAJ domain-containing							integral to membrane	heat shock protein binding				0		Lung NSC(96;4.3e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0737)														---	---	---	---
DNAJC15	29103	broad.mit.edu	37	13	43681780	43681780	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43681780delT	uc001uyy.2	+	6						NM_013238	NP_037370			DNAJ domain-containing							integral to membrane	heat shock protein binding				0		Lung NSC(96;4.3e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0737)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44219608	44219609	+	Intron	DEL	AT	-	-	rs78236784		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44219608_44219609delAT	uc001uzb.3	-						ENOX1_uc001uzc.3_Intron	NM_017993	NP_060463			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44243711	44243711	+	Intron	DEL	T	-	-	rs34292080		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44243711delT	uc001uzc.3	-						ENOX1_uc001uzb.3_5'Flank	NM_017993	NP_060463			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44265533	44265533	+	Intron	DEL	A	-	-	rs74832349		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44265533delA	uc001uzc.3	-							NM_017993	NP_060463			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44317049	44317052	+	Intron	DEL	ATAG	-	-	rs141441668		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44317049_44317052delATAG	uc001uzc.3	-							NM_017993	NP_060463			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	44649079	44649079	+	IGR	DEL	A	-	-	rs66756564		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44649079delA								LOC121838 (44481 upstream) : SERP2 (298899 downstream)																																			---	---	---	---
SERP2	387923	broad.mit.edu	37	13	44946583	44946584	+	5'Flank	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44946583_44946584delAA	uc001uzj.2	+						SERP2_uc001uzk.2_5'Flank	NM_001010897	NP_001010897			stress-associated endoplasmic reticulum protein						protein transport|transmembrane transport	endoplasmic reticulum membrane|integral to membrane					0		all_hematologic(4;1.49e-06)|Acute lymphoblastic leukemia(4;1.5e-06)|Lung NSC(96;0.00043)|Breast(139;0.0044)|Prostate(109;0.0137)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;0.00026)|BRCA - Breast invasive adenocarcinoma(63;0.123)														---	---	---	---
TSC22D1	8848	broad.mit.edu	37	13	45042512	45042512	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45042512delT	uc001uzn.3	-						TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358			TSC22 domain family, member 1 isoform 1						transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)														---	---	---	---
TSC22D1	8848	broad.mit.edu	37	13	45090339	45090340	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45090339_45090340delAA	uc001uzn.3	-						TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358			TSC22 domain family, member 1 isoform 1						transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)														---	---	---	---
TSC22D1	8848	broad.mit.edu	37	13	45103346	45103346	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45103346delA	uc001uzn.3	-						TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358			TSC22 domain family, member 1 isoform 1						transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)														---	---	---	---
NUFIP1	26747	broad.mit.edu	37	13	45550417	45550419	+	Intron	DEL	AAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45550417_45550419delAAG	uc001uzp.2	-							NM_012345	NP_036477			nuclear fragile X mental retardation protein						box C/D snoRNP assembly|positive regulation of transcription from RNA polymerase II promoter|RNA processing	actin cytoskeleton|cytosolic ribosome|nuclear matrix|nucleolus|perichromatin fibrils|pre-snoRNP complex|presynaptic active zone|transcription elongation factor complex	DNA binding|identical protein binding|protein binding, bridging|RNA binding|zinc ion binding				0		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	45616013	45616013	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45616013delA								KIAA1704 (8271 upstream) : GTF2F2 (78618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	45892497	45892497	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45892497delA								GTF2F2 (34260 upstream) : TPT1 (18807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	45908933	45908936	+	IGR	DEL	CTTC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45908933_45908936delCTTC								GTF2F2 (50696 upstream) : TPT1 (2368 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	46014351	46014351	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46014351delA								SLC25A30 (21835 upstream) : COG3 (24720 downstream)																																			---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46546314	46546314	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46546314delA	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)														---	---	---	---
LCP1	3936	broad.mit.edu	37	13	46752059	46752060	+	Intron	INS	-	A	A	rs149491022	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46752059_46752060insA	uc001vba.3	-							NM_002298	NP_002289			L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)				T	BCL6	NHL 								---	---	---	---
Unknown	0	broad.mit.edu	37	13	46852715	46852715	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46852715delA								LCP1 (96256 upstream) : C13orf18 (63424 downstream)																																			---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47226531	47226531	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47226531delT	uc001vbj.2	+						LRCH1_uc010acp.2_Intron|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931			leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47279680	47279681	+	Intron	INS	-	T	T	rs146461842	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47279680_47279681insT	uc001vbj.2	+						LRCH1_uc010acp.2_3'UTR|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931			leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47297333	47297333	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47297333delT	uc001vbj.2	+						LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931			leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	47379755	47379755	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47379755delT								ESD (8388 upstream) : HTR2A (27758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	47860549	47860550	+	IGR	DEL	TG	-	-	rs79824465		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47860549_47860550delTG								HTR2A (389499 upstream) : SUCLA2 (656242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	48067589	48067589	+	IGR	DEL	A	-	-	rs114870254	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48067589delA								HTR2A (596539 upstream) : SUCLA2 (449203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	48138167	48138168	+	IGR	DEL	TC	-	-	rs9534684	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48138167_48138168delTC								HTR2A (667117 upstream) : SUCLA2 (378624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	48232531	48232532	+	IGR	DEL	CA	-	-	rs72458219		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48232531_48232532delCA								HTR2A (761481 upstream) : SUCLA2 (284260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	48621845	48621845	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48621845delT								NUDT15 (563 upstream) : MED4 (5617 downstream)																																			---	---	---	---
MED4	29079	broad.mit.edu	37	13	48663717	48663717	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48663717delA	uc001vby.1	-						MED4_uc010tge.1_Intron|MED4_uc010tgf.1_Intron	NM_014166	NP_054885			mediator complex subunit 4						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		all_cancers(8;2.93e-25)|all_epithelial(8;4.38e-13)|all_lung(13;7.37e-06)|all_hematologic(8;8.61e-05)|Breast(56;0.000141)|Lung NSC(96;0.000518)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.00559)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;5.18e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	49154414	49154414	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49154414delA								RCBTB2 (44296 upstream) : CYSLTR2 (73451 downstream)																																			---	---	---	---
CAB39L	81617	broad.mit.edu	37	13	49993501	49993501	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49993501delA	uc001vcx.2	-						CAB39L_uc010adf.2_Intron	NM_001079670	NP_001073138			calcium binding protein 39-like						cell cycle arrest|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol	protein binding				0		Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226)														---	---	---	---
PHF11	51131	broad.mit.edu	37	13	50079929	50079929	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50079929delA	uc001vdb.2	+						PHF11_uc010tgl.1_Intron|PHF11_uc001vdc.2_Intron|PHF11_uc001vdd.2_Intron	NM_001040443	NP_001035533			PHD finger protein 11 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding				0		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)														---	---	---	---
PHF11	51131	broad.mit.edu	37	13	50084169	50084169	+	Intron	DEL	T	-	-	rs79693437		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50084169delT	uc001vdb.2	+						PHF11_uc010tgl.1_Intron|PHF11_uc001vdc.2_Intron|PHF11_uc001vdd.2_Intron	NM_001040443	NP_001035533			PHD finger protein 11 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding				0		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)														---	---	---	---
PHF11	51131	broad.mit.edu	37	13	50098427	50098427	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50098427delA	uc001vdb.2	+						PHF11_uc001vdc.2_Intron|PHF11_uc001vdd.2_Intron	NM_001040443	NP_001035533			PHD finger protein 11 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding				0		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)														---	---	---	---
RCBTB1	55213	broad.mit.edu	37	13	50147924	50147924	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50147924delT	uc001vde.1	-							NM_018191	NP_060661			regulator of chromosome condensation (RCC1) and						cell cycle|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(1)	1		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)														---	---	---	---
C13orf1	57213	broad.mit.edu	37	13	50504723	50504724	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50504723_50504724insA	uc001vdl.2	-						C13orf1_uc001vdm.2_Intron|C13orf1_uc010tgm.1_Intron|C13orf1_uc010adj.2_Intron	NM_020456	NP_065189			chromosome 13 open reading frame 1 isoform 1												0		Lung NSC(96;7.5e-06)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Acute lymphoblastic leukemia(7;0.117)		GBM - Glioblastoma multiforme(99;1.72e-10)|COAD - Colon adenocarcinoma(199;0.208)														---	---	---	---
TRIM13	10206	broad.mit.edu	37	13	50579812	50579812	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50579812delA	uc001vdq.1	+						DLEU2_uc001vdn.1_Intron|DLEU2_uc001vdo.1_Intron|TRIM13_uc001vdp.1_Intron|TRIM13_uc001vdr.1_Intron|TRIM13_uc001vds.1_Intron	NM_052811	NP_434698			ret finger protein 2 isoform 1						anatomical structure morphogenesis|ER-associated protein catabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination	cytoplasm|endoplasmic reticulum membrane|integral to membrane	protein binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)														---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	50726293	50726294	+	Intron	INS	-	CG	CG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50726293_50726294insCG	uc010adl.1	+						DLEU1_uc001vee.1_Intron|DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0																		---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	50770409	50770409	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50770409delT	uc010adl.1	+						DLEU1_uc001vee.1_Intron|DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron|uc001vek.1_Intron|uc001vel.1_Intron|uc001vem.1_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0																		---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	50773367	50773367	+	Intron	DEL	T	-	-	rs112595060		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50773367delT	uc010adl.1	+						DLEU1_uc001vee.1_Intron|DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron|uc001vek.1_Intron|uc001vel.1_Intron|uc001vem.1_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0																		---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	51016867	51016868	+	Intron	INS	-	T	T	rs149650274	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51016867_51016868insT	uc001vee.1	+						DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron|uc001vel.1_Intron|uc001vem.1_Intron|uc001veq.1_Intron|uc001ver.2_Intron|uc001ves.1_Intron|uc001vet.1_Intron|uc001veu.2_Intron|uc001vev.2_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	51235141	51235141	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51235141delT								DLEU1 (132471 upstream) : DLEU7 (51618 downstream)																																			---	---	---	---
DLEU7	220107	broad.mit.edu	37	13	51314058	51314058	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51314058delT	uc001vex.2	-							NM_198989	NP_945340			deleted in lymphocytic leukemia, 7												0		Acute lymphoblastic leukemia(7;1.03e-07)|Lung NSC(96;0.000818)|Breast(56;0.00122)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.25e-08)														---	---	---	---
RNASEH2B	79621	broad.mit.edu	37	13	51502127	51502127	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51502127delT	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)														---	---	---	---
GUCY1B2	2974	broad.mit.edu	37	13	51634722	51634722	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51634722delA	uc001vfd.3	-						GUCY1B2_uc010tgo.1_Intron|GUCY1B2_uc001vfc.3_Intron					SubName: Full=Guanylate cyclase 1, soluble, beta 2;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	51778862	51778862	+	IGR	DEL	A	-	-	rs36059563		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51778862delA								GUCY1B2 (123864 upstream) : FAM124A (17645 downstream)																																			---	---	---	---
FAM124A	220108	broad.mit.edu	37	13	51810601	51810602	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51810601_51810602insC	uc001vfg.1	+						FAM124A_uc001vfe.2_Intron|FAM124A_uc001vff.1_Intron	NM_145019	NP_659456			hypothetical protein LOC220108											central_nervous_system(1)	1		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	52046557	52046558	+	IGR	INS	-	TG	TG	rs150547073	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52046557_52046558insTG								INTS6 (19282 upstream) : WDFY2 (111926 downstream)																																			---	---	---	---
WDFY2	115825	broad.mit.edu	37	13	52204904	52204904	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52204904delT	uc001vfp.2	+						WDFY2_uc010ads.1_Intron|WDFY2_uc010adt.1_Intron	NM_052950	NP_443182			WD repeat and FYVE domain containing 2								metal ion binding				0		Breast(56;0.000208)|Lung NSC(96;0.000517)|Prostate(109;0.0041)|Hepatocellular(98;0.0652)|Myeloproliferative disorder(33;0.164)|all_neural(104;0.191)		GBM - Glioblastoma multiforme(99;9e-08)														---	---	---	---
WDFY2	115825	broad.mit.edu	37	13	52234342	52234342	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52234342delT	uc001vfp.2	+						WDFY2_uc010ads.1_Intron|WDFY2_uc010adt.1_Intron	NM_052950	NP_443182			WD repeat and FYVE domain containing 2								metal ion binding				0		Breast(56;0.000208)|Lung NSC(96;0.000517)|Prostate(109;0.0041)|Hepatocellular(98;0.0652)|Myeloproliferative disorder(33;0.164)|all_neural(104;0.191)		GBM - Glioblastoma multiforme(99;9e-08)														---	---	---	---
WDFY2	115825	broad.mit.edu	37	13	52286880	52286880	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52286880delA	uc001vfp.2	+						WDFY2_uc010ads.1_Intron|WDFY2_uc010adt.1_Intron	NM_052950	NP_443182			WD repeat and FYVE domain containing 2								metal ion binding				0		Breast(56;0.000208)|Lung NSC(96;0.000517)|Prostate(109;0.0041)|Hepatocellular(98;0.0652)|Myeloproliferative disorder(33;0.164)|all_neural(104;0.191)		GBM - Glioblastoma multiforme(99;9e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	52339920	52339920	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52339920delA								WDFY2 (3750 upstream) : DHRS12 (2211 downstream)																																			---	---	---	---
DHRS12	79758	broad.mit.edu	37	13	52364073	52364073	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52364073delT	uc001vfq.2	-						DHRS12_uc001vfr.1_Intron|DHRS12_uc001vfs.1_Intron					RecName: Full=Dehydrogenase/reductase SDR family member 12;          EC=1.1.-.-;								binding|oxidoreductase activity				0		Breast(56;0.00173)|Prostate(109;0.00899)|Lung NSC(96;0.0199)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.81e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	52496061	52496062	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52496061_52496062delTG								CCDC70 (55690 upstream) : ATP7B (10744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	52501949	52501949	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52501949delT								CCDC70 (61578 upstream) : ATP7B (4857 downstream)																																			---	---	---	---
ATP7B	540	broad.mit.edu	37	13	52546547	52546548	+	Intron	INS	-	TCAAT	TCAAT	rs145238171	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52546547_52546548insTCAAT	uc001vfw.2	-						ATP7B_uc010adv.2_Intron|ATP7B_uc001vfx.2_Intron|ATP7B_uc001vfy.2_Intron|ATP7B_uc010tgt.1_Intron|ATP7B_uc010tgu.1_Intron|ATP7B_uc010tgv.1_Intron|ATP7B_uc010tgw.1_Intron	NM_000053	NP_000044			ATPase, Cu++ transporting, beta polypeptide						ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)										Wilson_disease				---	---	---	---
ATP7B	540	broad.mit.edu	37	13	52568838	52568839	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52568838_52568839insA	uc001vfw.2	-						ATP7B_uc010adv.2_Intron|ATP7B_uc001vfx.2_Intron|ATP7B_uc001vfy.2_Intron|ATP7B_uc010tgt.1_Intron|ATP7B_uc010tgu.1_Intron|ATP7B_uc010tgv.1_Intron	NM_000053	NP_000044			ATPase, Cu++ transporting, beta polypeptide						ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)										Wilson_disease				---	---	---	---
NEK5	341676	broad.mit.edu	37	13	52674404	52674405	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52674404_52674405insT	uc001vge.2	-						NEK5_uc001vgf.2_Intron	NM_199289	NP_954983			NIMA-related kinase 5								ATP binding|metal ion binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)	1		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)														---	---	---	---
THSD1P1	374500	broad.mit.edu	37	13	52782354	52782354	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52782354delA	uc001vgm.1	-											Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	52940474	52940474	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52940474delT								THSD1P1 (74794 upstream) : THSD1 (10831 downstream)																																			---	---	---	---
CKAP2	26586	broad.mit.edu	37	13	53044741	53044741	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53044741delA	uc001vgv.2	+						CKAP2_uc001vgu.2_Intron|CKAP2_uc010tha.1_Intron	NM_001098525	NP_001091995			cytoskeleton associated protein 2 isoform 2						apoptosis|cell cycle	centrosome|microtubule|spindle pole				ovary(1)|skin(1)	2		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)														---	---	---	---
CKAP2	26586	broad.mit.edu	37	13	53045644	53045645	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53045644_53045645delAA	uc001vgv.2	+						CKAP2_uc001vgu.2_Intron|CKAP2_uc010tha.1_Intron	NM_001098525	NP_001091995			cytoskeleton associated protein 2 isoform 2						apoptosis|cell cycle	centrosome|microtubule|spindle pole				ovary(1)|skin(1)	2		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)														---	---	---	---
TPTE2P3	220115	broad.mit.edu	37	13	53152796	53152796	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53152796delA	uc001vgw.2	+							NR_002793				Homo sapiens TPTE and PTEN homologous inositol lipid phosphatase pseudogene, mRNA (cDNA clone IMAGE:5298506), with apparent retained intron.												0																		---	---	---	---
LECT1	11061	broad.mit.edu	37	13	53300646	53300646	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53300646delA	uc001vhf.2	-						LECT1_uc001vhg.2_Intron|LECT1_uc001vhh.2_Intron	NM_007015	NP_008946			leukocyte cell derived chemotaxin 1 isoform 1						cartilage development|proteoglycan metabolic process	endomembrane system|extracellular region|integral to membrane				ovary(2)	2		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.38e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	53699975	53699975	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53699975delT								OLFM4 (73789 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	53733545	53733545	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53733545delT								OLFM4 (107359 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54166455	54166455	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54166455delT								OLFM4 (540269 upstream) : MIR1297 (719652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54647153	54647153	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54647153delA								None (None upstream) : MIR1297 (238954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55476988	55476988	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55476988delT								MIR1297 (590805 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55844107	55844107	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55844107delA								MIR1297 (957924 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55909268	55909270	+	IGR	DEL	AAA	-	-	rs36044418		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55909268_55909270delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55997685	55997686	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55997685_55997686delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56120512	56120512	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56120512delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56253881	56253882	+	IGR	DEL	TG	-	-	rs662309	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56253881_56253882delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56791317	56791317	+	IGR	DEL	T	-	-	rs77687489		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56791317delT								None (None upstream) : PRR20C (923735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56800221	56800221	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56800221delT								None (None upstream) : PRR20C (914831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56812566	56812566	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56812566delA								None (None upstream) : PRR20C (902486 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56904104	56904104	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56904104delA								None (None upstream) : PRR20C (810948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56920034	56920034	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56920034delA								None (None upstream) : PRR20C (795018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57240799	57240800	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57240799_57240800delTT								None (None upstream) : PRR20C (474252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57242893	57242893	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57242893delA								None (None upstream) : PRR20C (472159 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57318531	57318534	+	IGR	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57318531_57318534delTTTT								None (None upstream) : PRR20C (396518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57320973	57320984	+	IGR	DEL	TCTCTCTCTCTG	-	-	rs71079877		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57320973_57320984delTCTCTCTCTCTG								None (None upstream) : PRR20C (394068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57448432	57448433	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57448432_57448433delAC								None (None upstream) : PRR20C (266619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57553659	57553659	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57553659delG								None (None upstream) : PRR20C (161393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	58354062	58354062	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58354062delT								PCDH17 (50997 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	58418899	58418900	+	IGR	DEL	TG	-	-	rs142211919	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58418899_58418900delTG								PCDH17 (115834 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	58817488	58817489	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58817488_58817489delAA								PCDH17 (514423 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	59972018	59972019	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59972018_59972019insA								None (None upstream) : DIAPH3 (267706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	59988220	59988220	+	IGR	DEL	T	-	-	rs79087022		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59988220delT								None (None upstream) : DIAPH3 (251505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	60035437	60035438	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60035437_60035438delAA								None (None upstream) : DIAPH3 (204287 downstream)																																			---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60251345	60251345	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60251345delA	uc001vht.2	-						DIAPH3_uc001vhs.2_Intron	NM_001042517	NP_001035982			diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60258186	60258186	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60258186delA	uc001vht.2	-						DIAPH3_uc001vhs.2_Intron	NM_001042517	NP_001035982			diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60303778	60303778	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60303778delA	uc001vht.2	-						DIAPH3_uc001vhs.2_Intron	NM_001042517	NP_001035982			diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60449555	60449555	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60449555delT	uc001vht.2	-						DIAPH3_uc001vhu.2_Intron|DIAPH3_uc001vhv.2_Intron	NM_001042517	NP_001035982			diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60457519	60457519	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60457519delT	uc001vht.2	-						DIAPH3_uc001vhu.2_Intron|DIAPH3_uc001vhv.2_Intron	NM_001042517	NP_001035982			diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60596773	60596773	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60596773delT	uc001vht.2	-						DIAPH3_uc001vhw.1_Intron|DIAPH3_uc010aed.1_Intron|DIAPH3_uc010aee.1_Intron|uc001vhx.2_Intron|uc001vhy.2_Intron	NM_001042517	NP_001035982			diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60607158	60607158	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60607158delT	uc001vht.2	-						DIAPH3_uc001vhw.1_Intron|DIAPH3_uc010aed.1_Intron|DIAPH3_uc010aee.1_Intron|uc001vhx.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	60913740	60913740	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60913740delG								DIAPH3 (175621 upstream) : TDRD3 (56851 downstream)																																			---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61056460	61056460	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61056460delT	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-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	61058809	61058809	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61058809delT	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	61296506	61296509	+	IGR	DEL	CGTA	-	-	rs148675039		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61296506_61296509delCGTA								TDRD3 (148494 upstream) : PCDH20 (687312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	61400153	61400155	+	IGR	DEL	TTT	-	-	rs79783167		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61400153_61400155delTTT								TDRD3 (252141 upstream) : PCDH20 (583666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	61792751	61792752	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61792751_61792752insG								TDRD3 (644739 upstream) : PCDH20 (191069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	62970454	62970455	+	IGR	INS	-	TG	TG	rs139443456	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62970454_62970455insTG								PCDH20 (968375 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63287223	63287223	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63287223delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63344656	63344657	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63344656_63344657delTC								None (None upstream) : OR7E156P (966911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63963309	63963309	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63963309delA								None (None upstream) : OR7E156P (348259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	64441912	64441912	+	IGR	DEL	A	-	-	rs72560080		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64441912delA								OR7E156P (125211 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65288399	65288399	+	IGR	DEL	T	-	-	rs66635407		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65288399delT								OR7E156P (971698 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65494639	65494639	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65494639delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65974154	65974154	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65974154delA								None (None upstream) : PCDH9 (902813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66028359	66028359	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66028359delA								None (None upstream) : PCDH9 (848608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66204630	66204631	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66204630_66204631insA								None (None upstream) : PCDH9 (672336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66376638	66376639	+	IGR	INS	-	AA	AA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66376638_66376639insAA								None (None upstream) : PCDH9 (500328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66441606	66441606	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66441606delA								None (None upstream) : PCDH9 (435361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66492728	66492729	+	IGR	INS	-	A	A	rs139402115	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66492728_66492729insA								None (None upstream) : PCDH9 (384238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66610828	66610829	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66610828_66610829delAA								None (None upstream) : PCDH9 (266138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66714138	66714138	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66714138delT								None (None upstream) : PCDH9 (162829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66841395	66841396	+	IGR	DEL	GT	-	-	rs139624907		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66841395_66841396delGT								None (None upstream) : PCDH9 (35571 downstream)																																			---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	66982862	66982862	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66982862delT	uc001vik.2	-						PCDH9_uc010aei.2_Intron|PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron|uc001vim.2_RNA	NM_203487	NP_982354			protocadherin 9 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	66983291	66983291	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66983291delA	uc001vik.2	-						PCDH9_uc010aei.2_Intron|PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron|uc001vim.2_RNA	NM_203487	NP_982354			protocadherin 9 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	66989877	66989877	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66989877delA	uc001vik.2	-						PCDH9_uc010aei.2_Intron|PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354			protocadherin 9 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67233809	67233809	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67233809delT	uc001vik.2	-						PCDH9_uc010aei.2_Intron|PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354			protocadherin 9 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67354315	67354316	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67354315_67354316delTT	uc001vik.2	-						PCDH9_uc010aei.2_Intron|PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354			protocadherin 9 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	67914740	67914740	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67914740delT								PCDH9 (110272 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	67959444	67959444	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67959444delT								PCDH9 (154976 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68576312	68576312	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68576312delT								PCDH9 (771844 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68761902	68761902	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68761902delA								PCDH9 (957434 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68939009	68939009	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68939009delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69347101	69347101	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69347101delA								None (None upstream) : KLHL1 (927625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69440828	69440828	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69440828delA	uc001vio.2	-											Homo sapiens cDNA clone IMAGE:4826430.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	69559827	69559827	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69559827delT								None (None upstream) : KLHL1 (714899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	70051177	70051178	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70051177_70051178delAA								None (None upstream) : KLHL1 (223548 downstream)																																			---	---	---	---
KLHL1	57626	broad.mit.edu	37	13	70525285	70525285	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70525285delT	uc001vip.2	-						KLHL1_uc010thm.1_Intron	NM_020866	NP_065917			kelch-like 1 protein						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	70895053	70895053	+	IGR	DEL	T	-	-	rs112520844		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70895053delT								ATXN8OS (181168 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71295509	71295509	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71295509delT								ATXN8OS (581624 upstream) : DACH1 (716589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71370957	71370957	+	IGR	DEL	T	-	-	rs34319763		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71370957delT								ATXN8OS (657072 upstream) : DACH1 (641141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71386591	71386592	+	IGR	INS	-	GCAGAGG	GCAGAGG	rs146586294	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71386591_71386592insGCAGAGG								ATXN8OS (672706 upstream) : DACH1 (625506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71471301	71471301	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71471301delA								ATXN8OS (757416 upstream) : DACH1 (540797 downstream)																																			---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72082600	72082600	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72082600delT	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)														---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72189962	72189963	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72189962_72189963delTG	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	72773198	72773198	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72773198delT								DACH1 (331868 upstream) : C13orf37 (509297 downstream)																																	OREG0002705	type=REGULATORY REGION|Gene=DACH1-FLJ22624|Dataset=Vista Enhancers|EvidenceSubtype=In-vivo LacZ Expression Assay	---	---	---	---
Unknown	0	broad.mit.edu	37	13	72773345	72773345	+	IGR	DEL	A	-	-	rs5804614		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72773345delA								DACH1 (332015 upstream) : C13orf37 (509150 downstream)																																	OREG0002705	type=REGULATORY REGION|Gene=DACH1-FLJ22624|Dataset=Vista Enhancers|EvidenceSubtype=In-vivo LacZ Expression Assay	---	---	---	---
Unknown	0	broad.mit.edu	37	13	72900659	72900659	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72900659delA								DACH1 (459329 upstream) : C13orf37 (381836 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73126372	73126373	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73126372_73126373delGT								DACH1 (685042 upstream) : C13orf37 (156122 downstream)																																			---	---	---	---
DIS3	22894	broad.mit.edu	37	13	73337441	73337441	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73337441delA	uc001vix.3	-						DIS3_uc001viy.3_Intron|DIS3_uc001viz.2_Intron	NM_014953	NP_055768			DIS3 mitotic control isoform a						CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding			central_nervous_system(1)	1		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)											Multiple Myeloma(4;0.011)			---	---	---	---
DIS3	22894	broad.mit.edu	37	13	73349322	73349322	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73349322delA	uc001vix.3	-						DIS3_uc001viy.3_Intron|DIS3_uc001viz.2_Intron	NM_014953	NP_055768			DIS3 mitotic control isoform a						CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding			central_nervous_system(1)	1		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)											Multiple Myeloma(4;0.011)			---	---	---	---
PIBF1	10464	broad.mit.edu	37	13	73505702	73505702	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73505702delT	uc001vjc.2	+						PIBF1_uc001vjb.2_Intron|PIBF1_uc010aep.2_Intron	NM_006346	NP_006337			progesterone-induced blocking factor 1							centrosome				ovary(1)|breast(1)	2		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)														---	---	---	---
PIBF1	10464	broad.mit.edu	37	13	73547716	73547716	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73547716delT	uc001vjc.2	+						PIBF1_uc001vjb.2_Intron|PIBF1_uc010aep.2_Intron	NM_006346	NP_006337			progesterone-induced blocking factor 1							centrosome				ovary(1)|breast(1)	2		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)														---	---	---	---
KLF5	688	broad.mit.edu	37	13	73637032	73637032	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73637032delT	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	73815179	73815180	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73815179_73815180insA								KLF5 (163504 upstream) : KLF12 (444970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73927333	73927333	+	IGR	DEL	T	-	-	rs141278386		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73927333delT								KLF5 (275658 upstream) : KLF12 (332817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	74023216	74023216	+	IGR	DEL	A	-	-	rs142121059		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74023216delA								KLF5 (371541 upstream) : KLF12 (236934 downstream)																																			---	---	---	---
KLF12	11278	broad.mit.edu	37	13	74261704	74261704	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74261704delT	uc001vjf.2	-	8					KLF12_uc010aeq.2_3'UTR	NM_007249	NP_009180			Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)														---	---	---	---
KLF12	11278	broad.mit.edu	37	13	74425568	74425568	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74425568delT	uc001vjf.2	-						KLF12_uc010aeq.2_Intron|KLF12_uc001vjg.3_Intron	NM_007249	NP_009180			Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)														---	---	---	---
KLF12	11278	broad.mit.edu	37	13	74532383	74532384	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74532383_74532384delTT	uc001vjf.2	-						KLF12_uc010aeq.2_Intron|KLF12_uc001vjg.3_Intron	NM_007249	NP_009180			Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)														---	---	---	---
KLF12	11278	broad.mit.edu	37	13	74710918	74710919	+	5'Flank	DEL	AA	-	-	rs113376192		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74710918_74710919delAA	uc001vjf.2	-						KLF12_uc010aeq.2_5'Flank|KLF12_uc001vjg.3_5'Flank	NM_007249	NP_009180			Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	74755499	74755499	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74755499delA								KLF12 (47105 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	74800096	74800096	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74800096delG								KLF12 (91702 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	74805341	74805341	+	5'Flank	DEL	T	-	-	rs72130934		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74805341delT	uc001vji.1	+											Homo sapiens cDNA FLJ32127 fis, clone PEBLM2000126.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	74996371	74996371	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74996371delA								KLF12 (287977 upstream) : LOC647288 (815519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75030033	75030033	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75030033delA								KLF12 (321639 upstream) : LOC647288 (781857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75143164	75143164	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75143164delA								KLF12 (434770 upstream) : LOC647288 (668726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75153005	75153005	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75153005delT								KLF12 (444611 upstream) : LOC647288 (658885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75320227	75320228	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75320227_75320228delAA								KLF12 (611833 upstream) : LOC647288 (491662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75385673	75385673	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75385673delA								KLF12 (677279 upstream) : LOC647288 (426217 downstream)																																			---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	75863376	75863376	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75863376delA	uc001vjl.1	-						TBC1D4_uc010tht.1_Intron|TBC1D4_uc010thu.1_Intron|TBC1D4_uc010aer.2_Intron|TBC1D4_uc010aes.2_Intron	NM_014832	NP_055647			TBC1 domain family, member 4							cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)														---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	75910536	75910536	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75910536delA	uc001vjl.1	-						TBC1D4_uc010aer.2_Intron|TBC1D4_uc010aes.2_Intron	NM_014832	NP_055647			TBC1 domain family, member 4							cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	76063400	76063400	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76063400delA								TBC1D4 (7150 upstream) : COMMD6 (35950 downstream)																																			---	---	---	---
COMMD6	170622	broad.mit.edu	37	13	76102190	76102190	+	Intron	DEL	A	-	-	rs67236741		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76102190delA	uc001vjo.1	-						COMMD6_uc001vjn.1_Intron|COMMD6_uc010aet.1_Intron|COMMD6_uc001vjp.1_Intron	NM_203495	NP_987091			COMM domain containing 6 isoform b							cytoplasm|nucleus	protein binding				0		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76423624	76423625	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76423624_76423625delTT	uc001vjv.2	+						LMO7_uc010thv.1_Intron|LMO7_uc010thw.1_Intron	NM_015842	NP_056667			LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	76445383	76445384	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76445383_76445384delTC	uc001vjy.1	+											Homo sapiens cDNA FLJ35379 fis, clone SKMUS2006481.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	76871749	76871749	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76871749delA								LMO7 (437745 upstream) : KCTD12 (582555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77130898	77130898	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77130898delT								LMO7 (696894 upstream) : KCTD12 (323406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77562830	77562830	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77562830delA								BTF3L1 (59607 upstream) : CLN5 (3229 downstream)																																			---	---	---	---
FBXL3	26224	broad.mit.edu	37	13	77586557	77586557	+	Intron	DEL	T	-	-	rs148463592		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77586557delT	uc001vkd.2	-							NM_012158	NP_036290			F-box and leucine-rich repeat protein 3						regulation of circadian rhythm|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity				0		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.218)		GBM - Glioblastoma multiforme(99;0.0521)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77834802	77834802	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77834802delA	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872			MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77861727	77861727	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77861727delT	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	77987879	77987879	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77987879delA								MYCBP2 (86702 upstream) : SCEL (121930 downstream)																																			---	---	---	---
SLAIN1	122060	broad.mit.edu	37	13	78281464	78281464	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78281464delT	uc010thy.1	+						SLAIN1_uc001vkk.1_Intron	NM_144595	NP_653196			SLAIN motif family, member 1 B											ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0853)														---	---	---	---
SLAIN1	122060	broad.mit.edu	37	13	78326014	78326014	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78326014delT	uc010thy.1	+						SLAIN1_uc001vkk.1_Intron|SLAIN1_uc001vkl.1_Intron|SLAIN1_uc010thz.1_Intron|SLAIN1_uc010aex.1_Intron|SLAIN1_uc010aey.1_Intron|SLAIN1_uc001vkm.2_Intron	NM_144595	NP_653196			SLAIN motif family, member 1 B											ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0853)												OREG0022451	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	13	78670370	78670370	+	Intron	DEL	A	-	-	rs150934546		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78670370delA	uc001vks.2	+						uc001vku.1_Intron					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	78738594	78738595	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78738594_78738595delGA	uc001vks.2	+						uc001vku.1_Intron					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	79076645	79076645	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79076645delT	uc001vks.2	+						uc001vku.1_Intron					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	79326305	79326306	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79326305_79326306insA								RNF219 (91605 upstream) : RBM26 (567794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79417894	79417894	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79417894delC								RNF219 (183194 upstream) : RBM26 (476206 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79533312	79533312	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79533312delA								RNF219 (298612 upstream) : RBM26 (360788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79661741	79661742	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79661741_79661742delAA								RNF219 (427041 upstream) : RBM26 (232358 downstream)																																			---	---	---	---
NDFIP2	54602	broad.mit.edu	37	13	80117019	80117019	+	Intron	DEL	T	-	-	rs113529957		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80117019delT	uc001vlf.2	+						NDFIP2_uc010tib.1_Intron|NDFIP2_uc001vlg.2_Intron	NM_019080	NP_061953			Nedd4 family interacting protein 2 isoform 1						negative regulation of gene expression|negative regulation of protein transport|negative regulation of transporter activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of protein ubiquitination	endoplasmic reticulum|Golgi membrane|integral to membrane|mitochondrion|multivesicular body membrane|perinuclear region of cytoplasm	signal transducer activity|WW domain binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0196)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	80927573	80927573	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80927573delA								SPRY2 (12487 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81084689	81084690	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81084689_81084690delTG								SPRY2 (169603 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81149690	81149690	+	IGR	DEL	C	-	-	rs80154477		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81149690delC								SPRY2 (234604 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81524631	81524631	+	IGR	DEL	A	-	-	rs35559408		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81524631delA								SPRY2 (609545 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81574075	81574075	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81574075delG								SPRY2 (658989 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81771980	81771980	+	IGR	DEL	A	-	-	rs5805114		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81771980delA								SPRY2 (856894 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81846601	81846601	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81846601delA								SPRY2 (931515 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81900155	81900155	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81900155delT								SPRY2 (985069 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82246917	82246917	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82246917delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82856104	82856104	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82856104delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82861722	82861722	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82861722delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83345247	83345248	+	IGR	DEL	TT	-	-	rs5805196		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83345247_83345248delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83370286	83370286	+	IGR	DEL	C	-	-	rs71438172		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83370286delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83559550	83559551	+	IGR	INS	-	AAC	AAC	rs141642503	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83559550_83559551insAAC								None (None upstream) : SLITRK1 (891793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83697711	83697711	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83697711delA								None (None upstream) : SLITRK1 (753633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83871842	83871844	+	IGR	DEL	TTT	-	-	rs142992551		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83871842_83871844delTTT								None (None upstream) : SLITRK1 (579500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	84240348	84240348	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84240348delA								None (None upstream) : SLITRK1 (210996 downstream)																																			---	---	---	---
SLITRK1	114798	broad.mit.edu	37	13	84456386	84456386	+	5'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84456386delT	uc001vlk.2	-	1						NM_052910	NP_443142			slit and trk like 1 protein precursor							integral to membrane				ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	84480499	84480499	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84480499delA								SLITRK1 (23971 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	84879595	84879598	+	IGR	DEL	TATG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84879595_84879598delTATG								SLITRK1 (423067 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	84890752	84890752	+	IGR	DEL	T	-	-	rs67191185		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84890752delT								SLITRK1 (434224 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85074575	85074575	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85074575delT								SLITRK1 (618047 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85150501	85150502	+	IGR	INS	-	AG	AG	rs142299312	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	85344550	85344550	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85344550delT								SLITRK1 (888022 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85404018	85404018	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85404018delA								SLITRK1 (947490 upstream) : SLITRK6 (962904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86327305	86327306	+	IGR	INS	-	C	C	rs145645813	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86327305_86327306insC								None (None upstream) : SLITRK6 (39616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86514794	86514794	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86514794delT								SLITRK6 (141311 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86551018	86551018	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86551018delA								SLITRK6 (177535 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87060100	87060100	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87060100delA								SLITRK6 (686617 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87569419	87569419	+	IGR	DEL	A	-	-	rs74326024		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87569419delA								None (None upstream) : SLITRK5 (755451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87661661	87661661	+	IGR	DEL	T	-	-	rs71718002		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87661661delT								None (None upstream) : SLITRK5 (663209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87886100	87886100	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87886100delA								None (None upstream) : SLITRK5 (438770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87939235	87939235	+	IGR	DEL	T	-	-	rs34551592		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87939235delT								None (None upstream) : SLITRK5 (385635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88102325	88102326	+	Intron	DEL	AA	-	-	rs34751657		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88102325_88102326delAA	uc001vlm.1	-											Homo sapiens clone IMAGE:32106, mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	88332816	88332816	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88332816delA								SLITRK5 (948 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89350274	89350274	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89350274delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89360724	89360724	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89360724delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89622632	89622632	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89622632delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89630405	89630405	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89630405delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89997405	89997405	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89997405delA								None (None upstream) : MIR622 (886031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90139449	90139450	+	IGR	INS	-	AC	AC	rs146472021	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90139449_90139450insAC								None (None upstream) : MIR622 (743986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90966857	90966858	+	IGR	DEL	AT	-	-	rs9522928	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90966857_90966858delAT								MIR622 (83326 upstream) : LOC144776 (576350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91091243	91091243	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91091243delT								MIR622 (207712 upstream) : LOC144776 (451965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91196044	91196044	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91196044delA								MIR622 (312513 upstream) : LOC144776 (347164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91293402	91293402	+	IGR	DEL	T	-	-	rs76198967		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91293402delT								MIR622 (409871 upstream) : LOC144776 (249806 downstream)																																			---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92208451	92208451	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92208451delA	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	92364552	92364553	+	Intron	INS	-	TG	TG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92364552_92364553insTG	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	92435997	92435997	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92435997delT	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	92789312	92789313	+	Intron	INS	-	T	T	rs112520958		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92789312_92789313insT	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	93106565	93106565	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93106565delT	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	93275419	93275419	+	Intron	DEL	A	-	-	rs76188645		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93275419delA	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	93577093	93577093	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93577093delT								GPC5 (57608 upstream) : GPC6 (301985 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	93596798	93596798	+	IGR	DEL	A	-	-	rs78759660		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93596798delA								GPC5 (77313 upstream) : GPC6 (282280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	93716406	93716409	+	IGR	DEL	AAAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93716406_93716409delAAAC								GPC5 (196921 upstream) : GPC6 (162669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	93792582	93792583	+	IGR	DEL	TC	-	-	rs161003	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93792582_93792583delTC								GPC5 (273097 upstream) : GPC6 (86495 downstream)																																			---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94423139	94423139	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94423139delT	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	94483810	94483810	+	Intron	DEL	T	-	-	rs67441086		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94483810delT	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	94525368	94525368	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94525368delT	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	94592667	94592670	+	Intron	DEL	ATGG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94592667_94592670delATGG	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	94927005	94927006	+	Intron	DEL	TT	-	-	rs71839602		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94927005_94927006delTT	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	95006603	95006603	+	Intron	DEL	A	-	-	rs74752854		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95006603delA	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	13	95626213	95626213	+	IGR	DEL	T	-	-	rs11330706		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95626213delT								SOX21 (261824 upstream) : ABCC4 (45871 downstream)																																			---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95696129	95696129	+	Intron	DEL	A	-	-	rs4148539		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	95864104	95864104	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95864104delA	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron|ABCC4_uc001vmf.2_Intron|ABCC4_uc010afl.1_Intron|ABCC4_uc010afm.1_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95876991	95876991	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95876991delA	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron|ABCC4_uc001vmf.2_Intron|ABCC4_uc010afl.1_Intron|ABCC4_uc010afm.1_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95882867	95882867	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95882867delA	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron|ABCC4_uc001vmf.2_Intron|ABCC4_uc010afl.1_Intron|ABCC4_uc010afm.1_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95926054	95926056	+	Intron	DEL	GTT	-	-	rs138418337	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95926054_95926056delGTT	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron|ABCC4_uc001vmf.2_Intron|ABCC4_uc010afl.1_Intron|ABCC4_uc010afm.1_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	96735875	96735876	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96735875_96735876insT								UGGT2 (30139 upstream) : HS6ST3 (7217 downstream)																																			---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	96743853	96743853	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96743853delC	uc001vmw.2	+							NM_153456	NP_703157			heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)																	---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	96770127	96770128	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96770127_96770128delTT	uc001vmw.2	+							NM_153456	NP_703157			heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)																	---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	96876589	96876589	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96876589delT	uc001vmw.2	+							NM_153456	NP_703157			heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)																	---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	96886355	96886356	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96886355_96886356delAA	uc001vmw.2	+							NM_153456	NP_703157			heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)																	---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	97246216	97246216	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97246216delT	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	97496437	97496437	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97496437delA								HS6ST3 (4626 upstream) : OXGR1 (141536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	97547987	97547987	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97547987delA								HS6ST3 (56176 upstream) : OXGR1 (89986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	97628994	97628994	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97628994delT								HS6ST3 (137183 upstream) : OXGR1 (8979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	97805575	97805576	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97805575_97805576delGT								OXGR1 (158971 upstream) : MBNL2 (68998 downstream)																																			---	---	---	---
RAP2A	5911	broad.mit.edu	37	13	98094057	98094057	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98094057delT	uc001vnd.2	+							NM_021033	NP_066361			RAP2A, member of RAS oncogene family precursor						actin cytoskeleton reorganization|cellular protein localization|establishment of protein localization|positive regulation of protein autophosphorylation|Rap protein signal transduction|regulation of dendrite morphogenesis|regulation of JNK cascade	recycling endosome membrane	GTP binding|GTPase activity|protein binding			central_nervous_system(1)	1	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.166)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	98275290	98275291	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98275290_98275291delTG								RAP2A (155039 upstream) : IPO5 (330638 downstream)																																			---	---	---	---
IPO5	3843	broad.mit.edu	37	13	98615627	98615630	+	Intron	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98615627_98615630delTTTT	uc001vne.2	+							NM_002271	NP_002262			importin 5						interspecies interaction between organisms|NLS-bearing substrate import into nucleus|ribosomal protein import into nucleus	cytoplasm|nuclear pore|nucleolus	GTPase inhibitor activity|protein transporter activity|Ran GTPase binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
FARP1	10160	broad.mit.edu	37	13	98874877	98874878	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98874877_98874878delTT	uc001vnj.2	+						FARP1_uc001vnh.2_Intron|FARP1_uc001vni.2_Intron	NM_005766	NP_005757			FERM, RhoGEF, and pleckstrin domain protein 1						regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)															---	---	---	---
FARP1	10160	broad.mit.edu	37	13	98918310	98918310	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98918310delT	uc001vnj.2	+						FARP1_uc001vnh.2_Intron	NM_005766	NP_005757			FERM, RhoGEF, and pleckstrin domain protein 1						regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)															---	---	---	---
FARP1	10160	broad.mit.edu	37	13	98958782	98958782	+	Intron	DEL	G	-	-	rs66993675		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98958782delG	uc001vnj.2	+						FARP1_uc001vnh.2_Intron	NM_005766	NP_005757			FERM, RhoGEF, and pleckstrin domain protein 1						regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)															---	---	---	---
DOCK9	23348	broad.mit.edu	37	13	99651545	99651548	+	Intron	DEL	CACA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99651545_99651548delCACA	uc001vnt.2	-						DOCK9_uc001vnv.1_Intron|DOCK9_uc010tir.1_Intron|DOCK9_uc010tit.1_Intron	NM_015296	NP_056111			dedicator of cytokinesis 9 isoform a						blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	99814776	99814776	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99814776delT								DOCK9 (76116 upstream) : UBAC2 (37903 downstream)																																			---	---	---	---
UBAC2	337867	broad.mit.edu	37	13	99933530	99933530	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99933530delT	uc001voa.3	+						UBAC2_uc010tiu.1_Intron|UBAC2_uc001vob.3_Intron|UBAC2_uc010tiv.1_Intron|UBAC2_uc001vod.2_Intron|UBAC2_uc001voc.2_Intron|UBAC2_uc010tiw.1_Intron	NM_001144072	NP_001137544			UBA domain containing 2 isoform 1							integral to membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	100118330	100118330	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100118330delT								UBAC2 (79579 upstream) : TM9SF2 (35398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	100242623	100242623	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100242623delA								TM9SF2 (27347 upstream) : CLYBL (16313 downstream)																																			---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100307335	100307336	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100307335_100307336delTT	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	100328854	100328854	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100328854delT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	100598290	100598290	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100598290delA								CLYBL (53467 upstream) : ZIC5 (16985 downstream)																																			---	---	---	---
PCCA	5095	broad.mit.edu	37	13	101122034	101122035	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101122034_101122035delAA	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron|PCCA_uc001vop.2_Intron	NM_000282	NP_000273			propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)													---	---	---	---
A2LD1	87769	broad.mit.edu	37	13	101229791	101229791	+	Intron	DEL	A	-	-	rs145711188	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101229791delA	uc001vor.2	-							NM_033110	NP_149101			AIG2-like domain 1						cellular modified amino acid catabolic process		acyltransferase activity|gamma-glutamylcyclotransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	101609047	101609048	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101609047_101609048delTG								TMTC4 (281944 upstream) : NALCN (97082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	101679063	101679063	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101679063delT								TMTC4 (351960 upstream) : NALCN (27067 downstream)																																			---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101805981	101805981	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101805981delC	uc001vox.1	-						NALCN_uc001voy.2_Intron	NM_052867	NP_443099			voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	102092578	102092578	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102092578delA								NALCN (23735 upstream) : ITGBL1 (12388 downstream)																																			---	---	---	---
ITGBL1	9358	broad.mit.edu	37	13	102243893	102243893	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102243893delT	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	102555589	102555590	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102555589_102555590delGT	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)																	---	---	---	---
FGF14	2259	broad.mit.edu	37	13	102646121	102646121	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102646121delA	uc001vpf.2	-							NM_175929	NP_787125			fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	103083171	103083171	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103083171delT								FGF14 (29047 upstream) : TPP2 (166115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	103087216	103087216	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103087216delT								FGF14 (33092 upstream) : TPP2 (162070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	103191891	103191891	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103191891delT								FGF14 (137767 upstream) : TPP2 (57395 downstream)																																			---	---	---	---
TPP2	7174	broad.mit.edu	37	13	103313601	103313603	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103313601_103313603delTTT	uc001vpi.3	+							NM_003291	NP_003282			tripeptidyl peptidase II						proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
LOC643677	643677	broad.mit.edu	37	13	103381996	103381996	+	Frame_Shift_Del	DEL	A	-	-	rs34874700		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103381996delA	uc001vpm.2	-	4	21191	c.21051delT	c.(21049-21051)TTTfs	p.F7017fs		NM_001146197	NP_001139669			hypothetical protein LOC643677												0																		---	---	---	---
LOC643677	643677	broad.mit.edu	37	13	103414244	103414244	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103414244delA	uc001vpm.2	-							NM_001146197	NP_001139669			hypothetical protein LOC643677												0																		---	---	---	---
SLC10A2	6555	broad.mit.edu	37	13	103709193	103709193	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103709193delT	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	103980994	103980995	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103980994_103980995insT								SLC10A2 (261798 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104352785	104352787	+	IGR	DEL	AAA	-	-	rs66996048		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104352785_104352787delAAA								SLC10A2 (633589 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104484605	104484605	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104484605delT								SLC10A2 (765409 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104575258	104575258	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104575258delA								SLC10A2 (856062 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104917632	104917632	+	IGR	DEL	G	-	-	rs3916947	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104917632delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	105222076	105222077	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105222076_105222077insG								None (None upstream) : DAOA (896139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	105656830	105656830	+	IGR	DEL	A	-	-	rs11342496		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105656830delA								None (None upstream) : DAOA (461386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107229105	107229105	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107229105delA								ARGLU1 (8591 upstream) : FAM155A (591775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107452589	107452589	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107452589delA								ARGLU1 (232075 upstream) : FAM155A (368291 downstream)																																			---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	108101603	108101603	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108101603delA	uc001vql.2	-							NM_001080396	NP_001073865			family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	108529759	108529759	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108529759delA								FAM155A (10299 upstream) : LIG4 (330035 downstream)																																			---	---	---	---
LIG4	3981	broad.mit.edu	37	13	108866519	108866519	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108866519delA	uc001vqn.2	-						LIG4_uc001vqo.2_Intron|LIG4_uc010agg.1_Intron|LIG4_uc010agf.2_Intron|LIG4_uc001vqp.2_Intron	NM_002312	NP_002303			DNA ligase IV						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					---	---	---	---
TNFSF13B	10673	broad.mit.edu	37	13	108959003	108959003	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108959003delT	uc001vqr.2	+						TNFSF13B_uc010agj.2_Intron	NM_006573	NP_006564			tumor necrosis factor superfamily, member 13b						cell proliferation|immune response|signal transduction	extracellular space|integral to membrane|plasma membrane|soluble fraction	cytokine activity|tumor necrosis factor receptor binding				0	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	109002000	109002000	+	IGR	DEL	T	-	-	rs113837345		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109002000delT								TNFSF13B (42636 upstream) : MYO16 (246500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	109206596	109206597	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109206596_109206597delAA								TNFSF13B (247232 upstream) : MYO16 (41903 downstream)																																			---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109250655	109250656	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109250655_109250656delAG	uc001vqt.1	+							NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109671320	109671322	+	Intron	DEL	TTG	-	-	rs74797710	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109671320_109671322delTTG	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc001vqu.1_Intron|MYO16_uc010tjh.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	109977634	109977635	+	IGR	INS	-	CACACA	CACACA	rs148233005	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109977634_109977635insCACACA								MYO16 (117279 upstream) : IRS2 (428551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110134788	110134788	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110134788delG								MYO16 (274433 upstream) : IRS2 (271398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110226268	110226268	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110226268delA								MYO16 (365913 upstream) : IRS2 (179918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110651405	110651405	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110651405delT								IRS2 (212491 upstream) : COL4A1 (149906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110781907	110781907	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110781907delT								IRS2 (342993 upstream) : COL4A1 (19404 downstream)																																			---	---	---	---
CARS2	79587	broad.mit.edu	37	13	111361430	111361430	+	5'Flank	DEL	T	-	-	rs113546139		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111361430delT	uc001vrd.2	-						CARS2_uc010tjm.1_Intron	NM_024537	NP_078813			cysteinyl-tRNA synthetase 2, mitochondrial						cysteinyl-tRNA aminoacylation	cytosol|mitochondrial matrix	ATP binding|cysteine-tRNA ligase activity|metal ion binding				0	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	111636862	111636862	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111636862delT								ANKRD10 (69446 upstream) : ARHGEF7 (130762 downstream)																																			---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111809922	111809922	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111809922delA	uc001vrs.2	+						ARHGEF7_uc001vrr.2_Intron|ARHGEF7_uc001vrt.2_Intron|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_Intron|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron	NM_001113511	NP_001106983			PAK-interacting exchange factor beta isoform c						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111835691	111835691	+	Intron	DEL	T	-	-	rs72184096		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111835691delT	uc001vrs.2	+						ARHGEF7_uc001vrr.2_Intron|ARHGEF7_uc001vrt.2_Intron|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_Intron|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron	NM_001113511	NP_001106983			PAK-interacting exchange factor beta isoform c						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111908011	111908013	+	Intron	DEL	AAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111908011_111908013delAAG	uc001vrs.2	+						ARHGEF7_uc001vrr.2_Intron|ARHGEF7_uc001vrt.2_Intron|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_Intron|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron|ARHGEF7_uc010tjo.1_Intron|ARHGEF7_uc010tjp.1_Intron|ARHGEF7_uc010agn.1_Intron	NM_001113511	NP_001106983			PAK-interacting exchange factor beta isoform c						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111912462	111912462	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111912462delA	uc001vrs.2	+						ARHGEF7_uc001vrr.2_Intron|ARHGEF7_uc001vrt.2_Intron|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_Intron|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron|ARHGEF7_uc010tjo.1_Intron|ARHGEF7_uc010tjp.1_Intron|ARHGEF7_uc010agn.1_Intron	NM_001113511	NP_001106983			PAK-interacting exchange factor beta isoform c						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111953300	111953300	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111953300delT	uc010tjo.1	+						ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron	NM_003899	NP_003890			PAK-interacting exchange factor beta isoform a						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	112134198	112134201	+	IGR	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112134198_112134201delTTTT								C13orf16 (137605 upstream) : SOX1 (587712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112683037	112683037	+	IGR	DEL	G	-	-	rs942036	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112683037delG								C13orf16 (686444 upstream) : SOX1 (38876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112702515	112702515	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112702515delG								C13orf16 (705922 upstream) : SOX1 (19398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112928128	112928128	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112928128delA								SOX1 (202108 upstream) : C13orf28 (102541 downstream)																																			---	---	---	---
C13orf28	122258	broad.mit.edu	37	13	113075068	113075069	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113075068_113075069delAC	uc001vsd.1	+							NM_145248	NP_660291			hypothetical protein LOC122258 precursor							extracellular region					0	all_lung(23;0.000633)|Lung NSC(43;0.0161)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0997)|Medulloblastoma(90;0.163)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	113128507	113128507	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113128507delA								C13orf28 (39506 upstream) : TUBGCP3 (10821 downstream)																																			---	---	---	---
TUBGCP3	10426	broad.mit.edu	37	13	113189083	113189083	+	Intron	DEL	T	-	-	rs76339402		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113189083delT	uc001vse.1	-						TUBGCP3_uc010tjq.1_Intron|TUBGCP3_uc001vsf.2_Intron	NM_006322	NP_006313			tubulin, gamma complex associated protein 3						G2/M transition of mitotic cell cycle|microtubule nucleation|single fertilization	centriole|cytosol|polar microtubule	gamma-tubulin binding|structural constituent of cytoskeleton			central_nervous_system(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)																	---	---	---	---
C13orf35	400165	broad.mit.edu	37	13	113331032	113331032	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113331032delA	uc001vsh.1	+							NM_207440	NP_997323			hypothetical protein LOC400165											ovary(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)		all cancers(43;0.201)															---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113365834	113365835	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113365834_113365835delAA	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron	NM_015205	NP_056020			ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)																---	---	---	---
F10	2159	broad.mit.edu	37	13	113797247	113797248	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113797247_113797248delAA	uc001vsx.2	+						F10_uc010agq.1_Intron|F10_uc001vsy.2_Intron|F10_uc001vsz.2_Intron	NM_000504	NP_000495			coagulation factor X preproprotein						blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|positive regulation of cell migration|positive regulation of protein kinase B signaling cascade|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen	calcium ion binding|phospholipid binding|protein binding|serine-type endopeptidase activity			pancreas(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Heparin(DB01109)|Menadione(DB00170)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
PCID2	55795	broad.mit.edu	37	13	113832825	113832825	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113832825delA	uc010tju.1	-						PCID2_uc001vtb.2_Intron|PCID2_uc010tjv.1_Intron|PCID2_uc010tjw.1_Intron|PCID2_uc001vte.2_Intron|PCID2_uc001vtd.2_Intron|PCID2_uc001vtf.2_Intron	NM_001127203	NP_001120675			PCI domain containing 2						negative regulation of apoptosis|negative regulation of cysteine-type endopeptidase activity|positive regulation of mitotic cell cycle spindle assembly checkpoint|positive regulation of transcription, DNA-dependent|regulation of mRNA stability|spleen development		protein binding				0	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)															---	---	---	---
PCID2	55795	broad.mit.edu	37	13	113847592	113847593	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113847592_113847593delAA	uc010tju.1	-						PCID2_uc010tjv.1_Intron|PCID2_uc010tjw.1_Intron|PCID2_uc001vte.2_Intron|PCID2_uc001vtd.2_Intron|PCID2_uc001vtf.2_Intron	NM_001127203	NP_001120675			PCI domain containing 2						negative regulation of apoptosis|negative regulation of cysteine-type endopeptidase activity|positive regulation of mitotic cell cycle spindle assembly checkpoint|positive regulation of transcription, DNA-dependent|regulation of mRNA stability|spleen development		protein binding				0	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)															---	---	---	---
CUL4A	8451	broad.mit.edu	37	13	113897490	113897490	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113897490delT	uc010tjy.1	+						CUL4A_uc010tjx.1_Intron|CUL4A_uc010agu.2_Intron|CUL4A_uc010tjz.1_Intron	NM_001008895	NP_001008895			cullin 4A isoform 1						cell cycle arrest|DNA repair|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	Cul4A-RING ubiquitin ligase complex	ubiquitin protein ligase binding			central_nervous_system(2)|skin(1)	3	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	113925818	113925821	+	IGR	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113925818_113925821delTTTT								CUL4A (6427 upstream) : LAMP1 (25648 downstream)																																			---	---	---	---
GRTP1	79774	broad.mit.edu	37	13	113988927	113988927	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113988927delA	uc001vtn.2	-						GRTP1_uc010tkb.1_Intron|GRTP1_uc010tkc.1_Intron	NM_024719	NP_078995			growth hormone regulated TBC protein 1							intracellular	Rab GTPase activator activity				0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0314)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0978)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	114025775	114025775	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114025775delC								GRTP1 (7312 upstream) : ADPRHL1 (50485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	114214135	114214136	+	IGR	INS	-	A	A	rs142676181	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114214135_114214136insA								TMCO3 (9593 upstream) : TFDP1 (24867 downstream)																																			---	---	---	---
TFDP1	7027	broad.mit.edu	37	13	114267907	114267908	+	Intron	INS	-	TGTC	TGTC	rs79999556		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114267907_114267908insTGTC	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)			---	---	---	---
CDC16	8881	broad.mit.edu	37	13	115012809	115012811	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115012809_115012811delTTT	uc001vuk.1	+						CDC16_uc001vul.1_Intron|CDC16_uc001vum.1_Intron|CDC16_uc001vun.1_Intron|CDC16_uc001vuo.1_Intron	NM_003903	NP_003894			anaphase-promoting complex, subunit 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cell proliferation|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	binding				0	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)															---	---	---	---
UPF3A	65110	broad.mit.edu	37	13	115045241	115045241	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115045241delT	uc001vup.2	+						UPF3A_uc010tkn.1_5'Flank|UPF3A_uc001vuq.2_5'Flank|UPF3A_uc001vus.2_5'Flank|UPF3A_uc001vur.2_5'Flank	NM_023011	NP_075387			UPF3 regulator of nonsense transcripts homolog A						mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)														---	---	---	---
UPF3A	65110	broad.mit.edu	37	13	115057211	115057211	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115057211delA	uc001vup.2	+	7	827	c.790delA	c.(790-792)AAAfs	p.K264fs	UPF3A_uc001vuq.2_Frame_Shift_Del_p.K231fs|UPF3A_uc001vus.2_RNA|UPF3A_uc001vur.2_RNA|UPF3A_uc001vut.2_Frame_Shift_Del_p.K63fs|UPF3A_uc001vuu.2_5'UTR	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A	264					mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)														---	---	---	---
UPF3A	65110	broad.mit.edu	37	13	115068575	115068575	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115068575delA	uc001vup.2	+						UPF3A_uc001vuq.2_Intron|UPF3A_uc001vus.2_Intron|UPF3A_uc001vur.2_Intron|UPF3A_uc001vut.2_Intron|UPF3A_uc001vuu.2_Intron	NM_023011	NP_075387			UPF3 regulator of nonsense transcripts homolog A						mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	19050195	19050196	+	IGR	INS	-	TAAA	TAAA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19050195_19050196insTAAA								None (None upstream) : OR11H12 (327398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19456335	19456335	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19456335delA								OR11H12 (77763 upstream) : POTEG (97030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19698789	19698789	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19698789delA								POTEG (113847 upstream) : P704P (285165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19746822	19746823	+	IGR	INS	-	C	C	rs34576740	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19746822_19746823insC								POTEG (161880 upstream) : P704P (237131 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19747418	19747418	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19747418delA								POTEG (162476 upstream) : P704P (236536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	20149342	20149343	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20149342_20149343delAA								P704P (129070 upstream) : OR4Q3 (66244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	20276505	20276505	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20276505delA								OR4M1 (27083 upstream) : OR4N2 (19103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	20300323	20300326	+	IGR	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20300323_20300326delTTTT								OR4N2 (3793 upstream) : OR4K2 (44101 downstream)																																			---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20845375	20845375	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20845375delA	uc001vxe.2	-						TEP1_uc010ahk.2_Intron|TEP1_uc010tlf.1_Intron|TEP1_uc010tlg.1_Intron|TEP1_uc010tlh.1_Intron	NM_007110	NP_009041			telomerase-associated protein 1						telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)														---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20878591	20878591	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20878591delT	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)														---	---	---	---
OSGEP	55644	broad.mit.edu	37	14	20918687	20918688	+	Intron	INS	-	T	T	rs149811749	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20918687_20918688insT	uc001vxf.2	-							NM_017807	NP_060277			O-sialoglycoprotein endopeptidase						proteolysis|tRNA processing		metal ion binding|metalloendopeptidase activity|protein binding				0	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0231)|READ - Rectum adenocarcinoma(17;0.196)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	21114704	21114704	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21114704delT								OR6S1 (4854 upstream) : ANG (37632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	21317542	21317542	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21317542delA								RNASE1 (46506 upstream) : RNASE3 (42020 downstream)																																			---	---	---	---
CHD8	57680	broad.mit.edu	37	14	21898261	21898262	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21898261_21898262insT	uc001was.1	-						CHD8_uc001war.1_Intron	NM_020920	NP_065971			chromodomain helicase DNA binding protein 8						ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22211704	22211704	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22211704delA	uc010aip.1	+											SubName: Full=Putative uncharacterized protein ENSP00000374934;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22592556	22592556	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22592556delA	uc001wbw.2	+						uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22652275	22652276	+	Intron	INS	-	A	A	rs140069365	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22652275_22652276insA	uc001wbw.2	+						uc010aiv.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22905224	22905233	+	Intron	DEL	ACACACACAC	-	-	rs35149290		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22905224_22905233delACACACACAC	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wds.1_Intron|uc001wdv.3_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
SLC7A7	9056	broad.mit.edu	37	14	23246781	23246781	+	Intron	DEL	A	-	-	rs111239567		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23246781delA	uc001wgr.3	-						SLC7A7_uc001wgs.3_Intron|SLC7A7_uc001wgt.3_Intron|SLC7A7_uc001wgu.3_Intron|SLC7A7_uc001wgv.3_Intron	NM_003982	NP_003973			solute carrier family 7 member 7						blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity			ovary(1)|breast(1)	2	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)														---	---	---	---
LRP10	26020	broad.mit.edu	37	14	23341527	23341529	+	In_Frame_Del	DEL	CCT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23341527_23341529delCCT	uc001whd.2	+	1	568_570	c.15_17delCCT	c.(13-18)ACCCTC>ACC	p.L11del	LRP10_uc001whe.2_5'Flank	NM_014045	NP_054764	Q7Z4F1	LRP10_HUMAN	low density lipoprotein receptor-related protein	11					endocytosis	coated pit|integral to membrane				central_nervous_system(1)	1	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)														---	---	---	---
CDH24	64403	broad.mit.edu	37	14	23523785	23523785	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23523785delC	uc001wil.2	-	5	974	c.714delG	c.(712-714)GGGfs	p.G238fs	CDH24_uc010akf.2_Frame_Shift_Del_p.G238fs|CDH24_uc001win.3_Frame_Shift_Del_p.G238fs	NM_022478	NP_071923	Q86UP0	CAD24_HUMAN	cadherin-like 24 isoform 1	238	Cadherin 2.|Extracellular (Potential).				adherens junction organization|cell junction assembly|cell-cell adhesion|homophilic cell adhesion	cell-cell junction|cell-cell junction|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|delta-catenin binding			central_nervous_system(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)												OREG0022594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ACIN1	22985	broad.mit.edu	37	14	23550267	23550267	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23550267delT	uc001wit.3	-						ACIN1_uc001wis.3_5'Flank|ACIN1_uc010akg.2_Intron|ACIN1_uc010tnj.1_Intron	NM_014977	NP_055792			apoptotic chromatin condensation inducer 1						apoptotic chromosome condensation|erythrocyte differentiation|positive regulation of monocyte differentiation	cytosol	ATPase activity|enzyme binding|nucleic acid binding|nucleotide binding			ovary(2)|large_intestine(1)|skin(1)	4	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)														---	---	---	---
SLC7A8	23428	broad.mit.edu	37	14	23631292	23631292	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23631292delA	uc001wiz.2	-						SLC7A8_uc010akj.2_Intron	NM_012244	NP_036376			solute carrier family 7 (cationic amino acid						blood coagulation|cellular amino acid metabolic process|leukocyte migration|metal ion homeostasis|response to toxin	basolateral plasma membrane|cytoplasm|integral to plasma membrane	neutral amino acid transmembrane transporter activity|organic cation transmembrane transporter activity|peptide antigen binding|protein binding|toxin transporter activity			ovary(1)	1	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)													---	---	---	---
SLC7A8	23428	broad.mit.edu	37	14	23650367	23650368	+	Intron	INS	-	A	A	rs141095198	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23650367_23650368insA	uc001wiz.2	-						SLC7A8_uc010akj.2_Intron	NM_012244	NP_036376			solute carrier family 7 (cationic amino acid						blood coagulation|cellular amino acid metabolic process|leukocyte migration|metal ion homeostasis|response to toxin	basolateral plasma membrane|cytoplasm|integral to plasma membrane	neutral amino acid transmembrane transporter activity|organic cation transmembrane transporter activity|peptide antigen binding|protein binding|toxin transporter activity			ovary(1)	1	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)													---	---	---	---
MYH6	4624	broad.mit.edu	37	14	23861417	23861419	+	Intron	DEL	TTT	-	-	rs75627904		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23861417_23861419delTTT	uc001wjv.2	-							NM_002471	NP_002462			myosin heavy chain 6						adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)														---	---	---	---
FAM158A	51016	broad.mit.edu	37	14	24609803	24609803	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24609803delA	uc001wmi.2	-							NM_016049	NP_057133			hypothetical protein LOC51016												0																		---	---	---	---
TM9SF1	10548	broad.mit.edu	37	14	24681761	24681761	+	Intron	DEL	T	-	-	rs113555572		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24681761delT	uc010tob.1	-						CHMP4A_uc001wni.2_Intron|CHMP4A_uc010toc.1_Intron|CHMP4A_uc001wnj.2_Intron	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)														---	---	---	---
STXBP6	29091	broad.mit.edu	37	14	25350327	25350327	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25350327delT	uc001wpu.2	-						STXBP6_uc001wpv.2_Intron|STXBP6_uc001wpw.2_Intron|STXBP6_uc001wpx.1_Intron	NM_014178	NP_054897			amisyn						vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	25711557	25711557	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25711557delT								STXBP6 (192386 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	25730235	25730236	+	IGR	INS	-	AAAA	AAAA	rs140900033	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25730235_25730236insAAAA								STXBP6 (211064 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	25894567	25894567	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25894567delG								STXBP6 (375396 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26053087	26053087	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26053087delT								STXBP6 (533916 upstream) : NOVA1 (862003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26596010	26596010	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26596010delT								None (None upstream) : NOVA1 (319080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26619034	26619035	+	IGR	DEL	CC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26619034_26619035delCC								None (None upstream) : NOVA1 (296055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	27343819	27343820	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27343819_27343820insT								NOVA1 (276859 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	27581360	27581361	+	IGR	DEL	TT	-	-	rs142193006		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27581360_27581361delTT								NOVA1 (514400 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	27596735	27596735	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27596735delT								NOVA1 (529775 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28480802	28480802	+	IGR	DEL	T	-	-	rs67125606		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28480802delT								None (None upstream) : FOXG1 (755485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28566657	28566657	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28566657delA								None (None upstream) : FOXG1 (669630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	29007867	29007867	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29007867delT								None (None upstream) : FOXG1 (228420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	29041021	29041021	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29041021delA								None (None upstream) : FOXG1 (195266 downstream)																																			---	---	---	---
FOXG1	2290	broad.mit.edu	37	14	29234805	29234805	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29234805delA	uc001wqe.2	+							NM_005249	NP_005240			forkhead box G1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	29327987	29327987	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29327987delT								C14orf23 (63988 upstream) : PRKD1 (717702 downstream)																																			---	---	---	---
PRKD1	5587	broad.mit.edu	37	14	30135669	30135669	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30135669delA	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)														---	---	---	---
SCFD1	23256	broad.mit.edu	37	14	31112379	31112379	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31112379delA	uc001wqm.1	+						SCFD1_uc001wqn.1_Intron|SCFD1_uc010tpg.1_Intron|SCFD1_uc010tph.1_Intron|SCFD1_uc010amf.1_Intron|SCFD1_uc010tpi.1_Intron|SCFD1_uc010amd.1_Intron|SCFD1_uc010ame.1_Intron	NM_016106	NP_057190			vesicle transport-related protein isoform a						post-Golgi vesicle-mediated transport|protein transport|regulation of ER to Golgi vesicle-mediated transport|response to toxin|retrograde vesicle-mediated transport, Golgi to ER|vesicle docking involved in exocytosis	cis-Golgi network|endoplasmic reticulum membrane|Golgi cisterna membrane|Golgi-associated vesicle|plasma membrane	syntaxin-5 binding				0	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)														---	---	---	---
SCFD1	23256	broad.mit.edu	37	14	31192049	31192049	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31192049delA	uc001wqm.1	+						SCFD1_uc001wqn.1_Intron|SCFD1_uc010tpg.1_Intron|SCFD1_uc010tph.1_Intron|SCFD1_uc010amf.1_Intron|SCFD1_uc010tpi.1_Intron	NM_016106	NP_057190			vesicle transport-related protein isoform a						post-Golgi vesicle-mediated transport|protein transport|regulation of ER to Golgi vesicle-mediated transport|response to toxin|retrograde vesicle-mediated transport, Golgi to ER|vesicle docking involved in exocytosis	cis-Golgi network|endoplasmic reticulum membrane|Golgi cisterna membrane|Golgi-associated vesicle|plasma membrane	syntaxin-5 binding				0	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)														---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31606025	31606025	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31606025delT	uc001wrc.1	-						HECTD1_uc001wrd.1_Intron	NM_015382	NP_056197			HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)														---	---	---	---
HEATR5A	25938	broad.mit.edu	37	14	31793890	31793891	+	Intron	DEL	TT	-	-	rs140519180		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31793890_31793891delTT	uc001wrf.3	-						HEATR5A_uc010ami.2_Intron|HEATR5A_uc001wrg.1_Intron	NM_015473	NP_056288			HEAT repeat containing 5A								binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)														---	---	---	---
HEATR5A	25938	broad.mit.edu	37	14	31818590	31818590	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31818590delA	uc001wrf.3	-						HEATR5A_uc010ami.2_Intron|HEATR5A_uc001wrg.1_Intron|HEATR5A_uc010tpk.1_Intron	NM_015473	NP_056288			HEAT repeat containing 5A								binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	32006111	32006111	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32006111delT								HEATR5A (79431 upstream) : NUBPL (24480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	32477556	32477557	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32477556_32477557delTC								NUBPL (147139 upstream) : C14orf128 (67069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	32484200	32484200	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32484200delT								NUBPL (153783 upstream) : C14orf128 (60426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	32667979	32667979	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32667979delA								ARHGAP5 (39047 upstream) : AKAP6 (130500 downstream)																																			---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	32838085	32838085	+	Intron	DEL	G	-	-	rs1951686		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32838085delG	uc001wrq.2	+						AKAP6_uc010aml.2_Intron	NM_004274	NP_004265			A-kinase anchor protein 6						protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33210556	33210556	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33210556delT	uc001wrq.2	+							NM_004274	NP_004265			A-kinase anchor protein 6						protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33294194	33294194	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33294194delA	uc001wrq.2	+							NM_004274	NP_004265			A-kinase anchor protein 6						protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	33833128	33833129	+	Intron	INS	-	TGTG	TGTG	rs148359376	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33833128_33833129insTGTG	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron|NPAS3_uc001wrw.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	34038825	34038825	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34038825delA	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron|NPAS3_uc001wrw.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	34249754	34249754	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34249754delA	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	34358561	34358562	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34358561_34358562delAA								NPAS3 (85180 upstream) : EGLN3 (34861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	34542515	34542516	+	IGR	DEL	AG	-	-	rs78482733		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34542515_34542516delAG								EGLN3 (122228 upstream) : C14orf147 (359629 downstream)																																			---	---	---	---
EAPP	55837	broad.mit.edu	37	14	34985336	34985336	+	3'UTR	DEL	A	-	-	rs144603764		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34985336delA	uc001wsd.1	-	6						NM_018453	NP_060923			E2F-associated phosphoprotein						negative regulation of transcription elongation from RNA polymerase II promoter|positive regulation of cell proliferation|positive regulation of transcription elongation from RNA polymerase II promoter	Golgi apparatus|nucleus|plasma membrane				ovary(1)	1	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00342)|Epithelial(34;0.18)	GBM - Glioblastoma multiforme(112;0.0196)														---	---	---	---
SNX6	58533	broad.mit.edu	37	14	35039268	35039269	+	Intron	DEL	GT	-	-	rs7148131	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35039268_35039269delGT	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419			sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	35387990	35387991	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35387990_35387991delTT								BAZ1A (43137 upstream) : C14orf19 (21137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	35448312	35448312	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35448312delA								C14orf19 (38610 upstream) : SRP54 (3792 downstream)																																			---	---	---	---
INSM2	84684	broad.mit.edu	37	14	36005056	36005057	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36005056_36005057insT	uc001wth.1	+	1	1809_1810	c.1598_1599insT	c.(1597-1599)ACTfs	p.T533fs		NM_032594	NP_115983	Q96T92	INSM2_HUMAN	insulinoma-associated protein IA-6	533	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)|skin(1)	2	Breast(36;0.122)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(9;2.16e-07)|Lung(238;2.63e-07)|Epithelial(34;0.00145)|all cancers(34;0.00452)	GBM - Glioblastoma multiforme(112;0.0223)														---	---	---	---
BRMS1L	84312	broad.mit.edu	37	14	36337009	36337009	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36337009delT	uc001wtl.2	+							NM_032352	NP_115728			breast cancer metastasis-suppressor 1-like						regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				skin(1)	1	Breast(36;0.137)|Hepatocellular(127;0.158)		Lung(8;1.7e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.00467)|all cancers(34;0.0157)|BRCA - Breast invasive adenocarcinoma(188;0.158)	GBM - Glioblastoma multiforme(112;0.0333)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	37066367	37066367	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37066367delT								NKX2-8 (14581 upstream) : PAX9 (60415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	37123071	37123071	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37123071delA								NKX2-8 (71285 upstream) : PAX9 (3711 downstream)																																			---	---	---	---
SLC25A21	89874	broad.mit.edu	37	14	37465902	37465902	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37465902delA	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	38167695	38167695	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38167695delT	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38631512	38631514	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38631512_38631514delAAA								FOXA1 (567023 upstream) : SSTR1 (45690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	38782170	38782171	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38782170_38782171delTT								CLEC14A (56596 upstream) : SEC23A (718952 downstream)																																			---	---	---	---
SEC23A	10484	broad.mit.edu	37	14	39540240	39540240	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39540240delA	uc001wup.1	-						SEC23A_uc010tqa.1_Intron|SEC23A_uc010tqb.1_Intron|SEC23A_uc010tqc.1_Intron	NM_006364	NP_006355			SEC23-related protein A						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)														---	---	---	---
SEC23A	10484	broad.mit.edu	37	14	39554851	39554852	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39554851_39554852insA	uc001wup.1	-						SEC23A_uc010tqa.1_Intron|SEC23A_uc010tqb.1_Intron|SEC23A_uc010tqc.1_Intron	NM_006364	NP_006355			SEC23-related protein A						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)														---	---	---	---
SEC23A	10484	broad.mit.edu	37	14	39560349	39560349	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39560349delA	uc001wup.1	-						SEC23A_uc010tqa.1_Intron|SEC23A_uc010tqb.1_Intron|SEC23A_uc010tqc.1_Intron	NM_006364	NP_006355			SEC23-related protein A						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	39611966	39611966	+	IGR	DEL	A	-	-	rs143481313		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39611966delA								SIP1 (5791 upstream) : TRAPPC6B (5049 downstream)																																			---	---	---	---
CTAGE5	4253	broad.mit.edu	37	14	39769403	39769403	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39769403delT	uc001wvg.3	+						CTAGE5_uc010tqe.1_Intron|CTAGE5_uc001wuz.3_Intron|CTAGE5_uc001wuy.3_Intron|CTAGE5_uc001wvb.3_Intron|CTAGE5_uc001wvc.3_Intron|CTAGE5_uc001wva.3_Intron|CTAGE5_uc001wve.1_Intron|CTAGE5_uc001wvh.3_Intron|CTAGE5_uc001wvf.3_Intron|CTAGE5_uc001wvi.3_Intron|CTAGE5_uc010amz.2_Intron|CTAGE5_uc001wvj.3_Intron	NM_005930	NP_005921			CTAGE family, member 5 isoform 1								enzyme activator activity|protein binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	40009603	40009605	+	IGR	DEL	AAA	-	-	rs111318373		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:40009603_40009605delAAA								FBXO33 (107899 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	40230435	40230435	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:40230435delA								FBXO33 (328731 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	40677966	40677966	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:40677966delA								FBXO33 (776262 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	40742897	40742897	+	IGR	DEL	T	-	-	rs33928473		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:40742897delT								FBXO33 (841193 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41174803	41174803	+	IGR	DEL	A	-	-	rs35472617		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41174803delA								None (None upstream) : LRFN5 (901961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41306223	41306223	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41306223delT								None (None upstream) : LRFN5 (770541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41366160	41366161	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41366160_41366161insT								None (None upstream) : LRFN5 (710603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41537673	41537673	+	IGR	DEL	C	-	-	rs141453881		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41537673delC								None (None upstream) : LRFN5 (539091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41881216	41881216	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41881216delA								None (None upstream) : LRFN5 (195548 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	42809843	42809843	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42809843delA								LRFN5 (436093 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	42972010	42972011	+	IGR	DEL	TT	-	-	rs111975827		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42972010_42972011delTT								LRFN5 (598260 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43972786	43972786	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43972786delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44359026	44359026	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44359026delA								None (None upstream) : FSCB (614329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44445424	44445424	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44445424delT								None (None upstream) : FSCB (527931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44760816	44760816	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44760816delA								None (None upstream) : FSCB (212539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	45393080	45393080	+	IGR	DEL	T	-	-	rs113302242		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45393080delT								C14orf28 (16621 upstream) : KLHL28 (448 downstream)																																			---	---	---	---
KLHL28	54813	broad.mit.edu	37	14	45414534	45414534	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45414534delA	uc001wvq.2	-	2	844	c.598delT	c.(598-600)TATfs	p.Y200fs	KLHL28_uc001wvr.2_Frame_Shift_Del_p.Y200fs|KLHL28_uc001wvt.3_Frame_Shift_Del_p.Y200fs	NM_017658	NP_060128	Q9NXS3	KLH28_HUMAN	BTB (POZ) domain containing 5	200										ovary(1)	1																		---	---	---	---
KLHL28	54813	broad.mit.edu	37	14	45429352	45429352	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45429352delA	uc001wvq.2	-						FAM179B_uc001wvv.2_5'Flank|FAM179B_uc001wvw.2_5'Flank|FAM179B_uc010anc.2_5'Flank|KLHL28_uc001wvr.2_Intron|FAM179B_uc010anb.1_5'Flank|FAM179B_uc001wvu.2_5'Flank	NM_017658	NP_060128			BTB (POZ) domain containing 5											ovary(1)	1																		---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45475110	45475110	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45475110delT	uc001wvv.2	+						FAM179B_uc001wvw.2_Intron|FAM179B_uc010anc.2_Intron|FAM179B_uc001wvu.2_Intron	NM_015091	NP_055906			hypothetical protein LOC23116								binding			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45541194	45541194	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45541194delT	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																		---	---	---	---
PRPF39	55015	broad.mit.edu	37	14	45584168	45584168	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45584168delT	uc001wvz.3	+	14					PRPF39_uc001wvy.3_3'UTR|PRPF39_uc010and.2_3'UTR|PRPF39_uc001wwa.1_3'UTR	NM_017922	NP_060392			PRP39 pre-mRNA processing factor 39 homolog						mRNA processing|RNA splicing	nucleus	binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	46009019	46009019	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46009019delT								C14orf106 (286414 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46384973	46384974	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46384973_46384974insA								C14orf106 (662368 upstream) : RPL10L (735248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46913859	46913859	+	IGR	DEL	C	-	-	rs34751424		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46913859delC								None (None upstream) : RPL10L (206363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	47231625	47231626	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47231625_47231626insA								RPL10L (110597 upstream) : MDGA2 (77204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	47296804	47296804	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47296804delA								RPL10L (175776 upstream) : MDGA2 (12026 downstream)																																			---	---	---	---
MDGA2	161357	broad.mit.edu	37	14	47928827	47928827	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47928827delT	uc001wwj.3	-						MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970			MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	49237679	49237679	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49237679delA								None (None upstream) : SDCCAG1 (795348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	49506001	49506002	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49506001_49506002delAC								None (None upstream) : SDCCAG1 (527025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	49763133	49763133	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49763133delT								None (None upstream) : SDCCAG1 (269894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	49833665	49833665	+	IGR	DEL	T	-	-	rs112831743		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49833665delT								None (None upstream) : SDCCAG1 (199362 downstream)																																			---	---	---	---
SDCCAG1	9147	broad.mit.edu	37	14	50295077	50295077	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50295077delA	uc001wxc.2	-						SDCCAG1_uc010anj.1_Intron|SDCCAG1_uc010tqi.1_Intron|SDCCAG1_uc001wxe.2_Intron|SDCCAG1_uc001wxd.1_Intron|SDCCAG1_uc010anq.1_Intron	NM_004713	NP_004704			serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)														---	---	---	---
SDCCAG1	9147	broad.mit.edu	37	14	50298108	50298108	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50298108delA	uc001wxc.2	-						SDCCAG1_uc010anj.1_Intron|SDCCAG1_uc010tqi.1_Intron|SDCCAG1_uc001wxe.2_Intron|SDCCAG1_uc001wxd.1_Intron|SDCCAG1_uc010anq.1_Intron	NM_004713	NP_004704			serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	50351831	50351831	+	IGR	DEL	A	-	-	rs145509265		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50351831delA								SDCCAG1 (32292 upstream) : ARF6 (7905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	50495770	50495770	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50495770delT								C14orf182 (21532 upstream) : C14orf183 (54600 downstream)																																			---	---	---	---
SOS2	6655	broad.mit.edu	37	14	50589494	50589494	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50589494delT	uc001wxs.3	-						SOS2_uc010ans.2_Intron|SOS2_uc010tql.1_Intron	NM_006939	NP_008870			son of sevenless homolog 2						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)																	---	---	---	---
SOS2	6655	broad.mit.edu	37	14	50670810	50670810	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50670810delT	uc001wxs.3	-						SOS2_uc010tql.1_Intron	NM_006939	NP_008870			son of sevenless homolog 2						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)																	---	---	---	---
L2HGDH	79944	broad.mit.edu	37	14	50708475	50708476	+	Intron	INS	-	A	A	rs142082924	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50708475_50708476insA	uc010tqn.1	-							NM_024884	NP_079160			L-2-hydroxyglutarate dehydrogenase precursor						2-oxoglutarate metabolic process|cellular protein metabolic process	integral to mitochondrial inner membrane	2-hydroxyglutarate dehydrogenase activity			ovary(2)	2	all_epithelial(31;0.000599)|Breast(41;0.0102)																	---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50887186	50887186	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50887186delA	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)																	---	---	---	---
ABHD12B	145447	broad.mit.edu	37	14	51368523	51368523	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51368523delT	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)																	---	---	---	---
FRMD6	122786	broad.mit.edu	37	14	52030387	52030388	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52030387_52030388insA	uc001wzb.2	+							NM_001042481	NP_001035946			FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)																	---	---	---	---
FRMD6	122786	broad.mit.edu	37	14	52043990	52043991	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52043990_52043991delAA	uc001wzb.2	+							NM_001042481	NP_001035946			FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)																	---	---	---	---
FRMD6	122786	broad.mit.edu	37	14	52174986	52174986	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52174986delA	uc001wzd.2	+						FRMD6_uc001wzb.2_Intron|FRMD6_uc001wzc.2_Intron|FRMD6_uc001wze.2_Intron	NM_152330	NP_689543			FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)																	---	---	---	---
GPR137C	283554	broad.mit.edu	37	14	53101641	53101641	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53101641delT	uc001wzu.3	+						GPR137C_uc001wzt.3_Intron	NM_001099652	NP_001093122			G protein-coupled receptor 137C							integral to membrane					0	Breast(41;0.0716)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	54446710	54446711	+	IGR	DEL	AA	-	-	rs71446482		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54446710_54446711delAA								BMP4 (23156 upstream) : CDKN3 (416962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54572390	54572390	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54572390delT								BMP4 (148836 upstream) : CDKN3 (291283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54629323	54629323	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54629323delC								BMP4 (205769 upstream) : CDKN3 (234350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54824405	54824405	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54824405delT								BMP4 (400851 upstream) : CDKN3 (39268 downstream)																																			---	---	---	---
KTN1	3895	broad.mit.edu	37	14	56150981	56150981	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	56184788	56184789	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56184788_56184789insT								KTN1 (33487 upstream) : RPL13AP3 (48174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56504692	56504692	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56504692delA								C14orf34 (241300 upstream) : PELI2 (80401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56505794	56505794	+	IGR	DEL	T	-	-	rs33989004		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56505794delT								C14orf34 (242402 upstream) : PELI2 (79299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56847124	56847124	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56847124delT								PELI2 (79094 upstream) : C14orf101 (199214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56964796	56964797	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56964796_56964797delAC								PELI2 (196766 upstream) : C14orf101 (81541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	57152855	57152856	+	IGR	INS	-	C	C	rs147660726	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57152855_57152856insC								C14orf101 (36625 upstream) : OTX2 (114571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	57453351	57453351	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57453351delT								OTX2 (176167 upstream) : EXOC5 (215845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	57654049	57654050	+	IGR	INS	-	GT	GT	rs138964597	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57654049_57654050insGT								OTX2 (376865 upstream) : EXOC5 (15146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	58188608	58188608	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58188608delC								SLC35F4 (124993 upstream) : C14orf37 (282201 downstream)																																			---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58681904	58681904	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58681904delT	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																		---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58719700	58719700	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58719700delT	uc010tro.1	-						PSMA3_uc001xdj.1_Intron|PSMA3_uc001xdk.1_Intron	NM_001001872	NP_001001872			hypothetical protein LOC145407 precursor							integral to membrane	binding				0																		---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58741619	58741620	+	Intron	DEL	AA	-	-	rs113544310		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58741619_58741620delAA	uc010tro.1	-						uc001xdl.2_Intron|uc001xdm.1_Intron|uc001xdn.1_Intron	NM_001001872	NP_001001872			hypothetical protein LOC145407 precursor							integral to membrane	binding				0																		---	---	---	---
TIMM9	26520	broad.mit.edu	37	14	58889833	58889833	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58889833delT	uc010aph.2	-						TIMM9_uc001xds.2_Intron|TIMM9_uc010api.2_Intron	NM_012460	NP_036592			translocase of inner mitochondrial membrane 9						protein import into mitochondrial inner membrane|sensory perception of sound|transmembrane transport	mitochondrial inner membrane presequence translocase complex|mitochondrial intermembrane space protein transporter complex	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	59042569	59042569	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59042569delA								KIAA0586 (27021 upstream) : DACT1 (58217 downstream)																																			---	---	---	---
C14orf135	64430	broad.mit.edu	37	14	60562510	60562510	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60562510delA	uc001xer.3	+						C14orf135_uc001xeq.2_Intron	NM_022495	NP_071940			hepatitis C virus F protein-binding protein 2							integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)														---	---	---	---
C14orf135	64430	broad.mit.edu	37	14	60581403	60581403	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60581403delT	uc001xer.3	+						C14orf135_uc001xeq.2_Intron	NM_022495	NP_071940			hepatitis C virus F protein-binding protein 2							integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	60682866	60682866	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60682866delT								DHRS7 (46305 upstream) : PPM1A (29604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	61047874	61047875	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61047874_61047875insT								SIX6 (69351 upstream) : SIX1 (63543 downstream)																																			---	---	---	---
SLC38A6	145389	broad.mit.edu	37	14	61518736	61518736	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)														---	---	---	---
PRKCH	5583	broad.mit.edu	37	14	61719919	61719919	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61719919delT	uc010tsa.1	+							NM_006255	NP_006246			protein kinase C, eta						intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)														---	---	---	---
PRKCH	5583	broad.mit.edu	37	14	61771379	61771379	+	Intron	DEL	A	-	-	rs111426448		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61771379delA	uc010tsa.1	+						uc001xfm.2_RNA	NM_006255	NP_006246			protein kinase C, eta						intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	62707292	62707292	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62707292delT								FLJ43390 (110060 upstream) : KCNH5 (466655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	62722584	62722585	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62722584_62722585delAA								FLJ43390 (125352 upstream) : KCNH5 (451362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	63065634	63065634	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63065634delA								FLJ43390 (468402 upstream) : KCNH5 (108313 downstream)																																			---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63367393	63367393	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63367393delA	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	63531138	63531139	+	Intron	INS	-	AGG	AGG	rs67842381		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63531138_63531139insAGG	uc001xfz.1	-						KCNH5_uc001xga.2_Intron	NM_172376	NP_758964			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	63579660	63579660	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63579660delA								KCNH5 (11076 upstream) : RHOJ (91485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	64058431	64058431	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64058431delT								PPP2R5E (48352 upstream) : WDR89 (5327 downstream)																																			---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64427327	64427327	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64427327delT	uc001xgm.2	+						SYNE2_uc001xgk.2_Intron|SYNE2_uc001xgl.2_Intron	NM_015180	NP_055995			spectrin repeat containing, nuclear envelope 2						centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64434881	64434881	+	Intron	DEL	A	-	-	rs78067424		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64434881delA	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron	NM_015180	NP_055995			spectrin repeat containing, nuclear envelope 2						centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64655326	64655326	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64655326delA	uc001xgm.2	+	98	18001	c.17771delA	c.(17770-17772)GAAfs	p.E5924fs	SYNE2_uc001xgl.2_Frame_Shift_Del_p.E5924fs|SYNE2_uc010apy.2_Frame_Shift_Del_p.E2309fs|SYNE2_uc001xgn.2_Frame_Shift_Del_p.E886fs|SYNE2_uc001xgo.2_RNA|SYNE2_uc010aqa.2_5'UTR|SYNE2_uc001xgq.2_Frame_Shift_Del_p.E289fs	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5924	Spectrin 5.|Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)														---	---	---	---
ESR2	2100	broad.mit.edu	37	14	64786124	64786125	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64786124_64786125delAA	uc001xgv.2	-						ESR2_uc001xgw.2_Intron|ESR2_uc001xgx.2_Intron	NM_001040276	NP_001035366			estrogen receptor beta isoform 2						cell-cell signaling|negative regulation of cell growth|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	mitochondrion|nucleoplasm	enzyme binding|estrogen receptor activity|receptor antagonist activity|sequence-specific DNA binding transcription factor activity|steroid binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Bicalutamide(DB01128)|Estradiol(DB00783)|Estramustine(DB01196)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)													---	---	---	---
C14orf50	145376	broad.mit.edu	37	14	65017760	65017760	+	Intron	DEL	A	-	-	rs76585972	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65017760delA	uc001xhl.1	+							NM_172365	NP_758953			hypothetical protein LOC145376											skin(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00382)|all cancers(60;0.00427)|BRCA - Breast invasive adenocarcinoma(234;0.0488)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	65158889	65158892	+	IGR	DEL	CCAT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65158889_65158892delCCAT								C14orf50 (102793 upstream) : PLEKHG3 (12301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	65848584	65848584	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65848584delT								MAX (279357 upstream) : LOC645431 (28729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	65851614	65851615	+	IGR	DEL	TT	-	-	rs71891860		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65851614_65851615delTT								MAX (282387 upstream) : LOC645431 (25698 downstream)																																			---	---	---	---
FUT8	2530	broad.mit.edu	37	14	66105071	66105071	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66105071delT	uc001xin.2	+						FUT8_uc001xio.2_Intron|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Intron|FUT8_uc001xiq.2_Intron	NM_178155	NP_835368			fucosyltransferase 8 isoform a						in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)														---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67239698	67239698	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67239698delT	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron	NM_001024218	NP_001019389			gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)				T	MLL	AL								---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67468870	67468870	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67468870delT	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389			gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)				T	MLL	AL								---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67590527	67590527	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67590527delT	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								---	---	---	---
MPP5	64398	broad.mit.edu	37	14	67733055	67733055	+	Intron	DEL	T	-	-	rs11319956		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67733055delT	uc001xjc.2	+						MPP5_uc001xjd.2_Intron|MPP5_uc001xjb.1_Intron	NM_022474	NP_071919			membrane protein, palmitoylated 5						tight junction assembly	cytoplasm|endomembrane system|tight junction	protein domain specific binding			ovary(1)	1				all cancers(60;0.000388)|OV - Ovarian serous cystadenocarcinoma(108;0.00762)|BRCA - Breast invasive adenocarcinoma(234;0.0106)														---	---	---	---
ATP6V1D	51382	broad.mit.edu	37	14	67809927	67809927	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67809927delT	uc001xjf.2	-						ATP6V1D_uc001xje.2_Intron	NM_015994	NP_057078			H(+)-transporting two-sector ATPase						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting two-sector ATPase complex, catalytic domain|vacuolar proton-transporting V-type ATPase complex	protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)|lung(1)	2				all cancers(60;0.000739)|OV - Ovarian serous cystadenocarcinoma(108;0.00597)|BRCA - Breast invasive adenocarcinoma(234;0.00957)														---	---	---	---
VTI1B	10490	broad.mit.edu	37	14	68126414	68126415	+	Intron	DEL	GA	-	-	rs74246590		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68126414_68126415delGA	uc001xjt.2	-						VTI1B_uc010aqp.2_Intron|VTI1B_uc001xju.2_Intron	NM_006370	NP_006361			vesicle transport through interaction with						cell proliferation|cellular membrane fusion|intracellular protein transport|vesicle docking involved in exocytosis	endomembrane system|integral to membrane					0				all cancers(60;0.000344)|OV - Ovarian serous cystadenocarcinoma(108;0.00212)|BRCA - Breast invasive adenocarcinoma(234;0.00941)														---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68391997	68391997	+	Intron	DEL	T	-	-	rs113443943		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68391997delT	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193			RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)				T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	69140593	69140594	+	Intron	INS	-	CA	CA	rs143867476	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69140593_69140594insCA	uc001xkg.1	+							NM_133510	NP_598194			RAD51-like 1 isoform 2						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)				T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	69148820	69148820	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69148820delT	uc001xkg.1	+							NM_133510	NP_598194			RAD51-like 1 isoform 2						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)				T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	69158421	69158422	+	Intron	INS	-	C	C	rs147745673	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69158421_69158422insC	uc001xkg.1	+							NM_133510	NP_598194			RAD51-like 1 isoform 2						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	69277886	69277886	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69277886delA								C14orf181 (14696 upstream) : ACTN1 (62955 downstream)																																			---	---	---	---
ACTN1	87	broad.mit.edu	37	14	69409331	69409334	+	Intron	DEL	AGAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69409331_69409334delAGAC	uc001xkl.2	-						ACTN1_uc010ttb.1_Intron|ACTN1_uc001xkm.2_Intron|ACTN1_uc001xkn.2_Intron|ACTN1_uc001xko.1_Intron|ACTN1_uc010ttd.1_Intron	NM_001102	NP_001093			actinin, alpha 1 isoform b						focal adhesion assembly|negative regulation of cellular component movement|platelet activation|platelet degranulation|regulation of apoptosis	actin cytoskeleton|cytosol|extracellular region|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|sarcomere	actin binding|calcium ion binding|integrin binding|vinculin binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	69454753	69454753	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69454753delT								ACTN1 (8670 upstream) : DCAF5 (62885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	69652847	69652847	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69652847delA								DCAF5 (32933 upstream) : EXD2 (5399 downstream)																																			---	---	---	---
EXD2	55218	broad.mit.edu	37	14	69655247	69655247	+	5'Flank	DEL	T	-	-	rs34070983		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69655247delT	uc001xkt.2	+						EXD2_uc001xku.2_5'Flank|EXD2_uc001xkv.2_5'Flank|EXD2_uc001xkw.2_5'Flank	NM_018199	NP_060669			exonuclease 3'-5' domain containing 2						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	69842321	69842321	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69842321delT								GALNTL1 (21138 upstream) : ERH (4519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	70666105	70666105	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70666105delT								SLC8A3 (10318 upstream) : ADAM21P1 (46366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	70695254	70695254	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70695254delT								SLC8A3 (39467 upstream) : ADAM21P1 (17217 downstream)																																			---	---	---	---
SYNJ2BP	55333	broad.mit.edu	37	14	70867893	70867893	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70867893delA	uc001xmc.3	-						SYNJ2BP_uc010arc.2_Intron	NM_018373	NP_060843			synaptojanin 2 binding protein							integral to membrane|mitochondrial outer membrane					0				all cancers(60;0.00367)|BRCA - Breast invasive adenocarcinoma(234;0.00716)|OV - Ovarian serous cystadenocarcinoma(108;0.0377)														---	---	---	---
MAP3K9	4293	broad.mit.edu	37	14	71205467	71205467	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71205467delA	uc001xmm.2	-						MAP3K9_uc010ttk.1_Intron|MAP3K9_uc001xmk.2_Intron|MAP3K9_uc001xml.2_Intron	NM_033141	NP_149132			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			stomach(2)|lung(1)|central_nervous_system(1)|skin(1)	5				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)														---	---	---	---
MAP3K9	4293	broad.mit.edu	37	14	71207814	71207814	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71207814delT	uc001xmm.2	-						MAP3K9_uc010ttk.1_Intron|MAP3K9_uc001xmk.2_Intron|MAP3K9_uc001xml.2_Intron	NM_033141	NP_149132			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			stomach(2)|lung(1)|central_nervous_system(1)|skin(1)	5				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71377106	71377108	+	Intron	DEL	TTC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71377106_71377108delTTC	uc001xmo.2	+						PCNX_uc001xmn.3_Intron|PCNX_uc010are.1_Intron	NM_014982	NP_055797			pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71455705	71455706	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71455705_71455706delTT	uc001xmo.2	+						PCNX_uc001xmn.3_Intron|PCNX_uc010are.1_Intron	NM_014982	NP_055797			pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71502766	71502766	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71502766delT	uc001xmo.2	+						PCNX_uc010are.1_Intron|PCNX_uc010arf.1_Intron	NM_014982	NP_055797			pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71522035	71522035	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71522035delT	uc001xmo.2	+						PCNX_uc010are.1_Intron|PCNX_uc010arf.1_Intron	NM_014982	NP_055797			pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	71623735	71623735	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71623735delA								PCNX (41636 upstream) : SNORD56B (241319 downstream)																																			---	---	---	---
RGS6	9628	broad.mit.edu	37	14	72873091	72873091	+	Intron	DEL	A	-	-	rs77051534		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72873091delA	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron	NM_004296	NP_004287			regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)														---	---	---	---
RGS6	9628	broad.mit.edu	37	14	73006730	73006731	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73006730_73006731delTT	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron|RGS6_uc010ttp.1_Intron|RGS6_uc001xmz.1_Intron	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)														---	---	---	---
PSEN1	5663	broad.mit.edu	37	14	73653642	73653642	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73653642delT	uc001xnr.2	+						PSEN1_uc001xnv.2_Intron|PSEN1_uc010ark.2_Intron|PSEN1_uc001xnt.1_Intron|PSEN1_uc001xnu.2_Intron	NM_000021	NP_000012			presenilin 1 isoform I-467						amyloid precursor protein catabolic process|anti-apoptosis|beta-amyloid metabolic process|cell-cell adhesion|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|smooth endoplasmic reticulum calcium ion homeostasis	apical plasma membrane|axon|cell cortex|cell surface|centrosome|ciliary rootlet|dendritic shaft|endoplasmic reticulum membrane|gamma-secretase complex|Golgi membrane|growth cone|integral to plasma membrane|kinetochore|lysosomal membrane|membrane raft|mitochondrial inner membrane|neuromuscular junction|neuronal cell body|nuclear outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum|smooth endoplasmic reticulum|Z disc	aspartic-type endopeptidase activity|beta-catenin binding|cadherin binding|calcium channel activity|PDZ domain binding			breast(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075)														---	---	---	---
NUMB	8650	broad.mit.edu	37	14	73744471	73744471	+	Intron	DEL	A	-	-	rs35278332		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73744471delA	uc001xny.1	-						NUMB_uc010aro.1_Intron|NUMB_uc010arp.1_Intron|NUMB_uc010arq.1_Intron|NUMB_uc010arr.1_Intron|NUMB_uc001xoa.1_Intron|NUMB_uc001xnz.1_Intron|NUMB_uc001xob.1_Intron|NUMB_uc001xod.1_Intron|NUMB_uc001xoc.1_Intron|NUMB_uc010ars.1_Intron|NUMB_uc010ttz.1_Intron|NUMB_uc001xoe.2_RNA	NM_001005743	NP_001005743			numb homolog isoform 1						axon guidance|lateral ventricle development|neuroblast division in subventricular zone|positive regulation of neurogenesis	integral to plasma membrane				ovary(2)|central_nervous_system(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)														---	---	---	---
NUMB	8650	broad.mit.edu	37	14	73865807	73865807	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73865807delT	uc001xny.1	-						NUMB_uc001xoa.1_Intron|NUMB_uc001xnz.1_Intron|NUMB_uc001xob.1_Intron|NUMB_uc001xod.1_Intron|NUMB_uc001xoc.1_Intron|NUMB_uc010ars.1_Intron|NUMB_uc001xof.1_Intron|NUMB_uc001xog.2_Intron|NUMB_uc001xoh.1_Intron	NM_001005743	NP_001005743			numb homolog isoform 1						axon guidance|lateral ventricle development|neuroblast division in subventricular zone|positive regulation of neurogenesis	integral to plasma membrane				ovary(2)|central_nervous_system(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	73934379	73934380	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73934379_73934380delCT	uc001xoi.1	+											Homo sapiens cDNA FLJ31314 fis, clone LIVER1000278.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	74076675	74076676	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74076675_74076676delTT								ACOT4 (14207 upstream) : ACOT6 (6872 downstream)																																			---	---	---	---
FAM161B	145483	broad.mit.edu	37	14	74401126	74401126	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74401126delA	uc001xpd.1	-							NM_152445	NP_689658			hypothetical protein LOC145483											ovary(1)	1																		---	---	---	---
FAM161B	145483	broad.mit.edu	37	14	74415980	74415980	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74415980delT	uc001xpd.1	-						COQ6_uc001xpe.2_5'Flank|COQ6_uc001xpf.2_5'Flank|COQ6_uc010tuk.1_5'Flank|COQ6_uc010tul.1_5'Flank|COQ6_uc010tum.1_5'Flank|COQ6_uc010tun.1_5'Flank|COQ6_uc001xpg.2_5'Flank|COQ6_uc001xph.2_5'Flank	NM_152445	NP_689658			hypothetical protein LOC145483											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	74674450	74674450	+	IGR	DEL	A	-	-	rs76601330		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74674450delA								LIN52 (7333 upstream) : VSX2 (31725 downstream)																																			---	---	---	---
KIAA0317	9870	broad.mit.edu	37	14	75137987	75137987	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75137987delT	uc001xqb.2	-						KIAA0317_uc010tut.1_Intron|KIAA0317_uc001xqc.2_Intron	NM_001039479	NP_001034568			hypothetical protein LOC9870						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|intracellular	ubiquitin-protein ligase activity			ovary(2)|kidney(1)|central_nervous_system(1)|pancreas(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00404)														---	---	---	---
KIAA0317	9870	broad.mit.edu	37	14	75163859	75163860	+	Intron	DEL	AC	-	-	rs112999456		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75163859_75163860delAC	uc001xqb.2	-						KIAA0317_uc010tut.1_Intron|KIAA0317_uc001xqc.2_Intron|KIAA0317_uc001xqd.1_Intron	NM_001039479	NP_001034568			hypothetical protein LOC9870						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|intracellular	ubiquitin-protein ligase activity			ovary(2)|kidney(1)|central_nervous_system(1)|pancreas(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00404)														---	---	---	---
YLPM1	56252	broad.mit.edu	37	14	75287731	75287734	+	Intron	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75287731_75287734delTTTT	uc001xqj.3	+						YLPM1_uc001xql.3_Intron|YLPM1_uc001xqm.1_Intron	NM_019589	NP_062535			YLP motif containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)														---	---	---	---
EIF2B2	8892	broad.mit.edu	37	14	75476005	75476005	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75476005delA	uc001xrc.1	+	8						NM_014239	NP_055054			eukaryotic translation initiation factor 2B,						cellular response to stimulus|myelination|oligodendrocyte development|ovarian follicle development|regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	ATP binding|GTP binding|protein binding|translation initiation factor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00661)														---	---	---	---
NEK9	91754	broad.mit.edu	37	14	75552430	75552430	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75552430delT	uc001xrl.2	-						NEK9_uc001xrj.2_Intron|NEK9_uc001xrk.2_Intron	NM_033116	NP_149107			NIMA-related kinase 9						cell division|mitosis	mitochondrion|nucleus	ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(2)|stomach(2)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00718)														---	---	---	---
NEK9	91754	broad.mit.edu	37	14	75555777	75555777	+	Intron	DEL	T	-	-	rs79548473		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75555777delT	uc001xrl.2	-						NEK9_uc001xrj.2_Intron|NEK9_uc001xrk.2_Intron	NM_033116	NP_149107			NIMA-related kinase 9						cell division|mitosis	mitochondrion|nucleus	ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(2)|stomach(2)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00718)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	75649791	75649791	+	IGR	DEL	A	-	-	rs72153011		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75649791delA								TMED10 (6442 upstream) : FOS (95690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	75820709	75820709	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75820709delT								FOS (71774 upstream) : JDP2 (73800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	76013543	76013545	+	IGR	DEL	CTT	-	-	rs67415289		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76013543_76013545delCTT								BATF (216 upstream) : FLVCR2 (31395 downstream)																																			---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76352963	76352963	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76352963delT	uc001xrx.2	+						TTLL5_uc010ask.1_Intron|TTLL5_uc001xrz.2_Intron|TTLL5_uc001xsa.2_Intron	NM_015072	NP_055887			tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
C14orf179	112752	broad.mit.edu	37	14	76493244	76493244	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76493244delA	uc010asm.1	+						C14orf179_uc001xsf.2_Intron|C14orf179_uc010asl.1_Intron|C14orf179_uc001xsg.2_Intron|C14orf179_uc010tve.1_Intron|C14orf179_uc001xse.2_Intron	NM_001102564	NP_001096034			hypothetical protein LOC112752 isoform 2						cilium morphogenesis|intraflagellar retrograde transport						0				BRCA - Breast invasive adenocarcinoma(234;0.0199)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	77106505	77106505	+	IGR	DEL	G	-	-	rs850741	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77106505delG								ESRRB (138327 upstream) : VASH1 (121730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77161763	77161763	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77161763delG								ESRRB (193585 upstream) : VASH1 (66472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77525100	77525101	+	Intron	DEL	AA	-	-	rs113373883		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77525100_77525101delAA	uc001xsz.2	-											Homo sapiens cDNA clone IMAGE:5271982.																														---	---	---	---
TMEM63C	57156	broad.mit.edu	37	14	77709045	77709045	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77709045delT	uc001xtf.2	+						TMEM63C_uc010asq.1_Intron	NM_020431	NP_065164			transmembrane protein 63C							integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)														---	---	---	---
POMT2	29954	broad.mit.edu	37	14	77750224	77750224	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77750224delA	uc001xti.2	-						POMT2_uc001xth.1_Intron	NM_013382	NP_037514			protein-O-mannosyltransferase 2						protein O-linked glycosylation	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)														---	---	---	---
VIPAR	63894	broad.mit.edu	37	14	77897067	77897068	+	Intron	DEL	AA	-	-	rs138727614		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77897067_77897068delAA	uc001xtt.1	-						VIPAR_uc001xtu.1_Intron|VIPAR_uc010tvj.1_Intron|VIPAR_uc001xtv.1_Intron	NM_022067	NP_071350			hypothetical protein LOC63894						endosome to lysosome transport|intracellular protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	early endosome|late endosome|recycling endosome	protein binding			central_nervous_system(1)	1																		---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79108268	79108268	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79108268delT	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	79134132	79134132	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79134132delT	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	79522551	79522551	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79522551delA	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	79750214	79750215	+	Intron	DEL	TA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79750214_79750215delTA	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc001xup.2_Intron|NRXN3_uc001xuq.2_Intron|NRXN3_uc010asw.2_Intron|NRXN3_uc001xur.3_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	80442088	80442088	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80442088delA								NRXN3 (111330 upstream) : DIO2 (221782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	80591828	80591829	+	IGR	DEL	AA	-	-	rs111479452		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80591828_80591829delAA								NRXN3 (261070 upstream) : DIO2 (72041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	80773058	80773058	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80773058delA	uc001xuw.1	+											Homo sapiens, clone IMAGE:5167652, mRNA.																														---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81253805	81253806	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81253805_81253806insA	uc001xux.2	-						C14orf145_uc010asz.1_Intron	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81302906	81302906	+	Intron	DEL	T	-	-	rs111834655		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81302906delT	uc001xux.2	-						C14orf145_uc010asz.1_5'Flank|C14orf145_uc001xuz.2_Intron|C14orf145_uc001xuy.1_Intron	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
TSHR	7253	broad.mit.edu	37	14	81557384	81557384	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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 						---	---	---	---
TSHR	7253	broad.mit.edu	37	14	81563267	81563268	+	Intron	INS	-	GT	GT	rs147149121	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81563267_81563268insGT	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 						---	---	---	---
Unknown	0	broad.mit.edu	37	14	84414583	84414584	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84414583_84414584delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86453578	86453579	+	IGR	INS	-	C	C	rs149006717	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86453578_86453579insC								FLRT2 (359309 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86553648	86553649	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86553648_86553649delAC								FLRT2 (459379 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87044838	87044838	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87044838delT								FLRT2 (950569 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87631239	87631239	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87631239delA								None (None upstream) : GALC (672925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	88043256	88043256	+	IGR	DEL	T	-	-	rs34907060		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88043256delT								None (None upstream) : GALC (260908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	88273291	88273291	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88273291delA								None (None upstream) : GALC (30873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	88639958	88639959	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88639958_88639959insA								GPR65 (161544 upstream) : KCNK10 (6495 downstream)																																			---	---	---	---
SPATA7	55812	broad.mit.edu	37	14	88880086	88880086	+	Intron	DEL	T	-	-	rs34039966		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88880086delT	uc001xwq.2	+						SPATA7_uc001xwr.2_Intron|SPATA7_uc001xws.2_Intron|SPATA7_uc001xwt.2_5'Flank	NM_018418	NP_060888			spermatogenesis-associated protein 7 isoform a						response to stimulus|visual perception					ovary(1)	1																		---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	88971527	88971527	+	Intron	DEL	T	-	-	rs80302635		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88971527delT	uc001xwv.3	-						PTPN21_uc010twc.1_Intron|PTPN21_uc010atf.1_Intron	NM_007039	NP_008970			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4																		---	---	---	---
TTC8	123016	broad.mit.edu	37	14	89327154	89327155	+	Intron	INS	-	T	T	rs113496415		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89327154_89327155insT	uc010ath.2	+						TTC8_uc001xxl.2_Intron|TTC8_uc010ati.2_Intron|TTC8_uc001xxm.2_Intron|TTC8_uc010atj.2_Intron|TTC8_uc001xxi.2_Intron|TTC8_uc001xxj.2_Intron|TTC8_uc001xxk.2_Intron	NM_198309	NP_938051			tetratricopeptide repeat domain 8 isoform B						cilium assembly|establishment of anatomical structure orientation|sensory processing	BBSome|centrosome|cilium membrane|microtubule basal body	protein binding				0														Bardet-Biedl_syndrome				---	---	---	---
TDP1	55775	broad.mit.edu	37	14	90455540	90455540	+	Intron	DEL	T	-	-	rs75923444		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90455540delT	uc001xxy.2	+						TDP1_uc010atm.2_Intron|TDP1_uc001xxz.2_Intron|TDP1_uc010atn.2_Intron|TDP1_uc001xya.2_Intron|TDP1_uc001xyb.2_Intron|TDP1_uc010ato.2_Intron|TDP1_uc001xyd.1_Intron	NM_018319	NP_060789			tyrosyl-DNA phosphodiesterase 1						cell death|double-strand break repair|single strand break repair	cytoplasm|nucleus	3'-tyrosyl-DNA phosphodiesterase activity|double-stranded DNA binding|exonuclease activity|protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)									Repair_of_DNA-protein_crosslinks					---	---	---	---
Unknown	0	broad.mit.edu	37	14	91296717	91296717	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91296717delT								TTC7B (13956 upstream) : RPS6KA5 (40450 downstream)																																			---	---	---	---
RPS6KA5	9252	broad.mit.edu	37	14	91358343	91358343	+	Intron	DEL	T	-	-	rs11362062		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91358343delT	uc001xys.2	-						RPS6KA5_uc010twi.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)														---	---	---	---
RPS6KA5	9252	broad.mit.edu	37	14	91372736	91372739	+	Intron	DEL	GAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91372736_91372739delGAAA	uc001xys.2	-						RPS6KA5_uc010twi.1_Intron|RPS6KA5_uc001xyt.2_Intron|RPS6KA5_uc010att.1_Intron	NM_004755	NP_004746			ribosomal protein S6 kinase, polypeptide 5						axon guidance|epidermal growth factor receptor signaling pathway|histone phosphorylation|innate immune response|interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	91544095	91544096	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91544095_91544096delAA								RPS6KA5 (17102 upstream) : C14orf159 (36261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	91564021	91564022	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91564021_91564022delTT								RPS6KA5 (37028 upstream) : C14orf159 (16335 downstream)																																			---	---	---	---
C14orf159	80017	broad.mit.edu	37	14	91690001	91690001	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91690001delT	uc001xzb.2	+						C14orf159_uc001xyx.2_Intron|C14orf159_uc001xyw.2_Intron|C14orf159_uc001xzc.2_Intron|C14orf159_uc001xza.2_Intron|C14orf159_uc001xyv.2_Intron|C14orf159_uc001xyz.2_Intron|C14orf159_uc001xze.2_Intron	NM_001102366	NP_001095836			hypothetical protein LOC80017 isoform a							mitochondrion				central_nervous_system(2)|ovary(1)	3		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)														---	---	---	---
CCDC88C	440193	broad.mit.edu	37	14	91871322	91871323	+	Intron	DEL	AG	-	-	rs57911960		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91871322_91871323delAG	uc010aty.2	-						CCDC88C_uc010twk.1_Intron|CCDC88C_uc001xzl.3_Intron	NM_001080414	NP_001073883			DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)																---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92597322	92597322	+	5'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92597322delA	uc001yah.1	+	3						NM_017437	NP_059133			cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	92735152	92735153	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92735152_92735153delTT								CPSF2 (104609 upstream) : SLC24A4 (53772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	92740050	92740051	+	IGR	INS	-	T	T	rs4141772		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92740050_92740051insT								CPSF2 (109507 upstream) : SLC24A4 (48874 downstream)																																			---	---	---	---
ITPK1	3705	broad.mit.edu	37	14	93583257	93583257	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93583257delA	uc001ybg.2	-						ITPK1_uc001ybe.2_5'Flank|ITPK1_uc001ybf.2_5'Flank|ITPK1_uc001ybh.2_5'Flank	NM_014216	NP_055031			inositol 1,3,4-triphosphate 5/6 kinase isoform						blood coagulation|inositol trisphosphate metabolic process|signal transduction	cytosol	ATP binding|hydrolase activity|inositol tetrakisphosphate 1-kinase activity|inositol-1,3,4-trisphosphate 5/6-kinase activity|isomerase activity|ligase activity|magnesium ion binding				0		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	93642114	93642114	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93642114delA								ITPK1 (59851 upstream) : MOAP1 (6429 downstream)																																			---	---	---	---
FAM181A	90050	broad.mit.edu	37	14	94395475	94395475	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94395475delC	uc001ybz.1	+	3	1337	c.1030delC	c.(1030-1032)CCCfs	p.P344fs	C14orf86_uc001yby.2_5'Flank|FAM181A_uc010aus.1_Frame_Shift_Del_p.P282fs|FAM181A_uc001yca.1_Frame_Shift_Del_p.P282fs	NM_138344	NP_612353	Q8N9Y4	F181A_HUMAN	hypothetical protein LOC90050	344											0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	94615223	94615223	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94615223delT								IFI27L2 (19266 upstream) : PPP4R4 (25426 downstream)																																			---	---	---	---
SERPINA11	256394	broad.mit.edu	37	14	94912511	94912511	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94912511delA	uc001ydd.1	-							NM_001080451	NP_001073920			serpin peptidase inhibitor, clade A (alpha-1						regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			kidney(1)	1				COAD - Colon adenocarcinoma(157;0.211)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	95117589	95117590	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95117589_95117590delAC								SERPINA13 (4259 upstream) : GSC (116971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	95245117	95245117	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95245117delA								GSC (8618 upstream) : DICER1 (307448 downstream)																																			---	---	---	---
DICER1	23405	broad.mit.edu	37	14	95591010	95591010	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95591010delA	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_				---	---	---	---
CLMN	79789	broad.mit.edu	37	14	95783937	95783939	+	Intron	DEL	AAA	-	-	rs10711295		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95783937_95783939delAAA	uc001yef.2	-							NM_024734	NP_079010			calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	95822914	95822914	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95822914delT								CLMN (36669 upstream) : C14orf139 (50692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	95977125	95977126	+	IGR	DEL	AA	-	-	rs79459277		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95977125_95977126delAA								C14orf49 (34952 upstream) : SNHG10 (22127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	96060392	96060393	+	IGR	INS	-	CCACATGTGCACA	CCACATGTGCACA	rs147631203	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96060392_96060393insCCACATGTGCACA								GLRX5 (49337 upstream) : TCL6 (56442 downstream)																																			---	---	---	---
TCL6	27004	broad.mit.edu	37	14	96120990	96120990	+	Intron	DEL	A	-	-	rs34140444		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96120990delA	uc001yeq.2	+						TCL6_uc001yep.1_Intron	NM_020554	NP_065579			SubName: Full=T-cell leukemia/lymphoma 6 ORF163;												0		all_cancers(154;0.103)		Epithelial(152;0.0655)|all cancers(159;0.149)|BRCA - Breast invasive adenocarcinoma(234;0.206)|COAD - Colon adenocarcinoma(157;0.207)				T	TRA@	T-ALL								---	---	---	---
BDKRB2	624	broad.mit.edu	37	14	96670467	96670467	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96670467delA	uc010avm.1	+						BDKRB2_uc010avl.1_5'Flank|BDKRB2_uc010twu.1_5'Flank|BDKRB2_uc001yfg.2_5'Flank	NM_000623	NP_000614			bradykinin receptor B2						arachidonic acid secretion|elevation of cytosolic calcium ion concentration|transmembrane receptor protein tyrosine kinase signaling pathway	endosome|integral to plasma membrane	bradykinin receptor activity|phosphatidylinositol phospholipase C activity|protease binding|protein heterodimerization activity|type 1 angiotensin receptor binding			ovary(3)|breast(1)|kidney(1)	5		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)														---	---	---	---
ATG2B	55102	broad.mit.edu	37	14	96824529	96824529	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96824529delG	uc001yfi.2	-							NM_018036	NP_060506			ATG2 autophagy related 2 homolog B											ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)														---	---	---	---
PAPOLA	10914	broad.mit.edu	37	14	96970083	96970083	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96970083delT	uc001yfq.2	+						PAPOLA_uc001yfo.2_Intron|PAPOLA_uc001yfp.2_Intron|PAPOLA_uc001yfr.2_Intron|PAPOLA_uc010twv.1_Intron|PAPOLA_uc010avp.2_Intron	NM_032632	NP_116021			poly(A) polymerase alpha						mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|RNA binding				0		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	97447998	97447999	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97447998_97447999insG								VRK1 (100048 upstream) : C14orf64 (943948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	97525906	97525906	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97525906delT								VRK1 (177956 upstream) : C14orf64 (866041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	97726009	97726009	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97726009delT								VRK1 (378059 upstream) : C14orf64 (665938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	97852874	97852874	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97852874delA								VRK1 (504924 upstream) : C14orf64 (539073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98020251	98020251	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98020251delT								VRK1 (672301 upstream) : C14orf64 (371696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98269420	98269421	+	IGR	DEL	TG	-	-	rs11160413	by1000genomes;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98269420_98269421delTG								VRK1 (921470 upstream) : C14orf64 (122526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98840556	98840556	+	IGR	DEL	T	-	-	rs138029151		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98840556delT								C14orf64 (396095 upstream) : C14orf177 (337394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99766758	99766758	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99766758delT								BCL11B (28936 upstream) : SETD3 (97326 downstream)																																			---	---	---	---
SETD3	84193	broad.mit.edu	37	14	99871696	99871696	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99871696delA	uc001ygc.2	-	10	1107	c.937delT	c.(937-939)TATfs	p.Y313fs		NM_032233	NP_115609	Q86TU7	SETD3_HUMAN	SET domain containing 3 isoform a	313	SET.				peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|peptidyl-lysine trimethylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone methyltransferase activity (H3-K36 specific)|transcription coactivator activity				0		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)																---	---	---	---
YY1	7528	broad.mit.edu	37	14	100725857	100725857	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100725857delA	uc001ygy.1	+							NM_003403	NP_003394			YY1 transcription factor						cell differentiation|cellular response to UV|double-strand break repair via homologous recombination|negative regulation of transcription from RNA polymerase II promoter|response to UV-C|spermatogenesis	Ino80 complex|nuclear matrix|plasma membrane	four-way junction DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding				0		Melanoma(154;0.152)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	100776182	100776182	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100776182delG								MIR345 (1889 upstream) : C14orf68 (13497 downstream)																																			---	---	---	---
WDR25	79446	broad.mit.edu	37	14	100931491	100931491	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100931491delT	uc010avx.2	+						WDR25_uc001yhm.2_Intron|WDR25_uc001yhn.2_Intron|WDR25_uc010avy.2_Intron|WDR25_uc001yho.2_Intron	NM_001161476	NP_001154948			WD repeat domain 25												0		Melanoma(154;0.212)																---	---	---	---
WDR25	79446	broad.mit.edu	37	14	100974667	100974667	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100974667delA	uc010avx.2	+						WDR25_uc001yhm.2_Intron|WDR25_uc001yhn.2_Intron|WDR25_uc010avy.2_Intron|WDR25_uc001yho.2_Intron	NM_001161476	NP_001154948			WD repeat domain 25												0		Melanoma(154;0.212)																---	---	---	---
BEGAIN	57596	broad.mit.edu	37	14	101004530	101004530	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101004530delC	uc010txa.1	-	6	1704	c.1558delG	c.(1558-1560)GACfs	p.D520fs	BEGAIN_uc001yhp.2_Frame_Shift_Del_p.D456fs|BEGAIN_uc001yhq.2_Frame_Shift_Del_p.D520fs	NM_001159531	NP_001153003	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	520						cytoplasm|membrane	protein binding				0		Melanoma(154;0.212)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	101377646	101377646	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101377646delT								MIR370 (96 upstream) : SNORD113-1 (13512 downstream)																																			---	---	---	---
WDR20	91833	broad.mit.edu	37	14	102642952	102642952	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102642952delT	uc001ykz.2	+						WDR20_uc001yky.1_Intron|WDR20_uc001yla.2_Intron|WDR20_uc001ylb.2_Intron|WDR20_uc010txu.1_Intron|WDR20_uc001ylc.2_Intron|WDR20_uc001yld.2_Intron|WDR20_uc001yle.2_Intron|WDR20_uc001ylf.2_Intron	NM_144574	NP_653175			WD repeat domain 20 isoform 2												0																		---	---	---	---
RAGE	5891	broad.mit.edu	37	14	102698299	102698300	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102698299_102698300insT	uc001ylm.2	-						RAGE_uc010txv.1_Intron|RAGE_uc001yln.2_Intron|RAGE_uc001ylh.2_Intron|RAGE_uc001yli.2_Intron|RAGE_uc001yll.2_Intron|RAGE_uc001ylj.2_Intron|RAGE_uc001ylk.2_Intron	NM_014226	NP_055041			MAPK/MAK/MRK overlapping kinase						signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
RAGE	5891	broad.mit.edu	37	14	102722909	102722909	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102722909delA	uc001ylm.2	-						RAGE_uc010txv.1_Intron|RAGE_uc001yln.2_Intron	NM_014226	NP_055041			MAPK/MAK/MRK overlapping kinase						signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
RAGE	5891	broad.mit.edu	37	14	102737904	102737904	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102737904delT	uc001ylm.2	-						RAGE_uc010txv.1_Intron|RAGE_uc001yln.2_Intron	NM_014226	NP_055041			MAPK/MAK/MRK overlapping kinase						signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
RAGE	5891	broad.mit.edu	37	14	102759096	102759096	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102759096delA	uc001ylm.2	-						RAGE_uc010txv.1_Intron|RAGE_uc001yln.2_Intron	NM_014226	NP_055041			MAPK/MAK/MRK overlapping kinase						signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
ZNF839	55778	broad.mit.edu	37	14	102797327	102797328	+	Intron	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102797327_102797328insG	uc001ylo.2	+						ZNF839_uc010awk.1_Intron|ZNF839_uc001ylp.2_Intron|ZNF839_uc001ylq.1_Intron|ZNF839_uc001ylr.2_Intron|ZNF839_uc001yls.2_5'Flank	NM_018335	NP_060805			zinc finger protein 839							intracellular	zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
RCOR1	23186	broad.mit.edu	37	14	103099011	103099012	+	Intron	INS	-	T	T	rs139502332	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103099011_103099012insT	uc001ymb.2	+							NM_015156	NP_055971			REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1																		---	---	---	---
TRAF3	7187	broad.mit.edu	37	14	103302836	103302836	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103302836delA	uc001ymc.1	+						TRAF3_uc001yme.1_Intron|TRAF3_uc001ymd.1_Intron|TRAF3_uc010txy.1_Intron	NM_145725	NP_663777			TNF receptor-associated factor 3 isoform 1						apoptosis|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|regulation of defense response to virus|regulation of interferon-beta production|regulation of proteolysis|toll-like receptor signaling pathway|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|endosome|internal side of plasma membrane|mitochondrion	signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)														---	---	---	---
AMN	81693	broad.mit.edu	37	14	103387681	103387681	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103387681delT	uc001ymg.3	+						AMN_uc001ymh.3_5'Flank	NM_030943	NP_112205			amnionless protein precursor						lipid metabolic process|lipoprotein metabolic process|multicellular organismal development	integral to membrane|plasma membrane					0				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
TNFAIP2	7127	broad.mit.edu	37	14	103602858	103602861	+	3'UTR	DEL	TTTT	-	-	rs11358000		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103602858_103602861delTTTT	uc001ymm.1	+	11					TNFAIP2_uc010awo.1_3'UTR|TNFAIP2_uc010txz.1_3'UTR	NM_006291	NP_006282			tumor necrosis factor, alpha-induced protein 2						angiogenesis|cell differentiation	extracellular space				central_nervous_system(1)	1		Melanoma(154;0.155)	Epithelial(46;0.191)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	103624701	103624701	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103624701delT								TNFAIP2 (20925 upstream) : EIF5 (175792 downstream)																																			---	---	---	---
KLC1	3831	broad.mit.edu	37	14	104096871	104096871	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104096871delT	uc001yno.2	+						KLC1_uc010tyd.1_Intron|KLC1_uc010tye.1_Intron|KLC1_uc001ynm.1_Intron|KLC1_uc001ynn.1_Intron|KLC1_uc010tyf.1_Intron	NM_182923	NP_891553			kinesin light chain 1 isoform 2						blood coagulation|microtubule-based movement|stress granule disassembly	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0		Melanoma(154;0.155)|all_epithelial(191;0.19)																---	---	---	---
TDRD9	122402	broad.mit.edu	37	14	104477673	104477674	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104477673_104477674delGT	uc001yom.3	+						TDRD9_uc001yon.3_Intron	NM_153046	NP_694591			tudor domain containing 9						cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	104681614	104681614	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104681614delG								KIF26A (34380 upstream) : C14orf180 (364442 downstream)																																			---	---	---	---
TMEM121	80757	broad.mit.edu	37	14	105991985	105991985	+	5'Flank	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105991985delC	uc001yrp.1	+							NM_025268	NP_079544			hole protein							integral to membrane					0		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.0959)|all cancers(159;0.235)														---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106131431	106131432	+	Intron	DEL	AG	-	-	rs150568146		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106131431_106131432delAG	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106131549	106131550	+	Intron	DEL	TT	-	-	rs139899819		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106131549_106131550delTT	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106846005	106846005	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106846005delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106922715	106922716	+	RNA	INS	-	TG	TG	rs149363398	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106922715_106922716insTG	uc010tyt.1	-	239		c.10391_10392insCA			uc010tyu.1_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106928021	106928021	+	Intron	DEL	A	-	-	rs112461101		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106928021delA	uc010tyt.1	-						uc010tyu.1_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106938366	106938367	+	Intron	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106938366_106938367insG	uc010tyt.1	-						uc010tyu.1_5'Flank|LOC100133469_uc001ysy.2_5'Flank					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107127960	107127960	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107127960delG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	20010729	20010730	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	20108579	20108580	+	IGR	INS	-	ATG	ATG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20108579_20108580insATG								None (None upstream) : GOLGA6L6 (628514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20111580	20111580	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20111580delG								None (None upstream) : GOLGA6L6 (625514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20126136	20126137	+	IGR	DEL	AG	-	-	rs34281620		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20126136_20126137delAG								None (None upstream) : GOLGA6L6 (610957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20138591	20138592	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20138591_20138592insA								None (None upstream) : GOLGA6L6 (598502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20615134	20615134	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20615134delC	uc001ytg.2	-						uc010tyx.1_Intron|uc001yth.3_Intron					RecName: Full=Putative HERC2-like protein 3;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	22440159	22440159	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22440159delT	uc001yug.2	-	1										full-length cDNA clone CS0DI014YE21 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	22778852	22778852	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22778852delA								GOLGA6L1 (32850 upstream) : TUBGCP5 (54543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	23090440	23090440	+	IGR	DEL	T	-	-	rs72257944		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23090440delT								NIPA1 (3597 upstream) : WHAMML1 (97291 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	23654734	23654734	+	IGR	DEL	A	-	-	rs111901864		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23654734delA								GOLGA8E (206311 upstream) : MKRN3 (155720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24168097	24168097	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24168097delT								NDN (235647 upstream) : PWRN2 (241829 downstream)																																			---	---	---	---
PWRN2	791115	broad.mit.edu	37	15	24411003	24411004	+	RNA	DEL	AA	-	-	rs148691390		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24411003_24411004delAA	uc010uad.1	-	1		c.4050_4051delTT			PWRN2_uc001ywl.2_RNA	NR_026647				Homo sapiens Prader-Willi region non-protein coding RNA 2 (PWRN2), non-coding RNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	24441692	24441693	+	IGR	DEL	AA	-	-	rs78641734		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24441692_24441693delAA								PWRN2 (26597 upstream) : PWRN1 (337146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	25002679	25002679	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25002679delA								C15orf2 (74087 upstream) : SNRPN (66115 downstream)																																			---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	26846561	26846562	+	Intron	DEL	AA	-	-	rs71420008		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26846561_26846562delAA	uc001zaz.2	-						GABRB3_uc010uae.1_Intron|GABRB3_uc001zba.2_Intron|GABRB3_uc001zbb.2_Intron	NM_000814	NP_000805			gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27404629	27404629	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27404629delA	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092			gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27502347	27502347	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27502347delT	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092			gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27654980	27654980	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27654980delT	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092			gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27710506	27710506	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27710506delC	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	27813463	27813464	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27813463_27813464insT								GABRG3 (35329 upstream) : OCA2 (186561 downstream)																																			---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28388214	28388214	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28388214delA	uc001zbj.2	-							NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28516818	28516818	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28516818delA	uc001zbj.2	-						HERC2_uc001zbl.1_Intron	NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	28913367	28913367	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28913367delT	uc010azc.2	+						uc010uao.1_Intron					Homo sapiens I.M.A.G.E. clone 321824, mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	29083707	29083707	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29083707delG	uc001zcj.2	+											Homo sapiens, Similar to hect domain and RLD 2, clone IMAGE:4581928, mRNA.																														---	---	---	---
APBA2	321	broad.mit.edu	37	15	29322933	29322936	+	Intron	DEL	TGTG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29322933_29322936delTGTG	uc001zck.2	+						APBA2_uc010azj.2_Intron|APBA2_uc010uat.1_Intron|APBA2_uc001zcl.2_Intron|APBA2_uc010uas.1_Intron	NM_005503	NP_005494			amyloid beta A4 precursor protein-binding,						nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)														---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29859050	29859051	+	Intron	INS	-	AC	AC	rs146482719	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29859050_29859051insAC	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
TJP1	7082	broad.mit.edu	37	15	30022801	30022801	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30022801delA	uc001zcr.2	-						TJP1_uc010azl.2_Intron|TJP1_uc001zcq.2_Intron|TJP1_uc001zcs.2_Intron	NM_003257	NP_003248			tight junction protein 1 isoform a						cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)														---	---	---	---
TJP1	7082	broad.mit.edu	37	15	30102051	30102051	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30102051delA	uc001zcr.2	-						TJP1_uc001zcq.2_Intron|TJP1_uc001zcs.2_Intron	NM_003257	NP_003248			tight junction protein 1 isoform a						cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)														---	---	---	---
MTMR15	22909	broad.mit.edu	37	15	31199272	31199272	+	Intron	DEL	T	-	-	rs74486196		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31199272delT	uc001zff.2	+						MTMR15_uc001zfc.3_Intron|MTMR15_uc010azw.2_Intron|MTMR15_uc001zfd.3_Intron|MTMR15_uc001zfe.2_Intron	NM_014967	NP_055782			myotubularin related protein 15 isoform a						double-strand break repair via homologous recombination|nucleotide-excision repair, DNA incision	nucleus	5'-3' exonuclease activity|5'-flap endonuclease activity|DNA binding|magnesium ion binding|phosphodiesterase I activity|ubiquitin binding				0		all_lung(180;2.23e-09)		all cancers(64;4.72e-15)|Epithelial(43;5.4e-11)|GBM - Glioblastoma multiforme(186;0.000136)|BRCA - Breast invasive adenocarcinoma(123;0.00402)|Lung(196;0.168)									Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
TRPM1	4308	broad.mit.edu	37	15	31359898	31359898	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31359898delT	uc001zfm.2	-						TRPM1_uc010azy.2_Intron|TRPM1_uc001zfl.2_Intron|uc010ubm.1_5'Flank|MIR211_hsa-mir-211|MI0000287_5'Flank|uc010ubn.1_5'Flank	NM_002420	NP_002411			transient receptor potential cation channel,						cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)														---	---	---	---
OTUD7A	161725	broad.mit.edu	37	15	31797101	31797101	+	Intron	DEL	T	-	-	rs68056263		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31797101delT	uc001zfq.2	-						OTUD7A_uc001zfr.2_Intron	NM_130901	NP_570971			OTU domain containing 7A							cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)														---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33187562	33187562	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33187562delA	uc001zhf.3	-							NM_001103184	NP_001096654			formin 1						actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)														---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33218473	33218473	+	Intron	DEL	A	-	-	rs72027856		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33218473delA	uc001zhf.3	-							NM_001103184	NP_001096654			formin 1						actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	33452385	33452385	+	Intron	DEL	A	-	-	rs35452985		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33452385delA	uc001zhh.2	-											RecName: Full=Formin-1; AltName: Full=Limb deformity protein homolog;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	33454626	33454627	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33454626_33454627insA	uc001zhh.2	-											RecName: Full=Formin-1; AltName: Full=Limb deformity protein homolog;																														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33757304	33757305	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33757304_33757305delTG	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	33825714	33825715	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33825714_33825715insA	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	33941160	33941160	+	Intron	DEL	A	-	-	rs112518422		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33941160delA	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	33961820	33961821	+	Intron	DEL	AT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33961820_33961821delAT	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	34061298	34061298	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34061298delT	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	34147406	34147406	+	Intron	DEL	T	-	-	rs72093198		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34147406delT	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)														---	---	---	---
AVEN	57099	broad.mit.edu	37	15	34158800	34158800	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34158800delT	uc001zhj.2	-	6						NM_020371	NP_065104			cell death regulator aven						anti-apoptosis|apoptosis	endomembrane system|intracellular|membrane|membrane fraction	protein binding			kidney(1)	1		all_lung(180;1.78e-08)		all cancers(64;1.66e-15)|GBM - Glioblastoma multiforme(113;1.42e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0359)														---	---	---	---
CHRM5	1133	broad.mit.edu	37	15	34315383	34315383	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34315383delA	uc001zhk.1	+						AVEN_uc001zhj.2_Intron|CHRM5_uc001zhl.1_Intron	NM_012125	NP_036257			cholinergic receptor, muscarinic 5						cell proliferation|inhibition of adenylate cyclase activity by muscarinic acetylcholine receptor signaling pathway	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	34405569	34405569	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34405569delC								PGBD4 (8979 upstream) : C15orf29 (27307 downstream)																																			---	---	---	---
ZNF770	54989	broad.mit.edu	37	15	35282187	35282187	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35282187delA	uc001ziw.2	-							NM_014106	NP_054825			zinc finger protein 770						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	35530357	35530357	+	IGR	DEL	T	-	-	rs141813373		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35530357delT								LOC723972 (95 upstream) : ATPBD4 (132814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	35845076	35845076	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35845076delA	uc001zjc.2	+											Homo sapiens, Similar to LOC161538, clone IMAGE:5199550, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	36192846	36192846	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36192846delT								ATPBD4 (354442 upstream) : C15orf41 (678966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	36593705	36593705	+	IGR	DEL	T	-	-	rs72334068		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36593705delT								ATPBD4 (755301 upstream) : C15orf41 (278107 downstream)																																			---	---	---	---
MEIS2	4212	broad.mit.edu	37	15	37392006	37392006	+	5'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37392006delA	uc001zjr.2	-	1					MEIS2_uc001zjl.2_5'Flank|MEIS2_uc010ucj.1_5'Flank|MEIS2_uc001zjm.2_5'Flank|MEIS2_uc001zjn.2_5'Flank|MEIS2_uc001zjo.2_5'UTR|MEIS2_uc001zjp.2_5'UTR|MEIS2_uc001zjs.2_5'UTR|MEIS2_uc001zju.2_Intron|MEIS2_uc001zjt.2_Intron	NM_170675	NP_733775			Meis homeobox 2 isoform c						negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)	2		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	37594899	37594899	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37594899delA								MEIS2 (201399 upstream) : TMCO5A (631928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	37984839	37984839	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37984839delT								MEIS2 (591339 upstream) : TMCO5A (241988 downstream)																																			---	---	---	---
TMCO5A	145942	broad.mit.edu	37	15	38228551	38228551	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38228551delA	uc001zjw.2	+	2	130	c.27delA	c.(25-27)TCAfs	p.S9fs	TMCO5A_uc001zjv.1_Frame_Shift_Del_p.S9fs|TMCO5A_uc010bbc.1_Frame_Shift_Del_p.S9fs	NM_152453	NP_689666	Q8N6Q1	TMC5A_HUMAN	transmembrane and coiled-coil domains 5A	9						integral to membrane				central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	38400303	38400304	+	IGR	DEL	GA	-	-	rs112757251		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38400303_38400304delGA								TMCO5A (140378 upstream) : SPRED1 (144748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38493493	38493493	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38493493delT	uc001zjy.2	-											Homo sapiens, clone IMAGE:3923347, mRNA.																														---	---	---	---
SPRED1	161742	broad.mit.edu	37	15	38638515	38638515	+	Intron	DEL	A	-	-	rs113279023		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38638515delA	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				---	---	---	---
RASGRP1	10125	broad.mit.edu	37	15	38842026	38842026	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38842026delA	uc001zke.3	-						RASGRP1_uc001zkd.3_Intron	NM_005739	NP_005730			RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)														---	---	---	---
GPR176	11245	broad.mit.edu	37	15	40104117	40104117	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40104117delA	uc001zkj.1	-						GPR176_uc010uck.1_Intron|GPR176_uc001zkk.1_Intron	NM_007223	NP_009154			G protein-coupled receptor 176						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)														---	---	---	---
SRP14	6727	broad.mit.edu	37	15	40329003	40329003	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40329003delA	uc001zkq.2	-						SRP14_uc001zkr.2_Intron|uc001zks.1_5'Flank	NM_003134	NP_003125			signal recognition particle 14kDa (homologous						negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding				0		all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	40343187	40343188	+	Intron	INS	-	AGG	AGG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40343187_40343188insAGG	uc001zks.1	+											Homo sapiens cDNA FLJ45796 fis, clone NT2RI2012542.																														---	---	---	---
BUB1B	701	broad.mit.edu	37	15	40477506	40477506	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40477506delC	uc001zkx.3	+	7	1104	c.892delC	c.(892-894)CCCfs	p.P298fs	BUB1B_uc010ucl.1_Frame_Shift_Del_p.P161fs	NM_001211	NP_001202	O60566	BUB1B_HUMAN	budding uninhibited by benzimidazoles 1 beta	298					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	40512758	40512758	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40512758delT	uc001zkx.3	+						PAK6_uc010bbl.2_Intron|PAK6_uc010bbm.2_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				---	---	---	---
C15orf23	90417	broad.mit.edu	37	15	40681927	40681927	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40681927delA	uc001zll.2	+						C15orf23_uc010ucp.1_Intron|C15orf23_uc001zlo.2_Intron|C15orf23_uc001zlm.2_Intron|C15orf23_uc001zln.2_Intron	NM_033286	NP_150628			TRAF4 associated factor 1 isoform a							nucleus	protein binding			ovary(1)|skin(1)	2		all_cancers(109;2.34e-14)|all_epithelial(112;9.21e-12)|Lung NSC(122;2.95e-09)|all_lung(180;6.03e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;3.39e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0798)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	40874114	40874114	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40874114delT								RPUSD2 (7453 upstream) : CASC5 (12333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	41128486	41128487	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41128486_41128487delAG								PPP1R14D (7579 upstream) : SPINT1 (7759 downstream)																																			---	---	---	---
RHOV	171177	broad.mit.edu	37	15	41168496	41168496	+	5'Flank	DEL	T	-	-	rs75644081		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41168496delT	uc001znd.2	-							NM_133639	NP_598378			ras homolog gene family, member V						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome membrane|plasma membrane	GTP binding|metal ion binding				0		all_cancers(109;1.42e-13)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.58e-05)|COAD - Colon adenocarcinoma(120;0.149)|BRCA - Breast invasive adenocarcinoma(123;0.163)														---	---	---	---
EXD1	161829	broad.mit.edu	37	15	41493078	41493078	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41493078delT	uc001znk.2	-						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																		---	---	---	---
NUSAP1	51203	broad.mit.edu	37	15	41647773	41647773	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41647773delT	uc001zns.3	+						NUSAP1_uc001znq.3_Intron|NUSAP1_uc001znr.3_Intron|NUSAP1_uc010bce.2_Intron|NUSAP1_uc001znt.3_Intron|NUSAP1_uc001znv.3_Intron|NUSAP1_uc001znu.3_Intron|NUSAP1_uc010ucw.1_Intron|NUSAP1_uc001znw.3_Intron	NM_016359	NP_057443			nucleolar and spindle associated protein 1						cytokinesis after mitosis|establishment of mitotic spindle localization|mitotic chromosome condensation|positive regulation of mitosis	chromosome|cytoplasm|nucleolus	DNA binding				0		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	41776076	41776076	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41776076delT								RTF1 (316 upstream) : ITPKA (10046 downstream)																																			---	---	---	---
MGA	23269	broad.mit.edu	37	15	41979230	41979230	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41979230delT	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	41984100	41984100	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41984100delT	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)														---	---	---	---
PLA2G4E	123745	broad.mit.edu	37	15	42302336	42302338	+	In_Frame_Del	DEL	CCA	-	-	rs28736629		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42302336_42302338delCCA	uc001zow.1	-	1	108_110	c.108_110delTGG	c.(106-111)GGTGGG>GGG	p.36_37GG>G		NM_001080490	NP_001073959	Q3MJ16	PA24E_HUMAN	phospholipase A2, group 4E	Error:Variant_position_missing_in_Q3MJ16_after_alignment					phospholipid catabolic process	cytosol|lysosomal membrane	metal ion binding|phospholipase A2 activity				0		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)														---	---	---	---
TMEM87A	25963	broad.mit.edu	37	15	42523218	42523219	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42523218_42523219insA	uc010udd.1	-							NM_015497	NP_056312			transmembrane protein 87A isoform 1							integral to membrane				ovary(1)	1		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)														---	---	---	---
SNAP23	8773	broad.mit.edu	37	15	42810223	42810223	+	Intron	DEL	T	-	-	rs35475710		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42810223delT	uc001zpz.1	+						SNAP23_uc001zqa.1_Intron	NM_003825	NP_003816			synaptosomal-associated protein 23 isoform						cellular membrane fusion|post-Golgi vesicle-mediated transport|protein transport|vesicle targeting	azurophil granule|cell junction|Golgi apparatus|nucleus|plasma membrane enriched fraction|specific granule|synapse|synaptosome	protein binding				0		all_cancers(109;7.14e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;1.18e-08)|all_lung(180;4.2e-08)|Melanoma(134;0.0179)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;2.62e-06)														---	---	---	---
LRRC57	255252	broad.mit.edu	37	15	42836388	42836388	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42836388delT	uc001zqd.1	-						LRRC57_uc001zqc.2_Intron	NM_153260	NP_694992			leucine rich repeat containing 57												0		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)														---	---	---	---
LRRC57	255252	broad.mit.edu	37	15	42837657	42837657	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42837657delA	uc001zqd.1	-						LRRC57_uc001zqc.2_Intron	NM_153260	NP_694992			leucine rich repeat containing 57												0		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)														---	---	---	---
HAUS2	55142	broad.mit.edu	37	15	42853339	42853339	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42853339delA	uc001zqe.2	+						HAUS2_uc010udi.1_Intron|HAUS2_uc001zqf.2_Intron	NM_018097	NP_060567			centrosomal protein 27kDa isoform 1						cell division|centrosome organization|G2/M transition of mitotic cell cycle|mitosis|spindle assembly	centrosome|cytosol|HAUS complex|microtubule|spindle					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	42950486	42950487	+	Intron	INS	-	GT	GT	rs139173925	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42950486_42950487insGT	uc001zqg.2	+						uc001zqh.2_Intron					Homo sapiens cDNA FLJ16106 fis, clone THYMU1000496, moderately similar to KINESIN-LIKE PROTEIN KIF1C.																														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43307840	43307840	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43307840delA	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	43363127	43363128	+	Intron	INS	-	A	A	rs112019760		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43363127_43363128insA	uc001zqq.2	-						UBR1_uc010udk.1_Intron	NM_174916	NP_777576			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43378119	43378124	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43378119_43378124delAAAAAA	uc001zqq.2	-						UBR1_uc010udk.1_Intron	NM_174916	NP_777576			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
TP53BP1	7158	broad.mit.edu	37	15	43748661	43748661	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43748661delT	uc001zrs.2	-	12	2278	c.2130delA	c.(2128-2130)AAAfs	p.K710fs	TP53BP1_uc010udp.1_Frame_Shift_Del_p.K710fs|TP53BP1_uc001zrq.3_Frame_Shift_Del_p.K715fs|TP53BP1_uc001zrr.3_Frame_Shift_Del_p.K715fs|TP53BP1_uc010udq.1_Frame_Shift_Del_p.K715fs	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3	710					double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)									Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					---	---	---	---
MFAP1	4236	broad.mit.edu	37	15	44097815	44097815	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44097815delT	uc001zth.1	-							NM_005926	NP_005917			microfibrillar-associated protein 1							microfibril				skin(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)														---	---	---	---
CTDSPL2	51496	broad.mit.edu	37	15	44741008	44741008	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44741008delA	uc001ztr.2	+						CTDSPL2_uc001zts.2_Intron|CTDSPL2_uc001ztt.2_Intron	NM_016396	NP_057480			CTD (carboxy-terminal domain, RNA polymerase II,								phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)														---	---	---	---
SPG11	80208	broad.mit.edu	37	15	44949207	44949207	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44949207delA	uc001ztx.2	-						SPG11_uc010ueh.1_Intron|SPG11_uc010uei.1_Intron|SPG11_uc001zua.1_Intron	NM_025137	NP_079413			spatacsin isoform 1						cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	45903012	45903014	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45903012_45903014delTTT								PLDN (1104 upstream) : SQRDL (20332 downstream)																																			---	---	---	---
SLC12A1	6557	broad.mit.edu	37	15	48526950	48526950	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48526950delA	uc001zwn.3	+						SLC12A1_uc010uew.1_Intron|SLC12A1_uc010bem.2_Intron|SLC12A1_uc010uex.1_Intron|SLC12A1_uc001zwq.3_Intron|SLC12A1_uc001zwr.3_Intron	NM_000338	NP_000329			sodium potassium chloride cotransporter 2						potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)													---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48763001	48763001	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48763001delA	uc001zwx.1	-						FBN1_uc010beo.1_5'Flank	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	48812686	48812686	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48812686delT	uc001zwx.1	-							NM_000138	NP_000129			fibrillin 1 precursor						heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)														---	---	---	---
GLDN	342035	broad.mit.edu	37	15	51689648	51689649	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51689648_51689649delTC	uc002aba.2	+						GLDN_uc002abb.2_Intron	NM_181789	NP_861454			gliomedin						cell differentiation|nervous system development	collagen|integral to membrane|plasma membrane				ovary(2)	2				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)														---	---	---	---
GNB5	10681	broad.mit.edu	37	15	52433631	52433632	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52433631_52433632delTT	uc002abt.1	-						GNB5_uc002abr.1_Intron|GNB5_uc002abs.1_Intron	NM_016194	NP_057278			guanine nucleotide-binding protein, beta-5							heterotrimeric G-protein complex	GTPase activity|signal transducer activity			lung(1)	1				all cancers(107;0.0163)														---	---	---	---
GNB5	10681	broad.mit.edu	37	15	52452149	52452149	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52452149delT	uc002abt.1	-						GNB5_uc002abr.1_Intron|GNB5_uc002abs.1_Intron|GNB5_uc002abu.3_Intron	NM_016194	NP_057278			guanine nucleotide-binding protein, beta-5							heterotrimeric G-protein complex	GTPase activity|signal transducer activity			lung(1)	1				all cancers(107;0.0163)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	53460154	53460155	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53460154_53460155delAA								ONECUT1 (377945 upstream) : WDR72 (345783 downstream)																																			---	---	---	---
WDR72	256764	broad.mit.edu	37	15	53810082	53810082	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53810082delA	uc002acj.2	-						WDR72_uc010bfh.1_Intron	NM_182758	NP_877435			WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)														---	---	---	---
WDR72	256764	broad.mit.edu	37	15	53992207	53992207	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53992207delT	uc002acj.2	-						WDR72_uc010bfi.1_Intron	NM_182758	NP_877435			WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	55285486	55285486	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55285486delA								UNC13C (364681 upstream) : RSL24D1 (188035 downstream)																																			---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55712613	55712613	+	Intron	DEL	A	-	-	rs143060404		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55712613delA	uc002acy.2	-						DYX1C1_uc010ugh.1_Intron|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.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)														---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55726958	55726958	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55726958delA	uc002acy.2	-						DYX1C1_uc010ugh.1_Intron|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.2_Intron|DYX1C1_uc002adc.2_Intron|DYX1C1_uc002add.2_Intron	NM_020739	NP_065790			cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)														---	---	---	---
NEDD4	4734	broad.mit.edu	37	15	56263823	56263823	+	Intron	DEL	A	-	-	rs147067892		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56263823delA	uc002adl.2	-							NM_006154	NP_006145			neural precursor cell expressed, developmentally						development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus	apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex	beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|breast(1)	4				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	56338611	56338611	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56338611delT								NEDD4 (52776 upstream) : RFX7 (40868 downstream)																																			---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57545439	57545439	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57545439delT	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron|TCF12_uc002aee.2_Intron|TCF12_uc010bft.2_Intron|TCF12_uc010ugo.1_Intron|TCF12_uc010ugp.1_Intron|TCF12_uc010ugq.1_Intron|TCF12_uc010ugr.1_Intron	NM_207038	NP_996921			transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)				T	TEC	extraskeletal myxoid chondrosarcoma								---	---	---	---
CGNL1	84952	broad.mit.edu	37	15	57701236	57701237	+	Intron	DEL	CA	-	-	rs72185255		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57701236_57701237delCA	uc002aeg.2	+						CGNL1_uc010bfw.2_Intron	NM_032866	NP_116255			cingulin-like 1							myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)														---	---	---	---
LIPC	3990	broad.mit.edu	37	15	58833693	58833693	+	Intron	DEL	G	-	-	rs41292504	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58833693delG	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)														---	---	---	---
RNF111	54778	broad.mit.edu	37	15	59321370	59321370	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59321370delT	uc002afv.2	+						RNF111_uc002afs.2_Intron|RNF111_uc002aft.2_Intron|RNF111_uc002afu.2_Intron|RNF111_uc002afw.2_5'Flank	NM_017610	NP_060080			ring finger protein 111						multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)														---	---	---	---
MYO1E	4643	broad.mit.edu	37	15	59547299	59547299	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59547299delT	uc002aga.2	-							NM_004998	NP_004989			myosin IE						actin filament-based movement	myosin complex	actin binding|ATP binding|ATPase activity, coupled|calmodulin binding|microfilament motor activity			central_nervous_system(3)	3				all cancers(107;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	59699491	59699492	+	IGR	DEL	TT	-	-	rs35677105		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59699491_59699492delTT								MYO1E (34420 upstream) : FAM81A (30880 downstream)																																			---	---	---	---
FAM81A	145773	broad.mit.edu	37	15	59745934	59745935	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59745934_59745935delAA	uc002agc.2	+						FAM81A_uc010uha.1_Intron	NM_152450	NP_689663			hypothetical protein LOC145773											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	59830471	59830471	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59830471delT								FAM81A (14720 upstream) : GCNT3 (73511 downstream)																																			---	---	---	---
ANXA2	302	broad.mit.edu	37	15	60678290	60678290	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60678290delA	uc002agn.2	-						ANXA2_uc002agk.2_Intron|ANXA2_uc002agl.2_Intron|ANXA2_uc002agm.2_Intron|ANXA2_uc010uhd.1_Intron|ANXA2_uc010bgj.2_Intron	NM_001136015	NP_001129487			annexin A2 isoform 2						angiogenesis|positive regulation of vesicle fusion|skeletal system development	basement membrane|melanosome|midbody|soluble fraction	calcium ion binding|calcium-dependent phospholipid binding|cytoskeletal protein binding|phospholipase inhibitor activity			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Tenecteplase(DB00031)													---	---	---	---
ANXA2	302	broad.mit.edu	37	15	60682362	60682362	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60682362delA	uc002agn.2	-						ANXA2_uc002agk.2_Intron|ANXA2_uc002agl.2_Intron|ANXA2_uc002agm.2_Intron|ANXA2_uc010uhd.1_Intron|ANXA2_uc010bgj.2_Intron	NM_001136015	NP_001129487			annexin A2 isoform 2						angiogenesis|positive regulation of vesicle fusion|skeletal system development	basement membrane|melanosome|midbody|soluble fraction	calcium ion binding|calcium-dependent phospholipid binding|cytoskeletal protein binding|phospholipase inhibitor activity			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Tenecteplase(DB00031)													---	---	---	---
NARG2	79664	broad.mit.edu	37	15	60758863	60758863	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60758863delA	uc002agp.2	-	5	693	c.458delT	c.(457-459)TTGfs	p.L153fs	NARG2_uc002ago.2_Frame_Shift_Del_p.L16fs|NARG2_uc010bgk.2_Frame_Shift_Del_p.L153fs|NARG2_uc002agr.1_Frame_Shift_Del_p.L153fs	NM_024611	NP_078887	Q659A1	NARG2_HUMAN	NMDA receptor regulated 2 isoform a	153						nucleus				ovary(1)|lung(1)	2																		---	---	---	---
RORA	6095	broad.mit.edu	37	15	61216007	61216007	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61216007delA	uc002agx.2	-							NM_134261	NP_599023			RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
RORA	6095	broad.mit.edu	37	15	61289107	61289108	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61289107_61289108delAA	uc002agx.2	-							NM_134261	NP_599023			RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
RORA	6095	broad.mit.edu	37	15	61371335	61371335	+	Intron	DEL	A	-	-	rs78494397		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61371335delA	uc002agx.2	-							NM_134261	NP_599023			RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	62083359	62083359	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62083359delT								RORA (561857 upstream) : VPS13C (61233 downstream)																																			---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62270972	62270972	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62270972delT	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	62284070	62284070	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62284070delA	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	62563040	62563040	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62563040delA								C2CD4B (105558 upstream) : MGC15885 (366331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62786909	62786909	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62786909delT								C2CD4B (329427 upstream) : MGC15885 (142462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62853865	62853865	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62853865delT								C2CD4B (396383 upstream) : MGC15885 (75506 downstream)																																			---	---	---	---
TLN2	83660	broad.mit.edu	37	15	62983890	62983890	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62983890delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	63252941	63252941	+	IGR	DEL	A	-	-	rs35745164		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63252941delA								TLN2 (116114 upstream) : TPM1 (81897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	63473603	63473603	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63473603delA								RPS27L (23862 upstream) : RAB8B (8125 downstream)																																			---	---	---	---
RAB8B	51762	broad.mit.edu	37	15	63552040	63552040	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63552040delT	uc002alz.2	+						RAB8B_uc010uih.1_Intron	NM_016530	NP_057614			RAB8B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			ovary(1)|kidney(1)	2																		---	---	---	---
USP3	9960	broad.mit.edu	37	15	63821378	63821380	+	Intron	DEL	TTT	-	-	rs11351032		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63821378_63821380delTTT	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)														---	---	---	---
TRIP4	9325	broad.mit.edu	37	15	64687574	64687575	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64687574_64687575delTT	uc002anm.2	+							NM_016213	NP_057297			thyroid hormone receptor interactor 4						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ligand-dependent nuclear receptor binding|transcription coactivator activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
TRIP4	9325	broad.mit.edu	37	15	64737319	64737319	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64737319delT	uc002anm.2	+							NM_016213	NP_057297			thyroid hormone receptor interactor 4						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ligand-dependent nuclear receptor binding|transcription coactivator activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
OAZ2	4947	broad.mit.edu	37	15	64987606	64987606	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64987606delT	uc002anp.2	-											Homo sapiens ornithine decarboxylase antizyme 2 (OAZ2) mRNA, complete cds.						polyamine metabolic process|regulation of cellular amino acid metabolic process	cytosol|nucleus	ornithine decarboxylase inhibitor activity|protein binding				0					L-Ornithine(DB00129)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	65166695	65166695	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65166695delA								PLEKHO2 (6496 upstream) : ANKDD1A (37406 downstream)																																			---	---	---	---
DPP8	54878	broad.mit.edu	37	15	65789893	65789893	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65789893delA	uc002aov.2	-						DPP8_uc002aow.2_Intron|DPP8_uc010uiv.1_Intron|DPP8_uc002aox.2_Intron|DPP8_uc002aoy.2_Intron|DPP8_uc002aoz.2_Intron|DPP8_uc010bhj.2_Intron|DPP8_uc002apa.2_Intron	NM_130434	NP_569118			dipeptidyl peptidase 8 isoform 1						immune response|proteolysis	cytoplasm|membrane|nucleus	aminopeptidase activity|dipeptidyl-peptidase activity|serine-type peptidase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	66140249	66140250	+	IGR	INS	-	AAC	AAC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66140249_66140250insAAC								DENND4A (55618 upstream) : RAB11A (21546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	66575756	66575756	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66575756delT								MEGF11 (29681 upstream) : DIS3L (9877 downstream)																																			---	---	---	---
DIS3L	115752	broad.mit.edu	37	15	66612761	66612761	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66612761delA	uc010ujm.1	+						DIS3L_uc010ujl.1_Intron|DIS3L_uc002app.2_Intron|DIS3L_uc002apq.2_Intron|DIS3L_uc010bho.2_Intron	NM_001143688	NP_001137160			DIS3 mitotic control homolog (S.						rRNA catabolic process	cytoplasm|exosome (RNase complex)	exonuclease activity|protein binding|ribonuclease activity|RNA binding			ovary(2)	2																		---	---	---	---
MAP2K1	5604	broad.mit.edu	37	15	66687868	66687868	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66687868delT	uc010bhq.2	+							NM_002755	NP_002746			mitogen-activated protein kinase kinase 1						activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|plasma membrane	ATP binding|MAP kinase kinase activity|protein serine/threonine kinase activity|protein tyrosine kinase activity				0														Cardiofaciocutaneous_syndrome				---	---	---	---
MAP2K1	5604	broad.mit.edu	37	15	66759908	66759908	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66759908delT	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				---	---	---	---
SMAD3	4088	broad.mit.edu	37	15	67486836	67486836	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67486836delT	uc002aqj.2	+	10					SMAD3_uc010ujr.1_3'UTR|SMAD3_uc010ujs.1_3'UTR|SMAD3_uc010ujt.1_3'UTR	NM_005902	NP_005893			mothers against decapentaplegic homolog 3						activation of caspase activity|cell cycle arrest|cell-cell junction organization|evasion of host defenses by virus|immune response|induction of apoptosis|negative regulation of cell growth|negative regulation of mitotic cell cycle|negative regulation of protein catabolic process|negative regulation of protein phosphorylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|protein stabilization|regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|transport|wound healing	cytosol|nuclear inner membrane|receptor complex	beta-catenin binding|co-SMAD binding|metal ion binding|protein homodimerization activity|protein kinase binding|R-SMAD binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor binding|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding			large_intestine(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)														---	---	---	---
IQCH	64799	broad.mit.edu	37	15	67665247	67665248	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67665247_67665248delAA	uc002aqo.1	+						IQCH_uc002aqn.1_Intron|IQCH_uc002aqq.1_Intron|IQCH_uc002aqp.1_Intron	NM_001031715	NP_001026885			IQ motif containing H isoform 1											skin(3)|ovary(1)	4				Colorectal(3;0.0856)												OREG0002848	type=REGULATORY REGION|Gene=FLJ12476(intragenic)|Dataset=Vista Enhancers|EvidenceSubtype=In-vivo LacZ Expression Assay	---	---	---	---
Unknown	0	broad.mit.edu	37	15	69052283	69052286	+	IGR	DEL	AGAG	-	-	rs9920458		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69052283_69052286delAGAG								CORO2B (32141 upstream) : ANP32A (18591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70035189	70035190	+	IGR	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70035189_70035190delGA								LOC145837 (171410 upstream) : C15orf50 (92383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70412094	70412095	+	IGR	DEL	CA	-	-	rs66550003		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70412094_70412095delCA								TLE3 (21838 upstream) : UACA (534800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70869827	70869827	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70869827delT								TLE3 (479571 upstream) : UACA (77068 downstream)																																			---	---	---	---
UACA	55075	broad.mit.edu	37	15	70973711	70973711	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70973711delA	uc002asr.2	-						UACA_uc010uke.1_Intron|UACA_uc002asq.2_Intron|UACA_uc010bin.1_Intron	NM_018003	NP_060473			uveal autoantigen with coiled-coil domains and							cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	71083401	71083402	+	IGR	DEL	AA	-	-	rs112108673		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71083401_71083402delAA								UACA (27551 upstream) : LARP6 (40489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	71360001	71360001	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71360001delT								LRRC49 (17567 upstream) : CT62 (42582 downstream)																																			---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71492142	71492143	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71492142_71492143delTG	uc002atb.1	+							NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71575306	71575308	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71575306_71575308delTTT	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71703216	71703217	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71703216_71703217delAC	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	72077855	72077855	+	IGR	DEL	A	-	-	rs75471600		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72077855delA								THSD4 (2133 upstream) : NR2E3 (25039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	72736310	72736310	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72736310delT								TMEM202 (35603 upstream) : ARIH1 (30357 downstream)																																			---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73357642	73357642	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73357642delT	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron	NM_002499	NP_002490			neogenin homolog 1 precursor						axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1																		---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73558929	73558929	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73558929delT	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron|NEO1_uc002avn.3_Intron	NM_002499	NP_002490			neogenin homolog 1 precursor						axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1																		---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73580951	73580951	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73580951delT	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																		---	---	---	---
ISLR2	57611	broad.mit.edu	37	15	74423522	74423522	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74423522delC	uc002axd.2	+						LOC283731_uc002axc.2_5'Flank|ISLR2_uc002axe.2_Intron|ISLR2_uc010bjg.2_Intron|ISLR2_uc010bjf.2_Intron	NM_001130136	NP_001123608			immunoglobulin superfamily containing						positive regulation of axon extension	cell surface|integral to membrane|plasma membrane					0																		---	---	---	---
CCDC33	80125	broad.mit.edu	37	15	74535645	74535645	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74535645delG	uc002axo.2	+							NM_025055	NP_079331			coiled-coil domain containing 33 isoform 1								protein binding			ovary(3)|skin(2)	5																		---	---	---	---
CCDC33	80125	broad.mit.edu	37	15	74568020	74568020	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74568020delT	uc002axo.2	+						CCDC33_uc002axp.2_Intron	NM_025055	NP_079331			coiled-coil domain containing 33 isoform 1								protein binding			ovary(3)|skin(2)	5																		---	---	---	---
CCDC33	80125	broad.mit.edu	37	15	74576135	74576136	+	Intron	INS	-	CACACA	CACACA	rs142112685	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74576135_74576136insCACACA	uc002axo.2	+						CCDC33_uc002axp.2_Intron	NM_025055	NP_079331			coiled-coil domain containing 33 isoform 1								protein binding			ovary(3)|skin(2)	5																		---	---	---	---
EDC3	80153	broad.mit.edu	37	15	74942202	74942203	+	Intron	DEL	GG	-	-	rs72445048		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74942202_74942203delGG	uc002ayn.2	-						EDC3_uc002ayo.2_Intron|EDC3_uc002aym.2_Intron	NM_001142443	NP_001135915			enhancer of mRNA decapping 3						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	75052308	75052308	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75052308delT								CYP1A2 (3367 upstream) : CSK (22117 downstream)																																			---	---	---	---
COX5A	9377	broad.mit.edu	37	15	75215755	75215755	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75215755delA	uc002azi.3	-							NM_004255	NP_004246			cytochrome c oxidase subunit Va precursor						respiratory electron transport chain	mitochondrial inner membrane	cytochrome-c oxidase activity|electron carrier activity|metal ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	75261648	75261649	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75261648_75261649delTT								RPP25 (11873 upstream) : SCAMP5 (26252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	75277271	75277271	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75277271delT								RPP25 (27496 upstream) : SCAMP5 (10630 downstream)																																			---	---	---	---
SCAMP5	192683	broad.mit.edu	37	15	75311041	75311041	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75311041delT	uc002azk.1	+						SCAMP5_uc002azl.1_Intron|SCAMP5_uc002azm.1_Intron|SCAMP5_uc002azn.1_Intron|SCAMP5_uc010uly.1_Intron	NM_138967	NP_620417			secretory carrier membrane protein 5						exocytosis|negative regulation of endocytosis|positive regulation of calcium ion-dependent exocytosis|positive regulation of cytokine secretion|protein transport|response to endoplasmic reticulum stress	cell junction|integral to membrane|recycling endosome membrane|synaptic vesicle membrane|trans-Golgi network membrane	protein binding			ovary(1)	1																		---	---	---	---
PTPN9	5780	broad.mit.edu	37	15	75768666	75768666	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75768666delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	76075102	76075102	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76075102delT	uc010umm.1	+						uc002bba.1_5'Flank					SubName: Full=cDNA FLJ59077, highly similar to Golgin subfamily A member 6;																														---	---	---	---
UBE2Q2	92912	broad.mit.edu	37	15	76164666	76164666	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76164666delA	uc002bbg.2	+						UBE2Q2_uc002bbh.2_Intron|UBE2Q2_uc010umn.1_Intron|UBE2Q2_uc002bbi.2_Intron	NM_173469	NP_775740			ubiquitin-conjugating enzyme E2Q 2 isoform 1						protein K48-linked ubiquitination	cytoplasm	ATP binding|ubiquitin-protein ligase activity			ovary(2)	2																		---	---	---	---
UBE2Q2	92912	broad.mit.edu	37	15	76191744	76191744	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76191744delT	uc002bbg.2	+						UBE2Q2_uc002bbh.2_Intron|UBE2Q2_uc010umn.1_Intron|UBE2Q2_uc002bbi.2_Intron	NM_173469	NP_775740			ubiquitin-conjugating enzyme E2Q 2 isoform 1						protein K48-linked ubiquitination	cytoplasm	ATP binding|ubiquitin-protein ligase activity			ovary(2)	2																		---	---	---	---
NRG4	145957	broad.mit.edu	37	15	76244934	76244934	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76244934delT	uc002bbo.2	-						NRG4_uc010bkm.1_Intron|NRG4_uc002bbn.2_Intron|NRG4_uc010bkn.2_Intron|NRG4_uc010bko.2_Intron	NM_138573	NP_612640			neuregulin 4							extracellular region|integral to membrane|plasma membrane	growth factor activity				0																		---	---	---	---
ETFA	2108	broad.mit.edu	37	15	76588097	76588097	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76588097delA	uc002bbt.2	-						ETFA_uc010bkq.1_Intron|ETFA_uc002bbu.1_Intron	NM_000126	NP_000117			electron transfer flavoprotein, alpha						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity				0																		---	---	---	---
ETFA	2108	broad.mit.edu	37	15	76598750	76598750	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76598750delG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	76611839	76611839	+	IGR	DEL	G	-	-	rs2456031	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76611839delG								ETFA (8029 upstream) : ISL2 (17308 downstream)																																			---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76804994	76804994	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76804994delA	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron	NM_020843	NP_065894			S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76927192	76927193	+	Intron	INS	-	TG	TG	rs148832890	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76927192_76927193insTG	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron	NM_020843	NP_065894			S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76927706	76927706	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76927706delA	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron	NM_020843	NP_065894			S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	77783908	77783908	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77783908delC								HMG20A (5965 upstream) : LINGO1 (121461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	78074196	78074196	+	IGR	DEL	C	-	-	rs151092710	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78074196delC								LINGO1 (85721 upstream) : LOC645752 (132363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	78624852	78624852	+	IGR	DEL	C	-	-	rs149068527	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78624852delC								WDR61 (32912 upstream) : CRABP1 (7814 downstream)																																			---	---	---	---
IREB2	3658	broad.mit.edu	37	15	78758544	78758544	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78758544delT	uc002bdr.2	+						IREB2_uc010unb.1_Intron|IREB2_uc002bdq.2_Intron	NM_004136	NP_004127			iron-responsive element binding protein 2								4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)														---	---	---	---
KIAA1024	23251	broad.mit.edu	37	15	79744546	79744549	+	Intron	DEL	TGTG	-	-	rs34276947		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79744546_79744549delTGTG	uc002bew.1	+							NM_015206	NP_056021			hypothetical protein LOC23251							integral to membrane				pancreas(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
FAH	2184	broad.mit.edu	37	15	80470744	80470745	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80470744_80470745insT	uc002bfj.2	+						FAH_uc002bfk.1_Intron|FAH_uc002bfm.1_Intron|FAH_uc002bfn.1_Intron|FAH_uc010bln.1_Intron|FAH_uc010blo.1_Intron	NM_000137	NP_000128			fumarylacetoacetase						L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	fumarylacetoacetase activity|metal ion binding				0														Tyrosinemia_type_1				---	---	---	---
Unknown	0	broad.mit.edu	37	15	80919354	80919355	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80919354_80919355delCT								ARNT2 (29082 upstream) : FAM108C1 (68297 downstream)																																			---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81172263	81172264	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81172263_81172264delAG	uc002bfw.1	+						KIAA1199_uc010unn.1_Intron	NM_018689	NP_061159			KIAA1199 precursor											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81228065	81228065	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81228065delT	uc002bfw.1	+						KIAA1199_uc010unn.1_Intron	NM_018689	NP_061159			KIAA1199 precursor											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
IL16	3603	broad.mit.edu	37	15	81473210	81473210	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81473210delT	uc010blq.1	+						IL16_uc002bgc.2_5'Flank|IL16_uc002bge.3_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	81677495	81677495	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81677495delT								TMC3 (11077 upstream) : MEX3B (656633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	81705818	81705818	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81705818delA								TMC3 (39400 upstream) : MEX3B (628310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	81721047	81721047	+	IGR	DEL	G	-	-	rs149934466		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81721047delG								TMC3 (54629 upstream) : MEX3B (613081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	82161676	82161676	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82161676delT								TMC3 (495258 upstream) : MEX3B (172452 downstream)																																			---	---	---	---
GOLGA6L10	647042	broad.mit.edu	37	15	83014189	83014190	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83014189_83014190delAA	uc010unt.1	-						uc002bhl.2_Intron|uc002bhm.2_Intron|GOLGA6L10_uc010uny.1_Intron|GOLGA6L10_uc002bia.1_5'Flank					Homo sapiens cDNA FLJ40113 fis, clone TESTI2008621.												0																		---	---	---	---
CPEB1	64506	broad.mit.edu	37	15	83277020	83277020	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83277020delT	uc002bit.2	-						CPEB1_uc002biu.2_Intron|CPEB1_uc010uof.1_Intron|CPEB1_uc002biv.2_Intron	NM_001079533	NP_001073001			cytoplasmic polyadenylation element binding						mRNA processing|regulation of translation	cell junction|cytoplasmic mRNA processing body|dendrite|postsynaptic density|postsynaptic membrane	nucleotide binding|RNA binding			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(143;0.229)															---	---	---	---
AP3B2	8120	broad.mit.edu	37	15	83360356	83360356	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83360356delA	uc010uoh.1	-						AP3B2_uc010uoi.1_Intron|AP3B2_uc010uoj.1_Intron|AP3B2_uc010uok.1_Intron	NM_004644	NP_004635			adaptor-related protein complex 3, beta 2						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	83381756	83381756	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83381756delT	uc002biz.2	-						uc002bja.2_RNA					Homo sapiens cDNA FLJ36177 fis, clone TESTI2026515.																														---	---	---	---
BTBD1	53339	broad.mit.edu	37	15	83699665	83699665	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83699665delA	uc002bjn.2	-						BTBD1_uc002bjo.2_Intron	NM_025238	NP_079514			BTB (POZ) domain containing 1 isoform 1							cytoplasmic mRNA processing body|protein complex	protein binding			ovary(1)|central_nervous_system(1)	2				all cancers(203;0.000186)														---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84629383	84629384	+	Intron	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84629383_84629384insG	uc002bjz.3	+						ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400			ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84638911	84638911	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84638911delA	uc002bjz.3	+						ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400			ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84660650	84660650	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84660650delA	uc002bjz.3	+						ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400			ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	84795466	84795466	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84795466delT								ADAMTSL3 (86875 upstream) : LOC388152 (72134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	84802478	84802478	+	IGR	DEL	T	-	-	rs67527764		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84802478delT								ADAMTSL3 (93887 upstream) : LOC388152 (65122 downstream)																																			---	---	---	---
SCAND2	54581	broad.mit.edu	37	15	85179251	85179251	+	Intron	DEL	A	-	-	rs74592536		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85179251delA	uc002bks.2	+						SCAND2_uc002bku.2_Intron|SCAND2_uc002bkt.2_Intron					RecName: Full=SCAN domain-containing protein 2;												0																		---	---	---	---
SEC11A	23478	broad.mit.edu	37	15	85252985	85252985	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85252985delT	uc002blb.1	-						SEC11A_uc002blc.1_Intron	NM_014300	NP_055115			SEC11-like 1						energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	endoplasmic reticulum membrane|integral to membrane|microsome	protein binding|serine-type peptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(143;0.199)															---	---	---	---
SLC28A1	9154	broad.mit.edu	37	15	85481647	85481647	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85481647delA	uc002blg.2	+						SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204			solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
SLC28A1	9154	broad.mit.edu	37	15	85484442	85484443	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85484442_85484443insT	uc002blg.2	+						SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204			solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	85820392	85820392	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85820392delA								PDE8A (138022 upstream) : AKAP13 (103479 downstream)																																			---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	86786376	86786376	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86786376delT	uc002blz.1	+							NM_152336	NP_689549			ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0																		---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	86884618	86884619	+	Intron	INS	-	AAC	AAC	rs140272978	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86884618_86884619insAAC	uc002blz.1	+							NM_152336	NP_689549			ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0																		---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	87089453	87089454	+	Intron	DEL	TT	-	-	rs66611676		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87089453_87089454delTT	uc002blz.1	+							NM_152336	NP_689549			ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0																		---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	87139825	87139825	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87139825delT	uc002blz.1	+							NM_152336	NP_689549			ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	87604749	87604750	+	IGR	DEL	AA	-	-	rs35253065		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87604749_87604750delAA								AGBL1 (32466 upstream) : NCRNA00052 (515410 downstream)																																			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88593718	88593719	+	Intron	DEL	GT	-	-	rs71710153		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88593718_88593719delGT	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	88873489	88873489	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88873489delT								NTRK3 (73828 upstream) : MRPL46 (129219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	88979215	88979216	+	IGR	INS	-	ACAC	ACAC	rs148381848	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88979215_88979216insACAC								NTRK3 (179554 upstream) : MRPL46 (23492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	89134246	89134246	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89134246delC	uc002bms.1	-											Homo sapiens cDNA FLJ30187 fis, clone BRACE2001239.																														---	---	---	---
ACAN	176	broad.mit.edu	37	15	89392632	89392632	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89392632delG	uc010upo.1	+						ACAN_uc002bmx.2_Intron|ACAN_uc010upp.1_Intron|ACAN_uc002bna.2_Intron	NM_013227	NP_037359			aggrecan isoform 2 precursor						cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)															---	---	---	---
RHCG	51458	broad.mit.edu	37	15	90027719	90027720	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90027719_90027720delGA	uc002bnz.2	-						RHCG_uc002boa.2_Intron|RHCG_uc010bnq.1_Intron	NM_016321	NP_057405			Rh family, C glycoprotein						amine transport|cellular ion homeostasis|epithelial cell differentiation|transepithelial ammonium transport	apical plasma membrane|basolateral plasma membrane|cytoplasmic vesicle|integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			kidney(1)	1	Lung NSC(78;0.0237)|all_lung(78;0.0478)																	---	---	---	---
KIF7	374654	broad.mit.edu	37	15	90184593	90184595	+	Intron	DEL	CTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90184593_90184595delCTT	uc002bof.2	-						KIF7_uc010upw.1_Intron	NM_198525	NP_940927			kinesin family member 7						microtubule-based movement|negative regulation of smoothened signaling pathway|positive regulation of smoothened signaling pathway	cilium	ATP binding|microtubule motor activity|protein binding			ovary(2)|lung(1)	3	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)															---	---	---	---
ZNF710	374655	broad.mit.edu	37	15	90587139	90587140	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90587139_90587140delTT	uc002bov.1	+							NM_198526	NP_940928			zinc finger protein 710						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)															---	---	---	---
IQGAP1	8826	broad.mit.edu	37	15	91027424	91027424	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91027424delG	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)															---	---	---	---
BLM	641	broad.mit.edu	37	15	91304139	91304139	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91304139delA	uc002bpr.2	+	7	1633	c.1536delA	c.(1534-1536)GGAfs	p.G512fs	BLM_uc010uqh.1_Frame_Shift_Del_p.G512fs|BLM_uc010uqi.1_Frame_Shift_Del_p.G137fs|BLM_uc010bnx.2_Frame_Shift_Del_p.G512fs|BLM_uc002bps.1_Frame_Shift_Del_p.G74fs	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				---	---	---	---
Unknown	0	broad.mit.edu	37	15	91508580	91508580	+	IGR	DEL	G	-	-	rs66937802		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91508580delG								RCCD1 (2227 upstream) : PRC1 (694 downstream)																																			---	---	---	---
SLCO3A1	28232	broad.mit.edu	37	15	92507663	92507664	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92507663_92507664delTT	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)															---	---	---	---
SLCO3A1	28232	broad.mit.edu	37	15	92653950	92653950	+	Intron	DEL	G	-	-	rs11322700		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92653950delG	uc002bqx.2	+						SLCO3A1_uc002bqy.2_Intron|SLCO3A1_uc010boc.1_Intron|SLCO3A1_uc002bqz.1_Intron	NM_013272	NP_037404			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)															---	---	---	---
ST8SIA2	8128	broad.mit.edu	37	15	92977209	92977209	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92977209delA	uc002bra.2	+						ST8SIA2_uc002brb.2_Intron	NM_006011	NP_006002			ST8 alpha-N-acetyl-neuraminide						axon guidance|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity				0	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	93966088	93966088	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93966088delC	uc002bsu.1	+						uc002bta.1_5'Flank|uc010ure.1_5'Flank|uc010urf.1_5'Flank|uc002btb.1_5'Flank|uc002btc.1_5'Flank					Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	94087471	94087472	+	Intron	INS	-	A	A	rs149229570	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94087471_94087472insA	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	94383966	94383967	+	Intron	DEL	TC	-	-	rs151253912		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94383966_94383967delTC	uc002bte.1	-											Homo sapiens cDNA clone IMAGE:5266107.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	95618695	95618696	+	IGR	INS	-	A	A	rs113643841		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95618695_95618696insA								MCTP2 (591515 upstream) : LOC145820 (357626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95634757	95634758	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95634757_95634758insC								MCTP2 (607577 upstream) : LOC145820 (341564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96481719	96481719	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96481719delA								LOC145820 (430645 upstream) : NR2F2 (387438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96600876	96600876	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96600876delT								LOC145820 (549802 upstream) : NR2F2 (268281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96616778	96616778	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96616778delA								LOC145820 (565704 upstream) : NR2F2 (252379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96945475	96945475	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96945475delA								NR2F2 (61985 upstream) : SPATA8 (381204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97115501	97115502	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97115501_97115502delTT								NR2F2 (232011 upstream) : SPATA8 (211177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97926140	97926140	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97926140delA								SPATA8 (597296 upstream) : LOC91948 (359706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98097472	98097472	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98097472delT								SPATA8 (768628 upstream) : LOC91948 (188374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98632177	98632177	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98632177delT								ARRDC4 (115110 upstream) : FAM169B (348214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98805118	98805118	+	IGR	DEL	A	-	-	rs66977440		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98805118delA								ARRDC4 (288051 upstream) : FAM169B (175273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	99103293	99103294	+	IGR	INS	-	A	A	rs145547872	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99103293_99103294insA								FAM169B (45682 upstream) : IGF1R (89467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	99132148	99132149	+	IGR	DEL	CA	-	-	rs34892902		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99132148_99132149delCA								FAM169B (74537 upstream) : IGF1R (60612 downstream)																																			---	---	---	---
IGF1R	3480	broad.mit.edu	37	15	99315136	99315137	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99315136_99315137delTT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	100084054	100084054	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100084054delT								LRRC28 (156774 upstream) : MEF2A (22079 downstream)																																			---	---	---	---
LYSMD4	145748	broad.mit.edu	37	15	100261508	100261508	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100261508delC	uc002bvj.1	-						LYSMD4_uc010bou.1_Intron					Homo sapiens cDNA FLJ32156 fis, clone PLACE6000137.						cell wall macromolecule catabolic process	integral to membrane					0	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)															---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100595210	100595210	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100595210delA	uc002bvv.1	-							NM_139057	NP_620688			ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)														---	---	---	---
LRRK1	79705	broad.mit.edu	37	15	101481612	101481617	+	Intron	DEL	TGTCTC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101481612_101481617delTGTCTC	uc002bwr.2	+						LRRK1_uc010usb.1_Intron|LRRK1_uc010usc.1_Intron|LRRK1_uc002bwq.1_Intron	NM_024652	NP_078928			leucine-rich repeat kinase 1						small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
PCSK6	5046	broad.mit.edu	37	15	101972833	101972833	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101972833delA	uc002bwy.2	-						PCSK6_uc010bpd.2_Intron|PCSK6_uc010bpe.2_Intron|PCSK6_uc002bxa.2_Intron|PCSK6_uc002bxb.2_Intron|PCSK6_uc002bxc.1_Intron|PCSK6_uc002bxd.1_Intron|PCSK6_uc002bxe.2_Intron|PCSK6_uc002bxg.1_Intron	NM_002570	NP_002561			paired basic amino acid cleaving system 4						glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	102089195	102089195	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102089195delA								PCSK6 (59008 upstream) : TM2D3 (83985 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	102287600	102287600	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102287600delT	uc010usj.1	+											RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	102382786	102382787	+	IGR	INS	-	TG	TG	rs145296118	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102382786_102382787insTG								OR4F15 (23460 upstream) : OR4F4 (79558 downstream)																																			---	---	---	---
LUC7L	55692	broad.mit.edu	37	16	240581	240581	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:240581delA	uc002cgc.1	-						LUC7L_uc002cga.1_Intron|LUC7L_uc002cgd.1_Intron|LUC7L_uc002cge.1_Intron|LUC7L_uc002cgb.1_Intron	NM_201412	NP_958815			LUC7-like isoform b								metal ion binding			central_nervous_system(1)	1		all_cancers(16;1.1e-06)|all_epithelial(16;2.71e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.0138)|all_lung(18;0.0306)																---	---	---	---
LUC7L	55692	broad.mit.edu	37	16	243153	243153	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:243153delT	uc002cgc.1	-						LUC7L_uc002cga.1_Intron|LUC7L_uc002cgd.1_Intron|LUC7L_uc002cge.1_Intron|LUC7L_uc002cgb.1_Intron	NM_201412	NP_958815			LUC7-like isoform b								metal ion binding			central_nervous_system(1)	1		all_cancers(16;1.1e-06)|all_epithelial(16;2.71e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.0138)|all_lung(18;0.0306)																---	---	---	---
AXIN1	8312	broad.mit.edu	37	16	350369	350369	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:350369delT	uc002cgp.1	-						AXIN1_uc002cgq.1_Intron	NM_003502	NP_003493			axin 1 isoform a						activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			breast(1)|liver(1)	2		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)																---	---	---	---
AXIN1	8312	broad.mit.edu	37	16	352889	352889	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:352889delT	uc002cgp.1	-						AXIN1_uc002cgq.1_Intron	NM_003502	NP_003493			axin 1 isoform a						activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			breast(1)|liver(1)	2		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)																---	---	---	---
PIGQ	9091	broad.mit.edu	37	16	626830	626830	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:626830delT	uc002cho.2	+						PIGQ_uc010bqw.2_Intron|PIGQ_uc002chm.2_3'UTR|PIGQ_uc002chn.2_Intron|PIGQ_uc010uui.1_Intron	NM_148920	NP_683721			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|carbohydrate metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			central_nervous_system(1)	1		Hepatocellular(780;0.00335)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	1084162	1084163	+	IGR	INS	-	TCCA	TCCA	rs149748787	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1084162_1084163insTCCA								SOX8 (47184 upstream) : LOC146336 (29921 downstream)																																			---	---	---	---
GNPTG	84572	broad.mit.edu	37	16	1409276	1409276	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1409276delT	uc002clm.2	+							NM_032520	NP_115909			N-acetylglucosamine-1-phosphotransferase, gamma							extracellular region|Golgi apparatus	protein binding			central_nervous_system(1)	1		Hepatocellular(780;0.0893)																---	---	---	---
UNKL	64718	broad.mit.edu	37	16	1427030	1427031	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1427030_1427031insC	uc010brn.1	-						UNKL_uc002cln.2_Intron|UNKL_uc002clo.2_Intron|UNKL_uc002clp.2_Intron					SubName: Full=Putative ubiquitin-protein ligase;          EC=6.3.2.19; Flags: Fragment;							cytoplasm|nucleus	ligase activity|nucleic acid binding|zinc ion binding				0		Hepatocellular(780;0.0893)																---	---	---	---
MAPK8IP3	23162	broad.mit.edu	37	16	1808219	1808219	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1808219delG	uc002cmk.2	+						MAPK8IP3_uc002cml.2_Intron|MAPK8IP3_uc010uvl.1_Intron	NM_015133	NP_055948			mitogen-activated protein kinase 8 interacting						vesicle-mediated transport	Golgi membrane	kinesin binding|MAP-kinase scaffold activity|protein kinase binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
C16orf73	254528	broad.mit.edu	37	16	1885864	1885865	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1885864_1885865delTT	uc002cne.2	-						FAHD1_uc002cnd.2_Intron|FAHD1_uc010brz.2_Intron|C16orf73_uc010uvq.1_Intron|C16orf73_uc010uvr.1_Intron	NM_152764	NP_689977			hypothetical protein LOC254528 isoform 2						meiosis	cytoplasm					0																		---	---	---	---
SEPX1	51734	broad.mit.edu	37	16	1992155	1992155	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1992155delA	uc010uvs.1	-							NM_016332	NP_057416			selenoprotein X, 1						protein repair	cytoplasm|nucleus	peptide-methionine-(S)-S-oxide reductase activity|zinc ion binding			ovary(1)	1					L-Methionine(DB00134)													---	---	---	---
TSC2	7249	broad.mit.edu	37	16	2100600	2100604	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2100600_2100604delTTTTT	uc002con.2	+						NTHL1_uc002col.1_5'Flank|NTHL1_uc002com.1_5'Flank|TSC2_uc010uvu.1_Intron|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				---	---	---	---
RNPS1	10921	broad.mit.edu	37	16	2304471	2304472	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2304471_2304472insT	uc002cpt.2	-						DCI_uc002cpr.2_5'Flank|DCI_uc002cps.2_5'Flank|RNPS1_uc002cpu.2_Intron|RNPS1_uc002cpv.2_Intron|RNPS1_uc002cpw.2_Intron|RNPS1_uc002cpx.2_Intron|RNPS1_uc010uwa.1_Intron	NM_080594	NP_542161			RNA-binding protein S1, serine-rich domain						mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|termination of RNA polymerase II transcription	cytosol|nuclear speck	mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(1)	1																		---	---	---	---
PDPK1	5170	broad.mit.edu	37	16	2636922	2636922	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2636922delT	uc002cqs.2	+						PDPK1_uc002cqt.2_Intron|PDPK1_uc010bsn.2_Intron|PDPK1_uc002cqu.2_Intron	NM_002613	NP_002604			3-phosphoinositide dependent protein kinase-1						actin cytoskeleton organization|activation of protein kinase B activity|insulin receptor signaling pathway|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|peptidyl-threonine phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|synaptic transmission|T cell costimulation|T cell receptor signaling pathway	cytosol|nucleoplasm|plasma membrane	3-phosphoinositide-dependent protein kinase activity|ATP binding			central_nervous_system(2)|ovary(1)	3		Ovarian(90;0.17)			Celecoxib(DB00482)													---	---	---	---
CCDC64B	146439	broad.mit.edu	37	16	3084713	3084713	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3084713delT	uc002ctf.3	-						CCDC64B_uc002cte.3_5'Flank	NM_001103175	NP_001096645			coiled-coil domain containing 64B												0																		---	---	---	---
ZNF263	10127	broad.mit.edu	37	16	3319046	3319047	+	Intron	INS	-	A	A	rs149447430	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3319046_3319047insA	uc010uww.1	+							NM_005741	NP_005732			zinc finger protein 263						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(3)|ovary(1)	4																		---	---	---	---
ZNF263	10127	broad.mit.edu	37	16	3338252	3338253	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3338252_3338253delAA	uc002cuq.2	+						ZNF263_uc010uww.1_Intron|ZNF263_uc002cur.2_5'Flank	NM_005741	NP_005732			zinc finger protein 263						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(3)|ovary(1)	4																		---	---	---	---
C16orf90	646174	broad.mit.edu	37	16	3546141	3546141	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3546141delA	uc002cvi.2	-							NM_001080524	NP_001073993			hypothetical protein LOC646174												0																		---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3821078	3821078	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3821078delT	uc002cvv.2	-						CREBBP_uc002cvw.2_Intron	NM_004380	NP_004371			CREB binding protein isoform a						cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)				T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3823681	3823681	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3823681delA	uc002cvv.2	-						CREBBP_uc002cvw.2_Intron	NM_004380	NP_004371			CREB binding protein isoform a						cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)				T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				---	---	---	---
ADCY9	115	broad.mit.edu	37	16	4039383	4039383	+	Intron	DEL	T	-	-	rs7206387	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4039383delT	uc002cvx.2	-							NM_001116	NP_001107			adenylate cyclase 9						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6																		---	---	---	---
ADCY9	115	broad.mit.edu	37	16	4058572	4058573	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4058572_4058573insT	uc002cvx.2	-							NM_001116	NP_001107			adenylate cyclase 9						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6																		---	---	---	---
DNAJA3	9093	broad.mit.edu	37	16	4499006	4499007	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4499006_4499007insT	uc002cwk.2	+						DNAJA3_uc002cwl.2_Intron|DNAJA3_uc010uxk.1_Intron	NM_005147	NP_005138			DnaJ (Hsp40) homolog, subfamily A, member 3						activation of caspase activity|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of cell proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein kinase activity|neuromuscular junction development|positive regulation of apoptosis|positive regulation of protein ubiquitination|protein folding|protein folding|protein stabilization|response to heat|response to interferon-gamma	cytosol|mitochondrial matrix|mitochondrial nucleoid|nucleus	ATP binding|heat shock protein binding|interferon-gamma receptor binding|metal ion binding|NF-kappaB binding|protein kinase binding			ovary(2)|breast(2)	4																		---	---	---	---
C16orf71	146562	broad.mit.edu	37	16	4794531	4794531	+	Intron	DEL	T	-	-	rs79094152		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4794531delT	uc002cxn.2	+							NM_139170	NP_631909			hypothetical protein LOC146562											central_nervous_system(1)	1																		---	---	---	---
PPL	5493	broad.mit.edu	37	16	4953722	4953722	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4953722delA	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																		---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6751037	6751037	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6751037delG	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	6991827	6991827	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6991827delT	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	7004187	7004190	+	Intron	DEL	ACTC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7004187_7004190delACTC	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	7268081	7268082	+	Intron	DEL	TG	-	-	rs113027730		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7268081_7268082delTG	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	7643669	7643670	+	Intron	DEL	TT	-	-	rs140556022		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7643669_7643670delTT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	8172749	8172749	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8172749delA								A2BP1 (409409 upstream) : TMEM114 (446754 downstream)																																			---	---	---	---
ABAT	18	broad.mit.edu	37	16	8805667	8805668	+	Intron	INS	-	GATA	GATA	rs149576218	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8805667_8805668insGATA	uc002czc.3	+						ABAT_uc002czd.3_5'Flank|ABAT_uc010buh.2_5'Flank	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)													---	---	---	---
C16orf72	29035	broad.mit.edu	37	16	9203650	9203650	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9203650delT	uc002czm.2	+						uc002czn.2_RNA	NM_014117	NP_054836			hypothetical protein LOC29035											large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	9584838	9584839	+	IGR	INS	-	T	T	rs138444983	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9584838_9584839insT								C16orf72 (371293 upstream) : GRIN2A (262428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9708168	9708168	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9708168delT								C16orf72 (494623 upstream) : GRIN2A (139099 downstream)																																			---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	10004877	10004878	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10004877_10004878delAA	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc010uyn.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879			N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	10329658	10329658	+	IGR	DEL	T	-	-	rs111805735		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10329658delT								GRIN2A (53047 upstream) : ATF7IP2 (150254 downstream)																																			---	---	---	---
ATF7IP2	80063	broad.mit.edu	37	16	10532277	10532280	+	Intron	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	10613650	10613651	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10613650_10613651delCT								ATF7IP2 (36156 upstream) : EMP2 (8629 downstream)																																			---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11154578	11154578	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11154578delT	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041			C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11210265	11210265	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11210265delA	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041			C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	11479893	11479893	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11479893delA								C16orf75 (34276 upstream) : LITAF (161689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	11552362	11552362	+	Intron	DEL	A	-	-	rs79402144		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11552362delA	uc002dax.1	-											Homo sapiens cDNA FLJ44575 fis, clone UTERU3018154.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	11841775	11841775	+	IGR	DEL	A	-	-	rs78892811		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11841775delA								TXNDC11 (5127 upstream) : ZC3H7A (2668 downstream)																																			---	---	---	---
RUNDC2A	84127	broad.mit.edu	37	16	12094979	12094979	+	Intron	DEL	T	-	-	rs75119546		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12094979delT	uc002dbw.1	+							NM_032167	NP_115543			RUN domain containing 2A											ovary(1)	1								T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
RUNDC2A	84127	broad.mit.edu	37	16	12142009	12142009	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12142009delT	uc002dbw.1	+							NM_032167	NP_115543			RUN domain containing 2A											ovary(1)	1								T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12274348	12274348	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12274348delT	uc002dby.3	+						SNX29_uc010uyx.1_Intron	NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	12714897	12714898	+	IGR	DEL	AT	-	-	rs59186687		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12714897_12714898delAT								SNX29 (46752 upstream) : CPPED1 (38759 downstream)																																			---	---	---	---
CPPED1	55313	broad.mit.edu	37	16	12801666	12801666	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12801666delA	uc002dca.3	-						CPPED1_uc002dcb.3_Intron|CPPED1_uc002dbz.3_5'Flank	NM_018340	NP_060810			calcineurin-like phosphoesterase domain								hydrolase activity|metal ion binding				0																		---	---	---	---
CPPED1	55313	broad.mit.edu	37	16	12810969	12810969	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12810969delA	uc002dca.3	-						CPPED1_uc002dcb.3_Intron	NM_018340	NP_060810			calcineurin-like phosphoesterase domain								hydrolase activity|metal ion binding				0																		---	---	---	---
CPPED1	55313	broad.mit.edu	37	16	12825719	12825719	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12825719delA	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	12952212	12952212	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12952212delA								CPPED1 (54468 upstream) : SHISA9 (43265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	12954678	12954678	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12954678delA								CPPED1 (56934 upstream) : SHISA9 (40799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	12960322	12960322	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12960322delT								CPPED1 (62578 upstream) : SHISA9 (35155 downstream)																																			---	---	---	---
SHISA9	729993	broad.mit.edu	37	16	13000996	13000997	+	Intron	INS	-	TCCC	TCCC	rs147623720	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13000996_13000997insTCCC	uc010uyy.1	+						SHISA9_uc002dcd.2_Intron	NM_001145204	NP_001138676			shisa homolog 9 isoform 1						regulation of short-term neuronal synaptic plasticity	cell junction|dendritic spine membrane|ionotropic glutamate receptor complex|synapse					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	13698102	13698102	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13698102delT								SHISA9 (363830 upstream) : ERCC4 (315912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13858455	13858455	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13858455delA								SHISA9 (524183 upstream) : ERCC4 (155559 downstream)																																			---	---	---	---
ERCC4	2072	broad.mit.edu	37	16	14016110	14016110	+	Intron	DEL	T	-	-	rs113434368		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14016110delT	uc002dce.2	+						ERCC4_uc010bva.2_Intron	NM_005236	NP_005227			excision repair cross-complementing rodent						double-strand break repair via homologous recombination|meiotic mismatch repair|negative regulation of telomere maintenance|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|nucleotide-excision repair, DNA incision, 5'-to lesion|resolution of meiotic recombination intermediates|telomere maintenance via telomere shortening|transcription-coupled nucleotide-excision repair	nuclear chromosome, telomeric region|nucleoplasm|nucleotide-excision repair factor 1 complex	damaged DNA binding|protein C-terminus binding|protein N-terminus binding|single-stranded DNA binding|single-stranded DNA specific endodeoxyribonuclease activity			lung(4)|ovary(3)|skin(2)|pancreas(1)	10								Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
MKL2	57496	broad.mit.edu	37	16	14321156	14321159	+	Intron	DEL	AAAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14321156_14321159delAAAG	uc010uza.1	+						MKL2_uc002dcg.2_Intron|MKL2_uc002dch.2_Intron|MKL2_uc010uzb.1_Intron	NM_014048	NP_054767			megakaryoblastic leukemia 2 protein						cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	14406397	14406398	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14406397_14406398delAA								MIR365-1 (3169 upstream) : PARN (123161 downstream)																																			---	---	---	---
PARN	5073	broad.mit.edu	37	16	14578766	14578766	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14578766delA	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron	NM_002582	NP_002573			poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2																		---	---	---	---
PARN	5073	broad.mit.edu	37	16	14649646	14649646	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14649646delA	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron	NM_002582	NP_002573			poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2																		---	---	---	---
PARN	5073	broad.mit.edu	37	16	14685894	14685894	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14685894delA	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron	NM_002582	NP_002573			poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2																		---	---	---	---
PARN	5073	broad.mit.edu	37	16	14721881	14721881	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14721881delA	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573			poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2																		---	---	---	---
BFAR	51283	broad.mit.edu	37	16	14737719	14737719	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14737719delA	uc002dco.2	+						BFAR_uc002dcm.2_Intron|BFAR_uc002dcn.2_Intron|BFAR_uc002dcp.2_Intron|BFAR_uc010uzh.1_5'Flank	NM_016561	NP_057645			bifunctional apoptosis regulator						anti-apoptosis|apoptosis	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	structural molecule activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
BFAR	51283	broad.mit.edu	37	16	14738020	14738022	+	Intron	DEL	AAA	-	-	rs75303738		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14738020_14738022delAAA	uc002dco.2	+						BFAR_uc002dcm.2_Intron|BFAR_uc002dcn.2_Intron|BFAR_uc002dcp.2_Intron|BFAR_uc010uzh.1_5'Flank	NM_016561	NP_057645			bifunctional apoptosis regulator						anti-apoptosis|apoptosis	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	structural molecule activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15078734	15078734	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15078734delT	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15152150	15152150	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15152150delA	uc002ddc.2	+						NTAN1_uc002ddd.2_5'Flank|NTAN1_uc010uzo.1_5'Flank	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
C16orf45	89927	broad.mit.edu	37	16	15650036	15650036	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15650036delA	uc002ddo.2	+						C16orf45_uc002ddp.2_Intron	NM_033201	NP_149978			hypothetical protein LOC89927 isoform 1											ovary(1)	1																		---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15870226	15870226	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15870226delA	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002dea.1_Intron	NM_002474	NP_002465			smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15								T	CBFB	AML								---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15918139	15918139	+	Intron	DEL	T	-	-	rs111277027		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15918139delT	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002deb.3_Intron	NM_002474	NP_002465			smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15								T	CBFB	AML								---	---	---	---
ABCC1	4363	broad.mit.edu	37	16	16206232	16206233	+	Intron	DEL	AA	-	-	rs71837610		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16206232_16206233delAA	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron|ABCC1_uc002del.3_Intron	NM_004996	NP_004987			ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
ABCC6	368	broad.mit.edu	37	16	16314754	16314755	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16314754_16314755insA	uc002den.3	-						ABCC6_uc010bvo.2_Intron|ABCC6_uc010uzz.1_Intron	NM_001171	NP_001162			ATP-binding cassette, sub-family C, member 6						response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	16724604	16724604	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16724604delT								LOC339047 (280167 upstream) : XYLT1 (471579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	16745666	16745667	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16745666_16745667insT								LOC339047 (301229 upstream) : XYLT1 (450516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	17570121	17570122	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17570121_17570122insA								XYLT1 (5383 upstream) : NOMO2 (941061 downstream)																																	OREG0023647	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	16	17835655	17835655	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17835655delC								XYLT1 (270917 upstream) : NOMO2 (675528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	17842212	17842212	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17842212delA								XYLT1 (277474 upstream) : NOMO2 (668971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18027200	18027200	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18027200delA								XYLT1 (462462 upstream) : NOMO2 (483983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18061962	18061962	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18061962delA								XYLT1 (497224 upstream) : NOMO2 (449221 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18116018	18116019	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18116018_18116019delAA								XYLT1 (551280 upstream) : NOMO2 (395164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18303290	18303290	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18303290delT								XYLT1 (738552 upstream) : NOMO2 (207893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18327267	18327268	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18327267_18327268delTC								XYLT1 (762529 upstream) : NOMO2 (183915 downstream)																																			---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18934964	18934964	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18934964delA	uc002dfm.2	-							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																		---	---	---	---
TMC5	79838	broad.mit.edu	37	16	19455699	19455699	+	Intron	DEL	G	-	-	rs4782248	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19455699delG	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron	NM_001105248	NP_001098718			transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1																		---	---	---	---
TMC5	79838	broad.mit.edu	37	16	19488576	19488577	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19488576_19488577insA	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron|TMC5_uc002dgd.1_Intron|TMC5_uc002dge.3_Intron|TMC5_uc002dgf.3_Intron|TMC5_uc002dgg.3_Intron	NM_001105248	NP_001098718			transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1																		---	---	---	---
C16orf62	57020	broad.mit.edu	37	16	19647070	19647071	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19647070_19647071insA	uc002dgn.1	+						C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Intron	NM_020314	NP_064710			hypothetical protein LOC57020							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	20633413	20633414	+	IGR	DEL	TG	-	-	rs5816127		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20633413_20633414delTG								ACSM2B (45718 upstream) : ACSM1 (1145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	21792433	21792434	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21792433_21792434delTT	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21806320	21806320	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21806320delT	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
RRN3P1	730092	broad.mit.edu	37	16	21827717	21827717	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21827717delA	uc010vbl.1	-						uc002diq.3_Intron|RRN3P1_uc002djl.2_Intron	NR_003370				SubName: Full=Putative uncharacterized protein ENSP00000219758;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	21902237	21902238	+	Intron	DEL	AA	-	-	rs55836110		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21902237_21902238delAA	uc002djs.3	-						uc010vbo.1_Intron|uc002dju.1_5'Flank					Homo sapiens cDNA FLJ45371 fis, clone BRHIP3017855, highly  similar to Homo sapiens nuclear pore complex interacting protein (NPIP).																														---	---	---	---
UQCRC2	7385	broad.mit.edu	37	16	21974275	21974275	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21974275delA	uc002djx.2	+						UQCRC2_uc002djy.2_Intron|UQCRC2_uc010bxa.2_Intron|UQCRC2_uc002djz.1_Intron	NM_003366	NP_003357			ubiquinol-cytochrome c reductase core protein II						aerobic respiration|oxidative phosphorylation|proteolysis|respiratory electron transport chain|transport		metalloendopeptidase activity|zinc ion binding			large_intestine(2)	2				GBM - Glioblastoma multiforme(48;0.0264)														---	---	---	---
VWA3A	146177	broad.mit.edu	37	16	22112162	22112163	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22112162_22112163insA	uc010vbq.1	+						VWA3A_uc010bxc.2_Intron	NM_173615	NP_775886			von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)														---	---	---	---
LOC653786	653786	broad.mit.edu	37	16	22554944	22554944	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22554944delT	uc002dlh.3	+							NR_003676				RecName: Full=Otoancorin; Flags: Precursor;												0																		---	---	---	---
HS3ST2	9956	broad.mit.edu	37	16	22856676	22856676	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22856676delT	uc002dli.2	+						HS3ST2_uc002dlj.2_Intron	NM_006043	NP_006034			heparan sulfate D-glucosaminyl							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(48;0.0299)														---	---	---	---
HS3ST2	9956	broad.mit.edu	37	16	22888454	22888454	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22888454delA	uc002dli.2	+						HS3ST2_uc002dlj.2_Intron	NM_006043	NP_006034			heparan sulfate D-glucosaminyl							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(48;0.0299)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	22940458	22940458	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22940458delT								HS3ST2 (12801 upstream) : USP31 (132271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	23065618	23065618	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23065618delA								HS3ST2 (137961 upstream) : USP31 (7111 downstream)																																			---	---	---	---
USP31	57478	broad.mit.edu	37	16	23128247	23128247	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23128247delC	uc002dll.2	-							NM_020718	NP_065769			ubiquitin specific peptidase 31						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(3)|lung(3)|breast(2)|pancreas(1)|skin(1)	10				GBM - Glioblastoma multiforme(48;0.0187)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	23259263	23259264	+	IGR	DEL	AA	-	-	rs79780436		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23259263_23259264delAA								SCNN1G (31063 upstream) : SCNN1B (54327 downstream)																																			---	---	---	---
GGA2	23062	broad.mit.edu	37	16	23486467	23486467	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23486467delA	uc002dlq.2	-						GGA2_uc010bxo.1_Intron	NM_015044	NP_055859			ADP-ribosylation factor binding protein 2						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|clathrin-coated vesicle|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.0386)														---	---	---	---
GGA2	23062	broad.mit.edu	37	16	23489547	23489547	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23489547delA	uc002dlq.2	-						GGA2_uc010bxo.1_Intron	NM_015044	NP_055859			ADP-ribosylation factor binding protein 2						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|clathrin-coated vesicle|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.0386)														---	---	---	---
PALB2	79728	broad.mit.edu	37	16	23649285	23649285	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23649285delA	uc002dlx.1	-							NM_024675	NP_078951			partner and localizer of BRCA2						double-strand break repair via homologous recombination	nucleoplasm	DNA binding|protein binding			lung(3)|breast(3)|ovary(2)|skin(1)|kidney(1)|pancreas(1)	11				GBM - Glioblastoma multiforme(48;0.0167)				F|N|Mis			Wilms tumor|medulloblastoma|AML ,breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia_type_N|Fanconi_Anemia|PALB2-associated_Familial_Breast_and_Pancreatic_Cancer|Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	16	23758348	23758348	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23758348delT								ERN2 (33527 upstream) : CHP2 (7600 downstream)																																			---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	23871561	23871561	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23871561delA	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	24013648	24013649	+	Intron	DEL	GC	-	-	rs4040053		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24013648_24013649delGC	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	24745518	24745518	+	Intron	DEL	A	-	-	rs113209421		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24745518delA	uc002dmm.2	+							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)														---	---	---	---
TNRC6A	27327	broad.mit.edu	37	16	24777049	24777049	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24777049delA	uc002dmm.2	+							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)														---	---	---	---
ZKSCAN2	342357	broad.mit.edu	37	16	25250585	25250586	+	3'UTR	DEL	AA	-	-	rs147070578		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25250585_25250586delAA	uc002dod.3	-	7					ZKSCAN2_uc010vcl.1_3'UTR	NM_001012981	NP_001012999			zinc finger with KRAB and SCAN domains 2						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|breast(1)	4				GBM - Glioblastoma multiforme(48;0.0378)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	25503288	25503288	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25503288delT								ZKSCAN2 (234433 upstream) : HS3ST4 (200059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25512643	25512644	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25512643_25512644insA								ZKSCAN2 (243788 upstream) : HS3ST4 (190703 downstream)																																			---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	26113479	26113479	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26113479delA	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	26242241	26242242	+	IGR	INS	-	CA	CA	rs139621728	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26242241_26242242insCA								HS3ST4 (93233 upstream) : C16orf82 (835977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26496616	26496619	+	IGR	DEL	GTGT	-	-	rs67638050		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26496616_26496619delGTGT								HS3ST4 (347608 upstream) : C16orf82 (581600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26520547	26520547	+	IGR	DEL	A	-	-	rs35304576		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26520547delA								HS3ST4 (371539 upstream) : C16orf82 (557672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27006684	27006684	+	IGR	DEL	A	-	-	rs74826171		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27006684delA								HS3ST4 (857676 upstream) : C16orf82 (71535 downstream)																																			---	---	---	---
GTF3C1	2975	broad.mit.edu	37	16	27509762	27509762	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27509762delT	uc002dov.1	-						GTF3C1_uc002dou.2_Intron	NM_001520	NP_001511			general transcription factor IIIC, polypeptide							transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5																		---	---	---	---
KIAA0556	23247	broad.mit.edu	37	16	27785719	27785719	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27785719delA	uc002dow.2	+							NM_015202	NP_056017			hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8																		---	---	---	---
GSG1L	146395	broad.mit.edu	37	16	27818884	27818884	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27818884delA	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																		---	---	---	---
XPO6	23214	broad.mit.edu	37	16	28120623	28120624	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28120623_28120624delTT	uc002dpa.1	-						XPO6_uc002dpb.1_Intron|XPO6_uc010vcp.1_Intron	NM_015171	NP_055986			exportin 6						protein export from nucleus		protein binding|protein transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
XPO6	23214	broad.mit.edu	37	16	28194265	28194265	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28194265delA	uc002dpa.1	-						XPO6_uc002dpb.1_Intron|XPO6_uc010vcp.1_Intron	NM_015171	NP_055986			exportin 6						protein export from nucleus		protein binding|protein transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	28271405	28271406	+	IGR	INS	-	TGTG	TGTG	rs138931229	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28271405_28271406insTGTG								XPO6 (48215 upstream) : SBK1 (32434 downstream)																																			---	---	---	---
RABEP2	79874	broad.mit.edu	37	16	28924713	28924713	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28924713delT	uc002drq.2	-						uc010vct.1_Intron|RABEP2_uc010vdf.1_Intron|RABEP2_uc010byn.2_Intron|RABEP2_uc002drr.2_Intron	NM_024816	NP_079092			rabaptin, RAB GTPase binding effector protein 2						endocytosis|protein transport	early endosome	growth factor activity|GTPase activator activity			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	29058446	29058446	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29058446delT	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	29181432	29181434	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29181432_29181434delTTT	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
SULT1A3	6818	broad.mit.edu	37	16	29472616	29472617	+	Intron	DEL	AA	-	-	rs149925755		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29472616_29472617delAA	uc002dsu.2	+						LOC440354_uc002dsp.3_Intron|SULT1A3_uc002dsw.2_Intron|SULT1A3_uc002dsz.2_Intron|SULT1A3_uc002dta.2_Intron|SULT1A3_uc010vdp.1_Intron|SULT1A3_uc002dtb.2_Intron|SULT1A3_uc010byw.2_5'Flank	NM_177552	NP_808220			sulfotransferase family, cytosolic, 1A,						3'-phosphoadenosine 5'-phosphosulfate metabolic process|catecholamine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity				0																		---	---	---	---
INO80E	283899	broad.mit.edu	37	16	30016653	30016653	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30016653delC	uc002dvg.1	+	7	726	c.625delC	c.(625-627)CCCfs	p.P209fs	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|INO80E_uc002dvh.1_RNA|INO80E_uc002dvi.1_3'UTR|INO80E_uc002dvj.1_RNA|INO80E_uc002dvk.1_Frame_Shift_Del_p.P170fs	NM_173618	NP_775889	Q8NBZ0	IN80E_HUMAN	INO80 complex subunit E	209	Pro-rich.				DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex				skin(1)	1																		---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	30056578	30056579	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30056578_30056579delGT	uc010bzb.1	-						uc002dtf.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	30082576	30082576	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30082576delT	uc010bzb.1	-						uc002dtf.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
TBC1D10B	26000	broad.mit.edu	37	16	30372304	30372304	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30372304delA	uc002dxu.2	-						TBC1D10B_uc002dxt.2_5'Flank	NM_015527	NP_056342			TBC1 domain family, member 10B							cytoplasm	Rab GTPase activator activity				0			Colorectal(24;0.193)															---	---	---	---
Unknown	0	broad.mit.edu	37	16	30472586	30472587	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30472586_30472587delAA								SEPHS2 (15362 upstream) : ITGAL (11396 downstream)																																			---	---	---	---
BCL7C	9274	broad.mit.edu	37	16	30854889	30854889	+	Intron	DEL	A	-	-	rs76501822		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30854889delA	uc002dzt.1	-							NM_004765	NP_004756			B-cell CLL/lymphoma 7C						apoptosis						0			Colorectal(24;0.198)															---	---	---	---
ITGAD	3681	broad.mit.edu	37	16	31428069	31428070	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31428069_31428070delCT	uc002ebv.1	+						ITGAD_uc010cap.1_Intron	NM_005353	NP_005344			integrin, alpha D precursor						cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1																		---	---	---	---
C16orf58	64755	broad.mit.edu	37	16	31503277	31503277	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31503277delC	uc002eci.1	-						C16orf58_uc002ecg.2_5'Flank|C16orf58_uc002ech.1_Intron	NM_022744	NP_073581			hypothetical protein LOC64755							integral to membrane				ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	32198504	32198504	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32198504delA	uc010vfv.1	-											Homo sapiens cDNA FLJ60890 complete cds, moderately similar to HECT domain and RCC1-like domain-containing protein 2.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	32410498	32410500	+	IGR	DEL	TTG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32410498_32410500delTTG								HERC2P4 (246624 upstream) : TP53TG3B (274341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32556942	32556942	+	IGR	DEL	A	-	-	rs76430736		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32556942delA								HERC2P4 (393068 upstream) : TP53TG3B (127899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32559919	32559920	+	IGR	INS	-	TT	TT	rs151318257		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32559919_32559920insTT								HERC2P4 (396045 upstream) : TP53TG3B (124921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32833684	32833685	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32833684_32833685delTC								TP53TG3B (144806 upstream) : SLC6A10P (55112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33340564	33340565	+	IGR	INS	-	TCA	TCA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33340564_33340565insTCA								SLC6A10P (444101 upstream) : MIR1826 (624943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33992107	33992108	+	IGR	DEL	TG	-	-	rs146428484		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33992107_33992108delTG								MIR1826 (26515 upstream) : UBE2MP1 (411694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34195874	34195876	+	IGR	DEL	AAT	-	-	rs149318354		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34195874_34195876delAAT								MIR1826 (230282 upstream) : UBE2MP1 (207926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34359802	34359803	+	IGR	DEL	AA	-	-	rs78630488		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34359802_34359803delAA								MIR1826 (394210 upstream) : UBE2MP1 (43999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34633095	34633095	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34633095delA								LOC283914 (7011 upstream) : LOC146481 (78690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	35002521	35002521	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35002521delT								LOC146481 (287554 upstream) : None (None downstream)																																			---	---	---	---
MYLK3	91807	broad.mit.edu	37	16	46774137	46774137	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46774137delC	uc002eei.3	-						MYLK3_uc010vge.1_Intron|MYLK3_uc002eej.1_5'Flank	NM_182493	NP_872299			myosin light chain kinase 3						cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis	cytosol	ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1)	7		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)																---	---	---	---
GPT2	84706	broad.mit.edu	37	16	46930365	46930365	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46930365delT	uc002eel.2	+						GPT2_uc002eem.2_Intron	NM_133443	NP_597700			glutamic pyruvate transaminase 2 isoform 1						2-oxoglutarate metabolic process|cellular amino acid biosynthetic process|L-alanine metabolic process	mitochondrial matrix	L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
DNAJA2	10294	broad.mit.edu	37	16	46993094	46993094	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46993094delT	uc002eeo.2	-						DNAJA2_uc002eep.2_Intron	NM_005880	NP_005871			DnaJ subfamily A member 2						positive regulation of cell proliferation|protein folding|response to heat	membrane	ATP binding|heat shock protein binding|metal ion binding|unfolded protein binding			lung(1)	1		all_cancers(37;0.00125)|all_lung(18;0.00338)|all_epithelial(9;0.00358)|Lung NSC(13;0.0309)|Breast(268;0.116)																---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47292700	47292700	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47292700delA	uc002eet.2	-						ITFG1_uc010vgg.1_Intron|ITFG1_uc010vgh.1_Intron	NM_030790	NP_110417			integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)																---	---	---	---
PHKB	5257	broad.mit.edu	37	16	47709431	47709436	+	Intron	DEL	CTCTCT	-	-	rs58621191		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47709431_47709436delCTCTCT	uc002eev.3	+						PHKB_uc002eeu.3_Intron|PHKB_uc002eew.3_Intron	NM_000293	NP_000284			phosphorylase kinase, beta isoform a						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	48200422	48200423	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48200422_48200423delTT								ABCC12 (10493 upstream) : ABCC11 (399 downstream)																																			---	---	---	---
SIAH1	6477	broad.mit.edu	37	16	48414375	48414375	+	Intron	DEL	A	-	-	rs78055790		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48414375delA	uc002efo.1	-						SIAH1_uc002efl.2_Intron	NM_003031	NP_003022			seven in absentia homolog 1 isoform a						axon guidance|cell cycle|neuron apoptosis|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	beta-catenin destruction complex|cytosol|nucleus	protein C-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)																---	---	---	---
N4BP1	9683	broad.mit.edu	37	16	48579939	48579939	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48579939delA	uc002efp.2	-							NM_153029	NP_694574			Nedd4 binding protein 1						negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination	nucleolus|PML body					0		all_cancers(37;0.179)|all_lung(18;0.11)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	49519873	49519874	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49519873_49519874delTC								C16orf78 (86556 upstream) : ZNF423 (4648 downstream)																																			---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49530372	49530373	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49530372_49530373delTC	uc002efs.2	-						ZNF423_uc010vgn.1_Intron	NM_015069	NP_055884			zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49583791	49583791	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49583791delT	uc002efs.2	-						ZNF423_uc010vgn.1_Intron	NM_015069	NP_055884			zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49654044	49654045	+	Intron	DEL	AC	-	-	rs68006357		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49654044_49654045delAC	uc002efs.2	-						ZNF423_uc010vgn.1_Intron	NM_015069	NP_055884			zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49738649	49738650	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49738649_49738650delCA	uc002efs.2	-							NM_015069	NP_055884			zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49834155	49834155	+	Intron	DEL	A	-	-	rs111441917		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49834155delA	uc002efs.2	-							NM_015069	NP_055884			zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
HEATR3	55027	broad.mit.edu	37	16	50128481	50128481	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50128481delG	uc002efw.2	+						HEATR3_uc002efx.2_Intron	NM_182922	NP_891552			HEAT repeat containing 3								binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	50270784	50270784	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50270784delT								PAPD5 (1567 upstream) : ADCY7 (29678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	50497090	50497090	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50497090delA								BRD7 (94261 upstream) : NKD1 (85151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51257230	51257231	+	IGR	INS	-	AA	AA	rs145358792		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51257230_51257231insAA								SALL1 (72047 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51462999	51462999	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51462999delT								SALL1 (277816 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51509017	51509018	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51509017_51509018insT								SALL1 (323834 upstream) : TOX3 (962900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51574616	51574616	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51574616delT								SALL1 (389433 upstream) : TOX3 (897302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51705813	51705813	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51705813delA								SALL1 (520630 upstream) : TOX3 (766105 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51837887	51837887	+	IGR	DEL	T	-	-	rs72186409		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51837887delT								SALL1 (652704 upstream) : TOX3 (634031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	52178987	52178987	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52178987delT								SALL1 (993804 upstream) : TOX3 (292931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	52233367	52233368	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52233367_52233368delCA								None (None upstream) : TOX3 (238550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	52626579	52626579	+	Intron	DEL	T	-	-	rs5816864		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52626579delT	uc002egx.2	-											Homo sapiens cDNA clone IMAGE:5172237.																														---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53332233	53332235	+	Intron	DEL	AAA	-	-	rs77259524		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53332233_53332235delAAA	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc010cbw.2_Intron	NM_025134	NP_079410			chromodomain helicase DNA binding protein 9						cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)																---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53348351	53348351	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53348351delA	uc002ehb.2	+	34	7449	c.7285delA	c.(7285-7287)AAAfs	p.K2429fs	CHD9_uc002egy.2_Frame_Shift_Del_p.K2413fs|CHD9_uc002ehc.2_Frame_Shift_Del_p.K2414fs|CHD9_uc002ehf.2_Frame_Shift_Del_p.K1527fs|CHD9_uc010cbw.2_Frame_Shift_Del_p.K495fs|CHD9_uc002ehg.1_Frame_Shift_Del_p.K436fs	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2429	A.T hook-like.|Binds A/T-rich DNA.				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-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53368579delA								CHD9 (7166 upstream) : RBL2 (99772 downstream)																																			---	---	---	---
FTO	79068	broad.mit.edu	37	16	53802820	53802820	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53802820delT	uc002ehr.2	+						FTO_uc010vha.1_Intron	NM_001080432	NP_001073901			fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	54378609	54378609	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54378609delC								IRX3 (58231 upstream) : IRX5 (586502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54423653	54423653	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54423653delT								IRX3 (103275 upstream) : IRX5 (541458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55081196	55081197	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55081196_55081197delTG								IRX5 (112803 upstream) : IRX6 (277274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55095586	55095586	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55095586delA								IRX5 (127193 upstream) : IRX6 (262885 downstream)																																			---	---	---	---
MMP2	4313	broad.mit.edu	37	16	55538873	55538873	+	Intron	DEL	T	-	-	rs34621950		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55538873delT	uc002ehz.3	+						MMP2_uc010vhd.1_Intron|MMP2_uc010ccc.2_Intron|MMP2_uc002eia.3_Intron	NM_004530	NP_004521			matrix metalloproteinase 2 isoform a						angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			large_intestine(3)|ovary(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	11		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)													---	---	---	---
CES7	221223	broad.mit.edu	37	16	55962155	55962156	+	5'Flank	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55962155_55962156delAA	uc002eir.2	-						CES7_uc002eiq.2_5'Flank					SubName: Full=Putative uncharacterized protein ENSP00000383269; Flags: Fragment;							extracellular region	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	56068667	56068668	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56068667_56068668delCT								CES7 (109295 upstream) : LOC283856 (58231 downstream)																																			---	---	---	---
GNAO1	2775	broad.mit.edu	37	16	56232382	56232382	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56232382delC	uc002eit.3	+						GNAO1_uc002eiu.3_Intron	NM_138736	NP_620073			guanine nucleotide binding protein, alpha						dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			lung(1)|breast(1)	2		all_neural(199;0.159)																---	---	---	---
GNAO1	2775	broad.mit.edu	37	16	56305372	56305372	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56305372delT	uc002eit.3	+						GNAO1_uc002eiu.3_Intron	NM_138736	NP_620073			guanine nucleotide binding protein, alpha						dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			lung(1)|breast(1)	2		all_neural(199;0.159)																---	---	---	---
AMFR	267	broad.mit.edu	37	16	56445588	56445588	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56445588delA	uc002eiy.2	-							NM_001144	NP_001135			autocrine motility factor receptor						endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|protein oligomerization|protein polyubiquitination	integral to endoplasmic reticulum membrane|integral to membrane of membrane fraction	protein binding|protein binding|receptor activity|ubiquitin-protein ligase activity|zinc ion binding			breast(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	56957326	56957328	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56957326_56957328delTTT								SLC12A3 (7566 upstream) : HERPUD1 (8420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	57120721	57120721	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57120721delA								NLRC5 (3285 upstream) : CPNE2 (5789 downstream)																																			---	---	---	---
RSPRY1	89970	broad.mit.edu	37	16	57250633	57250633	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57250633delA	uc002elb.2	+						RSPRY1_uc002elc.2_Intron|RSPRY1_uc002eld.2_Intron	NM_133368	NP_588609			ring finger and SPRY domain containing 1							extracellular region	zinc ion binding			ovary(1)	1																		---	---	---	---
GPR56	9289	broad.mit.edu	37	16	57694364	57694367	+	Intron	DEL	CTGT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57694364_57694367delCTGT	uc002emb.2	+						GPR56_uc002elz.1_Intron|GPR56_uc002ema.1_Intron|GPR56_uc002emc.2_Intron|GPR56_uc002emf.2_Intron|GPR56_uc010vhs.1_Intron|GPR56_uc002emd.2_Intron|GPR56_uc002eme.2_Intron|GPR56_uc010vht.1_Intron|GPR56_uc002emg.3_Intron|GPR56_uc010vhu.1_Intron	NM_005682	NP_005673			G protein-coupled receptor 56 isoform a						brain development|cell adhesion|cell-cell signaling|neuropeptide signaling pathway	integral to plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
TEPP	374739	broad.mit.edu	37	16	58012445	58012445	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58012445delA	uc002emw.3	+						TEPP_uc002emv.3_Intron	NM_199456	NP_955535			testis/prostate/placenta-expressed protein							extracellular region				kidney(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
ZNF319	57567	broad.mit.edu	37	16	58031628	58031628	+	Frame_Shift_Del	DEL	G	-	-	rs141462652		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58031628delG	uc002emx.1	-	2	1165	c.542delC	c.(541-543)CCGfs	p.P181fs		NM_020807	NP_065858	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	181					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
C16orf57	79650	broad.mit.edu	37	16	58048101	58048101	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58048101delT	uc002emz.2	+						C16orf57_uc010vib.1_Intron	NM_024598	NP_078874			hypothetical protein LOC79650												0																		---	---	---	---
NDRG4	65009	broad.mit.edu	37	16	58495025	58495025	+	5'Flank	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58495025delG	uc002enm.2	+						NDRG4_uc002enk.2_5'Flank	NM_001130487	NP_001123959			NDRG family member 4 isoform 2						cell differentiation|cell growth|multicellular organismal development|response to stress	cytoplasm				skin(1)	1																		---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58643276	58643276	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58643276delA	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc002enx.2_Intron|CNOT1_uc002enz.1_Intron	NM_016284	NP_057368			CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	58928188	58928188	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58928188delT								GOT2 (159942 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	58957594	58957595	+	IGR	INS	-	TCTCAGGGG	TCTCAGGGG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58957594_58957595insTCTCAGGGG								GOT2 (189348 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59295534	59295534	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59295534delT								GOT2 (527288 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59401455	59401455	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59401455delA								GOT2 (633209 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60038896	60038897	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60038896_60038897delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60195445	60195445	+	IGR	DEL	A	-	-	rs74349778		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60195445delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60739015	60739015	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60739015delA								None (None upstream) : CDH8 (948220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60835207	60835207	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60835207delA								None (None upstream) : CDH8 (852028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61274339	61274339	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61274339delA								None (None upstream) : CDH8 (412896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61450539	61450539	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61450539delT								None (None upstream) : CDH8 (236696 downstream)																																			---	---	---	---
CDH8	1006	broad.mit.edu	37	16	61835011	61835011	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61835011delA	uc002eog.1	-						CDH8_uc002eoh.2_Intron	NM_001796	NP_001787			cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	62599430	62599431	+	IGR	INS	-	AC	AC	rs149691824	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62599430_62599431insAC								CDH8 (529394 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	62813661	62813662	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62813661_62813662insT								CDH8 (743625 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63419357	63419357	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63419357delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63469150	63469150	+	IGR	DEL	A	-	-	rs75100638		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63469150delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63651737	63651739	+	IGR	DEL	CTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63651737_63651739delCTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64194200	64194201	+	IGR	DEL	AA	-	-	rs11322316		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64194200_64194201delAA								None (None upstream) : CDH11 (786484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64858406	64858406	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64858406delT								None (None upstream) : CDH11 (122279 downstream)																																			---	---	---	---
CDH11	1009	broad.mit.edu	37	16	65035704	65035704	+	Intron	DEL	A	-	-	rs79156754		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65035704delA	uc002eoi.2	-						CDH11_uc010cdn.2_Intron|CDH11_uc002eoj.2_Intron|CDH11_uc010vin.1_Intron|CDH11_uc010vio.1_Intron	NM_001797	NP_001788			cadherin 11, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)				T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			---	---	---	---
CDH11	1009	broad.mit.edu	37	16	65035710	65035715	+	Intron	DEL	AAAAAC	-	-	rs59669670	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65035710_65035715delAAAAAC	uc002eoi.2	-						CDH11_uc010cdn.2_Intron|CDH11_uc002eoj.2_Intron|CDH11_uc010vin.1_Intron|CDH11_uc010vio.1_Intron	NM_001797	NP_001788			cadherin 11, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)				T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			---	---	---	---
LOC283867	283867	broad.mit.edu	37	16	65342534	65342534	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65342534delT	uc010cdo.1	-						LOC283867_uc010cdp.1_Intron|LOC283867_uc002eol.1_Intron					Homo sapiens cDNA clone IMAGE:5276218.												0				OV - Ovarian serous cystadenocarcinoma(108;0.17)														---	---	---	---
TK2	7084	broad.mit.edu	37	16	66550095	66550095	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66550095delG	uc002eos.2	-						TK2_uc010vip.1_Intron|TK2_uc002eor.2_Intron|TK2_uc010cdq.2_Intron|TK2_uc010cdr.2_Intron|TK2_uc010viq.1_Intron|TK2_uc010vir.1_Intron	NM_004614	NP_004605			thymidine kinase 2, mitochondrial						pyrimidine base metabolic process|pyrimidine nucleoside salvage	mitochondrial matrix	ATP binding|phosphotransferase activity, alcohol group as acceptor|thymidine kinase activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0736)|Epithelial(162;0.237)												OREG0023857	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CMTM4	146223	broad.mit.edu	37	16	66724861	66724861	+	Intron	DEL	A	-	-	rs113936003		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66724861delA	uc002epz.2	-						CMTM4_uc002eqa.2_Intron	NM_178818	NP_848933			chemokine-like factor superfamily 4 isoform 1						chemotaxis	extracellular space|integral to membrane	cytokine activity			pancreas(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)														---	---	---	---
CCDC79	283847	broad.mit.edu	37	16	66811036	66811036	+	Intron	DEL	A	-	-	rs71671589		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66811036delA	uc010viv.1	-						CCDC79_uc002eqc.1_Intron|CCDC79_uc002eqd.1_Intron	NM_001136505	NP_001129977			coiled-coil domain containing 79						regulation of transcription, DNA-dependent		DNA binding				0																		---	---	---	---
NAE1	8883	broad.mit.edu	37	16	66852379	66852379	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66852379delA	uc002eqf.2	-						NAE1_uc002eqe.2_Intron|NAE1_uc002eqg.2_Intron|NAE1_uc010cdv.2_Intron|NAE1_uc010cdw.1_Intron	NM_003905	NP_003896			NEDD8 activating enzyme E1 subunit 1 isoform a						apoptosis|cell cycle|DNA replication|mitotic cell cycle DNA replication checkpoint|protein neddylation|signal transduction	cytoplasm|insoluble fraction|plasma membrane	catalytic activity|protein heterodimerization activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)													---	---	---	---
NAE1	8883	broad.mit.edu	37	16	66852580	66852580	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66852580delA	uc002eqf.2	-						NAE1_uc002eqe.2_Intron|NAE1_uc002eqg.2_Intron|NAE1_uc010cdv.2_Intron|NAE1_uc010cdw.1_Intron	NM_003905	NP_003896			NEDD8 activating enzyme E1 subunit 1 isoform a						apoptosis|cell cycle|DNA replication|mitotic cell cycle DNA replication checkpoint|protein neddylation|signal transduction	cytoplasm|insoluble fraction|plasma membrane	catalytic activity|protein heterodimerization activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)													---	---	---	---
NAE1	8883	broad.mit.edu	37	16	66855469	66855469	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66855469delA	uc002eqf.2	-						NAE1_uc002eqe.2_Intron|NAE1_uc002eqg.2_Intron|NAE1_uc010cdv.2_Intron|NAE1_uc010cdw.1_Intron	NM_003905	NP_003896			NEDD8 activating enzyme E1 subunit 1 isoform a						apoptosis|cell cycle|DNA replication|mitotic cell cycle DNA replication checkpoint|protein neddylation|signal transduction	cytoplasm|insoluble fraction|plasma membrane	catalytic activity|protein heterodimerization activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	66923703	66923704	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66923703_66923704delAA								PDP2 (1848 upstream) : CDH16 (18322 downstream)																																			---	---	---	---
CES8	283848	broad.mit.edu	37	16	67023015	67023015	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67023015delT	uc002eqv.2	+						CES8_uc010vix.1_Intron	NM_173815	NP_776176			carboxylesterase 8 (putative)							extracellular region	carboxylesterase activity				0																		---	---	---	---
KCTD19	146212	broad.mit.edu	37	16	67327340	67327340	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67327340delG	uc002esu.2	-						KCTD19_uc002est.2_Intron|KCTD19_uc010vjj.1_Intron	NM_001100915	NP_001094385			potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)														---	---	---	---
ATP6V0D1	9114	broad.mit.edu	37	16	67497479	67497479	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67497479delA	uc002ete.1	-						ATP6V0D1_uc010vjo.1_Intron	NM_004691	NP_004682			ATPase, H+ transporting, lysosomal, V0 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex					0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)														---	---	---	---
RLTPR	146206	broad.mit.edu	37	16	67683114	67683114	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67683114delC	uc002etn.2	+						RLTPR_uc010cel.1_Intron|RLTPR_uc010vjr.1_Intron	NM_001013838	NP_001013860			RGD motif, leucine rich repeats, tropomodulin											breast(1)	1		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)														---	---	---	---
GFOD2	81577	broad.mit.edu	37	16	67736375	67736376	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67736375_67736376delAA	uc002eub.2	-						GFOD2_uc002euc.2_Intron|GFOD2_uc010cen.2_Intron	NM_030819	NP_110446			glucose-fructose oxidoreductase domain							proteinaceous extracellular matrix	binding|oxidoreductase activity			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0151)|Epithelial(162;0.0505)|all cancers(182;0.242)														---	---	---	---
RANBP10	57610	broad.mit.edu	37	16	67772032	67772033	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67772032_67772033insT	uc002eud.2	-						RANBP10_uc010ceo.2_Intron|RANBP10_uc010vju.1_Intron|RANBP10_uc010vjv.1_Intron|RANBP10_uc010vjx.1_Intron|RANBP10_uc010vjy.1_Intron	NM_020850	NP_065901			RAN binding protein 10											ovary(1)	1		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)														---	---	---	---
TSNAXIP1	55815	broad.mit.edu	37	16	67854645	67854646	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67854645_67854646delAA	uc002euj.2	+						TSNAXIP1_uc010cep.2_Intron|TSNAXIP1_uc010vjz.1_Intron|TSNAXIP1_uc002euf.3_Intron|TSNAXIP1_uc010vka.1_Intron|TSNAXIP1_uc010vkb.1_Intron|TSNAXIP1_uc002eug.3_Intron|TSNAXIP1_uc002euh.3_Intron|TSNAXIP1_uc002eui.3_Intron|TSNAXIP1_uc002euk.2_5'Flank	NM_018430	NP_060900			translin-associated factor X interacting protein						cell differentiation|multicellular organismal development|spermatogenesis	perinuclear region of cytoplasm					0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)														---	---	---	---
DUS2L	54920	broad.mit.edu	37	16	68094750	68094751	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68094750_68094751insA	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	68138557	68138559	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68138557_68138559delTTT	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)														---	---	---	---
NFATC3	4775	broad.mit.edu	37	16	68248146	68248146	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68248146delA	uc002evo.1	+						NFATC3_uc010vkm.1_Intron|NFATC3_uc010vkn.1_Intron|NFATC3_uc010vkp.1_Intron|NFATC3_uc010vkq.1_Intron|NFATC3_uc002evm.1_Intron|NFATC3_uc002evn.1_Intron|NFATC3_uc010vks.1_Intron|NFATC3_uc010vkt.1_Intron|NFATC3_uc010vkv.1_Intron|NFATC3_uc010vkw.1_Intron|NFATC3_uc010vky.1_Intron|NFATC3_uc010vkz.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)														---	---	---	---
SMPD3	55512	broad.mit.edu	37	16	68430444	68430444	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68430444delC	uc002ewa.2	-							NM_018667	NP_061137			neutral sphingomyelin phosphodiesterase 3						cell cycle|multicellular organismal development|sphingomyelin catabolic process	Golgi membrane|integral to membrane|plasma membrane	metal ion binding|sphingomyelin phosphodiesterase activity			skin(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)											OREG0023901	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SMPD3	55512	broad.mit.edu	37	16	68455339	68455339	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68455339delG	uc002ewa.2	-							NM_018667	NP_061137			neutral sphingomyelin phosphodiesterase 3						cell cycle|multicellular organismal development|sphingomyelin catabolic process	Golgi membrane|integral to membrane|plasma membrane	metal ion binding|sphingomyelin phosphodiesterase activity			skin(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	68611548	68611548	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68611548delT								ZFP90 (10510 upstream) : CDH3 (66603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	68646916	68646916	+	IGR	DEL	A	-	-	rs112136679		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68646916delA								ZFP90 (45878 upstream) : CDH3 (31235 downstream)														p.?(1)																					---	---	---	---
CDH1	999	broad.mit.edu	37	16	68857140	68857141	+	Intron	INS	-	A	A	rs146046879		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68857140_68857141insA	uc002ewg.1	+						CDH1_uc010vlj.1_Intron|CDH1_uc010cfg.1_Intron	NM_004360	NP_004351			cadherin 1, type 1 preproprotein						adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response	actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm	cell adhesion molecule binding|gamma-catenin binding			breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1)	243		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)				Mis|N|F|S		lobular breast|gastric	gastric			Hereditary_Diffuse_Gastric_Cancer				---	---	---	---
CHTF8	54921	broad.mit.edu	37	16	69161828	69161829	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69161828_69161829insT	uc002ewn.1	-						CHTF8_uc002ewo.1_Intron|CHTF8_uc002ewp.1_Intron	NM_001040146	NP_001035236			chromosome transmission fidelity factor 8						cell cycle|DNA replication	nucleus	DNA binding				0																		---	---	---	---
NFAT5	10725	broad.mit.edu	37	16	69663524	69663525	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69663524_69663525delTT	uc002exm.1	+						NFAT5_uc002exh.1_Intron|NFAT5_uc002exi.2_Intron|NFAT5_uc002exj.1_Intron|NFAT5_uc002exk.1_Intron|NFAT5_uc002exl.1_Intron|NFAT5_uc002exn.1_Intron	NM_006599	NP_006590			nuclear factor of activated T-cells 5 isoform c						excretion|signal transduction|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
NFAT5	10725	broad.mit.edu	37	16	69718777	69718777	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69718777delT	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																		---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69829148	69829148	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69829148delA	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	69882354	69882354	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69882354delA	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																		---	---	---	---
DDX19A	55308	broad.mit.edu	37	16	70351678	70351678	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70351678delA	uc002eys.2	+						DDX19B_uc010vly.1_Intron|DDX19B_uc010vlv.1_Intron|DDX19B_uc010vlw.1_Intron|DDX19B_uc002eyo.2_Intron|DDX19B_uc002eyp.2_Intron|DDX19B_uc002eyq.2_Intron|DDX19B_uc002eyr.2_Intron|DDX19B_uc010vlx.1_Intron|uc002eyt.2_Intron	NM_007242	NP_009173			DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform						mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)																---	---	---	---
DDX19A	55308	broad.mit.edu	37	16	70354016	70354016	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70354016delT	uc002eys.2	+						DDX19B_uc010vly.1_Intron|DDX19B_uc010vlv.1_Intron|DDX19B_uc010vlw.1_Intron|DDX19B_uc002eyo.2_Intron|DDX19B_uc002eyp.2_Intron|DDX19B_uc002eyq.2_Intron|DDX19B_uc002eyr.2_Intron|DDX19B_uc010vlx.1_Intron|uc002eyt.2_Intron	NM_007242	NP_009173			DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform						mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)																---	---	---	---
DDX19A	55308	broad.mit.edu	37	16	70396075	70396076	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70396075_70396076delAA	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_Intron	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)																---	---	---	---
DDX19A	55308	broad.mit.edu	37	16	70399236	70399236	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70399236delA	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_Intron	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)																---	---	---	---
ST3GAL2	6483	broad.mit.edu	37	16	70417451	70417451	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70417451delA	uc002eyw.2	-						ST3GAL2_uc002eyx.2_Intron	NM_006927	NP_008858			ST3 beta-galactoside alpha-2,3-sialyltransferase						amino sugar metabolic process	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity			ovary(1)	1		Ovarian(137;0.0694)																---	---	---	---
ST3GAL2	6483	broad.mit.edu	37	16	70437899	70437899	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70437899delA	uc002eyx.2	-							NM_006927	NP_008858			ST3 beta-galactoside alpha-2,3-sialyltransferase						amino sugar metabolic process	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity			ovary(1)	1		Ovarian(137;0.0694)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	70618611	70618611	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70618611delT								SF3B3 (7041 upstream) : IL34 (61857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	70638889	70638889	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70638889delG								SF3B3 (27319 upstream) : IL34 (41579 downstream)																																			---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	71249474	71249474	+	Intron	DEL	A	-	-	rs66570981		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71249474delA	uc002ezr.2	-						HYDIN_uc002ezv.2_Intron|HYDIN_uc010vmc.1_Intron|HYDIN_uc010vmd.1_Intron|HYDIN_uc002ezw.3_Intron	NM_032821	NP_116210			hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	72288153	72288153	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72288153delT								PMFBP1 (81804 upstream) : ZFHX3 (528635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	72501281	72501281	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72501281delT	uc002fci.1	+											Homo sapiens cDNA FLJ38299 fis, clone FCBBF3017255.																														---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72839798	72839798	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72839798delT	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	73104610	73104611	+	IGR	DEL	TC	-	-	rs34143411		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73104610_73104611delTC								ZFHX3 (11373 upstream) : HTA (21637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73168404	73168405	+	IGR	DEL	TT	-	-	rs111533494		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73168404_73168405delTT								HTA (40734 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73213867	73213867	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73213867delA								HTA (86197 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73346291	73346291	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73346291delA								HTA (218621 upstream) : PSMD7 (984390 downstream)																																			---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74526264	74526264	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74526264delA	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139			golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2																		---	---	---	---
MLKL	197259	broad.mit.edu	37	16	74721733	74721733	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74721733delT	uc002fdb.2	-						MLKL_uc002fdc.2_Intron	NM_152649	NP_689862			mixed lineage kinase domain-like isoform 1								ATP binding|protein binding|protein kinase activity			stomach(2)	2																		---	---	---	---
FA2H	79152	broad.mit.edu	37	16	74801202	74801203	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74801202_74801203delAA	uc002fde.1	-						FA2H_uc010vmy.1_Intron	NM_024306	NP_077282			fatty acid 2-hydroxylase						cell death|electron transport chain|fatty acid biosynthetic process|sphingolipid metabolic process|transport	endoplasmic reticulum membrane|integral to membrane|microsome	heme binding|oxidoreductase activity				0																		---	---	---	---
ZNRF1	84937	broad.mit.edu	37	16	75082906	75082906	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75082906delT	uc002fdk.2	+						ZNRF1_uc010vmz.1_Intron|ZNRF1_uc002fdl.1_Intron|ZNRF1_uc010cgr.1_Intron	NM_032268	NP_115644			zinc and ring finger protein 1							cell junction|endosome|lysosome|synaptic vesicle membrane	ligase activity|protein binding|zinc ion binding				0																		---	---	---	---
LDHD	197257	broad.mit.edu	37	16	75153299	75153300	+	5'Flank	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75153299_75153300delTT	uc002fdm.2	-						LDHD_uc002fdn.2_5'Flank	NM_153486	NP_705690			D-lactate dehydrogenase isoform 1 precursor								D-lactate dehydrogenase (cytochrome) activity|flavin adenine dinucleotide binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	75165867	75165867	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75165867delA								LDHD (15202 upstream) : ZFP1 (16554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	75166724	75166725	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75166724_75166725delTT								LDHD (16059 upstream) : ZFP1 (15696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	76114308	76114309	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76114308_76114309delTG								TERF2IP (422980 upstream) : CNTNAP4 (196867 downstream)																																			---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77356311	77356311	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77356311delA	uc002ffc.3	-	14	2504	c.2085delT	c.(2083-2085)TTTfs	p.F695fs	ADAMTS18_uc010chc.1_Frame_Shift_Del_p.F283fs|ADAMTS18_uc002ffe.1_Frame_Shift_Del_p.F391fs	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	695	Cys-rich.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding	p.A696fs*18(2)		large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	77578708	77578709	+	IGR	INS	-	TC	TC	rs143488512	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77578708_77578709insTC								ADAMTS18 (109697 upstream) : NUDT7 (177702 downstream)																																			---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78435557	78435557	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78435557delT	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	78881670	78881670	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78881670delA	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	78962101	78962103	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78962101_78962103delTTT	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	79130960	79130960	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79130960delT	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	80155708	80155711	+	IGR	DEL	ATAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80155708_80155711delATAA								MAF (521086 upstream) : DYNLRB2 (419143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80317653	80317653	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80317653delA								MAF (683031 upstream) : DYNLRB2 (257201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80914963	80914964	+	Intron	INS	-	T	T	rs28385489		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80914963_80914964insT	uc002fft.1	-											Homo sapiens cDNA FLJ35683 fis, clone SPLEN2019131.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	80989559	80989559	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80989559delA								CDYL2 (151384 upstream) : C16orf61 (20142 downstream)																																			---	---	---	---
CENPN	55839	broad.mit.edu	37	16	81058306	81058306	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81058306delT	uc002ffx.2	+						CENPN_uc010vnl.1_Intron|CENPN_uc010vnm.1_Intron|CENPN_uc002ffy.3_Intron	NM_001100624	NP_001094094			centromere protein N isoform 2						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81694337	81694337	+	Intron	DEL	T	-	-	rs66465921		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81694337delT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron|CMIP_uc010vnq.1_Intron|CMIP_uc002fgr.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	82063915	82063915	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82063915delT								SDR42E1 (18822 upstream) : HSD17B2 (4943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	82274463	82274463	+	IGR	DEL	T	-	-	rs112391839		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82274463delT								MPHOSPH6 (70634 upstream) : CDH13 (386115 downstream)																																			---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82961770	82961777	+	Intron	DEL	TGTGTGTG	-	-	rs36232757		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82961770_82961777delTGTGTGTG	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83135375	83135376	+	Intron	INS	-	GA	GA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83135375_83135376insGA	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83368870	83368870	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83368870delC	uc002fgx.2	+						CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83783901	83783901	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83783901delA	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	84084994	84084994	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84084994delC								SLC38A8 (9232 upstream) : MBTPS1 (2377 downstream)																																			---	---	---	---
MBTPS1	8720	broad.mit.edu	37	16	84094451	84094451	+	Intron	DEL	T	-	-	rs71920773		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84094451delT	uc002fhi.2	-						MBTPS1_uc002fhh.2_Intron	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	84365865	84365865	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84365865delT								WFDC1 (2419 upstream) : ATP2C2 (36268 downstream)																																			---	---	---	---
CRISPLD2	83716	broad.mit.edu	37	16	84910108	84910108	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84910108delA	uc010voh.1	+						CRISPLD2_uc010vog.1_Intron|CRISPLD2_uc002fio.2_Intron|CRISPLD2_uc002fin.3_Intron	NM_031476	NP_113664			cysteine-rich secretory protein LCCL domain							extracellular region|transport vesicle					0																		---	---	---	---
ZDHHC7	55625	broad.mit.edu	37	16	85037800	85037800	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85037800delA	uc002fiq.2	-						ZDHHC7_uc010voi.1_Intron|ZDHHC7_uc002fir.1_Intron	NM_017740	NP_060210			zinc finger, DHHC-type containing 7 isoform 2							integral to membrane	acyltransferase activity|protein binding|zinc ion binding			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	85350416	85350416	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85350416delG								FAM92B (204302 upstream) : KIAA0182 (294613 downstream)																																	OREG0024001	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	16	85391553	85391553	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85391553delA								FAM92B (245439 upstream) : KIAA0182 (253476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85582785	85582785	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85582785delT								FAM92B (436671 upstream) : KIAA0182 (62244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85591176	85591177	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85591176_85591177delTT								FAM92B (445062 upstream) : KIAA0182 (53852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85867964	85867967	+	IGR	DEL	GGAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85867964_85867967delGGAA								COX4I1 (27359 upstream) : IRF8 (64807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86426367	86426367	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86426367delC								LOC732275 (47082 upstream) : FOXF1 (117766 downstream)																																			---	---	---	---
MTHFSD	64779	broad.mit.edu	37	16	86586595	86586595	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86586595delT	uc002fjn.2	-						MTHFSD_uc010voo.1_Intron|MTHFSD_uc002fjo.2_Intron|MTHFSD_uc002fjm.2_Intron|MTHFSD_uc010vop.1_Intron|MTHFSD_uc010voq.1_Intron|MTHFSD_uc010vor.1_Intron|MTHFSD_uc002fjp.2_Intron|FLJ30679_uc010vos.1_5'Flank	NM_001159377	NP_001152849			methenyltetrahydrofolate synthetase domain						folic acid-containing compound biosynthetic process		5-formyltetrahydrofolate cyclo-ligase activity|ATP binding|RNA binding				0																		---	---	---	---
ZCCHC14	23174	broad.mit.edu	37	16	87480090	87480090	+	Intron	DEL	A	-	-	rs112927994		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87480090delA	uc002fjz.1	-						ZCCHC14_uc002fka.1_Intron	NM_015144	NP_055959			zinc finger, CCHC domain containing 14						cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	87565946	87565947	+	IGR	DEL	TT	-	-	rs11335237		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87565946_87565947delTT								ZCCHC14 (40486 upstream) : JPH3 (69494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	87580295	87580295	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87580295delT								ZCCHC14 (54835 upstream) : JPH3 (55146 downstream)																																			---	---	---	---
BANP	54971	broad.mit.edu	37	16	88009223	88009224	+	Intron	DEL	CT	-	-	rs144806224		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88009223_88009224delCT	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)														---	---	---	---
BANP	54971	broad.mit.edu	37	16	88105395	88105396	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88105395_88105396delTT	uc002fkr.2	+						BANP_uc002fkp.2_Intron|BANP_uc002fkq.2_Intron|BANP_uc010vow.1_Intron|BANP_uc002fks.3_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	88468490	88468493	+	IGR	DEL	GATG	-	-	rs36187526		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88468490_88468493delGATG								BANP (357567 upstream) : ZNF469 (25386 downstream)																																			---	---	---	---
C16orf81	283860	broad.mit.edu	37	16	89224722	89224723	+	5'Flank	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89224722_89224723delTG	uc002fms.3	+							NR_024347				Homo sapiens cDNA FLJ36701 fis, clone UTERU2009147.												0																		---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89526892	89526892	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89526892delG	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407			ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)														---	---	---	---
C16orf7	9605	broad.mit.edu	37	16	89774962	89774962	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89774962delT	uc002fom.1	-						C16orf7_uc002fol.1_Intron	NM_004913	NP_004904			chromosome 16 open reading frame 7						ATP synthesis coupled proton transport		GTPase activator activity|transporter activity				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0273)														---	---	---	---
C16orf7	9605	broad.mit.edu	37	16	89783208	89783208	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89783208delG	uc002fom.1	-	3	323	c.198delC	c.(196-198)CCCfs	p.P66fs	C16orf7_uc002fol.1_5'UTR|uc002fon.1_RNA|uc002foo.1_Intron	NM_004913	NP_004904	Q9Y2B5	CP007_HUMAN	chromosome 16 open reading frame 7	66					ATP synthesis coupled proton transport		GTPase activator activity|transporter activity				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0273)														---	---	---	---
TCF25	22980	broad.mit.edu	37	16	89954031	89954031	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89954031delT	uc002fpb.2	+						TCF25_uc002fpc.2_Intron	NM_014972	NP_055787			NULP1						heart development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	90011211	90011215	+	IGR	DEL	AAAAA	-	-	rs113721666		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90011211_90011215delAAAAA								TUBB3 (8706 upstream) : DEF8 (3936 downstream)																																			---	---	---	---
RPH3AL	9501	broad.mit.edu	37	17	168321	168321	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:168321delA	uc002frd.1	-						RPH3AL_uc010vpy.1_Intron|RPH3AL_uc002fre.1_Intron|RPH3AL_uc002frf.1_Intron|RPH3AL_uc010cjl.1_Intron	NM_006987	NP_008918			rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	242100	242101	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:242100_242101delTT								RPH3AL (39524 upstream) : C17orf97 (18017 downstream)																																			---	---	---	---
FAM101B	359845	broad.mit.edu	37	17	290416	290417	+	3'UTR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:290416_290417insA	uc002frj.2	-	2						NM_182705	NP_874364			hypothetical protein LOC359845												0		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.0216)														---	---	---	---
VPS53	55275	broad.mit.edu	37	17	527002	527002	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:527002delA	uc002frn.2	-						VPS53_uc002frk.2_Intron|VPS53_uc010cjo.1_Intron|VPS53_uc002frl.2_Intron|VPS53_uc002frm.2_Intron|VPS53_uc002fro.2_Intron|VPS53_uc010cjp.1_Intron	NM_018289	NP_060759			vacuolar protein sorting 53 isoform 2						protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)														---	---	---	---
NXN	64359	broad.mit.edu	37	17	788738	788738	+	Intron	DEL	A	-	-	rs75847261		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:788738delA	uc002fsa.2	-						NXN_uc002fsb.1_Intron	NM_022463	NP_071908			nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)														---	---	---	---
ABR	29	broad.mit.edu	37	17	1004072	1004072	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1004072delT	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc002fsg.2_Intron|ABR_uc010cjq.1_Intron	NM_021962	NP_068781			active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	1170446	1170447	+	IGR	DEL	AA	-	-	rs35017337		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1170446_1170447delAA								ABR (79830 upstream) : TUSC5 (12510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	1206810	1206810	+	IGR	DEL	A	-	-	rs35485139		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1206810delA								TUSC5 (2529 upstream) : YWHAE (41026 downstream)																																			---	---	---	---
YWHAE	7531	broad.mit.edu	37	17	1265317	1265318	+	Intron	DEL	AT	-	-	rs34985093		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1265317_1265318delAT	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)														---	---	---	---
PITPNA	5306	broad.mit.edu	37	17	1442417	1442417	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1442417delT	uc002fst.3	-						PITPNA_uc010cjt.2_Intron|PITPNA_uc010cju.2_Intron	NM_006224	NP_006215			phosphatidylinositol transfer protein, alpha						axon guidance|lipid metabolic process|visual perception	cytoplasm	phosphatidylcholine transmembrane transporter activity|phosphatidylinositol transporter activity|protein binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0845)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	1805132	1805133	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1805132_1805133insC								RPA1 (2284 upstream) : RTN4RL1 (32840 downstream)																																			---	---	---	---
RTN4RL1	146760	broad.mit.edu	37	17	1847228	1847228	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1847228delT	uc002ftp.2	-							NM_178568	NP_848663			reticulon 4 receptor-like 1 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
SMG6	23293	broad.mit.edu	37	17	1976678	1976678	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1976678delT	uc002fub.1	-						SMG6_uc010vqv.1_Intron	NM_017575	NP_060045			Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4																		---	---	---	---
SMG6	23293	broad.mit.edu	37	17	2007249	2007249	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2007249delT	uc002fub.1	-						SMG6_uc010vqv.1_Intron	NM_017575	NP_060045			Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4																		---	---	---	---
MNT	4335	broad.mit.edu	37	17	2287891	2287892	+	3'UTR	INS	-	GTGTGT	GTGTGT	rs150110642		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2287891_2287892insGTGTGT	uc002fur.2	-	6						NM_020310	NP_064706			MAX binding protein						multicellular organismal development|negative regulation of cell proliferation|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			skin(1)	1				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	2431842	2431842	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2431842delT								METT10D (16642 upstream) : PAFAH1B1 (65081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	2475772	2475772	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2475772delT								METT10D (60572 upstream) : PAFAH1B1 (21151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	2483387	2483387	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2483387delT								METT10D (68187 upstream) : PAFAH1B1 (13536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	2975212	2975212	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2975212delC								OR1D4 (8257 upstream) : OR1D2 (20141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	3248343	3248344	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3248343_3248344insT								OR3A4 (33603 upstream) : OR1E1 (52416 downstream)																																			---	---	---	---
CAMKK1	84254	broad.mit.edu	37	17	3794404	3794404	+	5'Flank	DEL	G	-	-	rs72482584		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3794404delG	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)														---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3935311	3935311	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3935311delA	uc002fxe.2	-						ZZEF1_uc002fxh.2_Intron|ZZEF1_uc002fxi.2_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	4140102	4140102	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4140102delA	uc002fxq.1	-						ANKFY1_uc002fxn.2_Intron|ANKFY1_uc002fxo.2_Intron|ANKFY1_uc002fxp.2_Intron|ANKFY1_uc010ckp.2_Intron|ANKFY1_uc002fxr.2_Intron|ANKFY1_uc010vrz.1_Intron	NM_016376	NP_057460			ankyrin repeat and FYVE domain containing 1							endosome membrane	metal ion binding|protein binding			ovary(2)|skin(1)	3																		---	---	---	---
ANKFY1	51479	broad.mit.edu	37	17	4140431	4140431	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4140431delA	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																		---	---	---	---
GGT6	124975	broad.mit.edu	37	17	4461879	4461879	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4461879delG	uc002fyd.3	-	4	973	c.913delC	c.(913-915)CAGfs	p.Q305fs	GGT6_uc010vsb.1_Frame_Shift_Del_p.Q157fs|GGT6_uc002fyc.3_Frame_Shift_Del_p.Q273fs|GGT6_uc010vsc.1_Frame_Shift_Del_p.Q311fs	NM_001122890	NP_001116362	Q6P531	GGT6_HUMAN	gamma-glutamyltransferase 6 isoform a	305	Extracellular (Potential).				glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	4564654	4564655	+	IGR	INS	-	A	A	rs147217208	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4564654_4564655insA								ALOX15 (19065 upstream) : PELP1 (10025 downstream)																																			---	---	---	---
ZMYND15	84225	broad.mit.edu	37	17	4644575	4644575	+	Intron	DEL	T	-	-	rs112302834		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4644575delT	uc002fyt.2	+						CXCL16_uc002fyr.3_5'Flank|CXCL16_uc002fys.3_5'Flank|ZMYND15_uc002fyv.2_Intron|ZMYND15_uc002fyu.2_Intron	NM_032265	NP_115641			zinc finger, MYND-type containing 15 isoform 2								zinc ion binding				0																		---	---	---	---
KIF1C	10749	broad.mit.edu	37	17	4909026	4909027	+	Intron	DEL	TT	-	-	rs72032376		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4909026_4909027delTT	uc002gan.1	+							NM_006612	NP_006603			kinesin family member 1C						microtubule-based movement|retrograde vesicle-mediated transport, Golgi to ER	endoplasmic reticulum|Golgi apparatus|microtubule	ATP binding|microtubule motor activity			breast(2)	2																		---	---	---	---
KIF1C	10749	broad.mit.edu	37	17	4927147	4927147	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4927147delC	uc002gan.1	+	23	3339	c.3013delC	c.(3013-3015)CCCfs	p.P1005fs		NM_006612	NP_006603	O43896	KIF1C_HUMAN	kinesin family member 1C	1005	Pro-rich.				microtubule-based movement|retrograde vesicle-mediated transport, Golgi to ER	endoplasmic reticulum|Golgi apparatus|microtubule	ATP binding|microtubule motor activity			breast(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	5377326	5377326	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5377326delT								DHX33 (5145 upstream) : DERL2 (287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	5656160	5656161	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5656160_5656161delTT								NLRP1 (168328 upstream) : WSCD1 (316276 downstream)																																			---	---	---	---
ALOX12P2	245	broad.mit.edu	37	17	6773808	6773808	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6773808delT	uc002gdu.1	+						ALOX12P2_uc002gdv.2_Intron					Homo sapiens hair and skin epidermal-type 12-lipoxygenase-related protein (ALOX12E) mRNA, complete pseudogene sequence.												0																		---	---	---	---
MIR497	574456	broad.mit.edu	37	17	6921304	6921305	+	RNA	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6921304_6921305delCA	hsa-mir-497|MI0003138	-			c.37_38delCA			uc010vtj.1_5'Flank|MIR195_hsa-mir-195|MI0000489_5'Flank																	0																		---	---	---	---
DLG4	1742	broad.mit.edu	37	17	7094784	7094784	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7094784delA	uc002get.3	-						DLG4_uc010vtm.1_Intron|DLG4_uc010vtn.1_Intron|DLG4_uc010cly.2_Intron|DLG4_uc010vto.1_Intron	NM_001365	NP_001356			post-synaptic density protein 95 isoform 1						axon guidance|learning|protein complex assembly|protein localization to synapse|signal transduction|synaptic transmission	cell junction|cortical cytoskeleton|endocytic vesicle membrane|neuron spine|postsynaptic density|postsynaptic membrane|synaptosome	protein binding|protein C-terminus binding			ovary(1)|breast(1)	2																		---	---	---	---
FXR2	9513	broad.mit.edu	37	17	7502454	7502454	+	Intron	DEL	A	-	-	rs148282793		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7502454delA	uc002gia.1	-						FXR2_uc010vud.1_Intron	NM_004860	NP_004851			fragile X mental retardation syndrome related							cytosolic large ribosomal subunit	protein binding|RNA binding	p.?(1)			0				READ - Rectum adenocarcinoma(115;0.17)														---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7646597	7646597	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7646597delT	uc002giu.1	+						DNAH2_uc002git.2_Frame_Shift_Del_p.F763fs|DNAH2_uc010vuk.1_Frame_Shift_Del_p.F681fs	NM_020877	NP_065928			dynein heavy chain domain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)																---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7686121	7686121	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7686121delA	uc002giu.1	+							NM_020877	NP_065928			dynein heavy chain domain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)																---	---	---	---
ALOXE3	59344	broad.mit.edu	37	17	8014951	8014951	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8014951delA	uc010cnr.2	-						ALOXE3_uc002gka.2_Intron|ALOXE3_uc010vuo.1_Intron|ALOXE3_uc010vup.1_Intron	NM_021628	NP_067641			arachidonate lipoxygenase 3 isoform 2						leukotriene biosynthetic process		iron ion binding|lipoxygenase activity			skin(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
NDEL1	81565	broad.mit.edu	37	17	8361489	8361490	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8361489_8361490delTT	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																		---	---	---	---
PIK3R5	23533	broad.mit.edu	37	17	8808941	8808941	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8808941delC	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	9044611	9044612	+	Intron	INS	-	G	G	rs80154000	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9044611_9044612insG	uc002glw.3	+							NM_004822	NP_004813			netrin 1 precursor						apoptosis|axon guidance		protein binding				0																		---	---	---	---
NTN1	9423	broad.mit.edu	37	17	9119861	9119861	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9119861delA	uc002glw.3	+							NM_004822	NP_004813			netrin 1 precursor						apoptosis|axon guidance		protein binding				0																		---	---	---	---
NTN1	9423	broad.mit.edu	37	17	9127520	9127520	+	Intron	DEL	G	-	-	rs71361877		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9127520delG	uc002glw.3	+							NM_004822	NP_004813			netrin 1 precursor						apoptosis|axon guidance		protein binding				0																		---	---	---	---
STX8	9482	broad.mit.edu	37	17	9272624	9272624	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9272624delA	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
STX8	9482	broad.mit.edu	37	17	9334346	9334346	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9334346delT	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
STX8	9482	broad.mit.edu	37	17	9471827	9471827	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9471827delT	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
GAS7	8522	broad.mit.edu	37	17	9842932	9842934	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9842932_9842934delTTT	uc002gmg.1	-						GAS7_uc010vvc.1_Intron|GAS7_uc002gmh.1_Intron|GAS7_uc010vvd.1_Intron|GAS7_uc002gmi.2_Intron|GAS7_uc002gmj.1_Intron|GAS7_uc010coh.1_Intron	NM_201433	NP_958839			growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2								T	MLL	AML*								---	---	---	---
GAS7	8522	broad.mit.edu	37	17	9948358	9948361	+	Intron	DEL	AAAA	-	-	rs66854456		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9948358_9948361delAAAA	uc002gmg.1	-						GAS7_uc010coh.1_Intron	NM_201433	NP_958839			growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2								T	MLL	AML*								---	---	---	---
Unknown	0	broad.mit.edu	37	17	10175321	10175321	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10175321delA								GAS7 (73453 upstream) : MYH13 (28862 downstream)																																			---	---	---	---
MYH8	4626	broad.mit.edu	37	17	10302567	10302568	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10302567_10302568delTG	uc002gmm.2	-						uc002gml.1_Intron	NM_002472	NP_002463			myosin, heavy chain 8, skeletal muscle,						muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11														Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				---	---	---	---
Unknown	0	broad.mit.edu	37	17	10531668	10531668	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10531668delT								MYH2 (78651 upstream) : MYH3 (175 downstream)																																			---	---	---	---
SCO1	6341	broad.mit.edu	37	17	10591141	10591141	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10591141delT	uc002gmr.3	-						SCO1_uc002gms.3_Intron	NM_004589	NP_004580			cytochrome oxidase deficient homolog 1						cellular copper ion homeostasis|copper ion transport|generation of precursor metabolites and energy|respiratory chain complex IV assembly	mitochondrial inner membrane	copper ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	10705101	10705102	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10705101_10705102delTT	uc002gmz.2	-											Homo sapiens hypothetical gene supported by BC015790; BC041634, mRNA (cDNA clone IMAGE:4866059).																														---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11585098	11585098	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11585098delA	uc002gne.2	+						DNAH9_uc010coo.2_Intron	NM_001372	NP_001363			dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11719881	11719881	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11719881delT	uc002gne.2	+						DNAH9_uc010coo.2_Intron	NM_001372	NP_001363			dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11726387	11726388	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11726387_11726388insT	uc002gne.2	+						DNAH9_uc010coo.2_Intron	NM_001372	NP_001363			dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
MAP2K4	6416	broad.mit.edu	37	17	11996343	11996343	+	Intron	DEL	A	-	-	rs66524012		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11996343delA	uc002gnj.2	+						MAP2K4_uc002gnk.2_Intron|MAP2K4_uc010vvi.1_Intron|MAP2K4_uc010vvj.1_Intron	NM_003010	NP_003001			mitogen-activated protein kinase kinase 4						cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.?(1)		large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1)	58		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)				D|Mis|N		pancreatic|breast|colorectal								---	---	---	---
MAP2K4	6416	broad.mit.edu	37	17	12028819	12028819	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12028819delA	uc002gnj.2	+						MAP2K4_uc002gnk.2_Intron|MAP2K4_uc010vvi.1_Intron|MAP2K4_uc010vvj.1_Intron	NM_003010	NP_003001			mitogen-activated protein kinase kinase 4						cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.?(1)		large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1)	58		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)				D|Mis|N		pancreatic|breast|colorectal								---	---	---	---
MYOCD	93649	broad.mit.edu	37	17	12620615	12620615	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12620615delT	uc002gnn.2	+						MYOCD_uc002gno.2_Intron|MYOCD_uc002gnp.1_5'Flank	NM_153604	NP_705832			myocardin isoform 2						cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding			central_nervous_system(2)|skin(2)|ovary(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)														---	---	---	---
RICH2	9912	broad.mit.edu	37	17	12867808	12867808	+	Intron	DEL	A	-	-	rs112277916		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12867808delA	uc002gnr.3	+						RICH2_uc010vvk.1_Intron|RICH2_uc010vvl.1_Intron|RICH2_uc002gns.3_Intron|RICH2_uc010vvm.1_Intron|RICH2_uc010vvn.1_Intron	NM_014859	NP_055674			Rho GTPase-activating protein RICH2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
COX10	1352	broad.mit.edu	37	17	14099362	14099362	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14099362delA	uc002gof.3	+						COX10_uc010vvs.1_Intron|COX10_uc010vvt.1_Intron	NM_001303	NP_001294			heme A:farnesyltransferase precursor						heme a biosynthetic process|heme O biosynthetic process|respiratory chain complex IV assembly	integral to membrane|mitochondrial membrane	protoheme IX farnesyltransferase activity				0		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	14379190	14379190	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14379190delT								HS3ST3B1 (129698 upstream) : PMP22 (753907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14509251	14509259	+	IGR	DEL	GTTTGTTTG	-	-	rs56216439		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14509251_14509259delGTTTGTTTG								HS3ST3B1 (259759 upstream) : PMP22 (623838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14533734	14533734	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14533734delA								HS3ST3B1 (284242 upstream) : PMP22 (599363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14573897	14573898	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14573897_14573898delTT								HS3ST3B1 (324405 upstream) : PMP22 (559199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14608988	14608990	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14608988_14608990delTTT								HS3ST3B1 (359496 upstream) : PMP22 (524107 downstream)																																			---	---	---	---
CDRT4	284040	broad.mit.edu	37	17	15342591	15342592	+	Intron	DEL	AA	-	-	rs10707095		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15342591_15342592delAA	uc002gop.1	-						CDRT4_uc010vvw.1_Intron	NM_173622	NP_775893			CMT1A duplicated region transcript 4												0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0874)														---	---	---	---
NCOR1	9611	broad.mit.edu	37	17	16078689	16078689	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16078689delA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpp.1_Intron|NCOR1_uc002gpr.2_Intron|NCOR1_uc002gps.1_Intron|NCOR1_uc010coz.1_Intron|NCOR1_uc010cpb.1_Intron|NCOR1_uc010cpa.1_Intron|NCOR1_uc002gpu.2_Intron	NM_006311	NP_006302			nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)														---	---	---	---
PIGL	9487	broad.mit.edu	37	17	16154897	16154897	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16154897delA	uc002gpv.2	+						PIGL_uc010vwd.1_Intron	NM_004278	NP_004269			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminylphosphatidylinositol deacetylase activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)														---	---	---	---
C17orf76	388341	broad.mit.edu	37	17	16366656	16366656	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16366656delC	uc010cph.1	-						C17orf76_uc002gqh.2_Intron|NCRNA00188_uc010vwl.1_Intron|NCRNA00188_uc010vwm.1_Intron|NCRNA00188_uc010vwn.1_Intron|NCRNA00188_uc010cpe.2_Intron|NCRNA00188_uc010vwo.1_Intron|NCRNA00188_uc010vwp.1_Intron	NM_001113567	NP_001107039			hypothetical protein LOC388341 isoform 1												0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	16413135	16413136	+	IGR	DEL	TT	-	-	rs112075097		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16413135_16413136delTT								C17orf76 (17655 upstream) : ZNF287 (40495 downstream)																																			---	---	---	---
CCDC144A	9720	broad.mit.edu	37	17	16625450	16625450	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16625450delT	uc002gqk.1	+						CCDC144A_uc002gql.1_Intron|LOC162632_uc010cpj.1_Intron	NM_014695	NP_055510			coiled-coil domain containing 144A												0																		---	---	---	---
CCDC144A	9720	broad.mit.edu	37	17	16673986	16673986	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16673986delT	uc002gqk.1	+						LOC162632_uc010cpj.1_Intron	NM_014695	NP_055510			coiled-coil domain containing 144A												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	16905971	16905972	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16905971_16905972delAA								TNFRSF13B (30569 upstream) : MPRIP (40135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	16931323	16931323	+	IGR	DEL	T	-	-	rs78953875		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16931323delT								TNFRSF13B (55921 upstream) : MPRIP (14784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	17315498	17315498	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17315498delT								NT5M (64523 upstream) : MED9 (64802 downstream)																																			---	---	---	---
PEMT	10400	broad.mit.edu	37	17	17426312	17426313	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17426312_17426313insT	uc002grj.2	-						PEMT_uc002grk.2_Intron|PEMT_uc002grl.2_Intron|PEMT_uc010vwx.1_Intron	NM_148173	NP_680478			phosphatidylethanolamine N-methyltransferase						cell proliferation|phosphatidylcholine biosynthetic process	endoplasmic reticulum membrane|integral to membrane|mitochondrial membrane	phosphatidylethanolamine N-methyltransferase activity				0				Colorectal(2;0.0157)|READ - Rectum adenocarcinoma(2;0.0891)														---	---	---	---
C17orf39	79018	broad.mit.edu	37	17	17952960	17952961	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17952960_17952961delTT	uc002gsg.1	+							NM_024052	NP_076957			hypothetical protein LOC79018											skin(1)	1	all_neural(463;0.228)																	---	---	---	---
TOP3A	7156	broad.mit.edu	37	17	18192337	18192337	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18192337delT	uc002gsx.1	-						TOP3A_uc010cpz.1_Intron|TOP3A_uc010vxr.1_Intron|TOP3A_uc002gsw.1_Intron|TOP3A_uc010vxs.1_Intron	NM_004618	NP_004609			topoisomerase (DNA) III alpha						DNA topological change|meiosis	chromosome|PML body	ATP binding|DNA topoisomerase type I activity|protein binding|zinc ion binding			skin(3)	3																		---	---	---	---
PRPSAP2	5636	broad.mit.edu	37	17	18832049	18832049	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	18988562	18988562	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18988562delT								GRAP (38226 upstream) : GRAPL (42220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	19349125	19349125	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19349125delT								RNF112 (28538 upstream) : SLC47A1 (88042 downstream)																																			---	---	---	---
SLC47A1	55244	broad.mit.edu	37	17	19463171	19463171	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19463171delA	uc002gvy.1	+						SLC47A1_uc010vyy.1_Intron|SLC47A1_uc002gvx.2_Intron|SLC47A1_uc010vyz.1_Intron|SLC47A1_uc010cqp.1_Intron|SLC47A1_uc010cqq.1_Intron|SLC47A1_uc010vza.1_Intron|SLC47A1_uc010vzb.1_Intron|SLC47A1_uc010vzc.1_Intron	NM_018242	NP_060712			solute carrier family 47, member 1							integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)																	---	---	---	---
SLC47A1	55244	broad.mit.edu	37	17	19469749	19469749	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19469749delT	uc002gvy.1	+						SLC47A1_uc002gvx.2_Intron|SLC47A1_uc010vyz.1_Intron|SLC47A1_uc010cqp.1_Intron|SLC47A1_uc010cqq.1_Intron|SLC47A1_uc010vza.1_Intron|SLC47A1_uc010vzb.1_Intron|SLC47A1_uc010vzc.1_Intron	NM_018242	NP_060712			solute carrier family 47, member 1							integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)																	---	---	---	---
ULK2	9706	broad.mit.edu	37	17	19752998	19752998	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19752998delA	uc002gwm.3	-						ULK2_uc002gwn.2_Intron	NM_001142610	NP_001136082			unc-51-like kinase 2						signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)																	---	---	---	---
CYTSB	92521	broad.mit.edu	37	17	20016469	20016469	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20016469delT	uc002gwq.2	+						CYTSB_uc010cqx.2_Intron|CYTSB_uc002gwr.2_Intron|CYTSB_uc002gws.2_Intron	NM_001033553	NP_001028725			spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	20384029	20384029	+	IGR	DEL	T	-	-	rs141169224		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20384029delT								LGALS9B (13181 upstream) : CCDC144NL (382681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	20866843	20866843	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20866843delA	uc002gyk.1	+											Homo sapiens hypothetical protein LOC339260, mRNA (cDNA clone IMAGE:5168338), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	21098763	21098763	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21098763delA								DHRS7B (3928 upstream) : TMEM11 (2500 downstream)																																			---	---	---	---
TMEM11	8834	broad.mit.edu	37	17	21108879	21108879	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21108879delC	uc002gyp.2	-						TMEM11_uc002gyq.2_Intron	NM_003876	NP_003867			transmembrane protein 11						mitochondrion organization	integral to mitochondrial inner membrane|integral to plasma membrane	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	21228902	21228902	+	IGR	DEL	A	-	-	rs66723504		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21228902delA								MAP2K3 (10353 upstream) : KCNJ12 (50797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21232122	21232122	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21232122delT								MAP2K3 (13573 upstream) : KCNJ12 (47577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21237055	21237055	+	IGR	DEL	T	-	-	rs111986195		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21237055delT								MAP2K3 (18506 upstream) : KCNJ12 (42644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21333211	21333212	+	IGR	INS	-	GACT	GACT	rs112306969		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21333211_21333212insGACT								KCNJ12 (10032 upstream) : C17orf51 (98360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21353107	21353107	+	IGR	DEL	A	-	-	rs5819778		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21353107delA								KCNJ12 (29928 upstream) : C17orf51 (78465 downstream)																																			---	---	---	---
C17orf51	339263	broad.mit.edu	37	17	21466482	21466482	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21466482delT	uc002gyx.1	-											Homo sapiens cDNA FLJ12977 fis, clone NT2RP2006261.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	21507129	21507129	+	IGR	DEL	A	-	-	rs113637029		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21507129delA								C17orf51 (29398 upstream) : FAM27L (318241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21526577	21526578	+	IGR	INS	-	T	T	rs141423063		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21526577_21526578insT								C17orf51 (48846 upstream) : FAM27L (298792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21561660	21561660	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21561660delA								C17orf51 (83929 upstream) : FAM27L (263710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21564653	21564654	+	IGR	INS	-	C	C	rs112230591		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21564653_21564654insC								C17orf51 (86922 upstream) : FAM27L (260716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21731489	21731489	+	3'UTR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21731489delC	uc002gyy.3	+	2										SubName: Full=cDNA FLJ51326, highly similar to Homo sapiens ubiquitin B (UBB), mRNA;																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	22021080	22021080	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22021080delA	uc002gzb.1	+						uc002gzc.1_5'Flank					full-length cDNA clone CS0DA012YP03 of Neuroblastoma of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	22094218	22094218	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22094218delA								FLJ36000 (181148 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	22208225	22208225	+	IGR	DEL	T	-	-	rs150860792		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22208225delT								FLJ36000 (295155 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25263575	25263575	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25263575delA								None (None upstream) : WSB1 (357531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25285874	25285875	+	IGR	INS	-	CTCCTT	CTCCTT	rs73984730	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25285874_25285875insCTCCTT								None (None upstream) : WSB1 (335231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25297298	25297303	+	IGR	DEL	ATTTGT	-	-	rs140445727		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25297298_25297303delATTTGT								None (None upstream) : WSB1 (323803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25318216	25318216	+	IGR	DEL	T	-	-	rs111803514		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25318216delT								None (None upstream) : WSB1 (302890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25320354	25320354	+	IGR	DEL	A	-	-	rs71858721		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25320354delA								None (None upstream) : WSB1 (300752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25323057	25323058	+	IGR	DEL	AT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25323057_25323058delAT								None (None upstream) : WSB1 (298048 downstream)																																			---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25853466	25853466	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25853466delA	uc010crg.2	+						KSR1_uc002gzj.1_Intron	NM_014238	NP_055053			kinase suppressor of ras						Ras protein signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(1)	4	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25910016	25910016	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25910016delC	uc010crg.2	+	5	899	c.454delC	c.(454-456)CCCfs	p.P152fs	KSR1_uc002gzj.1_RNA	NM_014238	NP_055053	Q8IVT5	KSR1_HUMAN	kinase suppressor of ras	287	Poly-Pro.				Ras protein signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(1)	4	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	26339053	26339054	+	IGR	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26339053_26339054delGA								NOS2 (118644 upstream) : NLK (30634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	26530566	26530566	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26530566delT								NLK (7164 upstream) : PYY2 (23023 downstream)																																			---	---	---	---
SARM1	23098	broad.mit.edu	37	17	26726914	26726914	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26726914delT	uc010crl.1	+	12					SARM1_uc002hbe.1_3'UTR|SLC46A1_uc002hbf.1_Intron|SLC46A1_uc002hbg.1_Intron	NM_015077	NP_055892			sterile alpha and TIR motif containing 1						innate immune response	cytoplasm|intrinsic to membrane	binding|transmembrane receptor activity				0	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)														---	---	---	---
SDF2	6388	broad.mit.edu	37	17	26976512	26976512	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26976512delA	uc002hbw.2	-						SDF2_uc002hbx.2_Intron	NM_006923	NP_008854			stromal cell-derived factor 2 precursor						protein glycosylation	extracellular space|membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity				0	Lung NSC(42;0.00431)																	---	---	---	---
RPL23A	6147	broad.mit.edu	37	17	27047808	27047810	+	In_Frame_Del	DEL	AAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27047808_27047810delAAG	uc002hci.2	+	2	133_135	c.109_111delAAG	c.(109-111)AAGdel	p.K39del	RAB34_uc002hce.2_5'Flank|RAB34_uc002hcg.2_5'Flank|RAB34_uc002hcf.2_5'Flank|RAB34_uc010was.1_5'Flank|RAB34_uc010wat.1_5'Flank|RAB34_uc002hch.2_5'Flank|RAB34_uc010wau.1_5'Flank|RAB34_uc010wav.1_5'Flank|RPL23A_uc002hck.1_RNA|SNORD4A_uc002hcl.2_5'Flank|SNORD42A_uc002hcm.1_5'Flank|SNORD4B_uc002hcn.1_5'Flank	NM_000984	NP_000975	P62750	RL23A_HUMAN	ribosomal protein L23a	39					cell proliferation|endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleus	nucleotide binding|protein binding|rRNA binding|structural constituent of ribosome			ovary(1)	1	Lung NSC(42;0.00431)															OREG0024282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PHF12	57649	broad.mit.edu	37	17	27274003	27274004	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27274003_27274004delTT	uc002hdg.1	-						PHF12_uc010wbb.1_Intron|PHF12_uc002hdi.1_Intron|PHF12_uc002hdj.1_Intron|PHF12_uc010crw.1_Intron|PHF12_uc002hdk.1_Intron	NM_001033561	NP_001028733			PHD finger protein 12 isoform 1						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	protein binding|zinc ion binding			ovary(1)	1	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	27348210	27348210	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27348210delT								SEZ6 (14752 upstream) : PIPOX (21708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	27539998	27539999	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27539998_27539999delTT								MYO18A (32591 upstream) : CRYBA1 (33876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	27553148	27553148	+	IGR	DEL	A	-	-	rs35255154		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27553148delA								MYO18A (45741 upstream) : CRYBA1 (20727 downstream)																																			---	---	---	---
TAOK1	57551	broad.mit.edu	37	17	27785129	27785129	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27785129delA	uc002hdz.1	+						TAOK1_uc010wbe.1_Intron|TAOK1_uc010wbf.1_Intron	NM_020791	NP_065842			TAO kinase 1						mitotic prometaphase	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1)	4			Colorectal(6;0.198)															---	---	---	---
TAOK1	57551	broad.mit.edu	37	17	27822755	27822755	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27822755delA	uc002hdz.1	+						TAOK1_uc010wbe.1_Intron|TAOK1_uc010wbf.1_Intron|TAOK1_uc002heb.1_Intron	NM_020791	NP_065842			TAO kinase 1						mitotic prometaphase	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1)	4			Colorectal(6;0.198)															---	---	---	---
TAOK1	57551	broad.mit.edu	37	17	27861011	27861011	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27861011delA	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	28036694	28036695	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28036694_28036695insA	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.1_Intron|SSH2_uc002heq.2_Intron|SSH2_uc002her.2_Intron|SSH2_uc010csc.1_Intron	NM_033389	NP_203747			slingshot 2						actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2																		---	---	---	---
SSH2	85464	broad.mit.edu	37	17	28218612	28218612	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28218612delA	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																		---	---	---	---
EFCAB5	374786	broad.mit.edu	37	17	28270563	28270563	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28270563delT	uc002het.2	+						EFCAB5_uc010wbi.1_Intron|EFCAB5_uc010wbj.1_Intron|EFCAB5_uc010wbk.1_Intron|EFCAB5_uc010csd.2_Intron	NM_198529	NP_940931			EF-hand calcium binding domain 5 isoform a								calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
EFCAB5	374786	broad.mit.edu	37	17	28348155	28348155	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28348155delT	uc002het.2	+						EFCAB5_uc010wbi.1_Intron|EFCAB5_uc010wbj.1_Intron|EFCAB5_uc010wbk.1_Intron|EFCAB5_uc010csd.2_Intron|EFCAB5_uc010cse.2_Intron|EFCAB5_uc010csf.2_Intron	NM_198529	NP_940931			EF-hand calcium binding domain 5 isoform a								calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
CCDC55	84081	broad.mit.edu	37	17	28472713	28472713	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28472713delT	uc002heu.2	+						CCDC55_uc002hev.2_Intron|CCDC55_uc010wbl.1_Intron|CCDC55_uc010wbm.1_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																		---	---	---	---
SUZ12P	440423	broad.mit.edu	37	17	29094587	29094587	+	Intron	DEL	A	-	-	rs11310424		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29094587delA	uc002hfn.1	+						SUZ12P_uc002hfo.2_Intron|SUZ12P_uc002hfq.2_Intron					Homo sapiens cDNA clone IMAGE:5299523, containing frame-shift errors.												0																		---	---	---	---
CRLF3	51379	broad.mit.edu	37	17	29111122	29111122	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29111122delT	uc002hfr.3	-	8					CRLF3_uc010wbr.1_3'UTR	NM_015986	NP_057070			cytokine receptor-like factor 3						negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|positive regulation of cell cycle arrest|positive regulation of JAK-STAT cascade|positive regulation of transcription from RNA polymerase II promoter	cytoplasm					0		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)																---	---	---	---
NF1	4763	broad.mit.edu	37	17	29533435	29533435	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29533435delT	uc002hgg.2	+						NF1_uc002hge.1_Intron|NF1_uc002hgf.1_Intron|NF1_uc002hgh.2_Intron|NF1_uc010csn.1_Intron	NM_001042492	NP_001035957			neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	30082829	30082829	+	IGR	DEL	A	-	-	rs113381409		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30082829delA								MIR365-2 (180289 upstream) : C17orf79 (96056 downstream)																																			---	---	---	---
UTP6	55813	broad.mit.edu	37	17	30200273	30200273	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30200273delA	uc002hgr.2	-						UTP6_uc002hgq.2_Intron|UTP6_uc010cst.2_Intron	NM_018428	NP_060898			hepatocellular carcinoma-associated antigen 66						rRNA processing	nucleolus	binding			ovary(1)	1		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	30432703	30432703	+	IGR	DEL	T	-	-	rs67852851		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30432703delT								LRRC37B (52186 upstream) : RHOT1 (36770 downstream)																																			---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	30828529	30828529	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30828529delT	uc002hho.1	-							NM_015194	NP_056009			myosin ID							myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)															---	---	---	---
ACCN1	40	broad.mit.edu	37	17	31583850	31583850	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31583850delA	uc002hhu.2	-						ACCN1_uc002hht.2_Intron	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	31609496	31609497	+	Intron	DEL	TG	-	-	rs71895828	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31609496_31609497delTG	uc002hhu.2	-						ACCN1_uc002hht.2_Intron	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	32378838	32378839	+	Intron	DEL	AC	-	-	rs67311344		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32378838_32378839delAC	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	32586752	32586753	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32586752_32586753delCT								CCL2 (2534 upstream) : CCL7 (10487 downstream)																																			---	---	---	---
NLE1	54475	broad.mit.edu	37	17	33461424	33461425	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33461424_33461425delTT	uc002hiy.1	-						NLE1_uc010ctn.1_Intron|NLE1_uc002hiz.1_Intron	NM_018096	NP_060566			Notchless gene homolog isoform a							nucleolus				breast(3)|ovary(1)	4		Ovarian(249;0.17)																---	---	---	---
GGNBP2	79893	broad.mit.edu	37	17	34930247	34930249	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34930247_34930249delTTT	uc002hnb.2	+						GGNBP2_uc002hna.2_Intron|GGNBP2_uc002hnc.1_5'Flank	NM_024835	NP_079111			zinc finger protein 403						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasmic membrane-bounded vesicle				ovary(2)	2		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)														---	---	---	---
AATF	26574	broad.mit.edu	37	17	35406745	35406745	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35406745delA	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	35726591	35726591	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35726591delA	uc002hno.2	-						ACACA_uc002hnn.2_Intron|ACACA_uc002hnq.2_Intron	NM_198834	NP_942131			acetyl-Coenzyme A carboxylase alpha isoform 1						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)													---	---	---	---
SYNRG	11276	broad.mit.edu	37	17	35900094	35900094	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35900094delG	uc002hoa.2	-						SYNRG_uc010wde.1_Intron|SYNRG_uc010wdf.1_Intron|SYNRG_uc002hoc.2_Intron|SYNRG_uc002hoe.2_Intron|SYNRG_uc002hod.2_Intron|SYNRG_uc010wdg.1_Intron|SYNRG_uc002hob.2_Intron	NM_007247	NP_009178			synergin, gamma isoform 1						endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2																		---	---	---	---
GPR179	440435	broad.mit.edu	37	17	36500809	36500810	+	5'Flank	DEL	TT	-	-	rs148429715		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36500809_36500810delTT	uc002hpz.2	-							NM_001004334	NP_001004334			GPR158-like 1 precursor							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)																---	---	---	---
SRCIN1	80725	broad.mit.edu	37	17	36707421	36707421	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36707421delG	uc002hqd.2	-	15	3157	c.2932delC	c.(2932-2934)CGAfs	p.R978fs	SRCIN1_uc002hqf.1_Frame_Shift_Del_p.R850fs|SRCIN1_uc002hqe.2_Frame_Shift_Del_p.R832fs	NM_025248	NP_079524	Q9C0H9	SRCN1_HUMAN	SNAP25-interacting protein	850	Pro-rich.			R -> K (in Ref. 6; AA sequence).	exocytosis|negative regulation of protein tyrosine kinase activity|positive regulation of protein tyrosine kinase activity|regulation of cell migration|regulation of dendritic spine morphogenesis|substrate adhesion-dependent cell spreading	actin cytoskeleton|axon|cell junction|cytoplasm|dendrite|postsynaptic density|postsynaptic membrane	protein kinase binding				0																		---	---	---	---
SRCIN1	80725	broad.mit.edu	37	17	36710447	36710447	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36710447delA	uc002hqd.2	-						SRCIN1_uc002hqf.1_Intron|SRCIN1_uc002hqe.2_Intron|SRCIN1_uc002hqg.2_Intron	NM_025248	NP_079524			SNAP25-interacting protein						exocytosis|negative regulation of protein tyrosine kinase activity|positive regulation of protein tyrosine kinase activity|regulation of cell migration|regulation of dendritic spine morphogenesis|substrate adhesion-dependent cell spreading	actin cytoskeleton|axon|cell junction|cytoplasm|dendrite|postsynaptic density|postsynaptic membrane	protein kinase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	36779408	36779408	+	IGR	DEL	A	-	-	rs35961917		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36779408delA								SRCIN1 (17225 upstream) : C17orf96 (48553 downstream)																																			---	---	---	---
LASP1	3927	broad.mit.edu	37	17	37040276	37040277	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37040276_37040277delTT	uc002hra.2	+						LASP1_uc010wdy.1_Intron|LASP1_uc010cvq.2_Intron|LASP1_uc010wdz.1_Intron	NM_006148	NP_006139			LIM and SH3 protein 1							cortical actin cytoskeleton	ion transmembrane transporter activity|SH3/SH2 adaptor activity|zinc ion binding			lung(1)	1								T	MLL	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	17	37177537	37177537	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37177537delT								FBXO47 (53882 upstream) : PLXDC1 (42019 downstream)																																			---	---	---	---
CACNB1	782	broad.mit.edu	37	17	37338578	37338578	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37338578delA	uc002hrm.1	-						CACNB1_uc002hrl.1_Intron|CACNB1_uc002hrn.2_Intron|CACNB1_uc002hro.2_Intron	NM_000723	NP_000714			calcium channel, voltage-dependent, beta 1						axon guidance	voltage-gated calcium channel complex				large_intestine(1)|ovary(1)	2					Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Verapamil(DB00661)													---	---	---	---
STAC2	342667	broad.mit.edu	37	17	37373975	37373976	+	Intron	INS	-	A	A	rs79440560		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37373975_37373976insA	uc002hrs.2	-						STAC2_uc010cvt.2_Intron	NM_198993	NP_945344			SH3 and cysteine rich domain 2						intracellular signal transduction		metal ion binding			pancreas(1)	1																		---	---	---	---
NR1D1	9572	broad.mit.edu	37	17	38252308	38252309	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38252308_38252309delTC	uc002htz.1	-	5	1262_1263	c.636_637delGA	c.(634-639)GAGAAGfs	p.E212fs	NR1D1_uc010cwq.1_RNA|NR1D1_uc010cwr.1_Intron	NM_021724	NP_068370	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	212_213					cellular response to lipopolysaccharide|negative regulation of receptor biosynthetic process|negative regulation of toll-like receptor 4 signaling pathway|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin|nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding			skin(1)	1	Colorectal(19;0.000442)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	38260315	38260315	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38260315delT								NR1D1 (3342 upstream) : MSL1 (18475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	38370336	38370336	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38370336delA								RAPGEFL1 (18430 upstream) : WIPF2 (5238 downstream)																																			---	---	---	---
CDC6	990	broad.mit.edu	37	17	38447990	38447990	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38447990delT	uc002huj.1	+							NM_001254	NP_001245			cell division cycle 6 protein						cell division|DNA replication|DNA replication checkpoint|M/G1 transition of mitotic cell cycle|mitosis|negative regulation of cell proliferation|negative regulation of DNA replication|positive regulation of cell cycle cytokinesis|positive regulation of chromosome segregation|regulation of cyclin-dependent protein kinase activity|regulation of mitotic anaphase|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm|spindle midzone|spindle pole	ATP binding|kinase binding|nucleoside-triphosphatase activity			ovary(2)|breast(1)	3																		---	---	---	---
TOP2A	7153	broad.mit.edu	37	17	38562531	38562532	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38562531_38562532insT	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)													---	---	---	---
TOP2A	7153	broad.mit.edu	37	17	38563945	38563945	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38563945delA	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	38592134	38592135	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38592134_38592135delAC								TOP2A (17965 upstream) : IGFBP4 (7541 downstream)																																			---	---	---	---
TNS4	84951	broad.mit.edu	37	17	38633825	38633828	+	3'UTR	DEL	CAGG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38633825_38633828delCAGG	uc010cxb.2	-	13					TNS4_uc002huu.3_3'UTR	NM_032865	NP_116254			tensin 4 precursor						apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)															---	---	---	---
CCR7	1236	broad.mit.edu	37	17	38710799	38710799	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38710799delT	uc002huw.2	-	3						NM_001838	NP_001829			chemokine (C-C motif) receptor 7 precursor						cell maturation|immunological synapse formation|inflammatory response|interleukin-12 secretion|lymphocyte migration into lymph node|positive regulation of dendritic cell antigen processing and presentation|positive regulation of glycoprotein biosynthetic process|positive regulation of humoral immune response|positive regulation of hypersensitivity|positive regulation of interleukin-12 production|positive regulation of neutrophil chemotaxis|regulation of interferon-gamma production|regulation of interleukin-1 beta secretion|T cell costimulation	integral to membrane|intracellular	C-C chemokine receptor activity|chemokine (C-C motif) ligand 19 binding|chemokine (C-C motif) ligand 21 binding			breast(1)	1		Breast(137;0.000496)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	38870704	38870704	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38870704delC								KRT24 (10702 upstream) : KRT25 (33570 downstream)																																			---	---	---	---
KRT25	147183	broad.mit.edu	37	17	38910971	38910975	+	Intron	DEL	AAAAA	-	-	rs66622923		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38910971_38910975delAAAAA	uc002hve.2	-							NM_181534	NP_853512			keratin 25							cytoplasm|intermediate filament	structural molecule activity			ovary(2)	2		Breast(137;0.00526)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	39514901	39514901	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39514901delA								KRT33A (7845 upstream) : KRT33B (4846 downstream)																																			---	---	---	---
KRT13	3860	broad.mit.edu	37	17	39662028	39662028	+	5'Flank	DEL	T	-	-	rs72133811		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39662028delT	uc002hwu.1	-						KRT13_uc002hwv.1_5'Flank|KRT13_uc002hww.2_5'Flank|KRT13_uc010wfr.1_5'Flank|KRT13_uc010cxo.2_5'Flank|KRT13_uc002hwx.1_5'Flank	NM_153490	NP_705694			keratin 13 isoform a						epidermis development	intermediate filament	structural molecule activity			ovary(2)|skin(2)|pancreas(1)	5		Breast(137;0.000286)																---	---	---	---
HAP1	9001	broad.mit.edu	37	17	39885199	39885202	+	Intron	DEL	TTTA	-	-	rs66524308		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39885199_39885202delTTTA	uc002hxm.1	-						JUP_uc010wfs.1_Intron|HAP1_uc002hxn.1_Intron|HAP1_uc002hxo.1_Intron|HAP1_uc002hxp.1_Intron	NM_177977	NP_817084			huntingtin-associated protein 1 isoform 2						brain development|protein localization|synaptic transmission	actin cytoskeleton	protein binding			ovary(2)	2		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	39946867	39946867	+	IGR	DEL	T	-	-	rs1811138	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39946867delT								JUP (3903 upstream) : SC65 (11339 downstream)																																			---	---	---	---
TTC25	83538	broad.mit.edu	37	17	40105859	40105860	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40105859_40105860insT	uc002hyj.3	+						TTC25_uc010cxt.2_Intron	NM_031421	NP_113609			tetratricopeptide repeat domain 25							cytoplasm	protein binding			ovary(1)	1		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)																---	---	---	---
TTC25	83538	broad.mit.edu	37	17	40115791	40115791	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40115791delT	uc002hyj.3	+						TTC25_uc010cxt.2_Intron|CNP_uc002hyk.1_5'Flank|CNP_uc002hyl.1_5'Flank|CNP_uc010wfz.1_5'Flank|CNP_uc002hym.1_5'Flank|CNP_uc010wga.1_5'Flank	NM_031421	NP_113609			tetratricopeptide repeat domain 25							cytoplasm	protein binding			ovary(1)	1		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	40191813	40191813	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40191813delC								NKIRAS2 (14159 upstream) : DHX58 (61609 downstream)																																			---	---	---	---
KAT2A	2648	broad.mit.edu	37	17	40266348	40266348	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40266348delC	uc002hyx.2	-						DHX58_uc002hyv.3_5'Flank|DHX58_uc002hyw.3_5'Flank|DHX58_uc010wgf.1_5'Flank	NM_021078	NP_066564			general control of amino acid synthesis 5-like						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																		---	---	---	---
STAT5B	6777	broad.mit.edu	37	17	40401686	40401687	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40401686_40401687delTT	uc002hzh.2	-						STAT5B_uc002hzi.3_Intron	NM_012448	NP_036580			signal transducer and activator of transcription						2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|JAK-STAT cascade involved in growth hormone signaling pathway|oxaloacetate metabolic process|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|glucocorticoid receptor binding|sequence-specific DNA binding transcription factor activity			ovary(3)|lung(2)|skin(1)	6		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)													---	---	---	---
STAT3	6774	broad.mit.edu	37	17	40468976	40468977	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40468976_40468977delAA	uc002hzl.1	-						STAT3_uc002hzk.1_Intron|STAT3_uc002hzm.1_Intron|STAT3_uc010wgh.1_Intron|STAT3_uc002hzn.1_Intron|STAT3_uc010cyf.1_5'Flank	NM_139276	NP_644805			signal transducer and activator of transcription						cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)										Hyperimmunoglobulin_E_Recurrent_Infection_Syndrome				---	---	---	---
PTRF	284119	broad.mit.edu	37	17	40566430	40566430	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40566430delT	uc002hzo.2	-						PTRF_uc010wgi.1_Intron	NM_012232	NP_036364			polymerase I and transcript release factor						regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription initiation from RNA polymerase I promoter	caveola|cytosol|endoplasmic reticulum|microsome|mitochondrion|nucleoplasm	protein binding|rRNA primary transcript binding			breast(1)	1		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)														---	---	---	---
TUBG1	7283	broad.mit.edu	37	17	40765170	40765170	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40765170delA	uc002ian.2	+							NM_001070	NP_001061			tubulin, gamma 1						G2/M transition of mitotic cell cycle|meiotic spindle organization|protein polymerization	condensed nuclear chromosome|cytosol|gamma-tubulin complex|polar microtubule	GTP binding|GTPase activity|protein binding|structural constituent of cytoskeleton			ovary(1)	1		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.129)														---	---	---	---
LOC100190938	100190938	broad.mit.edu	37	17	40910163	40910163	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40910163delA	uc002ibd.1	-						LOC100190938_uc002ibe.3_Intron|LOC100190938_uc002ibf.3_Intron					Homo sapiens cDNA FLJ32559 fis, clone SPLEN1000144.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	40917133	40917134	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40917133_40917134insA								RAMP2 (2076 upstream) : VPS25 (8320 downstream)																																			---	---	---	---
BRCA1	672	broad.mit.edu	37	17	41283738	41283739	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41283738_41283739delAA	uc010whp.1	-						NBR2_uc002idf.2_Intron|NBR2_uc010czb.1_Intron|NBR2_uc002idg.2_Intron|NBR2_uc002idh.2_Intron	NM_007298	NP_009229			breast cancer 1, early onset isoform 4						androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)	52		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)				D|Mis|N|F|S		ovarian	breast|ovarian		Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_BRCA1_type	TCGA Ovarian(2;0.000030)			---	---	---	---
ETV4	2118	broad.mit.edu	37	17	41609865	41609865	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41609865delA	uc002idw.2	-						ETV4_uc002idv.2_5'Flank|ETV4_uc010wih.1_Intron|ETV4_uc010czh.2_Intron|ETV4_uc010wii.1_Intron|ETV4_uc002idx.2_Intron|ETV4_uc010wij.1_Intron	NM_001986	NP_001977			ets variant gene 4 (E1A enhancer binding						positive regulation of transcription, DNA-dependent	nucleolus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/ETV4(6)	bone(4)|soft_tissue(2)|ovary(1)	7		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)				T	EWSR1|TMPRSS2|DDX5|KLK2|CANT1	Ewing sarcoma|Prostate carcinoma								---	---	---	---
MPP3	4356	broad.mit.edu	37	17	41884348	41884348	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41884348delT	uc002iei.3	-						MPP3_uc002ieh.2_Intron|MPP3_uc002iej.2_Intron	NM_001932	NP_001923			palmitoylated membrane protein 3						signal transduction	cell surface|integral to plasma membrane	guanylate kinase activity			large_intestine(1)|skin(1)	2		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)														---	---	---	---
MPP3	4356	broad.mit.edu	37	17	41889846	41889846	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41889846delT	uc002iei.3	-						MPP3_uc002ieh.2_Intron|MPP3_uc002iej.2_Intron	NM_001932	NP_001923			palmitoylated membrane protein 3						signal transduction	cell surface|integral to plasma membrane	guanylate kinase activity			large_intestine(1)|skin(1)	2		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)														---	---	---	---
CCDC43	124808	broad.mit.edu	37	17	42756538	42756539	+	Intron	DEL	TA	-	-	rs78029716	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42756538_42756539delTA	uc002ihc.2	-						CCDC43_uc010czw.1_Intron	NM_144609	NP_653210			coiled-coil domain containing 43 isoform 1												0		Prostate(33;0.0322)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	42914726	42914726	+	IGR	DEL	A	-	-	rs149193880		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42914726delA								GJC1 (6547 upstream) : HIGD1B (10553 downstream)																																			---	---	---	---
FMNL1	752	broad.mit.edu	37	17	43309961	43309962	+	Intron	INS	-	GT	GT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43309961_43309962insGT	uc002iin.2	+						FMNL1_uc002iio.2_Intron|FMNL1_uc002iip.1_5'Flank	NM_005892	NP_005883			formin-like 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	43438137	43438137	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43438137delG								MAP3K14 (43723 upstream) : ARHGAP27 (33132 downstream)																																			---	---	---	---
CRHR1	1394	broad.mit.edu	37	17	43899264	43899264	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43899264delT	uc010dap.2	+						CRHR1_uc010wjx.1_Intron|CRHR1_uc002ijp.2_Intron|CRHR1_uc002ijm.2_Intron|CRHR1_uc002ijn.2_Intron|CRHR1_uc010dar.2_Intron|CRHR1_uc010dao.2_Intron|CRHR1_uc010daq.2_Intron|CRHR1_uc010das.1_Intron|CRHR1_uc002ijo.1_Intron	NM_001145146	NP_001138618			corticotropin releasing hormone receptor 1						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)														---	---	---	---
LOC100128977	100128977	broad.mit.edu	37	17	43928630	43928631	+	Intron	DEL	CA	-	-	rs66575115		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43928630_43928631delCA	uc010wjz.1	-							NR_024559				Homo sapiens cDNA clone IMAGE:4819956.												0																		---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44107957	44107958	+	3'UTR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44107957_44107958delAA	uc002ikb.2	-	14					KIAA1267_uc002ikc.2_3'UTR|KIAA1267_uc002ikd.2_3'UTR|KIAA1267_uc010dav.2_3'UTR|KIAA1267_uc010wkb.1_3'UTR|KIAA1267_uc010wkc.1_3'UTR	NM_015443	NP_056258			hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44260645	44260646	+	Intron	DEL	TT	-	-	rs68180932		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44260645_44260646delTT	uc002ikc.2	-						KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258			hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	44324687	44324687	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44324687delT								KIAA1267 (21970 upstream) : ARL17B (39176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	45133473	45133474	+	5'Flank	DEL	AA	-	-	rs71683829		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45133473_45133474delAA	uc010wkn.1	-						uc002ilc.1_RNA					Homo sapiens mRNA for ADP-ribosylation factor 7 variant protein.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	45191008	45191011	+	IGR	DEL	TTTT	-	-	rs71365040		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45191008_45191011delTTTT								GOSR2 (86014 upstream) : CDC27 (4302 downstream)																																			---	---	---	---
ITGB3	3690	broad.mit.edu	37	17	45369432	45369432	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45369432delT	uc002ilj.2	+						ITGB3_uc010wkr.1_Intron	NM_000212	NP_000203			integrin beta chain, beta 3 precursor						activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)													---	---	---	---
ITGB3	3690	broad.mit.edu	37	17	45386382	45386382	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45386382delC	uc002ilj.2	+						ITGB3_uc010wkr.1_Intron	NM_000212	NP_000203			integrin beta chain, beta 3 precursor						activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)													---	---	---	---
C17orf57	124989	broad.mit.edu	37	17	45470468	45470468	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45470468delA	uc002iln.2	+						C17orf57_uc002ilm.2_Intron	NM_152347	NP_689560			hypothetical protein LOC124989								calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
NPEPPS	9520	broad.mit.edu	37	17	45651873	45651874	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45651873_45651874delAC	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010dba.1_Intron	NM_006310	NP_006301			aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0																		---	---	---	---
NPEPPS	9520	broad.mit.edu	37	17	45696921	45696921	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45696921delA	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010wkv.1_Intron|NPEPPS_uc002ils.1_3'UTR	NM_006310	NP_006301			aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	45843017	45843017	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45843017delT								TBX21 (19532 upstream) : OSBPL7 (41716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	45948988	45948988	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45948988delT								SP6 (15748 upstream) : SP2 (24528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	45951408	45951410	+	IGR	DEL	TCT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45951408_45951410delTCT								SP6 (18168 upstream) : SP2 (22106 downstream)																																			---	---	---	---
SKAP1	8631	broad.mit.edu	37	17	46330608	46330608	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46330608delG	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717			src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0																		---	---	---	---
HOXB3	3213	broad.mit.edu	37	17	46635384	46635384	+	Intron	DEL	T	-	-	rs12451108	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46635384delT	uc010dbf.2	-						HOXB3_uc010wlm.1_Intron|HOXB3_uc010dbg.2_Intron|HOXB3_uc002ino.2_Intron|HOXB3_uc010wlk.1_Intron|HOXB3_uc010wll.1_Intron	NM_002146	NP_002137			homeobox B3						angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	46952062	46952062	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46952062delA								CALCOCO2 (9834 upstream) : ATP5G1 (18086 downstream)																																			---	---	---	---
UBE2Z	65264	broad.mit.edu	37	17	47000129	47000129	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47000129delA	uc002ioi.2	+							NM_023079	NP_075567			ubiquitin-conjugating enzyme E2Z						apoptosis	cytoplasm|nucleus	ATP binding|ubiquitin-protein ligase activity				0																		---	---	---	---
SNF8	11267	broad.mit.edu	37	17	47011678	47011679	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47011678_47011679delTT	uc002ioj.2	-						SNF8_uc002iok.2_Intron	NM_007241	NP_009172			EAP30 subunit of ELL complex						cellular membrane organization|endosome transport|protein transport|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytosol|late endosome membrane|transcription factor complex	transcription factor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	47032178	47032179	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47032178_47032179delTT								SNF8 (10024 upstream) : GIP (3739 downstream)																																			---	---	---	---
ZNF652	22834	broad.mit.edu	37	17	47388601	47388601	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47388601delA	uc002iov.3	-						ZNF652_uc002iow.2_Intron|ZNF652_uc002iou.3_Intron	NM_001145365	NP_001138837			zinc finger protein 652						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	47608152	47608154	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47608152_47608154delAAA								NGFR (15787 upstream) : NXPH3 (45144 downstream)																																			---	---	---	---
FAM117A	81558	broad.mit.edu	37	17	47860770	47860770	+	Intron	DEL	T	-	-	rs113094953		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47860770delT	uc010wlz.1	-							NM_030802	NP_110429			family with sequence similarity 117, member A											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	48038333	48038334	+	IGR	INS	-	CAA	CAA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48038333_48038334insCAA								TAC4 (112954 upstream) : DLX4 (8228 downstream)																																			---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48681076	48681076	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48681076delT	uc002irk.1	+						CACNA1G_uc002iri.1_Intron|CACNA1G_uc002irj.1_Intron|CACNA1G_uc002irl.1_Intron|CACNA1G_uc002irm.1_Intron|CACNA1G_uc002irn.1_Intron|CACNA1G_uc002iro.1_Intron|CACNA1G_uc002irp.1_Intron|CACNA1G_uc002irq.1_Intron|CACNA1G_uc002irr.1_Intron|CACNA1G_uc002irs.1_Intron|CACNA1G_uc002irt.1_Intron|CACNA1G_uc002irv.1_Intron|CACNA1G_uc002irw.1_Intron|CACNA1G_uc002iru.1_Intron|CACNA1G_uc002irx.1_Intron|CACNA1G_uc002iry.1_Intron|CACNA1G_uc002irz.1_Intron|CACNA1G_uc002isa.1_Intron|CACNA1G_uc002isb.1_Intron|CACNA1G_uc002isc.1_Intron|CACNA1G_uc002isd.1_Intron|CACNA1G_uc002ise.1_Intron|CACNA1G_uc002isf.1_Intron|CACNA1G_uc002isg.1_Intron|CACNA1G_uc002ish.1_Intron|CACNA1G_uc002isi.1_Intron|CACNA1G_uc002isj.2_Intron	NM_018896	NP_061496			voltage-dependent calcium channel alpha 1G						axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
ANKRD40	91369	broad.mit.edu	37	17	48783022	48783024	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48783022_48783024delTTT	uc002iso.2	-							NM_052855	NP_443087			ankyrin repeat domain 40												0			BRCA - Breast invasive adenocarcinoma(22;2.03e-09)															---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49075700	49075700	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49075700delT	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002itf.2_Intron|SPAG9_uc002ita.2_Intron|SPAG9_uc002ite.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49076858	49076859	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49076858_49076859delAA	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002itf.2_Intron|SPAG9_uc002ita.2_Intron|SPAG9_uc002ite.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49082678	49082679	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49082678_49082679insA	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002itf.2_Intron|SPAG9_uc002ita.2_Intron|SPAG9_uc002ite.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49110385	49110387	+	Intron	DEL	TTT	-	-	rs67602011		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49110385_49110387delTTT	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002itf.2_Intron|SPAG9_uc002ita.2_Intron|SPAG9_uc002ite.2_Intron|SPAG9_uc002itg.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	49223883	49223883	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49223883delA								SPAG9 (25657 upstream) : NME1 (7037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	49567654	49567654	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49567654delA								UTP18 (192364 upstream) : CA10 (140021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51016967	51016968	+	IGR	INS	-	G	G	rs112924456		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51016967_51016968insG								CA10 (779590 upstream) : KIF2B (883271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51502174	51502175	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51502174_51502175delAA								None (None upstream) : KIF2B (398064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51925495	51925496	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51925495_51925496delAC								KIF2B (22922 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	53659573	53659573	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53659573delG								MMD (160232 upstream) : TMEM100 (137417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	53911170	53911170	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53911170delT								PCTP (56423 upstream) : ANKFN1 (319666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	54068944	54068944	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54068944delT								PCTP (214197 upstream) : ANKFN1 (161892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	54858516	54858517	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54858516_54858517delTG								NOG (185565 upstream) : C17orf67 (10758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	55010781	55010781	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55010781delA								TRIM25 (19372 upstream) : COIL (4782 downstream)																																			---	---	---	---
COIL	8161	broad.mit.edu	37	17	55019885	55019885	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55019885delT	uc002iuu.2	-							NM_004645	NP_004636			coilin							Cajal body|nucleolus	protein C-terminus binding			ovary(1)	1	Breast(9;6.15e-08)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	55233476	55233476	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55233476delT								AKAP1 (34767 upstream) : MSI2 (99736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	56048485	56048485	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56048485delC								CUEDC1 (15801 upstream) : VEZF1 (425 downstream)																																			---	---	---	---
RNF43	54894	broad.mit.edu	37	17	56446074	56446075	+	Intron	DEL	AA	-	-	rs71365882		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56446074_56446075delAA	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)																	---	---	---	---
PPM1E	22843	broad.mit.edu	37	17	56985807	56985807	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56985807delT	uc002iwx.2	+						PPM1E_uc010ddd.2_Intron	NM_014906	NP_055721			protein phosphatase 1E						protein dephosphorylation	cytoplasm|nucleolus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(3)|lung(1)|skin(1)	5	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	57293778	57293778	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57293778delA								C17orf71 (1168 upstream) : GDPD1 (4056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	57489919	57489919	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57489919delA								YPEL2 (10824 upstream) : DHX40 (152967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	57540557	57540557	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57540557delA								YPEL2 (61462 upstream) : DHX40 (102329 downstream)																																			---	---	---	---
RPS6KB1	6198	broad.mit.edu	37	17	57995303	57995303	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57995303delT	uc002ixy.2	+						RPS6KB1_uc010ddj.1_Intron|RPS6KB1_uc010wom.1_Intron|RPS6KB1_uc010won.1_Intron|RPS6KB1_uc010woo.1_Intron	NM_003161	NP_003152			ribosomal protein S6 kinase, 70kDa, polypeptide						apoptosis|G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|negative regulation of apoptosis|phosphatidylinositol-mediated signaling|positive regulation of mitotic cell cycle|positive regulation of translational initiation|TOR signaling cascade	cell junction|cytoplasm|cytosol|mitochondrial outer membrane|nucleus|nucleus|synapse|synaptosome	ATP binding|protein binding|protein kinase activity			large_intestine(1)	1	all_cancers(5;1.63e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.57e-12)|all cancers(12;6.41e-11)															---	---	---	---
RNFT1	51136	broad.mit.edu	37	17	58033900	58033900	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58033900delA	uc002iya.2	-	7	1113	c.1020delT	c.(1018-1020)TTTfs	p.F340fs	RNFT1_uc002iyb.2_RNA|RNFT1_uc002iyc.2_Frame_Shift_Del_p.F78fs	NM_016125	NP_057209	Q5M7Z0	RNFT1_HUMAN	PTD016 protein	340	Helical; (Potential).					integral to membrane	zinc ion binding				0	all_cancers(5;1.58e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;7.95e-12)|all cancers(12;1.34e-10)															---	---	---	---
USP32	84669	broad.mit.edu	37	17	58277560	58277560	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58277560delA	uc002iyo.1	-						USP32_uc002iyn.1_Intron	NM_032582	NP_115971			ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)															---	---	---	---
PPM1D	8493	broad.mit.edu	37	17	58733813	58733814	+	Intron	INS	-	A	A	rs76607874		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58733813_58733814insA	uc002iyt.1	+						PPM1D_uc010ddm.1_Intron	NM_003620	NP_003611			protein phosphatase 1D						negative regulation of cell proliferation|protein dephosphorylation|response to radiation	nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein binding|protein serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)															---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	58858640	58858640	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58858640delT	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	59036509	59036509	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59036509delA	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyx.1_Intron|BCAS3_uc002iyy.3_Intron	NM_001099432	NP_001092902			breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)															---	---	---	---
INTS2	57508	broad.mit.edu	37	17	59974795	59974796	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
MED13	9969	broad.mit.edu	37	17	60101639	60101639	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60101639delA	uc002izo.2	-						MED13_uc002izp.2_Intron	NM_005121	NP_005112			mediator complex subunit 13						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
EFCAB3	146779	broad.mit.edu	37	17	60483827	60483827	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60483827delT	uc002izu.1	+						EFCAB3_uc010wpc.1_Intron	NM_173503	NP_775774			EF-hand calcium binding domain 3 isoform b								calcium ion binding			skin(1)	1			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)															---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60540928	60540928	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60540928delA	uc002izx.3	+											SubName: Full=Putative uncharacterized protein TLK1; Flags: Fragment;						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	60642069	60642069	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60642069delA	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																		---	---	---	---
MIR633	693218	broad.mit.edu	37	17	61021673	61021673	+	RNA	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61021673delA	hsa-mir-633|MI0003648	+			c.98delA																				0																		---	---	---	---
CYB561	1534	broad.mit.edu	37	17	61522538	61522538	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61522538delA	uc002jas.2	-						CYB561_uc010ddt.2_Intron|CYB561_uc002jat.2_Intron|CYB561_uc010wpf.1_Intron|CYB561_uc010wpg.1_Intron	NM_001017916	NP_001017916			cytochrome b-561						electron transport chain|transport	integral to plasma membrane	cytochrome-b5 reductase activity|ferric-chelate reductase activity|metal ion binding			ovary(1)	1				READ - Rectum adenocarcinoma(1115;0.0689)														---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61870025	61870025	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61870025delT	uc002jbu.2	+						DDX42_uc002jbv.2_Intron|DDX42_uc002jbw.1_Intron	NM_007372	NP_031398			DEAD box polypeptide 42 protein						protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	61978838	61978839	+	IGR	INS	-	T	T	rs147941855		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61978838_61978839insT								CSH2 (4851 upstream) : CSHL1 (8126 downstream)																																			---	---	---	---
DDX5	1655	broad.mit.edu	37	17	62498069	62498069	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62498069delA	uc002jek.2	-						DDX5_uc010deh.2_Intron|DDX5_uc002jej.2_Intron|DDX5_uc010wqa.1_Intron	NM_004396	NP_004387			DEAD (Asp-Glu-Ala-Asp) box polypeptide 5						cell growth|regulation of alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA helicase activity|transcription cofactor activity			ovary(2)|lung(1)	3	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)					T	ETV4	prostate								---	---	---	---
SMURF2	64750	broad.mit.edu	37	17	62591117	62591117	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62591117delA	uc002jep.1	-						SMURF2_uc002jeq.1_Intron|SMURF2_uc002jer.1_Intron	NM_022739	NP_073576			SMAD specific E3 ubiquitin protein ligase 2						BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)															---	---	---	---
SMURF2	64750	broad.mit.edu	37	17	62611385	62611385	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62611385delA	uc002jep.1	-						SMURF2_uc002jeq.1_Intron|SMURF2_uc002jer.1_Intron	NM_022739	NP_073576			SMAD specific E3 ubiquitin protein ligase 2						BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)															---	---	---	---
RGS9	8787	broad.mit.edu	37	17	63145247	63145247	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63145247delT	uc002jfe.2	+						RGS9_uc010dem.2_Intron|RGS9_uc002jfd.2_Intron|RGS9_uc002jff.2_Intron	NM_003835	NP_003826			regulator of G-protein signaling 9 isoform 1						intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			ovary(2)|skin(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	63284806	63284806	+	IGR	DEL	C	-	-	rs111332446		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63284806delC								RGS9 (60987 upstream) : AXIN2 (239879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	63513343	63513344	+	IGR	DEL	TT	-	-	rs11295227		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63513343_63513344delTT								RGS9 (289524 upstream) : AXIN2 (11341 downstream)																																			---	---	---	---
AXIN2	8313	broad.mit.edu	37	17	63553446	63553446	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63553446delA	uc002jfi.2	-						AXIN2_uc010den.1_Intron|AXIN2_uc002jfh.2_Intron	NM_004655	NP_004646			axin 2						cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2														Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				---	---	---	---
AXIN2	8313	broad.mit.edu	37	17	63567853	63567853	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63567853delA	uc010den.1	-							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				---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64328083	64328084	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64328083_64328084insT	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728			protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)													---	---	---	---
HELZ	9931	broad.mit.edu	37	17	65164098	65164098	+	Intron	DEL	T	-	-	rs35055892		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65164098delT	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	65247720	65247720	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65247720delA								HELZ (6401 upstream) : PSMD12 (88900 downstream)																																			---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65548584	65548584	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65548584delT	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65618983	65618983	+	Intron	DEL	A	-	-	rs112921919		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65618983delA	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
LOC651250	651250	broad.mit.edu	37	17	66118371	66118372	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66118371_66118372insT	uc002jgq.2	+						LOC651250_uc002kit.2_Intron|LOC651250_uc002jgo.1_Intron	NR_027418				Homo sapiens cDNA FLJ33831 fis, clone CTONG2003937.												0																		---	---	---	---
SLC16A6	9120	broad.mit.edu	37	17	66265043	66265043	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66265043delA	uc002jgz.1	-	6					ARSG_uc002jhc.2_Intron|SLC16A6_uc002jha.1_3'UTR	NM_004694	NP_004685			solute carrier family 16, member 6							integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity				0	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)													---	---	---	---
PRKAR1A	5573	broad.mit.edu	37	17	66519361	66519361	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66519361delT	uc002jhg.2	+						PRKAR1A_uc002jhh.2_Intron|PRKAR1A_uc002jhi.2_Intron|PRKAR1A_uc002jhj.2_Intron|PRKAR1A_uc002jhk.2_Intron|PRKAR1A_uc002jhl.2_Intron|PRKAR1A_uc002jhm.2_Intron	NM_212471	NP_997636			cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity|protein binding			adrenal_gland(4)|lung(3)|thyroid(2)|soft_tissue(2)|breast(1)	12	Breast(10;1.64e-13)							T|Mis|N|F|S	RET	papillary thyroid	myxoma|endocrine|papillary thyroid			Carney_Complex|Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial|Cardiac_Myxomas_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	17	66659558	66659558	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66659558delT								FAM20A (62463 upstream) : ABCA8 (203875 downstream)																																			---	---	---	---
ABCA9	10350	broad.mit.edu	37	17	66986939	66986939	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66986939delA	uc002jhu.2	-						ABCA9_uc010dez.2_Intron	NM_080283	NP_525022			ATP-binding cassette, sub-family A, member 9						transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	67354711	67354716	+	IGR	DEL	CACACA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67354711_67354716delCACACA								ABCA5 (31388 upstream) : MAP2K6 (56122 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69026449	69026449	+	IGR	DEL	T	-	-	rs71957996		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69026449delT								KCNJ2 (850268 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69498917	69498918	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69498917_69498918delTG								None (None upstream) : SOX9 (618243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69542969	69542969	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69542969delT								None (None upstream) : SOX9 (574192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69870752	69870752	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69870752delA								None (None upstream) : SOX9 (246409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70203376	70203377	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70203376_70203377insA								SOX9 (80824 upstream) : SLC39A11 (438709 downstream)																																			---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	70642714	70642714	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70642714delT	uc002jjb.2	-	10					SLC39A11_uc002jja.2_3'UTR	NM_001159770	NP_001153242			solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1																		---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	71074635	71074635	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71074635delT	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242			solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	71111640	71111640	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71111640delT								SLC39A11 (22787 upstream) : SSTR2 (49520 downstream)																																			---	---	---	---
C17orf80	55028	broad.mit.edu	37	17	71239688	71239691	+	Intron	DEL	TTTT	-	-	rs111267869		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71239688_71239691delTTTT	uc002jjm.3	+						C17orf80_uc010wqu.1_Intron|C17orf80_uc010dfj.2_Intron|C17orf80_uc002jjk.1_Intron|C17orf80_uc002jjl.3_Intron	NM_017941	NP_060411			lung cancer-related protein 8 isoform a							integral to membrane				skin(1)	1			LUSC - Lung squamous cell carcinoma(166;0.197)															---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71484164	71484164	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71484164delT	uc010dfm.2	-							NM_001144952	NP_001138424			sidekick 2						cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71590630	71590631	+	Intron	DEL	GA	-	-	rs55926990		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71590630_71590631delGA	uc010dfm.2	-							NM_001144952	NP_001138424			sidekick 2						cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	71700353	71700353	+	IGR	DEL	C	-	-	rs111686085		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71700353delC								SDK2 (60126 upstream) : C17orf54 (45056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	72031216	72031216	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72031216delG								C17orf54 (206540 upstream) : RPL38 (168579 downstream)																																			---	---	---	---
TTYH2	94015	broad.mit.edu	37	17	72226397	72226397	+	Intron	DEL	T	-	-	rs113300879		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72226397delT	uc002jkc.2	+						TTYH2_uc010wqw.1_Intron	NM_032646	NP_116035			tweety 2 isoform 1							chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4																		---	---	---	---
DNAI2	64446	broad.mit.edu	37	17	72281357	72281357	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72281357delC	uc002jkf.2	+						DNAI2_uc002jkg.2_Intron|DNAI2_uc010dfp.2_Intron	NM_023036	NP_075462			dynein, axonemal, intermediate polypeptide 2						cilium assembly	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	microtubule motor activity			ovary(2)|central_nervous_system(1)	3														Kartagener_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	17	72457664	72457665	+	IGR	DEL	AA	-	-	rs113706985		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72457664_72457665delAA								GPRC5C (10945 upstream) : CD300A (4857 downstream)																																			---	---	---	---
CD300E	342510	broad.mit.edu	37	17	72612304	72612304	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72612304delG	uc002jlb.1	-							NM_181449	NP_852114			CD300e molecule precursor							integral to membrane|plasma membrane	receptor activity			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
GGA3	23163	broad.mit.edu	37	17	73243032	73243032	+	Intron	DEL	A	-	-	rs75940499		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73243032delA	uc002jni.1	-						GGA3_uc002jnj.1_Intron|GGA3_uc010wrw.1_Intron|GGA3_uc002jnk.1_Intron|GGA3_uc010wrx.1_Intron|GGA3_uc010wry.1_Intron|GGA3_uc010wrz.1_Intron	NM_138619	NP_619525			ADP-ribosylation factor binding protein 3						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding			ovary(1)|breast(1)	2			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	73290622	73290622	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73290622delA								SLC25A19 (5092 upstream) : GRB2 (23536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	73706338	73706339	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73706338_73706339delAA								SAP30BP (2200 upstream) : ITGB4 (11177 downstream)																																			---	---	---	---
ITGB4	3691	broad.mit.edu	37	17	73737888	73737888	+	Intron	DEL	A	-	-	rs113801225		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73737888delA	uc002jpg.2	+						ITGB4_uc002jph.2_Intron|ITGB4_uc002jpi.3_Intron|ITGB4_uc010dgp.1_Intron|ITGB4_uc002jpj.2_Intron	NM_000213	NP_000204			integrin beta 4 isoform 1 precursor						cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
GALK1	2584	broad.mit.edu	37	17	73758414	73758414	+	Intron	DEL	G	-	-	rs115710194	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73758414delG	uc010wsi.1	-						GALK1_uc002jpk.2_Intron	NM_000154	NP_000145			galactokinase 1						galactose catabolic process	cytosol	ATP binding|galactokinase activity|galactose binding				0	all_cancers(13;1.5e-07)		all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
UNK	85451	broad.mit.edu	37	17	73809979	73809979	+	Intron	DEL	G	-	-	rs74319437	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73809979delG	uc002jpm.2	+							NM_001080419	NP_001073888			zinc finger CCCH-type domain containing 5								nucleic acid binding|zinc ion binding				0			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
UNC13D	201294	broad.mit.edu	37	17	73835181	73835181	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73835181delA	uc002jpp.2	-						UNC13D_uc010wsk.1_Intron|UNC13D_uc002jpq.1_Intron|UNC13D_uc010dgq.1_Intron	NM_199242	NP_954712			unc-13 homolog D						positive regulation of exocytosis|regulation of mast cell degranulation	exocytic vesicle|late endosome|lysosome|membrane|recycling endosome	protein binding			upper_aerodigestive_tract(1)|skin(1)	2			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)											Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
EXOC7	23265	broad.mit.edu	37	17	74090830	74090831	+	Intron	DEL	TT	-	-	rs35625794		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74090830_74090831delTT	uc002jqs.2	-						EXOC7_uc010dgv.1_Intron|EXOC7_uc002jqq.2_Intron|EXOC7_uc010wsw.1_Intron|EXOC7_uc010wsx.1_Intron|EXOC7_uc002jqr.2_Intron|EXOC7_uc010wsv.1_Intron|EXOC7_uc002jqu.2_Intron	NM_001145297	NP_001138769			exocyst complex component 7 isoform 4						exocytosis|protein transport	centriolar satellite|cytosol|exocyst|plasma membrane	protein binding				0			LUSC - Lung squamous cell carcinoma(166;0.187)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	74115923	74115923	+	IGR	DEL	T	-	-	rs35859558		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74115923delT								EXOC7 (16055 upstream) : FOXJ1 (16494 downstream)																																			---	---	---	---
RNF157	114804	broad.mit.edu	37	17	74164510	74164510	+	Intron	DEL	T	-	-	rs72171845		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74164510delT	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)															---	---	---	---
FAM100B	283991	broad.mit.edu	37	17	74258358	74258360	+	5'Flank	DEL	TTT	-	-	rs10714336		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74258358_74258360delTTT	uc010wsy.1	+							NM_182565	NP_872371			hypothetical protein LOC283991											central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(166;0.187)															---	---	---	---
PRPSAP1	5635	broad.mit.edu	37	17	74317036	74317036	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74317036delT	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																		---	---	---	---
CYGB	114757	broad.mit.edu	37	17	74524640	74524640	+	3'UTR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74524640delG	uc002jru.1	-	4					CYGB_uc002jrv.1_3'UTR|PRCD_uc002jrw.1_Intron	NM_134268	NP_599030			cytoglobin						response to oxidative stress	cytoplasm	heme binding|oxygen binding|oxygen transporter activity|peroxidase activity				0																		---	---	---	---
MFSD11	79157	broad.mit.edu	37	17	74738584	74738587	+	Intron	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74738584_74738587delTTTT	uc002jta.2	+						MFSD11_uc002jtb.2_Intron|MFSD11_uc010dha.2_Intron|MFSD11_uc002jtc.2_Intron|MFSD11_uc002jtd.3_Intron|MFSD11_uc010dhb.2_Intron|MFSD11_uc002jte.2_Intron	NM_024311	NP_077287			major facilitator superfamily domain containing							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	74806585	74806585	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74806585delT								MFSD11 (31249 upstream) : MGAT5B (58213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	74956337	74956337	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74956337delT								MGAT5B (9867 upstream) : C17orf86 (128388 downstream)																																			---	---	---	---
SEC14L1	6397	broad.mit.edu	37	17	75187626	75187626	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75187626delT	uc002jto.2	+						SEC14L1_uc010dhc.2_Intron|SEC14L1_uc010wth.1_Intron|SEC14L1_uc002jtm.2_Intron|SEC14L1_uc010wti.1_Intron	NM_003003	NP_002994			SEC14 (S. cerevisiae)-like 1 isoform a						transport	Golgi apparatus|integral to membrane	binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	75246986	75246986	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75246986delG								SEC14L1 (33807 upstream) : SEPT9 (30506 downstream)																																			---	---	---	---
SEPT9	10801	broad.mit.edu	37	17	75408807	75408807	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75408807delA	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_Intron|SEPT9_uc002jtx.1_Intron|SEPT9_uc010wtl.1_Intron	NM_001113491	NP_001106963			septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)															---	---	---	---
TNRC6C	57690	broad.mit.edu	37	17	76067505	76067505	+	Intron	DEL	T	-	-	rs75702970		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76067505delT	uc002jud.2	+						TNRC6C_uc002juf.2_Intron|TNRC6C_uc002jue.2_Intron	NM_018996	NP_061869			trinucleotide repeat containing 6C isoform 2						gene silencing by RNA|regulation of translation		nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)															---	---	---	---
PGS1	9489	broad.mit.edu	37	17	76384582	76384582	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76384582delT	uc002jvm.2	+						PGS1_uc010wtt.1_Intron	NM_024419	NP_077733			phosphatidylglycerophosphate synthase 1						phospholipid biosynthetic process	endoplasmic reticulum|mitochondrion	ATP binding|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity				0			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	76585857	76585857	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76585857delA								DNAH17 (117001 upstream) : CYTH1 (84274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	76608749	76608749	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76608749delT								DNAH17 (139893 upstream) : CYTH1 (61382 downstream)																																			---	---	---	---
CYTH1	9267	broad.mit.edu	37	17	76686624	76686625	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76686624_76686625insA	uc002jvw.2	-						CYTH1_uc010wtv.1_Intron	NM_017456	NP_059430			cytohesin 1 isoform 2						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1																		---	---	---	---
USP36	57602	broad.mit.edu	37	17	76813820	76813822	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76813820_76813822delAAA	uc002jvz.1	-						USP36_uc002jwa.1_Intron|USP36_uc002jwc.1_Intron	NM_025090	NP_079366			ubiquitin specific peptidase 36						ubiquitin-dependent protein catabolic process	nucleolus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|kidney(1)	5			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)															---	---	---	---
ENGASE	64772	broad.mit.edu	37	17	77073557	77073557	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77073557delT	uc002jwv.2	+	2	200	c.192delT	c.(190-192)AGTfs	p.S64fs	ENGASE_uc002jwu.1_Frame_Shift_Del_p.S64fs|ENGASE_uc010wtz.1_5'UTR|ENGASE_uc002jww.2_5'Flank	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	64						cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity			skin(1)	1																		---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77289544	77289545	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77289544_77289545insC	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044			hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)															---	---	---	---
CARD14	79092	broad.mit.edu	37	17	78164412	78164412	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78164412delA	uc002jxw.1	+						CARD14_uc002jxt.1_Intron|CARD14_uc002jxv.2_Intron|CARD14_uc010wud.1_Intron|CARD14_uc002jxx.2_Intron|CARD14_uc010dhu.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)															---	---	---	---
CARD14	79092	broad.mit.edu	37	17	78166028	78166028	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78166028delT	uc002jxw.1	+						CARD14_uc002jxt.1_Intron|CARD14_uc002jxv.2_Intron|CARD14_uc010wud.1_Intron|CARD14_uc002jxx.2_Intron|CARD14_uc010dhu.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)															---	---	---	---
FLJ35220	284131	broad.mit.edu	37	17	78398800	78398800	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78398800delT	uc002jym.1	+						FLJ35220_uc002jyk.2_Intron|FLJ35220_uc002jyl.1_Intron|FLJ35220_uc002jyn.2_Intron	NM_173627	NP_775898			hypothetical protein LOC284131 isoform 1						DNA repair		endodeoxyribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding				0	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)										Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
BAIAP2	10458	broad.mit.edu	37	17	79072221	79072221	+	Intron	DEL	T	-	-	rs113631114		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79072221delT	uc002jzg.2	+						BAIAP2_uc002jyz.3_Intron|BAIAP2_uc002jza.2_Intron|BAIAP2_uc002jzc.2_Intron|BAIAP2_uc002jzb.2_Intron|BAIAP2_uc002jzd.2_Intron|BAIAP2_uc002jzf.2_Intron|BAIAP2_uc002jze.2_Intron|BAIAP2_uc010wuh.1_Intron|BAIAP2_uc002jzh.2_Intron|BAIAP2_uc010wui.1_Intron	NM_017451	NP_059345			BAI1-associated protein 2 isoform 2						axonogenesis|filopodium assembly|insulin receptor signaling pathway|regulation of actin cytoskeleton organization|response to bacterium	cell junction|cytoskeleton|cytosol|filopodium|nucleus|ruffle	cytoskeletal adaptor activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding				0	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)															---	---	---	---
BAHCC1	57597	broad.mit.edu	37	17	79413303	79413303	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79413303delT	uc002kaf.2	+						BAHCC1_uc002kae.2_Intron	NM_001080519	NP_001073988			BAH domain and coiled-coil containing 1								DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)															---	---	---	---
NPLOC4	55666	broad.mit.edu	37	17	79531110	79531111	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79531110_79531111delAC	uc002kat.3	-						NPLOC4_uc002kau.3_3'UTR|NPLOC4_uc010wur.1_3'UTR|NPLOC4_uc002kar.2_5'Flank|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)															---	---	---	---
NPLOC4	55666	broad.mit.edu	37	17	79586905	79586906	+	Intron	DEL	AA	-	-	rs79411706		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79586905_79586906delAA	uc002kat.3	-						NPLOC4_uc002kau.3_Intron|NPLOC4_uc010wur.1_Intron	NM_017921	NP_060391			nuclear protein localization 4						cellular membrane fusion|ER-associated protein catabolic process|Golgi organization	cytosol|endoplasmic reticulum|nuclear outer membrane-endoplasmic reticulum membrane network|nucleus	zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)															---	---	---	---
TSPAN10	83882	broad.mit.edu	37	17	79608192	79608192	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79608192delA	uc010die.2	+						TSPAN10_uc002kaw.1_5'Flank|TSPAN10_uc010did.1_5'Flank	NM_031945	NP_114151			tetraspanin 10							integral to membrane				ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.175)|Lung NSC(278;0.192)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	79706572	79706573	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79706572_79706573delTT								SLC25A10 (18531 upstream) : GCGR (55453 downstream)																																			---	---	---	---
ANAPC11	51529	broad.mit.edu	37	17	79857433	79857433	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79857433delT	uc002kbv.1	+						ANAPC11_uc002kbw.1_Intron|ANAPC11_uc002kbx.1_Intron|ANAPC11_uc002kby.1_Intron|ANAPC11_uc002kbz.1_Intron|ANAPC11_uc002kca.1_Intron|ANAPC11_uc002kcb.1_Intron|ANAPC11_uc002kcc.1_Intron|ANAPC11_uc010dih.1_Intron|NPB_uc002kcd.2_5'Flank	NM_016476	NP_057560			APC11 anaphase promoting complex subunit 11						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	zinc ion binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	80239419	80239426	+	IGR	DEL	TGTCTGTG	-	-	rs36230322		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80239419_80239426delTGTCTGTG								CSNK1D (7846 upstream) : CD7 (33320 downstream)																																			---	---	---	---
HEXDC	284004	broad.mit.edu	37	17	80380301	80380301	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80380301delT	uc002kew.2	+						HEXDC_uc002kev.3_Intron|HEXDC_uc010diq.2_Intron					SubName: Full=Hexosaminidase (Glycosyl hydrolase family 20, catalytic domain) containing, isoform CRA_c; SubName: Full=Hexosaminidase D;						carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)|skin(1)	2	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)															---	---	---	---
FOXK2	3607	broad.mit.edu	37	17	80525803	80525813	+	Intron	DEL	TTTTTTTTTTT	-	-	rs5822539		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80525803_80525813delTTTTTTTTTTT	uc002kfn.2	+						FOXK2_uc002kfm.1_Intron|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505			forkhead box K2						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)															---	---	---	---
RAB40B	10966	broad.mit.edu	37	17	80631081	80631081	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80631081delA	uc002kft.2	-						RAB40B_uc002kfs.2_Intron	NM_006822	NP_006813			RAB40B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			central_nervous_system(1)	1	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)															---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80799197	80799197	+	Intron	DEL	T	-	-	rs112302012		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80799197delT	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|ZNF750_uc002kga.2_5'Flank	NM_005993	NP_005984			beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)															---	---	---	---
B3GNTL1	146712	broad.mit.edu	37	17	80928764	80928764	+	Intron	DEL	C	-	-	rs56800267	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80928764delC	uc002kgg.1	-						B3GNTL1_uc002kgf.1_Intron|B3GNTL1_uc002kge.1_Intron	NM_001009905	NP_001009905			UDP-GlcNAc:betaGal								transferase activity, transferring glycosyl groups			ovary(1)|pancreas(1)	2	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	81015841	81015842	+	IGR	INS	-	C	C	rs145436820	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:81015841_81015842insC								B3GNTL1 (6155 upstream) : METRNL (21725 downstream)																																			---	---	---	---
COLEC12	81035	broad.mit.edu	37	18	404261	404261	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:404261delA	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	826766	826766	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:826766delT								YES1 (14224 upstream) : ADCYAP1 (78178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	918968	918968	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:918968delT								ADCYAP1 (6797 upstream) : C18orf2 (335422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	999876	999877	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:999876_999877delAA								ADCYAP1 (87705 upstream) : C18orf2 (254513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1041024	1041024	+	IGR	DEL	A	-	-	rs35055547		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1041024delA								ADCYAP1 (128853 upstream) : C18orf2 (213366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1657737	1657737	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1657737delT								C18orf2 (250556 upstream) : METTL4 (879788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1709318	1709318	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1709318delA								C18orf2 (302137 upstream) : METTL4 (828207 downstream)																																			---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2762350	2762350	+	Intron	DEL	A	-	-	rs76381514	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2762350delA	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
LOC727896	727896	broad.mit.edu	37	18	2946534	2946534	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2946534delT	uc010wyu.1	-	1	88	c.1delA	c.(1-3)ATGfs	p.M1fs	LPIN2_uc002klo.2_Intron	NR_026659				Homo sapiens cDNA clone IMAGE:4614712, containing frame-shift errors.												0																		---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3134954	3134954	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3134954delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3222880	3222880	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3222880delT	uc002klp.2	-						MYOM1_uc002klq.2_5'Flank	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	3361987	3361987	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3361987delT								MYL12B (83707 upstream) : TGIF1 (50085 downstream)																																			---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3549336	3549336	+	Intron	DEL	T	-	-	rs66468936		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3549336delT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3581673	3581674	+	Intron	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3581673_3581674insG	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3924961	3924961	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3924961delT	uc010wyz.1	-							NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4274072	4274073	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4274072_4274073insT	uc010wyz.1	-							NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	4841836	4841836	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4841836delT								DLGAP1 (386570 upstream) : LOC642597 (301836 downstream)																																			---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5466734	5466734	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5466734delA	uc002kmt.1	-						EPB41L3_uc010wzh.1_Intron|EPB41L3_uc002kmu.1_Intron|EPB41L3_uc010dkq.1_Intron|EPB41L3_uc010dks.1_Intron|EPB41L3_uc002kmv.1_Intron	NM_012307	NP_036439			erythrocyte membrane protein band 4.1-like 3						cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5																		---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5474655	5474655	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5474655delA	uc002kmt.1	-						EPB41L3_uc010wzh.1_Intron|EPB41L3_uc002kmu.1_Intron|EPB41L3_uc010dkq.1_Intron|EPB41L3_uc010dks.1_Intron|EPB41L3_uc002kmv.1_Intron	NM_012307	NP_036439			erythrocyte membrane protein band 4.1-like 3						cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5																		---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6139495	6139496	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6139495_6139496delCA	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron|L3MBTL4_uc002kmy.3_Intron	NM_173464	NP_775735			l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	7246699	7246700	+	IGR	DEL	TT	-	-	rs67805910		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7246699_7246700delTT								LRRC30 (14658 upstream) : PTPRM (320614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	7268440	7268440	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7268440delA								LRRC30 (36399 upstream) : PTPRM (298874 downstream)																																			---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	7585615	7585615	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7585615delT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8034145	8034146	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8034145_8034146delTT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8217277	8217278	+	Intron	INS	-	T	T	rs140629913	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8217277_8217278insT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8305899	8305899	+	Intron	DEL	T	-	-	rs113326579		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8305899delT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	8930696	8930697	+	IGR	INS	-	G	G	rs138404493	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8930696_8930697insG								KIAA0802 (97921 upstream) : NDUFV2 (171978 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	9071239	9071239	+	IGR	DEL	A	-	-	rs71956327		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9071239delA								KIAA0802 (238464 upstream) : NDUFV2 (31436 downstream)																																			---	---	---	---
TWSG1	57045	broad.mit.edu	37	18	9344745	9344745	+	Intron	DEL	G	-	-	rs7233751	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9344745delG	uc002knz.2	+						TWSG1_uc002koa.2_Intron	NM_020648	NP_065699			twisted gastrulation precursor											ovary(1)|pancreas(1)	2																		---	---	---	---
RALBP1	10928	broad.mit.edu	37	18	9479327	9479327	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9479327delT	uc002kob.2	+						RALBP1_uc002koc.2_Intron	NM_006788	NP_006779			ralA binding protein 1						chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	9680299	9680299	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9680299delT								PPP4R1 (65699 upstream) : RAB31 (27929 downstream)																																			---	---	---	---
RAB31	11031	broad.mit.edu	37	18	9786961	9786961	+	Intron	DEL	A	-	-	rs73385038	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9786961delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	10065539	10065540	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10065539_10065540delAC								VAPA (105522 upstream) : APCDD1 (389085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11427018	11427018	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11427018delA								FAM38B (725039 upstream) : GNAL (262118 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11625311	11625311	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11625311delA								FAM38B (923332 upstream) : GNAL (63825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11668905	11668905	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11668905delA	uc002kpx.1	-						uc002kpy.2_5'Flank					DQ573573																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	11677867	11677867	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11677867delT								FAM38B (975888 upstream) : GNAL (11269 downstream)																																			---	---	---	---
GNAL	2774	broad.mit.edu	37	18	11711398	11711398	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11711398delT	uc002kqc.2	+							NM_182978	NP_892023			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1																		---	---	---	---
GNAL	2774	broad.mit.edu	37	18	11876464	11876464	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11876464delA	uc010dkz.2	+						GNAL_uc002kqc.2_Intron|GNAL_uc002kqd.2_Intron|GNAL_uc010wzt.1_Intron	NM_001142339	NP_001135811			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1																		---	---	---	---
TUBB6	84617	broad.mit.edu	37	18	12317467	12317467	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12317467delA	uc002kqw.2	+						TUBB6_uc002kqv.2_Intron|TUBB6_uc010dld.2_Intron|TUBB6_uc002kqx.2_Intron|TUBB6_uc002kqy.2_Intron	NM_032525	NP_115914			tubulin, beta 6						'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0				READ - Rectum adenocarcinoma(1;0.0649)														---	---	---	---
SPIRE1	56907	broad.mit.edu	37	18	12451072	12451072	+	Intron	DEL	A	-	-	rs76865998		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12451072delA	uc002kre.2	-						SPIRE1_uc002krc.2_Intron|SPIRE1_uc010wzw.1_Intron|SPIRE1_uc010wzx.1_Intron|SPIRE1_uc010wzy.1_Intron	NM_001128626	NP_001122098			spire homolog 1 isoform a							cytoskeleton|perinuclear region of cytoplasm	actin binding				0																		---	---	---	---
PTPN2	5771	broad.mit.edu	37	18	12812607	12812607	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12812607delA	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)																---	---	---	---
RNMT	8731	broad.mit.edu	37	18	13742337	13742339	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13742337_13742339delAAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	14876164	14876165	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14876164_14876165delAA								ANKRD30B (23427 upstream) : LOC644669 (437390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15171400	15171400	+	IGR	DEL	G	-	-	rs113649772		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15171400delG								ANKRD30B (318663 upstream) : LOC644669 (142155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15208265	15208266	+	IGR	INS	-	CTTC	CTTC	rs144580791	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15208265_15208266insCTTC								ANKRD30B (355528 upstream) : LOC644669 (105289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15390602	15390604	+	IGR	DEL	GTG	-	-	rs58894375		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15390602_15390604delGTG								LOC644669 (64684 upstream) : None (None downstream)																																			---	---	---	---
ROCK1	6093	broad.mit.edu	37	18	18591167	18591167	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18591167delT	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	18913054	18913055	+	Intron	DEL	CG	-	-	rs73432762	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18913054_18913055delCG	uc010xam.1	+						GREB1L_uc002ktf.1_Intron|GREB1L_uc010dlp.1_Intron	NM_001142966	NP_001136438			growth regulation by estrogen in breast							integral to membrane					0																		---	---	---	---
MIB1	57534	broad.mit.edu	37	18	19303208	19303208	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19303208delT	uc002ktp.2	+							NM_020774	NP_065825			mindbomb homolog 1						Notch signaling pathway	centrosome|nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(5;0.212)															---	---	---	---
MIB1	57534	broad.mit.edu	37	18	19421585	19421585	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19421585delT	uc002ktq.2	+						MIB1_uc002ktp.2_Intron	NM_020774	NP_065825			mindbomb homolog 1						Notch signaling pathway	centrosome|nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(5;0.212)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	19557187	19557187	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19557187delT								MIB1 (106277 upstream) : GATA6 (192229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	19587777	19587777	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19587777delA								MIB1 (136867 upstream) : GATA6 (161639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	19853450	19853451	+	IGR	INS	-	TCT	TCT	rs138748322	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19853450_19853451insTCT								GATA6 (71223 upstream) : CTAGE1 (140113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	19981298	19981299	+	IGR	INS	-	A	A	rs77978287		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19981298_19981299insA								GATA6 (199071 upstream) : CTAGE1 (12265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	20287363	20287363	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20287363delA								CTAGE1 (289485 upstream) : RBBP8 (225932 downstream)																																			---	---	---	---
RBBP8	5932	broad.mit.edu	37	18	20542915	20542915	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20542915delT	uc002ktw.2	+						RBBP8_uc002kty.2_Intron|RBBP8_uc002ktz.2_Intron|RBBP8_uc002kua.2_Intron|RBBP8_uc002ktx.1_Intron	NM_002894	NP_002885			retinoblastoma binding protein 8 isoform a						cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter	nucleus	damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)|lung(1)|skin(1)	3	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RBBP8	5932	broad.mit.edu	37	18	20586151	20586153	+	Intron	DEL	AAA	-	-	rs76247305		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20586151_20586153delAAA	uc002ktw.2	+						RBBP8_uc002kty.2_Intron|RBBP8_uc002ktz.2_Intron|RBBP8_uc002kua.2_Intron|RBBP8_uc010xap.1_Intron	NM_002894	NP_002885			retinoblastoma binding protein 8 isoform a						cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter	nucleus	damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)|lung(1)|skin(1)	3	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
C18orf45	85019	broad.mit.edu	37	18	20848768	20848769	+	Intron	DEL	GT	-	-	rs72363310		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20848768_20848769delGT	uc010xaq.1	-											Homo sapiens cDNA FLJ41629 fis, clone DFNES2010502.							integral to membrane					0	all_cancers(21;0.000238)|all_epithelial(16;5.29e-06)|Lung NSC(20;0.00925)|Colorectal(14;0.0202)|all_lung(20;0.0255)|Ovarian(20;0.127)																	---	---	---	---
C18orf8	29919	broad.mit.edu	37	18	21108849	21108849	+	Intron	DEL	T	-	-	rs112216095		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21108849delT	uc010xax.1	+						C18orf8_uc002kul.2_Intron|C18orf8_uc010xay.1_Intron|NPC1_uc010dlu.1_RNA	NM_013326	NP_037458			colon cancer-associated protein Mic1											ovary(1)	1	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	18	21176550	21176550	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21176550delA								NPC1 (9969 upstream) : ANKRD29 (3430 downstream)																																			---	---	---	---
LAMA3	3909	broad.mit.edu	37	18	21479182	21479182	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21479182delT	uc002kuq.2	+						LAMA3_uc002kur.2_Intron|LAMA3_uc002kus.3_Intron|LAMA3_uc002kut.3_Intron	NM_198129	NP_937762			laminin alpha 3 subunit isoform 1						cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
TTC39C	125488	broad.mit.edu	37	18	21577845	21577845	+	Intron	DEL	A	-	-	rs75125151		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21577845delA	uc002kuu.2	+							NM_153211	NP_694943			tetratricopeptide repeat domain 39C isoform 2								binding			ovary(1)	1																		---	---	---	---
TTC39C	125488	broad.mit.edu	37	18	21600707	21600707	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21600707delT	uc002kuw.2	+						TTC39C_uc002kuu.2_Intron	NM_001135993	NP_001129465			tetratricopeptide repeat domain 39C isoform 1								binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	23432557	23432558	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23432557_23432558delTG								ZNF521 (500343 upstream) : SS18 (163661 downstream)																																			---	---	---	---
KCTD1	284252	broad.mit.edu	37	18	24221035	24221035	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24221035delT	uc010xbk.1	-							NM_198991	NP_945342			potassium channel tetramerisation domain						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|voltage-gated potassium channel complex	transcription corepressor activity|transcription factor binding|voltage-gated potassium channel activity			ovary(1)	1	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)															---	---	---	---
CHST9	83539	broad.mit.edu	37	18	24672042	24672042	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24672042delT	uc002kwd.2	-						C18orf16_uc010xbm.1_Intron|CHST9_uc002kwe.2_Intron	NM_031422	NP_113610			GalNAc-4-sulfotransferase 2						carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)																	---	---	---	---
CHST9	83539	broad.mit.edu	37	18	24736125	24736126	+	Intron	DEL	AA	-	-	rs11299491		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24736125_24736126delAA	uc002kwe.2	-						C18orf16_uc010xbm.1_Intron	NM_031422	NP_113610			GalNAc-4-sulfotransferase 2						carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)																	---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25589920	25589920	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25589920delT	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	26151810	26151810	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26151810delT								CDH2 (394365 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26548879	26548879	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26548879delA								CDH2 (791434 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27157726	27157726	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27157726delA								None (None upstream) : MIR302F (721150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28791379	28791392	+	IGR	DEL	TGTGTGTGTGTGTG	-	-	rs72323446		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28791379_28791392delTGTGTGTGTGTGTG								DSC1 (48560 upstream) : DSG1 (106660 downstream)																																			---	---	---	---
DSG1	1828	broad.mit.edu	37	18	28923779	28923779	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28923779delT	uc002kwp.2	+						DSG1_uc010xbp.1_5'UTR	NM_001942	NP_001933			desmoglein 1 preproprotein						calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	29396351	29396351	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29396351delA								MCART2 (55508 upstream) : KIAA1012 (12786 downstream)																																			---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29417682	29417684	+	Intron	DEL	AAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29417682_29417684delAAG	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron	NM_014939	NP_055754			hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0																		---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29450471	29450471	+	Intron	DEL	A	-	-	rs35527481		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29450471delA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron	NM_014939	NP_055754			hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0																		---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29489050	29489050	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29489050delA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron|KIAA1012_uc002kxe.2_Intron	NM_014939	NP_055754			hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0																		---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29496810	29496813	+	Intron	DEL	AAAA	-	-	rs151187328		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29496810_29496813delAAAA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron|KIAA1012_uc002kxe.2_Intron	NM_014939	NP_055754			hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0																		---	---	---	---
RNF138	51444	broad.mit.edu	37	18	29701097	29701097	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29701097delA	uc002kxg.2	+						RNF138_uc002kxh.2_Intron	NM_016271	NP_057355			ring finger protein 138 isoform 1						Wnt receptor signaling pathway	intracellular	ligase activity|protein kinase binding|zinc ion binding				0																		---	---	---	---
MEP1B	4225	broad.mit.edu	37	18	29796832	29796832	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29796832delA	uc002kxj.3	+							NM_005925	NP_005916			meprin A beta precursor						digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	29848873	29848873	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29848873delT	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588			family with sequence similarity 59, member A											ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	30168229	30168229	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30168229delT								WBP11P1 (73633 upstream) : KLHL14 (84405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	31992545	31992545	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31992545delT								NOL4 (189099 upstream) : DTNA (80709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33155855	33155855	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33155855delT								INO80C (77900 upstream) : GALNT1 (5923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33380349	33380350	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33380349_33380350delAC								GALNT1 (88552 upstream) : MIR187 (104431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33561914	33561914	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33561914delT								C18orf21 (2674 upstream) : RPRD1A (7873 downstream)																																			---	---	---	---
RPRD1A	55197	broad.mit.edu	37	18	33626851	33626852	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33626851_33626852delAA	uc002kzf.1	-						RPRD1A_uc002kze.1_Intron|RPRD1A_uc002kzg.2_Intron|RPRD1A_uc010dmw.2_Intron|RPRD1A_uc010dmx.2_Intron	NM_018170	NP_060640			regulation of nuclear pre-mRNA domain containing											ovary(1)|breast(1)	2																		---	---	---	---
MOCOS	55034	broad.mit.edu	37	18	33836815	33836815	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33836815delT	uc002kzq.3	+							NM_017947	NP_060417			molybdenum cofactor sulfurase						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	lyase activity|Mo-molybdopterin cofactor sulfurase activity|molybdenum ion binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34205516	34205516	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34205516delC	uc002kzt.1	+	10	1097	c.1000delC	c.(1000-1002)CCCfs	p.P334fs	FHOD3_uc002kzr.1_Frame_Shift_Del_p.P334fs|FHOD3_uc002kzs.1_Frame_Shift_Del_p.P334fs|FHOD3_uc002kzu.1_Frame_Shift_Del_p.P159fs|FHOD3_uc010dmz.1_Frame_Shift_Del_p.P87fs	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	334	GBD/FH3.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34683767	34683768	+	Intron	DEL	AC	-	-	rs145289192		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34683767_34683768delAC	uc002kzz.2	+						KIAA1328_uc002lab.2_Intron|KIAA1328_uc002lac.1_Intron|KIAA1328_uc010dnc.1_Intron	NM_020776	NP_065827			hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)														---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34742848	34742848	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34742848delA	uc002kzz.2	+						KIAA1328_uc002lab.2_Intron|KIAA1328_uc002lac.1_Intron|KIAA1328_uc010dnc.1_Intron	NM_020776	NP_065827			hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)														---	---	---	---
CELF4	56853	broad.mit.edu	37	18	35093905	35093908	+	Intron	DEL	GTGT	-	-	rs144370407		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35093905_35093908delGTGT	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565			bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	35602810	35602813	+	IGR	DEL	GTGT	-	-	rs140526175		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35602810_35602813delGTGT								CELF4 (456810 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35944308	35944308	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35944308delA								CELF4 (798308 upstream) : LOC647946 (842580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36124407	36124407	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36124407delT								CELF4 (978407 upstream) : LOC647946 (662481 downstream)																																			---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	37335883	37335884	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37335883_37335884delAA	uc002lal.1	-											Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	37397743	37397743	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37397743delA								LOC647946 (17461 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	37796197	37796197	+	IGR	DEL	T	-	-	rs112768534		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37796197delT								LOC647946 (415915 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38383441	38383441	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38383441delA								None (None upstream) : KC6 (676797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39038277	39038277	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39038277delT								None (None upstream) : KC6 (21961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39117094	39117096	+	IGR	DEL	ACA	-	-	rs58437931		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39117094_39117096delACA								KC6 (16533 upstream) : PIK3C3 (418103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	40029367	40029368	+	Intron	INS	-	TGTGTGTGTT	TGTGTGTGTT	rs143488308	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40029367_40029368insTGTGTGTGTT	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	40306749	40306749	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40306749delA								PIK3C3 (645305 upstream) : RIT2 (16444 downstream)																																			---	---	---	---
RIT2	6014	broad.mit.edu	37	18	40456027	40456027	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40456027delA	uc002lav.2	-						RIT2_uc010dnf.2_Intron	NM_002930	NP_002921			Ras-like without CAAX 2						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1																		---	---	---	---
RIT2	6014	broad.mit.edu	37	18	40604750	40604750	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40604750delT	uc002lav.2	-						RIT2_uc010dnf.2_Intron	NM_002930	NP_002921			Ras-like without CAAX 2						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	41340190	41340190	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41340190delT								SYT4 (482575 upstream) : SETBP1 (919948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41578971	41578971	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41578971delA								SYT4 (721356 upstream) : SETBP1 (681167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41697457	41697458	+	IGR	DEL	AC	-	-	rs5824528		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41697457_41697458delAC								SYT4 (839842 upstream) : SETBP1 (562680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41872652	41872652	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41872652delT								None (None upstream) : SETBP1 (387486 downstream)																																			---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42296041	42296041	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42296041delT	uc010dni.2	+						SETBP1_uc002lay.2_Intron	NM_015559	NP_056374			SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42342104	42342105	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42342104_42342105delTT	uc010dni.2	+						SETBP1_uc002lay.2_Intron	NM_015559	NP_056374			SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42623405	42623406	+	Intron	DEL	AA	-	-	rs34933092		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42623405_42623406delAA	uc010dni.2	+							NM_015559	NP_056374			SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43121111	43121115	+	Intron	DEL	CAACA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43121111_43121115delCAACA	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron	NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43216750	43216750	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43216750delA	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron|SLC14A2_uc002lbe.2_Intron	NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43486621	43486621	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43486621delT	uc002lbm.2	-						KIAA1632_uc010xcq.1_Intron|KIAA1632_uc010xcr.1_Intron|KIAA1632_uc010xcs.1_Intron|KIAA1632_uc002lbn.2_Intron	NM_020964	NP_066015			hypothetical protein LOC57724						autophagy						0																		---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43529365	43529365	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
C18orf25	147339	broad.mit.edu	37	18	43790020	43790020	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43790020delA	uc002lbw.2	+						C18orf25_uc002lbx.2_Intron	NM_145055	NP_659492			ARKadia-like 1 isoform a											central_nervous_system(2)	2																		---	---	---	---
C18orf25	147339	broad.mit.edu	37	18	43830458	43830459	+	Intron	DEL	AC	-	-	rs33930478		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43830458_43830459delAC	uc002lbw.2	+						C18orf25_uc002lbx.2_Intron	NM_145055	NP_659492			ARKadia-like 1 isoform a											central_nervous_system(2)	2																		---	---	---	---
PIAS2	9063	broad.mit.edu	37	18	44402416	44402416	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44402416delA	uc002lck.2	-						PIAS2_uc010dnp.2_Intron|PIAS2_uc002lcl.2_Intron|PIAS2_uc010xda.1_Intron	NM_004671	NP_004662			protein inhibitor of activated STAT X isoform						androgen receptor signaling pathway|negative regulation of androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|PML body	androgen receptor binding|DNA binding|protein binding|SUMO ligase activity|transcription coactivator activity|zinc ion binding			ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
KATNAL2	83473	broad.mit.edu	37	18	44624593	44624593	+	Intron	DEL	A	-	-	rs3030956		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44624593delA	uc002lco.2	+						KATNAL2_uc010dnq.1_3'UTR|KATNAL2_uc002lcp.3_Intron	NM_031303	NP_112593			katanin p60 subunit A-like 2							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45786889	45786889	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45786889delA	uc010dnw.2	-						ZBTB7C_uc010dny.1_Intron|ZBTB7C_uc010dnz.1_Intron|ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449			zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45894341	45894341	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45894341delA	uc010dnw.2	-						ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449			zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	45986052	45986052	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45986052delT								ZBTB7C (50389 upstream) : KIAA0427 (79375 downstream)																																			---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46229283	46229283	+	Intron	DEL	A	-	-	rs35209703		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46229283delA	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron	NM_014772	NP_055587			hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46287569	46287569	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46287569delA	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron|KIAA0427_uc002lde.3_5'UTR	NM_014772	NP_055587			hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
SMAD7	4092	broad.mit.edu	37	18	46447012	46447012	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46447012delA	uc002ldg.2	-	4					SMAD7_uc002ldf.2_3'UTR|SMAD7_uc010xde.1_3'UTR	NM_005904	NP_005895			SMAD family member 7						adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex	activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding				0	Colorectal(1;0.0518)																	---	---	---	---
Unknown	0	broad.mit.edu	37	18	47196331	47196332	+	IGR	DEL	TT	-	-	rs11307739		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47196331_47196332delTT								LIPG (77055 upstream) : ACAA2 (113543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	47896274	47896274	+	IGR	DEL	T	-	-	rs112554641		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47896274delT								CXXC1 (81582 upstream) : SKA1 (5118 downstream)																																			---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48175383	48175383	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48175383delA	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	48274844	48274845	+	IGR	INS	-	CC	CC	rs140437919	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48274844_48274845insCC								MAPK4 (16649 upstream) : MRO (46646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	48656530	48656530	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48656530delT								SMAD4 (45121 upstream) : MEX3C (44392 downstream)																																			---	---	---	---
DCC	1630	broad.mit.edu	37	18	49900647	49900647	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49900647delG	uc002lfe.1	+							NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50341782	50341785	+	Intron	DEL	ACAC	-	-	rs35478640		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50341782_50341785delACAC	uc002lfe.1	+						DCC_uc010xdr.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50432877	50432880	+	Intron	DEL	TTTT	-	-	rs74178690		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50432877_50432880delTTTT	uc002lfe.1	+						DCC_uc010xdr.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50676539	50676539	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50676539delC	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50806228	50806229	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50806228_50806229delCT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50918705	50918705	+	Intron	DEL	T	-	-	rs35823251		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50918705delT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	51788073	51788073	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51788073delA								MBD2 (36915 upstream) : POLI (7776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	52213301	52213301	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52213301delT								C18orf54 (304898 upstream) : C18orf26 (41687 downstream)																																			---	---	---	---
RAB27B	5874	broad.mit.edu	37	18	52551371	52551371	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52551371delA	uc002lfr.2	+							NM_004163	NP_004154			RAB27B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi apparatus|plasma membrane	GTP binding|GTPase activity				0				Colorectal(16;0.0273)|READ - Rectum adenocarcinoma(59;0.219)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	52662521	52662521	+	IGR	DEL	A	-	-	rs113004913		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52662521delA								CCDC68 (35782 upstream) : TCF4 (227041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	52705548	52705549	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52705548_52705549delAA								CCDC68 (78809 upstream) : TCF4 (184013 downstream)																																			---	---	---	---
TCF4	6925	broad.mit.edu	37	18	53051266	53051266	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53051266delA	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)												OREG0024991	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TCF4	6925	broad.mit.edu	37	18	53239665	53239666	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53239665_53239666delGA	uc002lfz.2	-						TCF4_uc010xdx.1_Intron|TCF4_uc010dph.1_Intron|TCF4_uc010xdy.1_Intron|TCF4_uc002lga.2_Intron|TCF4_uc010dpi.2_Intron	NM_003199	NP_003190			transcription factor 4 isoform b						positive regulation of neuron differentiation|protein-DNA complex assembly|transcription initiation from RNA polymerase II promoter	transcription factor complex	E-box binding|protein C-terminus binding|protein heterodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity|TFIIB-class binding transcription factor activity|TFIIB-class transcription factor binding			ovary(1)|lung(1)	2				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	54148876	54148877	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54148876_54148877delAC								TCF4 (845691 upstream) : TXNL1 (121178 downstream)																																			---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54508240	54508240	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54508240delG	uc002lgk.1	+						WDR7_uc010dpk.1_Intron|WDR7_uc002lgl.1_Intron	NM_015285	NP_056100			rabconnectin-3 beta isoform 1											ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	54785487	54785487	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54785487delT								WDR7 (88451 upstream) : ST8SIA3 (234234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	54858675	54858676	+	IGR	DEL	GT	-	-	rs111340005		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54858675_54858676delGT								WDR7 (161639 upstream) : ST8SIA3 (161045 downstream)																																			---	---	---	---
ATP8B1	5205	broad.mit.edu	37	18	55346462	55346462	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55346462delA	uc002lgw.2	-						uc002lgv.1_Intron	NM_005603	NP_005594			ATPase, class I, type 8B, member 1						ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent	apical plasma membrane|integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			breast(5)|ovary(2)|central_nervous_system(2)|lung(1)	10		Colorectal(73;0.229)												Byler_disease				---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55937615	55937615	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55937615delC	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|NEDD4L_uc002lhh.2_Intron	NM_001144967	NP_001138439			neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4																		---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55992061	55992061	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55992061delT	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron|NEDD4L_uc002lhg.2_Intron|NEDD4L_uc002lhh.2_Intron|NEDD4L_uc010dpm.1_Intron	NM_001144967	NP_001138439			neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	56418629	56418630	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56418629_56418630delTT								MALT1 (1259 upstream) : ZNF532 (111431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58628956	58628956	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58628956delA								MC4R (588955 upstream) : CDH20 (372032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58660252	58660252	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58660252delT								MC4R (620251 upstream) : CDH20 (340736 downstream)																																			---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59075438	59075439	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59075438_59075439insA	uc002lif.2	+							NM_031891	NP_114097			cadherin 20, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)																---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59167188	59167188	+	Intron	DEL	T	-	-	rs7229087	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59167188delT	uc010dps.1	+						CDH20_uc002lif.2_Intron	NM_031891	NP_114097			cadherin 20, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	59235318	59235318	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59235318delT								CDH20 (12953 upstream) : RNF152 (246986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	59436782	59436783	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59436782_59436783insT								CDH20 (214417 upstream) : RNF152 (45521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	59608863	59608863	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59608863delT								RNF152 (48559 upstream) : PIGN (102597 downstream)																																			---	---	---	---
KIAA1468	57614	broad.mit.edu	37	18	59924114	59924114	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59924114delT	uc002lil.2	+						KIAA1468_uc002lik.1_Intron|KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_Intron	NM_020854	NP_065905			hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)																---	---	---	---
PHLPP1	23239	broad.mit.edu	37	18	60495241	60495242	+	Intron	INS	-	TG	TG	rs138353650	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60495241_60495242insTG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	61189626	61189626	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61189626delA								SERPINB5 (17309 upstream) : SERPINB12 (33767 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	61241301	61241312	+	IGR	DEL	AAACAAACAAAC	-	-	rs72464461		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61241301_61241312delAAACAAACAAAC								SERPINB12 (7059 upstream) : SERPINB13 (13222 downstream)																																			---	---	---	---
SERPINB2	5055	broad.mit.edu	37	18	61573559	61573559	+	Intron	DEL	C	-	-	rs112826446		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61573559delC	uc002ljp.1	+						SERPINB2_uc002ljq.1_Intron|SERPINB10_uc010xev.1_5'Flank	NM_002575	NP_002566			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	63697468	63697468	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63697468delA								CDH7 (149294 upstream) : CDH19 (473853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	64659090	64659090	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64659090delA								CDH19 (387874 upstream) : DSEL (514729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	65042307	65042308	+	IGR	DEL	TT	-	-	rs75002100		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65042307_65042308delTT								CDH19 (771091 upstream) : DSEL (131511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66165496	66165499	+	IGR	DEL	ATAA	-	-	rs36009088		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66165496_66165499delATAA								DSEL (981529 upstream) : TMX3 (175428 downstream)																																			---	---	---	---
CCDC102B	79839	broad.mit.edu	37	18	66414901	66414901	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66414901delC	uc002lkk.2	+						CCDC102B_uc002lkh.2_Intron	NM_001093729	NP_001087198			coiled-coil domain containing 102B											ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)																---	---	---	---
CCDC102B	79839	broad.mit.edu	37	18	66695870	66695871	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66695870_66695871delAC	uc002lkk.2	+						CCDC102B_uc002lki.2_Intron	NM_001093729	NP_001087198			coiled-coil domain containing 102B											ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	66807140	66807140	+	IGR	DEL	A	-	-	rs72140484		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66807140delA								CCDC102B (84714 upstream) : DOK6 (261151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	67029331	67029331	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67029331delT								CCDC102B (306905 upstream) : DOK6 (38960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	67046061	67046061	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67046061delT								CCDC102B (323635 upstream) : DOK6 (22230 downstream)																																			---	---	---	---
DOK6	220164	broad.mit.edu	37	18	67084169	67084169	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67084169delT	uc002lkl.2	+							NM_152721	NP_689934			docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)																---	---	---	---
DOK6	220164	broad.mit.edu	37	18	67309064	67309064	+	Intron	DEL	A	-	-	rs143429781	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67309064delA	uc002lkl.2	+							NM_152721	NP_689934			docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)																---	---	---	---
DOK6	220164	broad.mit.edu	37	18	67314294	67314295	+	Intron	INS	-	CTAT	CTAT	rs150522257	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67314294_67314295insCTAT	uc002lkl.2	+							NM_152721	NP_689934			docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)																---	---	---	---
DOK6	220164	broad.mit.edu	37	18	67488987	67488987	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67488987delT	uc002lkl.2	+							NM_152721	NP_689934			docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)																---	---	---	---
DOK6	220164	broad.mit.edu	37	18	67490862	67490865	+	Intron	DEL	TGTG	-	-	rs142252587		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67490862_67490865delTGTG	uc002lkl.2	+							NM_152721	NP_689934			docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)																---	---	---	---
CD226	10666	broad.mit.edu	37	18	67592684	67592684	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67592684delT	uc010dqo.2	-						CD226_uc002lkm.3_Intron	NM_006566	NP_006557			CD226 molecule precursor						cell adhesion|cell recognition|positive regulation of Fc receptor mediated stimulatory signaling pathway|positive regulation of immunoglobulin mediated immune response|positive regulation of mast cell activation|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	cell surface|integral to plasma membrane|membrane raft	cell adhesion molecule binding|integrin binding|protein kinase binding|receptor activity				0		Esophageal squamous(42;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	68065382	68065382	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68065382delT								SOCS6 (67948 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	68587217	68587217	+	IGR	DEL	A	-	-	rs33997882		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68587217delA								SOCS6 (589783 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	68904134	68904135	+	IGR	DEL	TT	-	-	rs113679881		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68904134_68904135delTT								SOCS6 (906700 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69263843	69263843	+	IGR	DEL	T	-	-	rs75832271		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69263843delT								None (None upstream) : CBLN2 (940072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69489290	69489293	+	IGR	DEL	TGTT	-	-	rs5826115		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69489290_69489293delTGTT								None (None upstream) : CBLN2 (714622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69807029	69807029	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69807029delG								None (None upstream) : CBLN2 (396886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69850224	69850224	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69850224delA								None (None upstream) : CBLN2 (353691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69874758	69874758	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69874758delT								None (None upstream) : CBLN2 (329157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	70142700	70142700	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70142700delT								None (None upstream) : CBLN2 (61215 downstream)																																			---	---	---	---
CBLN2	147381	broad.mit.edu	37	18	70206408	70206408	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70206408delA	uc002lku.2	-						CBLN2_uc002lkv.2_Intron	NM_182511	NP_872317			cerebellin 2 precursor							integral to membrane					0		Esophageal squamous(42;0.131)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	71004972	71004972	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71004972delA	uc002llc.1	+											Homo sapiens cDNA clone IMAGE:4667929, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	71412134	71412134	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71412134delA								NETO1 (877324 upstream) : FBXO15 (328454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71534035	71534035	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71534035delT								NETO1 (999225 upstream) : FBXO15 (206553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71734228	71734228	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71734228delC								None (None upstream) : FBXO15 (6360 downstream)																																			---	---	---	---
FBXO15	201456	broad.mit.edu	37	18	71795570	71795571	+	Intron	DEL	AA	-	-	rs34174491		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71795570_71795571delAA	uc002lle.2	-						FBXO15_uc002llf.2_Intron	NM_152676	NP_689889			F-box protein 15 isoform 1											ovary(2)|pancreas(1)	3		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)														---	---	---	---
ZNF407	55628	broad.mit.edu	37	18	72365819	72365819	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72365819delA	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	72455320	72455321	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72455320_72455321delTG	uc002llw.2	+						ZNF407_uc010xfc.1_Intron|ZNF407_uc010dqu.1_Intron	NM_017757	NP_060227			zinc finger protein 407 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)														---	---	---	---
ZADH2	284273	broad.mit.edu	37	18	72909864	72909865	+	3'UTR	INS	-	TT	TT	rs145659695	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72909864_72909865insTT	uc002llx.2	-	2					ZADH2_uc010dqv.2_3'UTR	NM_175907	NP_787103			zinc binding alcohol dehydrogenase domain							peroxisome	oxidoreductase activity|zinc ion binding				0		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	73089334	73089334	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73089334delA								TSHZ1 (87434 upstream) : C18orf62 (32493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73214592	73214592	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73214592delA								C18orf62 (75003 upstream) : ZNF516 (857027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73756579	73756580	+	IGR	INS	-	AC	AC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73756579_73756580insAC								C18orf62 (616990 upstream) : ZNF516 (315039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	74496289	74496290	+	IGR	DEL	GT	-	-	rs143560228		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74496289_74496290delGT								LOC284276 (224506 upstream) : ZNF236 (39826 downstream)																																			---	---	---	---
ZNF236	7776	broad.mit.edu	37	18	74680459	74680459	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74680459delA	uc002lmi.2	+	31					ZNF236_uc002lmj.2_RNA	NM_007345	NP_031371			zinc finger protein 236						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	74939581	74939584	+	IGR	DEL	AGTC	-	-	rs148880442		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74939581_74939584delAGTC								MBP (94807 upstream) : GALR1 (22424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75170580	75170580	+	IGR	DEL	T	-	-	rs68068926		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75170580delT								GALR1 (188486 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75238730	75238731	+	IGR	DEL	TG	-	-	rs148942639		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75238730_75238731delTG								GALR1 (256636 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75836981	75836981	+	IGR	DEL	T	-	-	rs11327589		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75836981delT								GALR1 (854887 upstream) : SALL3 (903294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75856744	75856744	+	IGR	DEL	A	-	-	rs78433627		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75856744delA								GALR1 (874650 upstream) : SALL3 (883531 downstream)																																			---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	77041498	77041498	+	Intron	DEL	A	-	-	rs35595923		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77041498delA	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmz.1_Intron	NM_198531	NP_940933			ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)														---	---	---	---
C18orf22	79863	broad.mit.edu	37	18	77802768	77802768	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77802768delA	uc002lns.2	+						C18orf22_uc010drh.2_Intron|C18orf22_uc010dri.1_Intron|C18orf22_uc002lnt.2_Intron	NM_024805	NP_079081			hypothetical protein LOC79863 precursor						rRNA processing	mitochondrion					0		all_cancers(4;3.21e-14)|all_epithelial(4;7.11e-09)|all_lung(4;0.00366)|Lung NSC(4;0.00683)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0545)|all_hematologic(56;0.15)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;6.46e-08)|BRCA - Breast invasive adenocarcinoma(31;0.00376)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	251753	251753	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:251753delA								FLJ45445 (49544 upstream) : PPAP2C (29293 downstream)																																			---	---	---	---
HCN2	610	broad.mit.edu	37	19	603265	603265	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:603265delG	uc002lpe.2	+							NM_001194	NP_001185			hyperpolarization activated cyclic						cell-cell signaling|muscle contraction	voltage-gated potassium channel complex	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
PRSSL1	400668	broad.mit.edu	37	19	691213	691213	+	Intron	DEL	A	-	-	rs147436553		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:691213delA	uc002lpl.1	-						PRSSL1_uc010xfs.1_Intron	NM_214710	NP_999875			protease, serine-like 1 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
LPPR3	79948	broad.mit.edu	37	19	817291	817291	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:817291delT	uc002lpx.1	-						LPPR3_uc010dru.1_5'Flank|LPPR3_uc002lpw.1_Intron|LPPR3_uc002lpy.1_Intron	NM_024888	NP_079164			plasticity-related protein 2							integral to membrane	phosphatidate phosphatase activity				0																		---	---	---	---
PRTN3	5657	broad.mit.edu	37	19	845409	845409	+	Intron	DEL	A	-	-	rs77190755		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:845409delA	uc002lqa.1	+							NM_002777	NP_002768			myeloblastin						collagen catabolic process|positive regulation of cell proliferation|proteolysis		protein binding|serine-type endopeptidase activity			ovary(1)	1		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
MUM1	84939	broad.mit.edu	37	19	1372107	1372107	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1372107delT	uc010xgm.1	+						MUM1_uc002lrz.2_Intron|MUM1_uc002lsb.2_Intron|MUM1_uc002lsd.2_5'Flank					SubName: Full=MUM1 protein;						chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
APC2	10297	broad.mit.edu	37	19	1461863	1461863	+	Intron	DEL	C	-	-	rs9916972		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1461863delC	uc002lsr.1	+						APC2_uc002lss.1_Intron|APC2_uc002lst.1_Intron|APC2_uc002lsu.1_Intron|C19orf25_uc010xgn.1_Intron	NM_005883	NP_005874			adenomatosis polyposis coli 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|Wnt receptor signaling pathway	actin filament|catenin complex|cytoplasmic microtubule|Golgi membrane|lamellipodium membrane|perinuclear region of cytoplasm	beta-catenin binding|microtubule binding			breast(3)|pancreas(1)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	1542219	1542220	+	IGR	DEL	TC	-	-	rs2003289	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1542219_1542220delTC								PLK5P (6764 upstream) : MEX3D (12449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	1666505	1666506	+	IGR	INS	-	CTC	CTC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1666505_1666506insCTC								TCF3 (14179 upstream) : ONECUT3 (87156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	1677366	1677367	+	IGR	DEL	TT	-	-	rs75111299		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1677366_1677367delTT								TCF3 (25040 upstream) : ONECUT3 (76295 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	1929049	1929049	+	IGR	DEL	A	-	-	rs74327615		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1929049delA								SCAMP4 (3038 upstream) : CSNK1G2 (12112 downstream)																																			---	---	---	---
MOBKL2A	126308	broad.mit.edu	37	19	2095757	2095757	+	Intron	DEL	T	-	-	rs112997414		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2095757delT	uc002luv.2	-						C19orf36_uc002luw.1_5'Flank|C19orf36_uc002lux.1_5'Flank|C19orf36_uc010xgw.1_5'Flank	NM_130807	NP_570719			MOB-LAK							intracellular	metal ion binding			lung(1)	1		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
DOT1L	84444	broad.mit.edu	37	19	2164709	2164709	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2164709delT	uc002lvb.3	+							NM_032482	NP_115871			DOT1-like, histone H3 methyltransferase							nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SPPL2B	56928	broad.mit.edu	37	19	2348517	2348518	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2348517_2348518delTC	uc002lvs.2	+						SPPL2B_uc002lvr.2_Intron	NM_152988	NP_694533			signal peptide peptidase-like 2B isoform 2							Golgi membrane|integral to membrane	aspartic-type endopeptidase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SPPL2B	56928	broad.mit.edu	37	19	2349072	2349073	+	Intron	DEL	CC	-	-	rs68057588		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2349072_2349073delCC	uc002lvs.2	+						SPPL2B_uc002lvr.2_Intron	NM_152988	NP_694533			signal peptide peptidase-like 2B isoform 2							Golgi membrane|integral to membrane	aspartic-type endopeptidase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	2486196	2486196	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2486196delA								GADD45B (7939 upstream) : GNG7 (25022 downstream)																																			---	---	---	---
GNG7	2788	broad.mit.edu	37	19	2698265	2698265	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2698265delA	uc002lwd.2	-							NM_052847	NP_443079			guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SGTA	6449	broad.mit.edu	37	19	2757306	2757306	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2757306delC	uc002lwi.1	-							NM_003021	NP_003012			small glutamine-rich tetratricopeptide						interspecies interaction between organisms	cytoplasm	protein binding			ovary(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
TLE2	7089	broad.mit.edu	37	19	3032940	3032940	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3032940delT	uc010dti.2	-							NM_001144761	NP_001138233			transducin-like enhancer protein 2 isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
PIP5K1C	23396	broad.mit.edu	37	19	3642657	3642657	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3642657delA	uc002lyj.1	-						PIP5K1C_uc010xhq.1_Intron|PIP5K1C_uc010xhr.1_Intron	NM_012398	NP_036530			phosphatidylinositol-4-phosphate 5-kinase, type						axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)														---	---	---	---
PIP5K1C	23396	broad.mit.edu	37	19	3678976	3678977	+	Intron	INS	-	GATG	GATG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3678976_3678977insGATG	uc002lyj.1	-						PIP5K1C_uc010xhq.1_Intron|PIP5K1C_uc010xhr.1_Intron	NM_012398	NP_036530			phosphatidylinositol-4-phosphate 5-kinase, type						axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)														---	---	---	---
ZFR2	23217	broad.mit.edu	37	19	3867302	3867303	+	Intron	INS	-	GG	GG	rs139361358	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3867302_3867303insGG	uc002lyw.2	-						ZFR2_uc010xhx.1_Intron|ZFR2_uc002lyx.3_Intron|ZFR2_uc010xhy.1_Intron	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)														---	---	---	---
CCDC94	55702	broad.mit.edu	37	19	4265594	4265594	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4265594delT	uc002lzv.3	+							NM_018074	NP_060544			coiled-coil domain containing 94												0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0348)|STAD - Stomach adenocarcinoma(1328;0.183)														---	---	---	---
TMEM146	257062	broad.mit.edu	37	19	5739321	5739321	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5739321delT	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	5753573	5753573	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5753573delA	uc002mda.2	+						TMEM146_uc010duj.1_Intron	NM_152784	NP_689997			transmembrane protein 146 precursor							integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	5778767	5778767	+	IGR	DEL	T	-	-	rs111505087		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5778767delT								TMEM146 (26 upstream) : PRR22 (4204 downstream)																																			---	---	---	---
RFX2	5990	broad.mit.edu	37	19	6075284	6075286	+	Intron	DEL	GGA	-	-	rs8113072		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6075284_6075286delGGA	uc002meb.2	-						RFX2_uc002mec.2_Intron|RFX2_uc010xiy.1_Intron	NM_000635	NP_000626			regulatory factor X2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(4)|ovary(1)|skin(1)	6																		---	---	---	---
MLLT1	4298	broad.mit.edu	37	19	6251781	6251781	+	Intron	DEL	A	-	-	rs140498097		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6251781delA	uc002mek.2	-							NM_005934	NP_005925			myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|protein binding			skin(1)	1								T	MLL	AL								---	---	---	---
ACER1	125981	broad.mit.edu	37	19	6314481	6314481	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6314481delA	uc002mel.2	-							NM_133492	NP_597999			alkaline ceramidase 1							endoplasmic reticulum membrane|integral to membrane	ceramidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	6579600	6579600	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6579600delA								TNFSF9 (43661 upstream) : CD70 (3535 downstream)																																			---	---	---	---
VAV1	7409	broad.mit.edu	37	19	6852736	6852736	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6852736delA	uc002mfu.1	+						VAV1_uc010xjh.1_Intron|VAV1_uc010dva.1_Intron|VAV1_uc002mfv.1_Intron	NM_005428	NP_005419			vav 1 guanine nucleotide exchange factor						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16																		---	---	---	---
EMR1	2015	broad.mit.edu	37	19	6913192	6913192	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6913192delT	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)																	---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8187561	8187561	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8187561delT	uc002mjf.2	-							NM_032447	NP_115823			fibrillin 3 precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11																		---	---	---	---
LASS4	79603	broad.mit.edu	37	19	8322325	8322325	+	Intron	DEL	T	-	-	rs113321728		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8322325delT	uc002mjg.2	+						LASS4_uc002mjh.2_Intron|LASS4_uc002mji.2_Intron|LASS4_uc010dvz.2_Intron	NM_024552	NP_078828			LAG1 homolog, ceramide synthase 4							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			ovary(1)	1																		---	---	---	---
PRAM1	84106	broad.mit.edu	37	19	8567648	8567648	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8567648delT	uc002mkd.2	-						PRAM1_uc002mkc.2_5'Flank	NM_032152	NP_115528			PML-RARA regulated adaptor molecule 1								lipid binding|protein binding				0																		---	---	---	---
MYO1F	4542	broad.mit.edu	37	19	8634962	8634963	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8634962_8634963delTT	uc002mkg.2	-						MYO1F_uc002mkh.2_Intron|MYO1F_uc010xkf.1_Intron	NM_012335	NP_036467			myosin IF							unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	9286400	9286400	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9286400delT								ZNF317 (12311 upstream) : OR7D2 (9870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9337914	9337914	+	IGR	DEL	T	-	-	rs113475297		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9337914delT								OR7D4 (12401 upstream) : OR7E24 (23806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9574357	9574357	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9574357delT								ZNF266 (28123 upstream) : ZNF560 (2674 downstream)																																			---	---	---	---
ZNF121	7675	broad.mit.edu	37	19	9687007	9687008	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9687007_9687008delAA	uc010xkp.1	-						ZNF121_uc010dwt.2_Intron|ZNF121_uc010xkq.1_Intron	NM_001008727	NP_001008727			zinc finger protein 121						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZNF562	54811	broad.mit.edu	37	19	9785247	9785247	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9785247delT	uc010xks.1	-						ZNF562_uc002mly.2_Intron|ZNF562_uc002mlx.2_Intron|ZNF562_uc010xkt.1_Intron|ZNF562_uc010xku.1_Intron|ZNF562_uc010xkv.1_Intron|ZNF562_uc010xkw.1_Intron	NM_001130032	NP_001123504			zinc finger protein 562 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
COL5A3	50509	broad.mit.edu	37	19	10117130	10117131	+	Intron	DEL	TT	-	-	rs35938123		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10117130_10117131delTT	uc002mmq.1	-							NM_015719	NP_056534			collagen, type V, alpha 3 preproprotein						collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)															---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10573779	10573779	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10573779delT	uc002moj.2	+						PDE4A_uc002mok.2_Intron|PDE4A_uc002mol.2_Intron|PDE4A_uc002mom.2_Intron|PDE4A_uc002mon.2_Intron|PDE4A_uc002moo.2_Intron	NM_001111307	NP_001104777			phosphodiesterase 4A isoform 1						signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)													---	---	---	---
CARM1	10498	broad.mit.edu	37	19	10991843	10991843	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10991843delA	uc002mpz.2	+						CARM1_uc010dxn.2_Intron	NM_199141	NP_954592			coactivator-associated arginine						cellular lipid metabolic process|histone H3-R2 methylation|interspecies interaction between organisms|pathogenesis|positive regulation of fat cell differentiation|regulation of estrogen receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleoplasm	beta-catenin binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-R17 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein-arginine omega-N asymmetric methyltransferase activity|transcription regulatory region DNA binding				0																		---	---	---	---
LDLR	3949	broad.mit.edu	37	19	11210620	11210620	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11210620delT	uc002mqk.3	+						LDLR_uc010xlk.1_Intron|LDLR_uc010xll.1_Intron|LDLR_uc010xlm.1_Intron|LDLR_uc010xln.1_Intron|LDLR_uc010xlo.1_Intron	NM_000527	NP_000518			low density lipoprotein receptor precursor						cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)|skin(2)	4		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)													---	---	---	---
DOCK6	57572	broad.mit.edu	37	19	11335904	11335904	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11335904delA	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																		---	---	---	---
TSPAN16	26526	broad.mit.edu	37	19	11422999	11423001	+	Intron	DEL	AAA	-	-	rs149530459		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11422999_11423001delAAA	uc002mqv.1	+						TSPAN16_uc002mqu.1_Intron|uc002mqw.1_Intron	NM_012466	NP_036598			transmembrane 4 superfamily member 16							integral to membrane				skin(1)	1																		---	---	---	---
RGL3	57139	broad.mit.edu	37	19	11504635	11504636	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11504635_11504636delTG	uc002mrn.2	-						RGL3_uc002mrm.2_Intron					SubName: Full=FLJ00153 protein; Flags: Fragment;						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1																		---	---	---	---
RGL3	57139	broad.mit.edu	37	19	11521522	11521522	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11521522delT	uc002mrp.2	-						RGL3_uc002mrn.2_Intron|RGL3_uc002mrm.2_Intron|RGL3_uc002mro.2_Intron	NM_001035223	NP_001030300			ral guanine nucleotide dissociation						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1																		---	---	---	---
ELAVL3	1995	broad.mit.edu	37	19	11566921	11566921	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11566921delT	uc002mry.1	-						ELAVL3_uc002mrx.1_Intron	NM_001420	NP_001411			ELAV-like protein 3 isoform 1						cell differentiation|nervous system development		AU-rich element binding|nucleotide binding			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
ZNF653	115950	broad.mit.edu	37	19	11595888	11595889	+	Intron	INS	-	A	A	rs144338386	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11595888_11595889insA	uc002mrz.1	-							NM_138783	NP_620138			zinc finger protein 653						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ECSIT	51295	broad.mit.edu	37	19	11618821	11618821	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11618821delG	uc002msb.2	-	5	915	c.781delC	c.(781-783)CAGfs	p.Q261fs	ZNF653_uc002mrz.1_5'Flank|ECSIT_uc002msa.1_RNA|ECSIT_uc010dyc.1_Frame_Shift_Del_p.Q261fs|ECSIT_uc010dyd.2_Frame_Shift_Del_p.Q261fs|ECSIT_uc010xma.1_Frame_Shift_Del_p.Q47fs	NM_016581	NP_057665	Q9BQ95	ECSIT_HUMAN	evolutionarily conserved signaling intermediate	261					innate immune response|regulation of oxidoreductase activity	mitochondrion	oxidoreductase activity, acting on NADH or NADPH|protein binding			ovary(1)	1																		---	---	---	---
ZNF440	126070	broad.mit.edu	37	19	11928491	11928491	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11928491delA	uc002msp.1	+							NM_152357	NP_689570			zinc finger protein 440						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF440	126070	broad.mit.edu	37	19	11940914	11940914	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11940914delA	uc002msp.1	+							NM_152357	NP_689570			zinc finger protein 440						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
C19orf43	79002	broad.mit.edu	37	19	12843726	12843726	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12843726delT	uc002muu.2	-							NM_024038	NP_076943			hypothetical protein MGC2803												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	12892656	12892657	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12892656_12892657delTT								HOOK2 (6222 upstream) : JUNB (9629 downstream)																																			---	---	---	---
RNASEH2A	10535	broad.mit.edu	37	19	12922432	12922432	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12922432delA	uc002mvg.1	+						RNASEH2A_uc002mvf.1_Intron	NM_006397	NP_006388			ribonuclease H2, large subunit						DNA replication|RNA catabolic process	nucleus|ribonuclease H2 complex	metal ion binding|ribonuclease H activity|RNA binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
MAST1	22983	broad.mit.edu	37	19	12948572	12948573	+	5'Flank	DEL	TT	-	-	rs35858668		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12948572_12948573delTT	uc002mvm.2	+						RTBDN_uc002mvh.1_5'Flank|RTBDN_uc002mvj.2_5'Flank|MAST1_uc002mvk.2_Intron|MAST1_uc002mvl.2_5'Flank	NM_014975	NP_055790			microtubule associated serine/threonine kinase						cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	13092301	13092302	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13092301_13092302delTT								DAND5 (6734 upstream) : NFIX (14282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	13100034	13100034	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13100034delT								DAND5 (14467 upstream) : NFIX (6550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	13284694	13284694	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13284694delT								IER2 (18978 upstream) : CACNA1A (32562 downstream)																																			---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13387838	13387838	+	Intron	DEL	A	-	-	rs34471308		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13387838delA	uc010dze.2	-						CACNA1A_uc010xnd.1_5'Flank|CACNA1A_uc002mwx.3_5'Flank|CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc010xne.1_Intron	NM_001127221	NP_001120693			calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)											OREG0025295	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13610148	13610148	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13610148delT	uc010dze.2	-						CACNA1A_uc002mwy.3_Intron	NM_001127221	NP_001120693			calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
MRI1	84245	broad.mit.edu	37	19	13882018	13882018	+	Intron	DEL	A	-	-	rs113973693		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13882018delA	uc002mxe.2	+						MRI1_uc002mxf.2_Intron	NM_001031727	NP_001026897			translation initiation factor eIF-2B subunit						L-methionine salvage from methylthioadenosine	cell projection|cytoplasm|nucleus	identical protein binding|S-methyl-5-thioribose-1-phosphate isomerase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	13980589	13980590	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13980589_13980590delCA								MIR23A (33116 upstream) : MIR181C (4923 downstream)																																			---	---	---	---
NANOS3	342977	broad.mit.edu	37	19	13989596	13989596	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13989596delT	uc002mxj.3	+							NM_001098622	NP_001092092			nanos homolog 3						anti-apoptosis|germ cell development|multicellular organismal development|oogenesis|regulation of cell cycle|regulation of translation|spermatogenesis	cytoplasmic mRNA processing body|nucleus|stress granule	RNA binding|zinc ion binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(19;2e-21)															---	---	---	---
C19orf57	79173	broad.mit.edu	37	19	14011958	14011960	+	Intron	DEL	TTT	-	-	rs111701966		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14011958_14011960delTTT	uc002mxl.1	-						C19orf57_uc002mxm.1_Intron	NM_024323	NP_077299			hypothetical protein LOC79173						multicellular organismal development		protein binding			ovary(2)|upper_aerodigestive_tract(1)	3			OV - Ovarian serous cystadenocarcinoma(19;2e-21)															---	---	---	---
DCAF15	90379	broad.mit.edu	37	19	14067112	14067112	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14067112delC	uc002mxt.2	+						PODNL1_uc010xnj.1_5'Flank|PODNL1_uc002mxs.2_5'Flank	NM_138353	NP_612362			DDB1 and CUL4 associated factor 15											central_nervous_system(1)	1																		---	---	---	---
RFX1	5989	broad.mit.edu	37	19	14105532	14105533	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14105532_14105533delTG	uc002mxv.2	-						RFX1_uc010dzi.2_Intron	NM_002918	NP_002909			regulatory factor X1						immune response	nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			lung(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)															---	---	---	---
RLN3	117579	broad.mit.edu	37	19	14137725	14137726	+	5'Flank	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14137725_14137726delAA	uc002mxw.1	+						RLN3_uc010dzj.1_5'Flank	NM_080864	NP_543140			relaxin 3 preproprotein							extracellular region	hormone activity				0																		---	---	---	---
ASF1B	55723	broad.mit.edu	37	19	14232736	14232736	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14232736delT	uc002mye.2	-							NM_018154	NP_060624			anti-silencing function 1B						cell differentiation|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus					0																		---	---	---	---
LPHN1	22859	broad.mit.edu	37	19	14277909	14277909	+	Intron	DEL	A	-	-	rs79500350		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14277909delA	uc010xnn.1	-						LPHN1_uc010xno.1_Intron|uc002myf.2_Intron	NM_001008701	NP_001008701			latrophilin 1 isoform 1 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	14405724	14405724	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14405724delA								LPHN1 (88727 upstream) : CD97 (86489 downstream)																																			---	---	---	---
GIPC1	10755	broad.mit.edu	37	19	14599746	14599746	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14599746delT	uc002myt.2	-						GIPC1_uc002myu.2_Intron|GIPC1_uc002myv.2_Intron|GIPC1_uc002myw.2_Intron|GIPC1_uc002myx.2_Intron|GIPC1_uc002myy.2_Intron|LOC100130932_uc010xnq.1_5'Flank	NM_005716	NP_005707			regulator of G-protein signalling 19 interacting						endothelial cell migration|G-protein coupled receptor protein signaling pathway|glutamate secretion|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|protein targeting|regulation of protein stability|regulation of synaptic plasticity|synaptic transmission	cell cortex|dendritic shaft|dendritic spine|membrane fraction|soluble fraction|synaptic vesicle|vesicle membrane	actin binding|myosin binding|protein homodimerization activity|receptor binding				0																		---	---	---	---
EMR3	84658	broad.mit.edu	37	19	14762192	14762192	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
BRD4	23476	broad.mit.edu	37	19	15411454	15411454	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15411454delA	uc002nat.3	-						BRD4_uc002nau.3_Intron	NM_014299	NP_055114			bromodomain-containing protein 4 isoform short						interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle	condensed nuclear chromosome|cytoplasm	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)					T	NUT|C15orf55	lethal midline carcinoma of young people								---	---	---	---
AKAP8L	26993	broad.mit.edu	37	19	15520761	15520761	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15520761delT	uc002naw.1	-						AKAP8L_uc002nax.1_Intron|AKAP8L_uc010xoh.1_Intron|AKAP8L_uc002nay.1_Intron	NM_014371	NP_055186			A kinase (PRKA) anchor protein 8-like							cytoplasm|nuclear matrix	DEAD/H-box RNA helicase binding|DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	15578652	15578652	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15578652delC								RASAL3 (3270 upstream) : PGLYRP2 (807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	15840891	15840891	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15840891delT								OR10H2 (1029 upstream) : OR10H3 (11312 downstream)																																			---	---	---	---
EPS15L1	58513	broad.mit.edu	37	19	16482574	16482574	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16482574delA	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	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																		---	---	---	---
EPS15L1	58513	broad.mit.edu	37	19	16559641	16559642	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16559641_16559642delAA	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																		---	---	---	---
CALR3	125972	broad.mit.edu	37	19	16590241	16590241	+	Intron	DEL	A	-	-	rs67714289		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16590241delA	uc002ned.2	-						MED26_uc002nee.2_Intron	NM_145046	NP_659483			calreticulin 3 precursor						protein folding	endoplasmic reticulum lumen	calcium ion binding|sugar binding|unfolded protein binding				0																		---	---	---	---
CHERP	10523	broad.mit.edu	37	19	16648369	16648369	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16648369delC	uc002nei.1	-						MED26_uc002nee.2_Intron|CHERP_uc002nej.2_Intron	NM_006387	NP_006378			calcium homeostasis endoplasmic reticulum						cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing	endoplasmic reticulum|perinuclear region of cytoplasm	RNA binding			ovary(2)	2																		---	---	---	---
NWD1	284434	broad.mit.edu	37	19	16887753	16887753	+	Intron	DEL	A	-	-	rs112284735		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16887753delA	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_Intron					RecName: Full=NACHT and WD repeat domain-containing protein 1;								ATP binding			skin(3)|ovary(2)|pancreas(2)	7																		---	---	---	---
ANKLE1	126549	broad.mit.edu	37	19	17396069	17396070	+	Intron	DEL	AA	-	-	rs34050017		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17396069_17396070delAA	uc002nga.2	+						ANKLE1_uc010xpm.1_Intron|ANKLE1_uc010eao.1_Intron|ANKLE1_uc010xpn.1_Intron|ANKLE1_uc002nfy.2_Intron|ANKLE1_uc002nfz.2_Intron	NM_152363	NP_689576			ankyrin repeat domain 41							nuclear envelope					0																		---	---	---	---
PLVAP	83483	broad.mit.edu	37	19	17490652	17490652	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17490652delA	uc002ngk.1	-							NM_031310	NP_112600			plasmalemma vesicle associated protein							caveola|integral to membrane|perinuclear region of cytoplasm					0																		---	---	---	---
SLC27A1	376497	broad.mit.edu	37	19	17595390	17595390	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17595390delA	uc002ngu.1	+						SLC27A1_uc002ngt.1_Intron|SLC27A1_uc010xpp.1_Intron	NM_198580	NP_940982			solute carrier family 27, member 1						cardiolipin biosynthetic process|fatty acid metabolic process|long-chain fatty acid transport|negative regulation of phospholipid biosynthetic process|phosphatidic acid biosynthetic process|phosphatidylcholine biosynthetic process|phosphatidylethanolamine biosynthetic process|phosphatidylinositol biosynthetic process|phosphatidylserine biosynthetic process|transmembrane transport	endomembrane system|integral to membrane	fatty acid transporter activity|nucleotide binding				0																		---	---	---	---
FAM129C	199786	broad.mit.edu	37	19	17638538	17638538	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17638538delT	uc010xpr.1	+						FAM129C_uc010xpq.1_Intron|FAM129C_uc010xps.1_Intron|FAM129C_uc010xpt.1_Intron	NM_173544	NP_775815			B-cell novel protein 1 isoform a												0																		---	---	---	---
FAM129C	199786	broad.mit.edu	37	19	17663932	17663932	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17663932delT	uc010xpr.1	+						GLT25D1_uc002nhc.1_5'Flank	NM_173544	NP_775815			B-cell novel protein 1 isoform a												0																		---	---	---	---
GLT25D1	79709	broad.mit.edu	37	19	17673471	17673471	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17673471delA	uc002nhc.1	+							NM_024656	NP_078932			glycosyltransferase 25 domain containing 1						lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity				0																		---	---	---	---
SLC5A5	6528	broad.mit.edu	37	19	17993148	17993149	+	Intron	DEL	TT	-	-	rs78838816		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17993148_17993149delTT	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	18395964	18395964	+	IGR	DEL	T	-	-	rs35945463		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18395964delT								JUND (3532 upstream) : LSM4 (21754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	18447927	18447927	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18447927delA								LSM4 (13926 upstream) : PGPEP1 (3481 downstream)																																			---	---	---	---
PGPEP1	54858	broad.mit.edu	37	19	18452722	18452723	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18452722_18452723delTT	uc002nis.1	+						PGPEP1_uc002nir.1_Intron|PGPEP1_uc002nit.1_Intron|PGPEP1_uc010xqg.1_Intron	NM_017712	NP_060182			pyroglutamyl-peptidase I								cysteine-type peptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	18636921	18636921	+	IGR	DEL	A	-	-	rs141795467		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18636921delA								ELL (3984 upstream) : FKBP8 (5647 downstream)																																			---	---	---	---
CRLF1	9244	broad.mit.edu	37	19	18711016	18711016	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18711016delT	uc010ebt.1	-							NM_004750	NP_004741			cytokine receptor-like factor 1 precursor						negative regulation of neuron apoptosis|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein	extracellular space	cytokine binding|protein heterodimerization activity|receptor activity			central_nervous_system(1)	1																		---	---	---	---
UPF1	5976	broad.mit.edu	37	19	18973650	18973650	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18973650delA	uc002nkg.2	+						UPF1_uc002nkf.2_Intron|UPF1_uc002nkh.2_Intron	NM_002911	NP_002902			regulator of nonsense transcripts 1						cell cycle|DNA repair|DNA replication|histone mRNA catabolic process|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational termination	chromatin|cytoplasmic mRNA processing body|exon-exon junction complex	ATP binding|ATP-dependent RNA helicase activity|chromatin binding|DNA binding|protein binding|protein binding|RNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
COPE	11316	broad.mit.edu	37	19	19013565	19013566	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19013565_19013566insA	uc002nkk.2	-						COPE_uc002nkl.2_Intron|COPE_uc002nkm.2_Intron|COPE_uc002nkn.2_Intron	NM_007263	NP_009194			epsilon subunit of coatomer protein complex						COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	binding|structural molecule activity				0																		---	---	---	---
ARMC6	93436	broad.mit.edu	37	19	19156981	19156981	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19156981delT	uc002nld.2	+						ARMC6_uc002nlc.2_Intron|ARMC6_uc010xql.1_Intron|ARMC6_uc002nle.2_Intron|ARMC6_uc010xqm.1_Intron	NM_033415	NP_219483			armadillo repeat containing 6								protein binding				0			OV - Ovarian serous cystadenocarcinoma(5;5.66e-06)|Epithelial(12;0.000391)															---	---	---	---
SLC25A42	284439	broad.mit.edu	37	19	19212549	19212549	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19212549delC	uc002nlf.1	+						SLC25A42_uc010xqn.1_Intron	NM_178526	NP_848621			solute carrier family 25, member 42						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)															---	---	---	---
LOC729991-MEF2B	4207	broad.mit.edu	37	19	19288517	19288517	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19288517delG	uc010xqo.1	-						LOC729991-MEF2B_uc010xqp.1_Intron|LOC729991-MEF2B_uc002nlo.2_Intron|LOC729991-MEF2B_uc002nlp.2_Intron|LOC729991_uc002nlq.2_Intron	NM_005919	NP_005910			myocyte enhancer factor 2B isoform b						muscle organ development	transcription factor complex	histone deacetylase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
LOC729991-MEF2B	4207	broad.mit.edu	37	19	19299643	19299643	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19299643delT	uc010xqp.1	-						LOC729991-MEF2B_uc002nlo.2_Intron|LOC729991-MEF2B_uc002nlp.2_Intron|LOC729991_uc002nlq.2_Intron|LOC729991_uc002nlr.3_Intron|LOC729991-MEF2B_uc010ecb.2_Intron	NM_001145785	NP_001139257			myocyte enhancer factor 2B isoform a						muscle organ development	transcription factor complex	histone deacetylase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
RFXANK	8625	broad.mit.edu	37	19	19307690	19307690	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19307690delA	uc002nls.2	+						RFXANK_uc002nlt.2_Intron|RFXANK_uc002nlu.2_Intron|RFXANK_uc002nlv.2_Intron|RFXANK_uc002nlw.2_Intron	NM_003721	NP_003712			regulatory factor X-associated							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(2)	2			Epithelial(12;0.00228)															---	---	---	---
PBX4	80714	broad.mit.edu	37	19	19685449	19685449	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19685449delT	uc002nmy.2	-						PBX4_uc010xqz.1_Intron|PBX4_uc010xra.1_Intron	NM_025245	NP_079521			pre-B-cell leukemia homeobox 4								sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
LOC284440	284440	broad.mit.edu	37	19	19870506	19870525	+	Intron	DEL	CCTTCCTTCCTTCCTTCCTT	-	-	rs10401655	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19870506_19870525delCCTTCCTTCCTTCCTTCCTT	uc010ech.2	-						LOC284440_uc002nof.3_Intron	NR_026956				Homo sapiens cDNA FLJ12356 fis, clone MAMMA1002339.												0																		---	---	---	---
LOC284440	284440	broad.mit.edu	37	19	19877580	19877580	+	Intron	DEL	A	-	-	rs111841762		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19877580delA	uc010ech.2	-						LOC284440_uc002nof.3_Intron	NR_026956				Homo sapiens cDNA FLJ12356 fis, clone MAMMA1002339.												0																		---	---	---	---
ZNF253	56242	broad.mit.edu	37	19	19991618	19991618	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19991618delT	uc002noj.2	+						ZNF253_uc002nok.2_Intron|ZNF253_uc002nol.2_Intron	NM_021047	NP_066385			zinc finger protein 253						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	20107878	20107880	+	IGR	DEL	AAA	-	-	rs77433034		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20107878_20107880delAAA								ZNF93 (62113 upstream) : ZNF682 (7349 downstream)																																			---	---	---	---
ZNF486	90649	broad.mit.edu	37	19	20294985	20294985	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20294985delT	uc002nou.2	+							NM_052852	NP_443084			zinc finger protein 486						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	20437227	20437228	+	IGR	INS	-	T	T	rs77138358		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20437227_20437228insT								LOC284441 (66724 upstream) : ZNF826 (13850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	20922497	20922497	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20922497delT								ZNF626 (78095 upstream) : ZNF85 (183583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	21042032	21042032	+	IGR	DEL	A	-	-	rs35187507		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21042032delA								ZNF626 (197630 upstream) : ZNF85 (64048 downstream)																																			---	---	---	---
ZNF85	7639	broad.mit.edu	37	19	21111909	21111910	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21111909_21111910delTT	uc002npg.3	+						ZNF85_uc002npf.2_Intron|ZNF85_uc002nph.1_Intron	NM_003429	NP_003420			zinc finger protein 85							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
ZNF431	170959	broad.mit.edu	37	19	21348102	21348102	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21348102delA	uc002npp.2	+						ZNF431_uc010ecq.2_Intron|ZNF431_uc010ecr.2_Intron	NM_133473	NP_597730			zinc finger protein 431						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
ZNF738	148203	broad.mit.edu	37	19	21565051	21565051	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21565051delT	uc002nps.3	+	5						NR_027130				SubName: Full=cDNA FLJ14673 fis, clone NT2RP2003714, moderately similar to Zinc finger protein 430;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	21823322	21823322	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21823322delT								ZNF429 (84254 upstream) : ZNF100 (83522 downstream)																																			---	---	---	---
ZNF100	163227	broad.mit.edu	37	19	21918601	21918601	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21918601delT	uc002nqi.2	-						ZNF100_uc002nqh.2_Intron	NM_173531	NP_775802			zinc finger protein 100						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	21957944	21957949	+	IGR	DEL	CTCTCC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21957944_21957949delCTCTCC								ZNF100 (7514 upstream) : ZNF43 (29804 downstream)																																			---	---	---	---
ZNF208	7757	broad.mit.edu	37	19	22128709	22128709	+	Intron	DEL	A	-	-	rs111989265		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22128709delA	uc002nqo.1	-											Homo sapiens cDNA FLJ38917 fis, clone NT2NE2008997, moderately similar to ZINC FINGER PROTEIN 91.											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)																---	---	---	---
ZNF492	57615	broad.mit.edu	37	19	22814454	22814454	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22814454delT	uc002nqw.3	+							NM_020855	NP_065906			zinc finger protein 492						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	22930608	22930608	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22930608delT								ZNF492 (80136 upstream) : ZNF99 (8401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23083906	23083906	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23083906delT								ZNF99 (131122 upstream) : ZNF91 (437513 downstream)																																			---	---	---	---
ZNF675	171392	broad.mit.edu	37	19	23867447	23867447	+	Intron	DEL	A	-	-	rs35113707		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23867447delA	uc002nri.2	-							NM_138330	NP_612203			zinc finger protein 675						bone resorption|cytokine-mediated signaling pathway|hemopoiesis|I-kappaB kinase/NF-kappaB cascade|negative regulation of JNK cascade|negative regulation of osteoclast differentiation|negative regulation of protein kinase activity|negative regulation of transcription, DNA-dependent|regulation of ossification|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|kidney(1)	2		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)																---	---	---	---
RPSAP58	388524	broad.mit.edu	37	19	23982830	23982832	+	Intron	DEL	TTT	-	-	rs74175774		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23982830_23982832delTTT	uc002nrn.2	+							NM_002295	NP_002286			ribosomal protein SA												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	24563869	24563869	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24563869delT								LOC100101266 (217620 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27852418	27852419	+	IGR	INS	-	ATC	ATC	rs143744412		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27852418_27852419insATC								None (None upstream) : LOC148189 (428983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27871639	27871639	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27871639delG								None (None upstream) : LOC148189 (409763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28002350	28002350	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28002350delT								None (None upstream) : LOC148189 (279052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28440990	28440991	+	IGR	INS	-	A	A	rs145497395	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28440990_28440991insA								LOC148189 (156142 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28663465	28663466	+	IGR	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28663465_28663466delTC								LOC148189 (378617 upstream) : LOC148145 (792574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28877620	28877621	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28877620_28877621delAG								LOC148189 (592772 upstream) : LOC148145 (578419 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29883974	29883974	+	RNA	DEL	T	-	-	rs72290975		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29883974delT	uc002nse.1	-	8		c.1657delA								Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	30627813	30627813	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30627813delT								C19orf2 (121202 upstream) : ZNF536 (235515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30691167	30691167	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30691167delT								C19orf2 (184556 upstream) : ZNF536 (172161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31206800	31206800	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31206800delT								ZNF536 (157835 upstream) : DKFZp566F0947 (433983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31402382	31402382	+	IGR	DEL	T	-	-	rs5827746		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31402382delT								ZNF536 (353417 upstream) : DKFZp566F0947 (238401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31846295	31846295	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31846295delA								TSHZ3 (6105 upstream) : ZNF507 (990219 downstream)																																			---	---	---	---
TDRD12	91646	broad.mit.edu	37	19	33252973	33252973	+	Intron	DEL	T	-	-	rs71336961		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33252973delT	uc002ntq.2	+						TDRD12_uc002ntr.3_Intron					RecName: Full=Tudor domain-containing protein 12; AltName: Full=ES cell-associated transcript 8 protein;								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	Esophageal squamous(110;0.137)																	---	---	---	---
TDRD12	91646	broad.mit.edu	37	19	33266568	33266568	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33266568delT	uc002ntq.2	+						TDRD12_uc002ntr.3_Intron					RecName: Full=Tudor domain-containing protein 12; AltName: Full=ES cell-associated transcript 8 protein;								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	Esophageal squamous(110;0.137)																	---	---	---	---
TDRD12	91646	broad.mit.edu	37	19	33304347	33304347	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33304347delC	uc002ntq.2	+						uc002nts.1_5'Flank					RecName: Full=Tudor domain-containing protein 12; AltName: Full=ES cell-associated transcript 8 protein;								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	Esophageal squamous(110;0.137)																	---	---	---	---
CCDC123	84902	broad.mit.edu	37	19	33418514	33418514	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33418514delT	uc002nty.2	-						CCDC123_uc002ntx.2_Intron|CCDC123_uc010edg.2_Intron|CCDC123_uc002ntz.1_Intron	NM_032816	NP_116205			coiled-coil domain containing 123							centrosome|spindle pole					0	Esophageal squamous(110;0.137)																	---	---	---	---
RHPN2	85415	broad.mit.edu	37	19	33514359	33514359	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33514359delG	uc002nuf.2	-						RHPN2_uc010xro.1_Intron|RHPN2_uc002nue.2_Intron	NM_033103	NP_149094			rhophilin, Rho GTPase binding protein 2						signal transduction	perinuclear region of cytoplasm	protein binding			central_nervous_system(5)|ovary(1)	6	Esophageal squamous(110;0.137)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	33770172	33770172	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33770172delT								SLC7A10 (53416 upstream) : CEBPA (20670 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34267827	34267827	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34267827delC								CHST8 (3414 upstream) : KCTD15 (19924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34522957	34522957	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34522957delA								KCTD15 (216292 upstream) : LSM14A (140395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34598387	34598389	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34598387_34598389delTTT								KCTD15 (291722 upstream) : LSM14A (64963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	35128512	35128512	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35128512delA	uc002nvo.1	-											Homo sapiens cDNA FLJ36176 fis, clone TESTI2026491.																														---	---	---	---
GRAMD1A	57655	broad.mit.edu	37	19	35492512	35492512	+	Intron	DEL	T	-	-	rs113097476		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35492512delT	uc010xse.1	+						GRAMD1A_uc002nxi.1_Intron|GRAMD1A_uc002nxk.2_Intron|GRAMD1A_uc002nxl.2_Intron	NM_020895	NP_065946			GRAM domain containing 1A isoform 1							integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)															---	---	---	---
LOC100128675	100128675	broad.mit.edu	37	19	35557800	35557801	+	Intron	INS	-	CAA	CAA	rs147318605	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35557800_35557801insCAA	uc010xsi.1	-							NR_024562				SubName: Full=cDNA FLJ57934;												0																		---	---	---	---
FXYD5	53827	broad.mit.edu	37	19	35650030	35650031	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35650030_35650031delAA	uc002nyg.1	+						FXYD5_uc010xsq.1_Intron|FXYD5_uc002nyh.1_Intron	NM_014164	NP_054883			FXYD domain-containing ion transport regulator 5						microvillus assembly|negative regulation of calcium-dependent cell-cell adhesion	integral to membrane	actin binding|cadherin binding|ion channel activity				0	all_lung(56;9.4e-09)|Lung NSC(56;1.4e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.75e-22)|OV - Ovarian serous cystadenocarcinoma(14;3.17e-20)|all cancers(14;7.07e-19)|LUSC - Lung squamous cell carcinoma(66;0.0221)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	35699374	35699374	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35699374delT								FXYD5 (38589 upstream) : FAM187B (16330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	35895631	35895631	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35895631delT	uc002nzf.1	+											Homo sapiens cDNA FLJ46220 fis, clone TESTI4013774.																														---	---	---	---
DMKN	93099	broad.mit.edu	37	19	35993607	35993607	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35993607delA	uc002nzm.3	-						DMKN_uc002nzi.3_5'Flank|DMKN_uc002nzj.2_Intron|DMKN_uc002nzk.3_Intron|DMKN_uc002nzl.3_Intron|DMKN_uc002nzo.3_Intron|DMKN_uc002nzn.3_Intron|DMKN_uc002nzw.2_Intron|DMKN_uc002nzr.2_Intron|DMKN_uc002nzp.2_Intron|DMKN_uc002nzq.2_Intron|DMKN_uc002nzt.2_Intron|DMKN_uc002nzs.2_Intron|DMKN_uc002nzu.2_Intron|DMKN_uc002nzv.2_Intron|DMKN_uc010xsv.1_Intron|DMKN_uc010xsw.1_Intron	NM_033317	NP_201574			dermokine isoform 2 precursor							extracellular region				large_intestine(1)|ovary(1)|skin(1)	3	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)															---	---	---	---
UPK1A	11045	broad.mit.edu	37	19	36167098	36167098	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36167098delT	uc002oaw.2	+						UPK1A_uc010eeh.2_Intron|uc002oax.1_5'Flank	NM_007000	NP_008931			uroplakin 1A						epithelial cell differentiation|protein oligomerization	endoplasmic reticulum|integral to membrane	monosaccharide binding|protein homodimerization activity				0	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36223002	36223002	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36223002delG	uc010eei.2	+	28	5631	c.5631delG	c.(5629-5631)TTGfs	p.L1877fs		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	1877					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)															---	---	---	---
TYROBP	7305	broad.mit.edu	37	19	36397022	36397023	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36397022_36397023delTT	uc002ocm.2	-						TYROBP_uc002ocn.2_Intron	NM_003332	NP_003323			TYRO protein tyrosine kinase binding protein						axon guidance|cell junction assembly|cellular defense response|intracellular signal transduction|regulation of immune response	integral to plasma membrane|intracellular	identical protein binding|receptor signaling protein activity				0	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	36600957	36600957	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36600957delA								WDR62 (4945 upstream) : POLR2I (3655 downstream)																																			---	---	---	---
ZFP14	57677	broad.mit.edu	37	19	36841040	36841041	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36841040_36841041delAA	uc002odx.1	-						ZFP14_uc010xtd.1_Intron|ZFP14_uc010eex.1_Intron	NM_020917	NP_065968			zinc finger protein 14-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
ZNF566	84924	broad.mit.edu	37	19	36967259	36967260	+	Intron	INS	-	T	T	rs144333679	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36967259_36967260insT	uc002oea.3	-						ZNF566_uc010xte.1_Intron|ZNF566_uc010xtf.1_Intron|ZNF566_uc002oeb.3_Intron|ZNF566_uc002oec.3_Intron|ZNF566_uc010xtg.1_Intron	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)																	---	---	---	---
ZNF790	388536	broad.mit.edu	37	19	37327355	37327355	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37327355delA	uc002oew.2	-							NM_206894	NP_996777			zinc finger protein 790						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|skin(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	37335236	37335236	+	IGR	DEL	A	-	-	rs66661957		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37335236delA								ZNF790 (5952 upstream) : ZNF345 (6031 downstream)																																			---	---	---	---
ZNF569	148266	broad.mit.edu	37	19	37918654	37918654	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37918654delA	uc002ogi.2	-						ZNF569_uc002ogh.2_Intron|ZNF569_uc002ogj.2_Intron	NM_152484	NP_689697			zinc finger protein 569						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|skin(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF540	163255	broad.mit.edu	37	19	38053280	38053280	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38053280delT	uc002ogq.2	+						uc002ogm.2_Intron|uc002ogn.2_Intron|ZNF540_uc002ogo.2_Intron|ZNF540_uc002ogp.2_Intron|ZNF571_uc002ogr.1_Intron	NM_152606	NP_689819			zinc finger protein 540						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF540	163255	broad.mit.edu	37	19	38101926	38101927	+	Intron	DEL	TT	-	-	rs71977978		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38101926_38101927delTT	uc002ogq.2	+						ZNF540_uc002ogu.2_Intron|ZNF540_uc010efq.2_Intron	NM_152606	NP_689819			zinc finger protein 540						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF573	126231	broad.mit.edu	37	19	38235028	38235028	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38235028delA	uc002ohe.2	-						ZNF573_uc010efs.2_Intron|ZNF573_uc002ohd.2_Intron|ZNF573_uc002ohf.2_Intron|ZNF573_uc002ohg.2_Intron	NM_152360	NP_689573			zinc finger protein 573						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)															---	---	---	---
ZNF573	126231	broad.mit.edu	37	19	38235309	38235310	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38235309_38235310delAA	uc002ohe.2	-						ZNF573_uc010efs.2_Intron|ZNF573_uc002ohd.2_Intron|ZNF573_uc002ohf.2_Intron|ZNF573_uc002ohg.2_Intron	NM_152360	NP_689573			zinc finger protein 573						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	38368635	38368635	+	IGR	DEL	A	-	-	rs77853590		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38368635delA								ZNF573 (60695 upstream) : WDR87 (6837 downstream)																																			---	---	---	---
PPP1R14A	94274	broad.mit.edu	37	19	38749794	38749794	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38749794delA	uc002ohq.2	-						PPP1R14A_uc010efv.2_5'Flank	NM_033256	NP_150281			protein phosphatase 1, regulatory (inhibitor)						regulation of phosphorylation	cytoplasm	protein binding|protein phosphatase inhibitor activity				0	all_cancers(60;9.57e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
MAP4K1	11184	broad.mit.edu	37	19	39082007	39082007	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39082007delA	uc002oix.1	-						MAP4K1_uc002oiw.1_Intron|MAP4K1_uc002oiy.1_Intron	NM_007181	NP_009112			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|peptidyl-serine phosphorylation		ATP binding|MAP kinase kinase kinase kinase activity|protein binding|small GTPase regulator activity			skin(4)|lung(3)|ovary(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)															---	---	---	---
EIF3K	27335	broad.mit.edu	37	19	39112740	39112741	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39112740_39112741delTT	uc002oiz.1	+						EIF3K_uc010xuh.1_Intron|EIF3K_uc010xui.1_Intron	NM_013234	NP_037366			eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex|nucleus	protein binding|ribosome binding|translation initiation factor activity			ovary(1)|central_nervous_system(1)	2	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)															---	---	---	---
LGALS4	3960	broad.mit.edu	37	19	39297034	39297035	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39297034_39297035insA	uc002ojg.2	-						LGALS4_uc010xuj.1_Intron	NM_006149	NP_006140			galectin-4						cell adhesion	cytosol|plasma membrane	sugar binding			ovary(1)|skin(1)	2	all_cancers(60;1.02e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)															---	---	---	---
NFKBIB	4793	broad.mit.edu	37	19	39395119	39395120	+	Intron	INS	-	TCTT	TCTT	rs145766902	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39395119_39395120insTCTT	uc002ojw.2	+						NFKBIB_uc010egk.1_Intron|NFKBIB_uc002ojx.2_Intron|NFKBIB_uc002ojy.2_Intron	NM_002503	NP_002494			nuclear factor of kappa light polypeptide gene						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|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|nucleus	protein binding|signal transducer activity|transcription coactivator activity			lung(1)|kidney(1)	2	all_cancers(60;4.39e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)															---	---	---	---
NCCRP1	342897	broad.mit.edu	37	19	39686511	39686512	+	5'Flank	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39686511_39686512delAG	uc002okq.1	+							NM_001001414	NP_001001414			non-specific cytotoxic cell receptor protein 1						protein catabolic process					ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	39700028	39700029	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39700028_39700029delCA								SYCN (5122 upstream) : IL28B (34244 downstream)																																			---	---	---	---
PLEKHG2	64857	broad.mit.edu	37	19	39907794	39907794	+	Intron	DEL	T	-	-	rs111240744		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39907794delT	uc010xuz.1	+						PLEKHG2_uc010xuy.1_Intron|PLEKHG2_uc002olj.2_Intron|PLEKHG2_uc010xva.1_Intron	NM_022835	NP_073746			common-site lymphoma/leukemia guanine nucleotide						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			skin(2)|pancreas(1)|breast(1)	4	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
SUPT5H	6829	broad.mit.edu	37	19	39941995	39941995	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39941995delT	uc002olo.3	+						SUPT5H_uc010xvb.1_Intron|SUPT5H_uc002olp.3_Intron|SUPT5H_uc002olq.3_Intron|SUPT5H_uc002oln.3_Intron|SUPT5H_uc002olr.3_Intron	NM_001111020	NP_001104490			suppressor of Ty 5 homolog isoform a						cell cycle|chromatin remodeling|mRNA capping|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to organic substance|retroviral genome replication|transcription elongation from RNA polymerase II promoter	nucleoplasm	enzyme binding|protein heterodimerization activity			ovary(3)|pancreas(1)	4	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
CLC	1178	broad.mit.edu	37	19	40226833	40226833	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40226833delA	uc002omh.2	-							NM_001828	NP_001819			Charcot-Leyden crystal protein						lipid catabolic process|multicellular organismal development		carboxylesterase activity|lysophospholipase activity|sugar binding				0	all_cancers(60;2.99e-06)|all_lung(34;4.7e-08)|Lung NSC(34;5.46e-08)|Ovarian(47;0.06)	Renal(1328;0.000147)|Hepatocellular(1079;0.0202)|Myeloproliferative disorder(2;0.0255)	Epithelial(26;6.43e-25)|OV - Ovarian serous cystadenocarcinoma(5;1.07e-24)|all cancers(26;8.38e-23)	GBM - Glioblastoma multiforme(1328;4.97e-06)|STAD - Stomach adenocarcinoma(1328;0.00655)														---	---	---	---
AKT2	208	broad.mit.edu	37	19	40787404	40787404	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40787404delA	uc002onf.2	-						AKT2_uc010egt.2_Intron|AKT2_uc010xvj.1_Intron|AKT2_uc010egu.1_Intron|AKT2_uc010xvk.1_5'Flank	NM_001626	NP_001617			AKT2 kinase						insulin receptor signaling pathway|negative regulation of plasma membrane long-chain fatty acid transport|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2			Lung(22;0.000499)					A		ovarian|pancreatic 								---	---	---	---
HIPK4	147746	broad.mit.edu	37	19	40889492	40889492	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40889492delT	uc002onp.2	-							NM_144685	NP_653286			homeodomain interacting protein kinase 4							cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)|stomach(1)	2			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	41152231	41152231	+	IGR	DEL	T	-	-	rs66710377		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41152231delT								LTBP4 (16506 upstream) : NUMBL (19583 downstream)																																			---	---	---	---
ITPKC	80271	broad.mit.edu	37	19	41234123	41234124	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41234123_41234124delTT	uc002oot.2	+							NM_025194	NP_079470			inositol 1,4,5-trisphosphate 3-kinase C							cytoplasm|nucleus	ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity				0			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)															---	---	---	---
SNRPA	6626	broad.mit.edu	37	19	41265110	41265110	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41265110delA	uc002ooz.2	+						SNRPA_uc002opa.2_Intron	NM_004596	NP_004587			small nuclear ribonucleoprotein polypeptide A							nucleoplasm|spliceosomal complex	nucleotide binding|protein binding|RNA binding			skin(2)|ovary(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)															---	---	---	---
CYP2F1	1572	broad.mit.edu	37	19	41653488	41653488	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41653488delA	uc010xvw.1	+											SubName: Full=cDNA FLJ51986, highly similar to Homo sapiens cytochrome P450, family 2, subfamily F, polypeptide 1 (CYP2F1), mRNA;						naphthalene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0																		---	---	---	---
BCKDHA	593	broad.mit.edu	37	19	41914527	41914527	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41914527delT	uc002oqq.2	+						CYP2F1_uc010xvw.1_Intron|BCKDHA_uc002oqm.3_Intron|BCKDHA_uc002oqp.1_Intron|BCKDHA_uc002oqr.2_Intron|BCKDHA_uc010xvz.1_Intron	NM_000709	NP_000700			branched chain keto acid dehydrogenase E1, alpha						branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|alpha-ketoacid dehydrogenase activity|carboxy-lyase activity|metal ion binding|protein binding				0																		---	---	---	---
CYP2F1	1572	broad.mit.edu	37	19	42044023	42044024	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42044023_42044024insA	uc010xvw.1	+											SubName: Full=cDNA FLJ51986, highly similar to Homo sapiens cytochrome P450, family 2, subfamily F, polypeptide 1 (CYP2F1), mRNA;						naphthalene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	42255156	42255156	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42255156delA								CEACAM5 (20720 upstream) : CEACAM6 (4242 downstream)																																			---	---	---	---
ARHGEF1	9138	broad.mit.edu	37	19	42404070	42404071	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42404070_42404071delAA	uc002orx.2	+						ARHGEF1_uc002ory.2_Intron|ARHGEF1_uc002orz.2_Intron|ARHGEF1_uc002osa.2_Intron|ARHGEF1_uc002osb.2_Intron|ARHGEF1_uc002osc.2_Intron|ARHGEF1_uc002osd.2_Intron|ARHGEF1_uc002ose.2_5'Flank	NM_004706	NP_004697			Rho guanine nucleotide exchange factor 1 isoform						cell proliferation|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol|plasma membrane	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(3)|large_intestine(1)	4		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)														---	---	---	---
GRIK5	2901	broad.mit.edu	37	19	42538152	42538152	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42538152delA	uc002osj.1	-						GRIK5_uc002osi.1_Intron|GRIK5_uc010eib.1_Intron	NM_002088	NP_002079			glutamate receptor KA2 precursor							cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity				0		Prostate(69;0.059)			L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	42957418	42957420	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42957418_42957420delAAA	uc010eif.1	+						uc002ott.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron					Homo sapiens cDNA FLJ39530 fis, clone PUAEN2004400.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	43073167	43073167	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43073167delT	uc010eif.1	+						uc010eig.1_Intron|uc010eih.1_Intron					Homo sapiens cDNA FLJ39530 fis, clone PUAEN2004400.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	43158151	43158151	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43158151delA								CEACAM8 (59069 upstream) : PSG3 (67644 downstream)																																			---	---	---	---
PSG3	5671	broad.mit.edu	37	19	43228338	43228338	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43228338delT	uc002oue.2	-						PSG3_uc002ouf.2_Intron|PSG3_uc010eil.2_Intron	NM_021016	NP_066296			pregnancy specific beta-1-glycoprotein 3						defense response|female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43671000	43671001	+	Intron	DEL	AA	-	-	rs67158836		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43671000_43671001delAA	uc010xwk.1	-											SubName: Full=Pregnancy-specific beta-1 glycoprotein; Flags: Fragment;						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	43797093	43797093	+	IGR	DEL	T	-	-	rs79823213		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43797093delT								PSG9 (23411 upstream) : PRG1 (56115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	44209389	44209390	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44209389_44209390delTT								PLAUR (34887 upstream) : IRGC (10824 downstream)																																			---	---	---	---
ZNF221	7638	broad.mit.edu	37	19	44458941	44458942	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44458941_44458942delAA	uc002oxx.2	+						ZNF221_uc010ejb.1_Intron	NM_013359	NP_037491			zinc finger protein 221						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1		Prostate(69;0.0352)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	45110912	45110912	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45110912delA								CEACAM22P (50762 upstream) : PVR (36186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	45222185	45222185	+	IGR	DEL	A	-	-	rs113598502		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45222185delA								CEACAM16 (8201 upstream) : BCL3 (29793 downstream)																																			---	---	---	---
BCL3	602	broad.mit.edu	37	19	45262880	45262880	+	3'UTR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45262880delG	uc010xxe.1	+	9						NM_005178	NP_005169			B-cell CLL/lymphoma 3						DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|I-kappaB kinase/NF-kappaB cascade|maintenance of protein location in nucleus|negative regulation of apoptosis|negative regulation of interleukin-8 biosynthetic process|negative regulation of transcription, DNA-dependent|positive regulation of translation|protein import into nucleus, translocation|regulation of DNA binding|regulation of NF-kappaB import into nucleus|response to UV-C|response to virus	Bcl3-Bcl10 complex|Bcl3/NF-kappaB2 complex|nucleus|perinuclear region of cytoplasm	protein binding, bridging|transcription factor binding			ovary(1)|lung(1)	2	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)						T	IGH@	CLL 								---	---	---	---
Unknown	0	broad.mit.edu	37	19	45333746	45333746	+	IGR	DEL	A	-	-	rs60311827	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45333746delA								BCAM (9069 upstream) : PVRL2 (15647 downstream)																																			---	---	---	---
APOC1P1	342	broad.mit.edu	37	19	45431268	45431268	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45431268delA	uc010eju.2	+											Homo sapiens clone DKFZp781C1677 mRNA sequence.												0																		---	---	---	---
CLPTM1	1209	broad.mit.edu	37	19	45470052	45470052	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45470052delA	uc002pai.2	+						CLPTM1_uc010ejv.1_Intron|CLPTM1_uc010xxf.1_Intron|CLPTM1_uc010xxg.1_Intron	NM_001294	NP_001285			cleft lip and palate associated transmembrane						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)														---	---	---	---
RELB	5971	broad.mit.edu	37	19	45505596	45505596	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45505596delT	uc002paj.1	+							NM_006509	NP_006500			reticuloendotheliosis viral oncogene homolog B							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00986)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	45635574	45635574	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45635574delT	uc002pas.2	+											Homo sapiens leucine rich repeat containing 68, mRNA (cDNA clone IMAGE:5573062), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	45833506	45833506	+	IGR	DEL	T	-	-	rs71338768		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45833506delT								CKM (7372 upstream) : KLC3 (10492 downstream)																																			---	---	---	---
KLC3	147700	broad.mit.edu	37	19	45852955	45852955	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45852955delG	uc002pbf.1	+						KLC3_uc010ejy.1_Intron|KLC3_uc002pbg.1_Intron	NM_177417	NP_803136			kinesin light chain 3							cytoplasm|kinesin complex|microtubule	microtubule motor activity			ovary(1)	1		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	45985489	45985489	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45985489delT								ERCC1 (3403 upstream) : RTN2 (3062 downstream)																																			---	---	---	---
VASP	7408	broad.mit.edu	37	19	46025137	46025137	+	Intron	DEL	A	-	-	rs78597113		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46025137delA	uc002pcg.2	+						VASP_uc010eki.2_Intron|VASP_uc002pci.2_Intron	NM_003370	NP_003361			vasodilator-stimulated phosphoprotein						axon guidance|cell junction assembly|T cell receptor signaling pathway	actin cytoskeleton|cytosol|filopodium membrane|focal adhesion|lamellipodium membrane	actin binding|profilin binding|SH3 domain binding				0		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)														---	---	---	---
QPCTL	54814	broad.mit.edu	37	19	46198544	46198544	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46198544delA	uc010xxr.1	+						QPCTL_uc010ekn.2_Intron	NM_017659	NP_060129			glutaminyl-peptide cyclotransferase-like isoform						peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase|proteolysis	Golgi membrane|integral to membrane	acyltransferase activity|glutaminyl-peptide cyclotransferase activity|peptidase activity|protein binding|zinc ion binding			skin(1)	1		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0059)|GBM - Glioblastoma multiforme(486;0.0882)|Epithelial(262;0.208)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	46737294	46737295	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46737294_46737295delCA								IGFL1 (2796 upstream) : HIF3A (63010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	46846764	46846777	+	IGR	DEL	TTTTCCTTCCTTCC	-	-	rs71814107		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46846764_46846777delTTTTCCTTCCTTCC								HIF3A (75 upstream) : PPP5C (3517 downstream)																																			---	---	---	---
ZC3H4	23211	broad.mit.edu	37	19	47583160	47583160	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47583160delA	uc002pga.3	-						ZC3H4_uc002pgb.1_Intron	NM_015168	NP_055983			zinc finger CCCH-type containing 4								nucleic acid binding|zinc ion binding			skin(4)|ovary(2)	6		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	47847095	47847095	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47847095delA								GPR77 (1823 upstream) : DHX34 (5451 downstream)																																			---	---	---	---
DHX34	9704	broad.mit.edu	37	19	47861714	47861716	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47861714_47861716delTTT	uc010xyn.1	+						DHX34_uc010elc.1_Intron	NM_014681	NP_055496			DEAH (Asp-Glu-Ala-His) box polypeptide 34							intracellular	ATP binding|ATP-dependent helicase activity|RNA binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	48099986	48099986	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48099986delA								ZNF541 (40873 upstream) : GLTSCR1 (11467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	48347455	48347456	+	IGR	DEL	TC	-	-	rs35973815		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48347455_48347456delTC								CRX (871 upstream) : SULT2A1 (26267 downstream)																																			---	---	---	---
SULT2A1	6822	broad.mit.edu	37	19	48381603	48381603	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48381603delT	uc002phr.2	-							NM_003167	NP_003158			bile-salt sulfotransferase 2A1						3'-phosphoadenosine 5'-phosphosulfate metabolic process|bile acid catabolic process|cellular lipid metabolic process|digestion|sulfation|xenobiotic metabolic process	cytosol	bile-salt sulfotransferase activity			ovary(1)|pancreas(1)	2		all_cancers(25;3.02e-09)|all_lung(116;6.48e-07)|all_epithelial(76;7.35e-07)|Lung NSC(112;1.56e-06)|all_neural(266;0.0146)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000254)|all cancers(93;0.000545)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.0552)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	48402939	48402940	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48402939_48402940delTT								SULT2A1 (13285 upstream) : SNAR-A13 (7995 downstream)																																			---	---	---	---
LIG1	3978	broad.mit.edu	37	19	48662338	48662339	+	Intron	DEL	TT	-	-	rs141596835		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48662338_48662339delTT	uc002pia.1	-						LIG1_uc002phz.1_Intron|LIG1_uc002pib.1_Intron|LIG1_uc010xzf.1_Intron|LIG1_uc010xzg.1_Intron|LIG1_uc010xzh.1_Intron	NM_000234	NP_000225			DNA ligase I						anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)								NER					---	---	---	---
LIG1	3978	broad.mit.edu	37	19	48671083	48671083	+	Intron	DEL	A	-	-	rs113009303		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48671083delA	uc002pia.1	-						LIG1_uc002phz.1_5'Flank|LIG1_uc002pib.1_Intron|LIG1_uc010xzf.1_Intron|LIG1_uc010xzg.1_Intron|LIG1_uc010xzh.1_Intron|uc002pic.3_5'Flank	NM_000234	NP_000225			DNA ligase I						anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)								NER					---	---	---	---
SYNGR4	23546	broad.mit.edu	37	19	48875002	48875002	+	Intron	DEL	T	-	-	rs112725407		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48875002delT	uc002piz.2	+							NM_012451	NP_036583			synaptogyrin 4							integral to membrane					0		all_epithelial(76;5.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|Prostate(7;0.0143)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)														---	---	---	---
SYNGR4	23546	broad.mit.edu	37	19	48878739	48878739	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48878739delA	uc002piz.2	+							NM_012451	NP_036583			synaptogyrin 4							integral to membrane					0		all_epithelial(76;5.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|Prostate(7;0.0143)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)														---	---	---	---
GRWD1	83743	broad.mit.edu	37	19	48950512	48950513	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48950512_48950513insT	uc002pjd.2	+							NM_031485	NP_113673			glutamate-rich WD repeat containing 1							nucleolus				ovary(1)	1		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)														---	---	---	---
BCAT2	587	broad.mit.edu	37	19	49311658	49311660	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49311658_49311660delAAA	uc002pkr.2	-						BCAT2_uc002pkp.2_5'Flank|BCAT2_uc002pkq.3_Intron|BCAT2_uc002pks.2_Intron|BCAT2_uc002pkt.2_Intron|BCAT2_uc010emh.1_Intron|BCAT2_uc010emi.1_Intron|BCAT2_uc002pku.1_5'Flank|BCAT2_uc010emj.1_Intron	NM_001190	NP_001181			branched chain aminotransferase 2, mitochondrial							mitochondrial matrix	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity			ovary(1)	1		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.000366)|Epithelial(262;0.0195)|GBM - Glioblastoma multiforme(486;0.0224)	L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|Pyridoxal Phosphate(DB00114)													---	---	---	---
BCAT2	587	broad.mit.edu	37	19	49313994	49313997	+	Intron	DEL	TTTT	-	-	rs35945446		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49313994_49313997delTTTT	uc002pkr.2	-						BCAT2_uc002pkq.3_Intron|BCAT2_uc002pks.2_Intron|BCAT2_uc002pkt.2_Intron|BCAT2_uc010emh.1_Intron|BCAT2_uc010emi.1_Intron|BCAT2_uc002pku.1_5'Flank|BCAT2_uc010emj.1_Intron	NM_001190	NP_001181			branched chain aminotransferase 2, mitochondrial							mitochondrial matrix	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity			ovary(1)	1		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.000366)|Epithelial(262;0.0195)|GBM - Glioblastoma multiforme(486;0.0224)	L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|Pyridoxal Phosphate(DB00114)													---	---	---	---
HSD17B14	51171	broad.mit.edu	37	19	49328536	49328536	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49328536delG	uc002pkv.1	-						HSD17B14_uc010emk.1_Intron	NM_016246	NP_057330			dehydrogenase/reductase (SDR family) member 10						steroid catabolic process	centrosome|cytosol	estradiol 17-beta-dehydrogenase activity|protein binding|testosterone 17-beta-dehydrogenase (NADP+) activity				0		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)														---	---	---	---
HSD17B14	51171	broad.mit.edu	37	19	49335635	49335636	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49335635_49335636insA	uc002pkv.1	-						HSD17B14_uc010emk.1_Intron	NM_016246	NP_057330			dehydrogenase/reductase (SDR family) member 10						steroid catabolic process	centrosome|cytosol	estradiol 17-beta-dehydrogenase activity|protein binding|testosterone 17-beta-dehydrogenase (NADP+) activity				0		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)														---	---	---	---
CGB	1082	broad.mit.edu	37	19	49556905	49556906	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49556905_49556906insC	uc010yad.1	-						CGB8_uc002pmc.2_Intron	NM_033183	NP_149439			chorionic gonadotropin, beta polypeptide 8						apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Choriogonadotropin alfa(DB00097)													---	---	---	---
TRPM4	54795	broad.mit.edu	37	19	49677088	49677088	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49677088delA	uc002pmw.2	+						TRPM4_uc010emu.2_Intron|TRPM4_uc010yak.1_Intron|TRPM4_uc002pmx.2_Intron|TRPM4_uc010emv.2_Intron|TRPM4_uc010yal.1_Intron	NM_017636	NP_060106			transient receptor potential cation channel,						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)														---	---	---	---
TRPM4	54795	broad.mit.edu	37	19	49684585	49684586	+	Intron	DEL	CT	-	-	rs11668638	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49684585_49684586delCT	uc002pmw.2	+						TRPM4_uc010emu.2_Intron|TRPM4_uc010yak.1_Intron|TRPM4_uc002pmx.2_Intron|TRPM4_uc010emv.2_Intron|TRPM4_uc010yal.1_Intron|TRPM4_uc002pmy.2_5'Flank	NM_017636	NP_060106			transient receptor potential cation channel,						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)														---	---	---	---
TRPM4	54795	broad.mit.edu	37	19	49708123	49708123	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49708123delT	uc002pmw.2	+						TRPM4_uc010emu.2_Intron|TRPM4_uc010yak.1_Intron|TRPM4_uc002pmx.2_Intron|TRPM4_uc010emv.2_Intron|TRPM4_uc010yal.1_Intron|TRPM4_uc002pmy.2_Intron	NM_017636	NP_060106			transient receptor potential cation channel,						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	49755911	49755911	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49755911delA								TRPM4 (40820 upstream) : SLC6A16 (36983 downstream)																																			---	---	---	---
TEAD2	8463	broad.mit.edu	37	19	49850473	49850473	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49850473delG	uc002pnj.2	-	9	974	c.883delC	c.(883-885)CATfs	p.H295fs	TEAD2_uc002png.2_Frame_Shift_Del_p.H298fs|TEAD2_uc002pnh.2_Frame_Shift_Del_p.H299fs|TEAD2_uc002pni.2_Frame_Shift_Del_p.H298fs|TEAD2_uc010yao.1_Frame_Shift_Del_p.H167fs|TEAD2_uc010emw.2_Frame_Shift_Del_p.H298fs	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2	295	Transcriptional activation (Potential).				hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)														---	---	---	---
ALDH16A1	126133	broad.mit.edu	37	19	49963972	49963974	+	Intron	DEL	TTT	-	-	rs140597019		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49963972_49963974delTTT	uc002pnt.2	+						ALDH16A1_uc010yar.1_Intron|ALDH16A1_uc010yas.1_Intron|ALDH16A1_uc010yat.1_Intron	NM_153329	NP_699160			aldehyde dehydrogenase 16 family, member A1								oxidoreductase activity|protein binding			skin(1)	1		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)														---	---	---	---
RCN3	57333	broad.mit.edu	37	19	50044190	50044191	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50044190_50044191delTT	uc002poj.2	+							NM_020650	NP_065701			reticulocalbin 3, EF-hand calcium binding domain							endoplasmic reticulum lumen	calcium ion binding|protein binding			ovary(1)	1		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0159)														---	---	---	---
AP2A1	160	broad.mit.edu	37	19	50290603	50290604	+	Intron	DEL	TG	-	-	rs66888841		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50290603_50290604delTG	uc002ppn.2	+						AP2A1_uc010enj.1_Intron|AP2A1_uc002ppo.2_Intron	NM_014203	NP_055018			adaptor-related protein complex 2, alpha 1						axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|Golgi to endosome transport|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|clathrin coat of trans-Golgi network vesicle|cytosol	protein binding|protein transporter activity			ovary(2)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)														---	---	---	---
FUZ	80199	broad.mit.edu	37	19	50316026	50316027	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50316026_50316027insC	uc002ppq.1	-						FUZ_uc002ppr.1_Intron|FUZ_uc002pps.1_Intron|FUZ_uc002ppt.1_Intron|FUZ_uc002ppu.1_Intron|FUZ_uc002ppv.1_Intron|FUZ_uc010ybd.1_Intron	NM_025129	NP_079405			fuzzy homolog						cilium assembly|embryonic body morphogenesis|embryonic skeletal system morphogenesis|establishment of planar polarity|hair follicle development|neural tube closure|protein transport|regulation of smoothened signaling pathway	cytoplasm|cytoskeleton					0		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;0.00793)|GBM - Glioblastoma multiforme(134;0.0116)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	50345037	50345038	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50345037_50345038delAA	uc002ppy.3	-											Homo sapiens cDNA FLJ34894 fis, clone NT2NE2017982.																														---	---	---	---
C19orf41	126123	broad.mit.edu	37	19	50657070	50657070	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50657070delA	uc002prp.1	-							NM_152358	NP_689571			hypothetical protein LOC126123 precursor							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	50686613	50686613	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50686613delT								C19orf41 (20075 upstream) : MYH14 (20272 downstream)																																			---	---	---	---
MYH14	79784	broad.mit.edu	37	19	50747236	50747237	+	Intron	DEL	TT	-	-	rs112359962		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50747236_50747237delTT	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)														---	---	---	---
MYH14	79784	broad.mit.edu	37	19	50781795	50781795	+	Intron	DEL	A	-	-	rs34458457		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50781795delA	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron|MYH14_uc010ycb.1_5'Flank	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)														---	---	---	---
NR1H2	7376	broad.mit.edu	37	19	50870807	50870808	+	Intron	DEL	CT	-	-	rs78432723		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50870807_50870808delCT	uc002prv.3	+						NAPSA_uc002prx.2_5'Flank					Homo sapiens NR1H2 mRNA for liver X receptor beta, complete cds.						negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of pinocytosis|negative regulation of transcription, DNA-dependent|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)														---	---	---	---
SHANK1	50944	broad.mit.edu	37	19	51204852	51204852	+	Intron	DEL	T	-	-	rs34977465		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51204852delT	uc002psx.1	-							NM_016148	NP_057232			SH3 and multiple ankyrin repeat domains 1						cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)														---	---	---	---
KLK1	3816	broad.mit.edu	37	19	51323227	51323227	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51323227delT	uc002ptk.1	-	4	600	c.561delA	c.(559-561)AAAfs	p.K187fs	KLK1_uc010ycg.1_RNA	NM_002257	NP_002248	P06870	KLK1_HUMAN	kallikrein 1 preproprotein	187	Peptidase S1.				proteolysis	nucleus	serine-type endopeptidase activity				0		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00399)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
ETFB	2109	broad.mit.edu	37	19	51863274	51863274	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51863274delA	uc002pwh.2	-							NM_001985	NP_001976			electron-transfer-flavoprotein, beta polypeptide						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity				0		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)														---	---	---	---
LIM2	3982	broad.mit.edu	37	19	51883616	51883616	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51883616delC	uc002pwm.2	-						LIM2_uc002pwl.2_Intron	NM_001161748	NP_001155220			lens intrinsic membrane protein 2, 19kDa isoform						cell-cell junction assembly	cell junction|integral to membrane	structural constituent of eye lens				0		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000214)|OV - Ovarian serous cystadenocarcinoma(262;0.00985)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	51943264	51943264	+	IGR	DEL	A	-	-	rs33992341		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51943264delA								SIGLEC10 (21813 upstream) : SIGLEC8 (10838 downstream)																																			---	---	---	---
CEACAM18	729767	broad.mit.edu	37	19	51979530	51979530	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51979530delA	uc002pwv.1	+							NM_001080405	NP_001073874			carcinoembryonic antigen-related cell adhesion							integral to membrane				skin(1)	1		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	52274287	52274287	+	IGR	DEL	A	-	-	rs35155020		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52274287delA								FPR2 (510 upstream) : FPR3 (24124 downstream)																																			---	---	---	---
ZNF615	284370	broad.mit.edu	37	19	52512142	52512142	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52512142delA	uc002pye.1	-						ZNF615_uc002pyf.1_5'Flank|ZNF615_uc002pyg.1_5'Flank|ZNF615_uc002pyh.1_5'Flank|ZNF615_uc010epi.1_5'Flank|ZNF615_uc010ydg.1_5'Flank	NM_198480	NP_940882			zinc finger protein 615						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)														---	---	---	---
ZNF880	400713	broad.mit.edu	37	19	52877717	52877718	+	Intron	DEL	TT	-	-	rs77187934		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52877717_52877718delTT	uc002pzc.2	+						ZNF880_uc002pzb.3_Intron	NM_001145434	NP_001138906			zinc finger protein LOC400713						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0																		---	---	---	---
ZNF28	7576	broad.mit.edu	37	19	53308527	53308527	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53308527delA	uc002qad.2	-						ZNF28_uc002qac.2_Intron|ZNF28_uc010eqe.2_Intron	NM_006969	NP_008900			zinc finger protein 28						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)														---	---	---	---
ZNF320	162967	broad.mit.edu	37	19	53388287	53388287	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53388287delA	uc002qag.2	-						ZNF320_uc010eqi.1_Intron|ZNF320_uc002qah.2_Intron|ZNF320_uc002qai.2_Intron	NM_207333	NP_997216			zinc finger protein 320						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0534)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	53713507	53713507	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53713507delC								ZNF665 (16888 upstream) : ZNF677 (25131 downstream)																																			---	---	---	---
ZNF677	342926	broad.mit.edu	37	19	53757634	53757634	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53757634delT	uc002qbf.1	-						ZNF677_uc002qbg.1_Intron|ZNF677_uc002qbh.2_Intron	NM_182609	NP_872415			zinc finger protein 677						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00352)														---	---	---	---
ZNF765	91661	broad.mit.edu	37	19	53905183	53905183	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53905183delA	uc010ydx.1	+						ZNF765_uc002qbm.2_Intron|ZNF765_uc002qbn.2_Intron	NM_001040185	NP_001035275			zinc finger protein 765						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00379)														---	---	---	---
MIR518B	574474	broad.mit.edu	37	19	54204651	54204651	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54204651delT	hsa-mir-518b|MI0003156	+																							0																		---	---	---	---
MIR517C	574492	broad.mit.edu	37	19	54242862	54242863	+	5'Flank	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54242862_54242863delTC	hsa-mir-517c|MI0003174	+						MIR520H_hsa-mir-520h|MI0003175_5'Flank|uc010yeb.1_5'Flank																	0																		---	---	---	---
PRKCG	5582	broad.mit.edu	37	19	54387922	54387923	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54387922_54387923delAG	uc002qcq.1	+						PRKCG_uc010eqz.1_Intron|PRKCG_uc010yef.1_Intron|PRKCG_uc010yeg.1_Intron|PRKCG_uc010yeh.1_Intron	NM_002739	NP_002730			protein kinase C, gamma						activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|synaptic transmission	cytosol	ATP binding|protein kinase C activity|zinc ion binding			lung(4)|ovary(2)|pancreas(2)|large_intestine(1)	9	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)														---	---	---	---
PPP1R12C	54776	broad.mit.edu	37	19	55608669	55608670	+	Intron	DEL	CA	-	-	rs71827383		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55608669_55608670delCA	uc002qix.2	-						PPP1R12C_uc010yfs.1_Intron|PPP1R12C_uc002qiy.2_Intron	NM_017607	NP_060077			protein phosphatase 1, regulatory subunit 12C							cytoplasm				ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)														---	---	---	---
PPP1R12C	54776	broad.mit.edu	37	19	55608827	55608829	+	Intron	DEL	CAC	-	-	rs80252875		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55608827_55608829delCAC	uc002qix.2	-						PPP1R12C_uc010yfs.1_Intron|PPP1R12C_uc002qiy.2_Intron	NM_017607	NP_060077			protein phosphatase 1, regulatory subunit 12C							cytoplasm				ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)														---	---	---	---
SAPS1	22870	broad.mit.edu	37	19	55763517	55763517	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55763517delA	uc002qjw.3	-							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)														---	---	---	---
FAM71E2	284418	broad.mit.edu	37	19	55867575	55867575	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55867575delA	uc002qkr.2	-						COX6B2_uc002qkm.2_5'Flank|COX6B2_uc002qkn.2_5'Flank|COX6B2_uc002qko.2_5'Flank|COX6B2_uc002qkp.1_5'Flank	NM_001145402	NP_001138874			hypothetical protein LOC284418												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	56100871	56100871	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56100871delA								ZNF579 (8660 upstream) : FIZ1 (1867 downstream)																																			---	---	---	---
U2AF2	11338	broad.mit.edu	37	19	56173837	56173837	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56173837delC	uc002qlu.2	+						U2AF2_uc002qlt.2_Intron	NM_007279	NP_009210			U2 (RNU2) small nuclear RNA auxiliary factor 2						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	nucleoplasm|spliceosomal complex	enzyme binding|nucleotide binding|RNA binding			ovary(1)	1		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)														---	---	---	---
ZNF444	55311	broad.mit.edu	37	19	56671783	56671783	+	3'UTR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56671783delC	uc002qmm.2	+	5					ZNF444_uc002qmn.1_3'UTR	NM_018337	NP_060807			zinc finger protein 444						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0531)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	56677188	56677188	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56677188delA								ZNF444 (4926 upstream) : GALP (10201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	57238175	57238175	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57238175delT	uc010ygp.1	+											Homo sapiens cDNA clone IMAGE:4793694.																														---	---	---	---
ZIM2	23619	broad.mit.edu	37	19	57287026	57287026	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57287026delA	uc002qnr.2	-						uc010ygp.1_Intron|uc002qnp.1_Intron|ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron	NM_015363	NP_056178			zinc finger, imprinted 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)														---	---	---	---
PEG3	5178	broad.mit.edu	37	19	57338785	57338785	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57338785delA	uc002qnu.2	-						ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_5'Flank|PEG3_uc002qnv.2_Intron|PEG3_uc002qnw.2_Intron|PEG3_uc002qnx.2_Intron|PEG3_uc010etr.2_Intron	NM_001146186	NP_001139658			paternally expressed 3 isoform 1						apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57408842	57408844	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57408842_57408844delTTT								MIMT1 (48920 upstream) : USP29 (222665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	57589327	57589327	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57589327delA								MIMT1 (229405 upstream) : USP29 (42182 downstream)																																			---	---	---	---
ZIM3	114026	broad.mit.edu	37	19	57646555	57646555	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57646555delT	uc002qnz.1	-	5	1536	c.1150delA	c.(1150-1152)ATCfs	p.I384fs		NM_052882	NP_443114	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	384	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)														---	---	---	---
ZNF547	284306	broad.mit.edu	37	19	57895732	57895732	+	Intron	DEL	A	-	-	rs66592720		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57895732delA	uc002qpm.3	+											RecName: Full=Zinc finger protein 547;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)														---	---	---	---
ZNF549	256051	broad.mit.edu	37	19	58048306	58048306	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58048306delA	uc002qpb.1	+						ZNF547_uc002qpm.3_Intron|ZNF549_uc010eud.1_Intron|ZNF549_uc002qpa.1_Intron	NM_153263	NP_694995			zinc finger protein 549						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)														---	---	---	---
ZNF776	284309	broad.mit.edu	37	19	58215377	58215377	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58215377delA	uc002qpx.2	+						ZNF154_uc002qpy.2_Intron|ZNF154_uc010euf.2_Intron	NM_173632	NP_775903			zinc finger protein 776						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0256)														---	---	---	---
ZNF587	84914	broad.mit.edu	37	19	58282224	58282224	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58282224delT	uc002qqb.2	+						ZNF586_uc002qqd.2_Intron|ZNF586_uc002qqe.2_Intron|ZNF586_uc010euh.2_Intron|ZNF586_uc002qqf.1_Intron	NM_032828	NP_116217			zinc finger protein 587						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)														---	---	---	---
ZNF418	147686	broad.mit.edu	37	19	58436829	58436830	+	Intron	DEL	AA	-	-	rs34948790		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58436829_58436830delAA	uc002qqs.1	-						ZNF418_uc010yhn.1_Intron	NM_133460	NP_597717			zinc finger protein 418						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)														---	---	---	---
ZNF544	27300	broad.mit.edu	37	19	58759286	58759286	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58759286delT	uc010euo.2	+						ZNF544_uc010eun.1_Intron|ZNF544_uc010yhw.1_Intron|ZNF544_uc010yhx.1_Intron|ZNF544_uc010yhy.1_Intron|ZNF544_uc002qrt.3_Intron|ZNF544_uc002qru.3_Intron|ZNF544_uc002qrv.2_Intron	NM_014480	NP_055295			zinc finger protein 544						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)														---	---	---	---
RPS5	6193	broad.mit.edu	37	19	58896095	58896095	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58896095delA	uc002qsn.2	+						RPS5_uc002qso.2_5'Flank	NM_001009	NP_001000			ribosomal protein S5						endocrine pancreas development|regulation of translational fidelity|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	mRNA binding|structural constituent of ribosome				0		all_cancers(17;1.71e-22)|all_epithelial(17;1.69e-16)|Lung NSC(17;2.25e-06)|all_lung(17;9.97e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Breast(46;0.0194)|Ovarian(87;0.0443)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.171)|GBM - Glioblastoma multiforme(193;0.0323)|Lung(386;0.0543)|LUSC - Lung squamous cell carcinoma(496;0.176)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	58943362	58943362	+	IGR	DEL	A	-	-	rs79774564		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58943362delA								ZNF584 (13672 upstream) : ZNF132 (820 downstream)																																			---	---	---	---
SLC27A5	10998	broad.mit.edu	37	19	58995018	58995018	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58995018delA	uc002qtb.2	-											Homo sapiens very long-chain acyl-CoA synthetase homolog 2 mRNA, complete cds.						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)														---	---	---	---
TRIB3	57761	broad.mit.edu	37	20	373202	373202	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:373202delT	uc002wdm.2	+						TRIB3_uc002wdn.2_Intron	NM_021158	NP_066981			tribbles 3						apoptosis|cellular lipid metabolic process|insulin receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fatty acid biosynthetic process|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein binding|positive regulation of ubiquitin-protein ligase activity|regulation of glucose transport|regulation of MAP kinase activity|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	ATP binding|protein kinase activity|protein kinase binding|protein kinase inhibitor activity|transcription corepressor activity|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity			central_nervous_system(2)	2		all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231)		Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112)														---	---	---	---
RBCK1	10616	broad.mit.edu	37	20	409871	409872	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:409871_409872delTT	uc002wdp.3	+						RBCK1_uc002wdq.3_Intron|RBCK1_uc010fzy.2_Intron|RBCK1_uc002wdr.3_Intron	NM_031229	NP_112506			RanBP-type and C3HC4-type zinc finger containing						interspecies interaction between organisms|negative regulation of NF-kappaB transcription factor activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|proteasomal ubiquitin-dependent protein catabolic process|protein linear polyubiquitination|T cell receptor signaling pathway	LUBAC complex	protein binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)																---	---	---	---
SCRT2	85508	broad.mit.edu	37	20	656896	656896	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:656896delA	uc002wec.2	-						SRXN1_uc002web.2_5'Flank	NM_033129	NP_149120			scratch 2 protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	1160477	1160477	+	IGR	DEL	T	-	-	rs73893636	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1160477delT								PSMF1 (12053 upstream) : C20orf46 (738 downstream)																																			---	---	---	---
SNPH	9751	broad.mit.edu	37	20	1258268	1258269	+	Intron	INS	-	TG	TG	rs140756165	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1258268_1258269insTG	uc002wes.2	+						SNPH_uc002wet.2_Intron	NM_014723	NP_055538			syntaphilin						synaptic vesicle docking involved in exocytosis	cell junction|integral to membrane|synapse|synaptosome	syntaxin-1 binding			ovary(2)	2																		---	---	---	---
FKBP1A	2280	broad.mit.edu	37	20	1347896	1347896	+	Intron	DEL	A	-	-	rs111958500		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1347896delA	uc010gac.2	-						uc002wew.2_Intron|uc002wex.2_Intron					Homo sapiens FKBP12-Exip2 mRNA for FK506 binding protein12, complete cds.						'de novo' protein folding|beta-amyloid formation|fibril organization|heart trabecula formation|negative regulation of protein phosphatase type 2B activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of protein binding|positive regulation of protein ubiquitination|protein maturation by protein folding|protein refolding|regulation of activin receptor signaling pathway|regulation of immune response|regulation of ryanodine-sensitive calcium-release channel activity|SMAD protein complex assembly|T cell activation|ventricular cardiac muscle tissue morphogenesis	axon|cytosol|sarcoplasmic reticulum membrane|terminal cisterna	activin binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity|signal transducer activity|SMAD binding|type I transforming growth factor beta receptor binding				0					Pimecrolimus(DB00337)|Sirolimus(DB00877)|Tacrolimus(DB00864)													---	---	---	---
SIRPA	140885	broad.mit.edu	37	20	1879852	1879852	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1879852delA	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)														---	---	---	---
SIRPA	140885	broad.mit.edu	37	20	1912700	1912703	+	Intron	DEL	ATTC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1912700_1912703delATTC	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	2220311	2220311	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2220311delT								STK35 (91115 upstream) : TGM3 (56302 downstream)																																			---	---	---	---
TGM3	7053	broad.mit.edu	37	20	2282354	2282354	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2282354delT	uc002wfx.3	+							NM_003245	NP_003236			transglutaminase 3 precursor						cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)|skin(1)	9					L-Glutamine(DB00130)													---	---	---	---
TGM6	343641	broad.mit.edu	37	20	2383177	2383177	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2383177delC	uc002wfy.1	+						TGM6_uc010gal.1_Intron	NM_198994	NP_945345			transglutaminase 6						cell death|peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(3)|skin(1)	4					L-Glutamine(DB00130)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	2438433	2438433	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2438433delG								TGM6 (25034 upstream) : SNRPB (3848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	2662692	2662692	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2662692delA								IDH3B (17849 upstream) : EBF4 (10832 downstream)																																			---	---	---	---
EBF4	57593	broad.mit.edu	37	20	2675769	2675769	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2675769delT	uc002wgt.3	+						EBF4_uc002wgs.3_Intron	NM_001110514	NP_001103984			early B-cell factor 4						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	2771622	2771622	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2771622delT								EBF4 (30869 upstream) : CPXM1 (3094 downstream)																																			---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	2983149	2983149	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2983149delT	uc010zqd.1	+						PTPRA_uc002whj.2_Intron|PTPRA_uc010zqc.1_Intron|PTPRA_uc002whk.2_Intron|PTPRA_uc002whl.2_Intron|PTPRA_uc002whm.2_Intron|PTPRA_uc002whn.2_Intron|PTPRA_uc002who.2_Intron	NM_002836	NP_002827			protein tyrosine phosphatase, receptor type, A						axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	2989556	2989556	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2989556delA	uc010zqd.1	+						PTPRA_uc002whj.2_Intron|PTPRA_uc002whk.2_Intron|PTPRA_uc002whl.2_Intron|PTPRA_uc002whm.2_Intron|PTPRA_uc002whn.2_Intron|PTPRA_uc002who.2_Intron	NM_002836	NP_002827			protein tyrosine phosphatase, receptor type, A						axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	3006599	3006600	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3006599_3006600insT	uc010zqd.1	+						PTPRA_uc002whj.2_Intron|PTPRA_uc002whk.2_Intron|PTPRA_uc002whl.2_Intron|PTPRA_uc002whm.2_Intron|PTPRA_uc002whn.2_Intron|PTPRA_uc002who.2_Intron	NM_002836	NP_002827			protein tyrosine phosphatase, receptor type, A						axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
DDRGK1	65992	broad.mit.edu	37	20	3181263	3181264	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3181263_3181264delGT	uc002wic.2	-						DDRGK1_uc010gaw.2_Intron|DDRGK1_uc010gax.1_Intron	NM_023935	NP_076424			DDRGK domain containing 1 precursor							endoplasmic reticulum	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	3426771	3426772	+	IGR	INS	-	C	C	rs147077908	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3426771_3426772insC								C20orf194 (38184 upstream) : ATRN (24893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	3440236	3440237	+	IGR	DEL	GT	-	-	rs71331051		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3440236_3440237delGT								C20orf194 (51649 upstream) : ATRN (11428 downstream)																																			---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3524375	3524376	+	Intron	DEL	AA	-	-	rs142720669		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3524375_3524376delAA	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3565278	3565278	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3577009	3577009	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3577009delT	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
CDC25B	994	broad.mit.edu	37	20	3775020	3775021	+	5'Flank	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3775020_3775021insT	uc002wjn.2	+						CDC25B_uc010zqk.1_Intron|CDC25B_uc010zql.1_Intron|CDC25B_uc010zqm.1_Intron|CDC25B_uc002wjl.2_5'Flank|CDC25B_uc002wjm.2_5'Flank|CDC25B_uc002wjo.2_5'Flank|CDC25B_uc002wjp.2_5'Flank	NM_021873	NP_068659			cell division cycle 25B isoform 1						cell division|G2/M transition of mitotic cell cycle|mitosis|positive regulation of cell proliferation	cytosol|microtubule organizing center|nucleoplasm	protein binding|protein tyrosine phosphatase activity			lung(3)|ovary(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	3816140	3816142	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3816140_3816142delAAA								C20orf29 (10186 upstream) : MAVS (11307 downstream)																																			---	---	---	---
MAVS	57506	broad.mit.edu	37	20	3835072	3835072	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3835072delA	uc002wjw.3	+						MAVS_uc002wjv.2_Intron|MAVS_uc010zqn.1_Intron|MAVS_uc002wjx.3_Intron|MAVS_uc002wjy.3_5'Flank	NM_020746	NP_065797			virus-induced signaling adapter						activation of innate immune response|cellular response to exogenous dsRNA|defense response to bacterium|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of chemokine (C-C motif) ligand 5 production|positive regulation of defense response to virus by host|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interleukin-8 production|positive regulation of IP-10 production|positive regulation of protein import into nucleus, translocation|positive regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|response to virus	integral to membrane|mitochondrial outer membrane	CARD domain binding|protein kinase binding|signal transducer activity				0																		---	---	---	---
MAVS	57506	broad.mit.edu	37	20	3839446	3839446	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3839446delT	uc002wjw.3	+						MAVS_uc010zqn.1_Intron|MAVS_uc002wjx.3_Intron|MAVS_uc002wjy.3_Intron	NM_020746	NP_065797			virus-induced signaling adapter						activation of innate immune response|cellular response to exogenous dsRNA|defense response to bacterium|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of chemokine (C-C motif) ligand 5 production|positive regulation of defense response to virus by host|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interleukin-8 production|positive regulation of IP-10 production|positive regulation of protein import into nucleus, translocation|positive regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|response to virus	integral to membrane|mitochondrial outer membrane	CARD domain binding|protein kinase binding|signal transducer activity				0																		---	---	---	---
PANK2	80025	broad.mit.edu	37	20	3884279	3884279	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3884279delT	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																		---	---	---	---
PANK2	80025	broad.mit.edu	37	20	3897857	3897858	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3897857_3897858delTT	uc002wkc.2	+						PANK2_uc002wkb.2_Intron|PANK2_uc002wkd.2_Intron|PANK2_uc002wke.2_Intron|PANK2_uc002wkf.2_Intron|uc002wkg.2_5'Flank|MIR103-2_hsa-mir-103-2|MI0000108_5'Flank	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	4413545	4413545	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4413545delA	uc002wks.2	-											Homo sapiens, clone IMAGE:5170855, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	4588471	4588472	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4588471_4588472delAA								ADRA1D (358812 upstream) : PRNP (78325 downstream)																																			---	---	---	---
PRNP	5621	broad.mit.edu	37	20	4674730	4674730	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4674730delA	uc002wku.2	+						PRNP_uc002wkv.2_Intron|PRNP_uc002wkw.2_Intron|PRNP_uc002wkx.2_Intron|PRNP_uc002wkt.1_Intron|PRNP_uc002wky.2_Intron	NM_001080122	NP_001073591			prion protein preproprotein						axon guidance|cell cycle arrest|cellular copper ion homeostasis|metabolic process|negative regulation of activated T cell proliferation|negative regulation of calcineurin-NFAT signaling pathway|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-2 production|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of T cell receptor signaling pathway|protein homooligomerization|response to oxidative stress	anchored to membrane|endoplasmic reticulum|extrinsic to membrane|Golgi apparatus|membrane raft|nucleus|plasma membrane	copper ion binding|identical protein binding|microtubule binding			central_nervous_system(1)	1					Tetracycline(DB00759)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	4809203	4809203	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4809203delA								RASSF2 (4912 upstream) : SLC23A2 (23799 downstream)																																			---	---	---	---
SLC23A2	9962	broad.mit.edu	37	20	4851223	4851223	+	Intron	DEL	A	-	-	rs6116561		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4851223delA	uc002wlg.1	-						SLC23A2_uc010zqr.1_Intron|SLC23A2_uc002wlh.1_Intron|SLC23A2_uc002wli.2_Intron	NM_005116	NP_005107			solute carrier family 23 (nucleobase						L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	5183442	5183443	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5183442_5183443delAC								CDS2 (11455 upstream) : PROKR2 (99244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	5522651	5522651	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5522651delT								LOC149837 (37409 upstream) : GPCPD1 (2430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	5622804	5622805	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5622804_5622805delAA								GPCPD1 (31132 upstream) : C20orf196 (108238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	5727128	5727128	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5727128delG								GPCPD1 (135456 upstream) : C20orf196 (3915 downstream)																																			---	---	---	---
CHGB	1114	broad.mit.edu	37	20	5891506	5891506	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5891506delT	uc002wmg.2	+						CHGB_uc010zqz.1_5'Flank	NM_001819	NP_001810			chromogranin B precursor							extracellular region	hormone activity			breast(3)|skin(2)|ovary(1)	6																		---	---	---	---
TRMT6	51605	broad.mit.edu	37	20	5921479	5921479	+	Intron	DEL	T	-	-	rs11335317		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5921479delT	uc002wmh.1	-						TRMT6_uc010zra.1_Intron	NM_015939	NP_057023			tRNA methyltransferase 6						regulation of translational initiation|tRNA processing	nucleus	protein binding|translation initiation factor activity			pancreas(1)	1																		---	---	---	---
CRLS1	54675	broad.mit.edu	37	20	5990940	5990940	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5990940delA	uc002wmn.3	+						CRLS1_uc010gbq.2_Intron|CRLS1_uc010gbr.2_Intron|CRLS1_uc010gbs.1_Intron	NM_019095	NP_061968			cardiolipin synthase 1 isoform 1						phospholipid biosynthetic process	integral to membrane|mitochondrial inner membrane	phosphotransferase activity, for other substituted phosphate groups				0																		---	---	---	---
CRLS1	54675	broad.mit.edu	37	20	5997101	5997102	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5997101_5997102delGT	uc002wmn.3	+						CRLS1_uc010gbq.2_Intron|CRLS1_uc010gbr.2_Intron	NM_019095	NP_061968			cardiolipin synthase 1 isoform 1						phospholipid biosynthetic process	integral to membrane|mitochondrial inner membrane	phosphotransferase activity, for other substituted phosphate groups				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	6132162	6132162	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6132162delT								FERMT1 (27971 upstream) : BMP2 (616583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	6769067	6769067	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6769067delC								BMP2 (8157 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7466309	7466309	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7466309delA								BMP2 (705399 upstream) : HAO1 (397322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7541743	7541743	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7541743delT								BMP2 (780833 upstream) : HAO1 (321888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7687127	7687128	+	IGR	INS	-	GAC	GAC	rs148149123	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7687127_7687128insGAC								BMP2 (926217 upstream) : HAO1 (176503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7701372	7701372	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7701372delG								BMP2 (940462 upstream) : HAO1 (162259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7720629	7720630	+	IGR	DEL	AA	-	-	rs4813840	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7720629_7720630delAA								BMP2 (959719 upstream) : HAO1 (143001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7746865	7746867	+	IGR	DEL	CAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7746865_7746867delCAA								BMP2 (985955 upstream) : HAO1 (116764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7791329	7791329	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7791329delT								None (None upstream) : HAO1 (72302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7961701	7961701	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7961701delT								HAO1 (40608 upstream) : TMX4 (15 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	8054655	8054655	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8054655delA								TMX4 (54262 upstream) : PLCB1 (40445 downstream)																																			---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8249348	8249349	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8249348_8249349insT	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	8322642	8322642	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8322642delA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	8871591	8871591	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8871591delT								PLCB1 (6046 upstream) : PLCB4 (178110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	8885908	8885910	+	IGR	DEL	AAA	-	-	rs144253101		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8885908_8885910delAAA								PLCB1 (20363 upstream) : PLCB4 (163791 downstream)																																			---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9064026	9064027	+	Intron	DEL	AC	-	-	rs72314605		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9064026_9064027delAC	uc010gbx.2	+						PLCB4_uc010gbw.1_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9173459	9173459	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9173459delA	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9269054	9269054	+	Intron	DEL	T	-	-	rs66531078		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9269054delT	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9423027	9423029	+	Intron	DEL	TTT	-	-	rs113662916		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9423027_9423029delTTT	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron|PLCB4_uc002wnh.2_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
PAK7	57144	broad.mit.edu	37	20	9778901	9778901	+	Intron	DEL	A	-	-	rs71331382		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9778901delA	uc002wnl.2	-						PAK7_uc002wnk.2_Intron|PAK7_uc002wnj.2_Intron|PAK7_uc010gby.1_Intron	NM_020341	NP_065074			p21-activated kinase 7								ATP binding|protein binding|protein serine/threonine kinase activity			lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1)	23			COAD - Colon adenocarcinoma(9;0.194)															---	---	---	---
SNAP25	6616	broad.mit.edu	37	20	10204318	10204318	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10204318delA	uc002wnq.1	+						SNAP25_uc002wnr.1_Intron|SNAP25_uc002wns.1_Intron|SNAP25_uc010gca.1_Intron|SNAP25_uc010gcb.1_Intron|SNAP25_uc010gcc.1_Intron	NM_130811	NP_570824			synaptosomal-associated protein 25 isoform						energy reserve metabolic process|glutamate secretion|neurotransmitter uptake|synaptic vesicle docking involved in exocytosis	cell junction|growth cone|perinuclear region of cytoplasm|synapse|synaptosome				skin(2)	2					Botulinum Toxin Type A(DB00083)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	10296837	10296837	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10296837delA								SNAP25 (8772 upstream) : MKKS (88996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10300910	10300910	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10300910delA								SNAP25 (12845 upstream) : MKKS (84923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10971329	10971330	+	IGR	INS	-	AC	AC	rs143029968	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10971329_10971330insAC								JAG1 (316635 upstream) : BTBD3 (900147 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11205582	11205582	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11205582delA								JAG1 (550888 upstream) : BTBD3 (665895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11252241	11252241	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11252241delA	uc002wnx.2	-											Homo sapiens hypothetical protein LOC339593, mRNA (cDNA clone IMAGE:5166493), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	11412419	11412419	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11412419delT								JAG1 (757725 upstream) : BTBD3 (459058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11418702	11418702	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11418702delT								JAG1 (764008 upstream) : BTBD3 (452775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11551643	11551644	+	IGR	DEL	TT	-	-	rs35869588		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11551643_11551644delTT								JAG1 (896949 upstream) : BTBD3 (319833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11621432	11621432	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11621432delG								JAG1 (966738 upstream) : BTBD3 (250045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11687504	11687505	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11687504_11687505insA								None (None upstream) : BTBD3 (183972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11727879	11727880	+	IGR	INS	-	AAAAGAAAAGAAAA	AAAAGAAAAGAAAA	rs148111754	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11727879_11727880insAAAAGAAAAGAAAA								None (None upstream) : BTBD3 (143597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11739384	11739385	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11739384_11739385delTT								None (None upstream) : BTBD3 (132092 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12080901	12080901	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12080901delT								BTBD3 (173659 upstream) : SPTLC3 (908726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12437256	12437256	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12437256delA								BTBD3 (530014 upstream) : SPTLC3 (552371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12589639	12589639	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12589639delA								BTBD3 (682397 upstream) : SPTLC3 (399988 downstream)																																			---	---	---	---
SPTLC3	55304	broad.mit.edu	37	20	13064332	13064332	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13064332delT	uc002wod.1	+							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)													---	---	---	---
SPTLC3	55304	broad.mit.edu	37	20	13136711	13136712	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13136711_13136712delAC	uc002wod.1	+							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	13310375	13310375	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13310375delT	uc010zri.1	-											Homo sapiens cDNA FLJ20212 fis, clone COLF1860.						asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0																		---	---	---	---
TASP1	55617	broad.mit.edu	37	20	13434710	13434712	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	13678140	13678141	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13678140_13678141delAA								TASP1 (58557 upstream) : ESF1 (16829 downstream)																																			---	---	---	---
ESF1	51575	broad.mit.edu	37	20	13723124	13723124	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13723124delA	uc002woj.2	-							NM_016649	NP_057733			ABT1-associated protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1																		---	---	---	---
C20orf7	79133	broad.mit.edu	37	20	13769424	13769424	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13769424delT	uc002wom.2	+						C20orf7_uc002wol.1_Intron|C20orf7_uc002won.2_Intron|C20orf7_uc002woo.2_Intron	NM_024120	NP_077025			hypothetical protein LOC79133 isoform 1						mitochondrial respiratory chain complex I assembly	extrinsic to mitochondrial inner membrane	methyltransferase activity				0		Myeloproliferative disorder(85;0.00878)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	14073899	14073899	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14073899delT	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	14083490	14083490	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14083490delT	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	14200582	14200582	+	Intron	DEL	G	-	-	rs115851199	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14200582delG	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	14728274	14728274	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14728274delT	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	14738753	14738753	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14738753delA	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	14841606	14841606	+	Intron	DEL	A	-	-	rs113452509		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14841606delA	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	15164150	15164150	+	Intron	DEL	A	-	-	rs72425908		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15164150delA	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	15381688	15381688	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15381688delT	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	15418479	15418479	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15418479delT	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	15614214	15614214	+	Intron	DEL	T	-	-	rs11476372		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15614214delT	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	15658709	15658709	+	Intron	DEL	A	-	-	rs34539368		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15658709delA	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	15847570	15847570	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15847570delG	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	15948034	15948034	+	Intron	DEL	A	-	-	rs6080063	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15948034delA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	16019810	16019810	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16019810delG	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron|MACROD2_uc002wpd.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	16227249	16227249	+	IGR	DEL	A	-	-	rs77632141		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16227249delA								MACROD2 (193410 upstream) : KIF16B (25500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	16626477	16626478	+	IGR	DEL	GT	-	-	rs33983158		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16626477_16626478delGT								KIF16B (72399 upstream) : SNRPB2 (84151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	16936893	16936894	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16936893_16936894delAA								OTOR (204085 upstream) : PCSK2 (269858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17048636	17048637	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17048636_17048637insC								OTOR (315828 upstream) : PCSK2 (158115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17079904	17079904	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17079904delA								OTOR (347096 upstream) : PCSK2 (126848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17141816	17141817	+	IGR	DEL	AA	-	-	rs139657218		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17141816_17141817delAA								OTOR (409008 upstream) : PCSK2 (64935 downstream)																																			---	---	---	---
PCSK2	5126	broad.mit.edu	37	20	17389042	17389042	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17389042delA	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585			proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
BFSP1	631	broad.mit.edu	37	20	17548599	17548601	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17548599_17548601delAAA	uc010zro.1	-						DSTN_uc002wpq.2_5'Flank|DSTN_uc002wpr.2_5'Flank	NM_001161705	NP_001155177			filensin isoform 2							cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens			central_nervous_system(1)	1																		---	---	---	---
RRBP1	6238	broad.mit.edu	37	20	17599607	17599607	+	5'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17599607delT	uc010zrp.1	-	1					RRBP1_uc002wpt.1_Intron|RRBP1_uc002wpu.2_Intron|RRBP1_uc002wpv.1_Intron|RRBP1_uc002wpw.1_Intron|RRBP1_uc010gcl.1_Intron					Homo sapiens mRNA for KIAA1398 protein, partial cds.						protein transport|translation|transmembrane transport	integral to endoplasmic reticulum membrane|ribosome	receptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	17779581	17779581	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17779581delT								BANF2 (63064 upstream) : SNX5 (142665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17896842	17896842	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17896842delA								BANF2 (180325 upstream) : SNX5 (25404 downstream)																																			---	---	---	---
OVOL2	58495	broad.mit.edu	37	20	18007756	18007756	+	Intron	DEL	T	-	-	rs67779488		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18007756delT	uc002wqi.1	-							NM_021220	NP_067043			zinc finger protein 339						negative regulation of keratinocyte differentiation|negative regulation of Notch signaling pathway|negative regulation of transcription by competitive promoter binding|regulation of cell cycle|regulation of keratinocyte proliferation|transcription, DNA-dependent	nucleus	DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
CSRP2BP	57325	broad.mit.edu	37	20	18126425	18126425	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18126425delA	uc002wqj.2	+						CSRP2BP_uc002wqk.2_Intron	NM_020536	NP_065397			CSRP2 binding protein						histone H3 acetylation	Ada2/Gcn5/Ada3 transcription activator complex|cytoplasm	LIM domain binding|N-acetyltransferase activity			lung(3)|ovary(2)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	18235586	18235586	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18235586delA								CSRP2BP (66571 upstream) : ZNF133 (33535 downstream)																																			---	---	---	---
C20orf12	55184	broad.mit.edu	37	20	18365748	18365748	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18365748delA	uc010zsa.1	-						C20orf12_uc010zrz.1_Intron|C20orf12_uc002wqp.3_Intron|C20orf12_uc002wqr.3_Intron|C20orf12_uc002wqs.3_Intron|C20orf12_uc002wqq.3_Intron	NM_001099407	NP_001092877			hypothetical protein LOC55184							intracellular	zinc ion binding			ovary(1)	1		Myeloproliferative disorder(85;0.0122)																---	---	---	---
RBBP9	10741	broad.mit.edu	37	20	18471327	18471327	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18471327delT	uc002wqy.2	-							NM_006606	NP_006597			retinoblastoma binding protein 9							cytoplasm|nucleus	hydrolase activity			haematopoietic_and_lymphoid_tissue(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	18908707	18908707	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18908707delC								C20orf79 (113674 upstream) : SLC24A3 (284583 downstream)																																			---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19243678	19243681	+	Intron	DEL	TGTG	-	-	rs140444429		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19243678_19243681delTGTG	uc002wrl.2	+						LOC100130264_uc010zsd.1_Intron	NM_020689	NP_065740			solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1																		---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19436730	19436730	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19436730delT	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	19441087	19441088	+	Intron	DEL	TC	-	-	rs145856041		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19441087_19441088delTC	uc002wrl.2	+							NM_020689	NP_065740			solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1																		---	---	---	---
RIN2	54453	broad.mit.edu	37	20	19935338	19935352	+	Intron	DEL	CCCTGTGCCCCTCAC	-	-	rs2063312	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19935338_19935352delCCCTGTGCCCCTCAC	uc002wro.1	+						RIN2_uc010gcu.1_Intron|RIN2_uc010gcv.1_Intron	NM_018993	NP_061866			Ras and Rab interactor 2						endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5																		---	---	---	---
RIN2	54453	broad.mit.edu	37	20	19978623	19978624	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19978623_19978624delTT	uc002wro.1	+						RIN2_uc010gcu.1_Intron|RIN2_uc010gcv.1_Intron	NM_018993	NP_061866			Ras and Rab interactor 2						endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5																		---	---	---	---
NAA20	51126	broad.mit.edu	37	20	20003957	20003958	+	Intron	DEL	AA	-	-	rs146423575		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20003957_20003958delAA	uc002wrp.2	+						NAA20_uc002wrq.2_Intron|NAA20_uc002wrr.2_Intron	NM_016100	NP_057184			N-acetyltransferase 5 isoform a							cytoplasm|nucleus	peptide alpha-N-acetyltransferase activity				0																		---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20125230	20125231	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20125230_20125231delAG	uc002wru.2	+						C20orf26_uc010gcw.1_Intron|C20orf26_uc010zse.1_Intron|C20orf26_uc010zsf.1_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20221219	20221219	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20221219delT	uc002wru.2	+						C20orf26_uc010zse.1_Intron|C20orf26_uc002wrw.2_Intron|C20orf26_uc002wrv.2_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20314778	20314779	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20314778_20314779insT	uc002wru.2	+						C20orf26_uc002wrw.2_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
RALGAPA2	57186	broad.mit.edu	37	20	20385939	20385939	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20385939delT	uc002wrz.2	-						RALGAPA2_uc010gcx.2_Intron|RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076			akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1																		---	---	---	---
RALGAPA2	57186	broad.mit.edu	37	20	20539321	20539321	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20539321delA	uc002wrz.2	-						RALGAPA2_uc010gcx.2_Intron|RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076			akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	20735589	20735590	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20735589_20735590insT								RALGAPA2 (42323 upstream) : PLK1S1 (371034 downstream)																																			---	---	---	---
PLK1S1	55857	broad.mit.edu	37	20	21153239	21153239	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21153239delA	uc002wsb.2	+						PLK1S1_uc010zsh.1_Intron|PLK1S1_uc010zsi.1_Intron|PLK1S1_uc010zsj.1_Intron|uc002wsc.2_Intron|PLK1S1_uc002wsd.2_Intron	NM_018474	NP_060944			polo-like kinase 1 substrate 1 isoform 1						spindle organization	centrosome	protein kinase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	21454156	21454156	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21454156delT								NKX2-4 (76109 upstream) : NKX2-2 (37508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21651731	21651732	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21651731_21651732insA								NKX2-2 (157067 upstream) : PAX1 (34565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21735886	21735886	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21735886delT								PAX1 (39266 upstream) : LOC284788 (645085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21913916	21913916	+	IGR	DEL	A	-	-	rs113159148		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21913916delA								PAX1 (217296 upstream) : LOC284788 (467055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21948006	21948006	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21948006delT								PAX1 (251386 upstream) : LOC284788 (432965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21975743	21975743	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21975743delT								PAX1 (279123 upstream) : LOC284788 (405228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22219495	22219498	+	IGR	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22219495_22219498delTTTT								PAX1 (522875 upstream) : LOC284788 (161473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22357686	22357688	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22357686_22357688delAAA								PAX1 (661066 upstream) : LOC284788 (23283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22483733	22483733	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22483733delT								LOC284788 (82452 upstream) : C20orf56 (57461 downstream)																																			---	---	---	---
CD93	22918	broad.mit.edu	37	20	23066469	23066469	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23066469delC	uc002wsv.2	-	1	509	c.361delG	c.(361-363)GAGfs	p.E121fs		NM_012072	NP_036204	Q9NPY3	C1QR1_HUMAN	CD93 antigen precursor	121	Extracellular (Potential).|C-type lectin.				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding			large_intestine(2)	2	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	23553248	23553248	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23553248delT								CST9L (3862 upstream) : CST9 (29801 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24023634	24023635	+	IGR	INS	-	T	T	rs72536521		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24023634_24023635insT								GGTLC1 (54218 upstream) : TMEM90B (426200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24217202	24217203	+	IGR	DEL	TG	-	-	rs74271752		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24217202_24217203delTG								GGTLC1 (247786 upstream) : TMEM90B (232632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24396955	24396955	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24396955delA								GGTLC1 (427539 upstream) : TMEM90B (52880 downstream)																																			---	---	---	---
ACSS1	84532	broad.mit.edu	37	20	24997615	24997616	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24997615_24997616delTT	uc002wub.2	-						ACSS1_uc002wuc.2_Intron|ACSS1_uc010gdc.2_Intron|ACSS1_uc002wud.1_Intron|ACSS1_uc002wua.2_Intron	NM_032501	NP_115890			acyl-CoA synthetase short-chain family member 1						acetyl-CoA biosynthetic process|ethanol oxidation|xenobiotic metabolic process	mitochondrial matrix	acetate-CoA ligase activity|AMP binding|ATP binding|protein binding			ovary(1)|skin(1)	2					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	25159938	25159938	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25159938delA								LOC284798 (30512 upstream) : ENTPD6 (16401 downstream)																																			---	---	---	---
ABHD12	26090	broad.mit.edu	37	20	25368369	25368369	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25368369delA	uc002wus.1	-						ABHD12_uc002wuq.2_Intron|ABHD12_uc002wur.2_Intron|ABHD12_uc002wut.1_Intron|ABHD12_uc002wuu.1_Intron	NM_001042472	NP_001035937			abhydrolase domain containing 12 isoform a							integral to membrane	acylglycerol lipase activity			skin(1)	1																		---	---	---	---
NINL	22981	broad.mit.edu	37	20	25474777	25474778	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25474777_25474778delCA	uc002wux.1	-						NINL_uc010gdn.1_Intron|NINL_uc010gdo.1_Intron|NINL_uc010ztf.1_Intron	NM_025176	NP_079452			ninein-like						G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25614671	25614673	+	Intron	DEL	TTC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25614671_25614673delTTC	uc002wuz.2	+											Homo sapiens zinc finger protein 337, mRNA (cDNA clone IMAGE:4826085).																														---	---	---	---
FAM182B	728882	broad.mit.edu	37	20	25759814	25759814	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25759814delA	uc010zth.1	-						FAM182B_uc002wvd.1_Intron|FAM182B_uc002wve.2_Intron|FAM182B_uc010zti.1_Intron	NR_027061				Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25930638	25930638	+	IGR	DEL	A	-	-	rs111792046		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25930638delA								FAM182B (81852 upstream) : LOC100134868 (59797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25968396	25968397	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25968396_25968397delGT								FAM182B (119610 upstream) : LOC100134868 (22038 downstream)																																			---	---	---	---
C20orf191	149934	broad.mit.edu	37	20	26089857	26089858	+	Intron	INS	-	C	C	rs149500400	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26089857_26089858insC	uc002wvj.3	-							NR_003678				SubName: Full=Putative uncharacterized protein ENSP00000323172;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	29422881	29422883	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29422881_29422883delAAA								None (None upstream) : FRG1B (188996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29552823	29552824	+	IGR	INS	-	AC	AC	rs145559505	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29552823_29552824insAC								None (None upstream) : FRG1B (59055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29555208	29555208	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29555208delC								None (None upstream) : FRG1B (56671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29572296	29572297	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	29588082	29588083	+	IGR	INS	-	C	C	rs139764885		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29588082_29588083insC								None (None upstream) : FRG1B (23796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29854223	29854223	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29854223delT								DEFB115 (6788 upstream) : DEFB116 (36793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	30038164	30038164	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30038164delA								DEFB123 (105 upstream) : DEFB124 (15145 downstream)																																			---	---	---	---
HM13	81502	broad.mit.edu	37	20	30122888	30122889	+	Intron	INS	-	A	A	rs78093425		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30122888_30122889insA	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	30161468	30161468	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30161468delT								HM13 (4100 upstream) : ID1 (31624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	30168835	30168835	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30168835delA								HM13 (11467 upstream) : ID1 (24257 downstream)																																			---	---	---	---
BCL2L1	598	broad.mit.edu	37	20	30257262	30257262	+	Intron	DEL	T	-	-	rs78282173		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30257262delT	uc002wwl.2	-						BCL2L1_uc002wwk.2_Intron|BCL2L1_uc002wwm.2_Intron|BCL2L1_uc002wwn.2_Intron	NM_138578	NP_612815			BCL2-like 1 isoform 1						induction of apoptosis by intracellular signals|negative regulation of establishment of protein localization in plasma membrane|negative regulation of survival gene product expression|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|release of cytochrome c from mitochondria|response to cytokine stimulus	integral to membrane|mitochondrial outer membrane|nuclear membrane	BH3 domain binding|identical protein binding			lung(1)|central_nervous_system(1)	2	all_cancers(5;3.47e-06)|all_epithelial(3;1.83e-06)|Lung NSC(7;2.08e-06)|all_lung(7;3.63e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;2.97e-06)|all cancers(5;3.21e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00052)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)															---	---	---	---
BCL2L1	598	broad.mit.edu	37	20	30260665	30260665	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30260665delT	uc002wwl.2	-						BCL2L1_uc002wwk.2_Intron|BCL2L1_uc002wwm.2_Intron|BCL2L1_uc002wwn.2_Intron	NM_138578	NP_612815			BCL2-like 1 isoform 1						induction of apoptosis by intracellular signals|negative regulation of establishment of protein localization in plasma membrane|negative regulation of survival gene product expression|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|release of cytochrome c from mitochondria|response to cytokine stimulus	integral to membrane|mitochondrial outer membrane|nuclear membrane	BH3 domain binding|identical protein binding			lung(1)|central_nervous_system(1)	2	all_cancers(5;3.47e-06)|all_epithelial(3;1.83e-06)|Lung NSC(7;2.08e-06)|all_lung(7;3.63e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;2.97e-06)|all cancers(5;3.21e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00052)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)															---	---	---	---
BCL2L1	598	broad.mit.edu	37	20	30277892	30277892	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30277892delT	uc002wwl.2	-						BCL2L1_uc002wwk.2_Intron|BCL2L1_uc002wwm.2_Intron|BCL2L1_uc002wwn.2_Intron	NM_138578	NP_612815			BCL2-like 1 isoform 1						induction of apoptosis by intracellular signals|negative regulation of establishment of protein localization in plasma membrane|negative regulation of survival gene product expression|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|release of cytochrome c from mitochondria|response to cytokine stimulus	integral to membrane|mitochondrial outer membrane|nuclear membrane	BH3 domain binding|identical protein binding			lung(1)|central_nervous_system(1)	2	all_cancers(5;3.47e-06)|all_epithelial(3;1.83e-06)|Lung NSC(7;2.08e-06)|all_lung(7;3.63e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;2.97e-06)|all cancers(5;3.21e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00052)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	30314806	30314806	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30314806delA								BCL2L1 (3077 upstream) : TPX2 (12098 downstream)																																			---	---	---	---
TPX2	22974	broad.mit.edu	37	20	30370538	30370538	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30370538delA	uc002wwp.1	+						TPX2_uc010gdv.1_Intron	NM_012112	NP_036244			TPX2, microtubule-associated protein homolog						activation of protein kinase activity|apoptosis|cell division|cell proliferation|mitosis|regulation of mitotic spindle organization	cytoplasm|microtubule|nucleus|spindle pole	ATP binding|GTP binding|protein kinase binding			large_intestine(1)|ovary(1)	2			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)															---	---	---	---
MYLK2	85366	broad.mit.edu	37	20	30414943	30414943	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30414943delA	uc002wwq.2	+						MYLK2_uc002wws.2_Intron	NM_033118	NP_149109			skeletal myosin light chain kinase						cardiac muscle tissue morphogenesis|regulation of muscle filament sliding		ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			lung(2)|skin(2)|ovary(1)|central_nervous_system(1)	6			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	30591908	30591908	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30591908delT								XKR7 (5653 upstream) : C20orf160 (6337 downstream)																																			---	---	---	---
HCK	3055	broad.mit.edu	37	20	30687113	30687113	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30687113delG	uc002wxh.2	+						HCK_uc010gdy.2_Intron|HCK_uc002wxi.2_Intron	NM_002110	NP_002101			hemopoietic cell kinase isoform p61HCK						interspecies interaction between organisms|mesoderm development|regulation of defense response to virus by virus|viral reproduction	caveola|cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|ovary(2)|central_nervous_system(2)|pancreas(1)	9			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
POFUT1	23509	broad.mit.edu	37	20	30808544	30808546	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30808544_30808546delAAA	uc002wxp.2	+						POFUT1_uc010ztt.1_Intron|POFUT1_uc010ztu.1_Intron	NM_015352	NP_056167			protein O-fucosyltransferase 1 isoform 1						fucose metabolic process|Notch signaling pathway|O-glycan processing|regulation of transcription, DNA-dependent	endoplasmic reticulum|membrane	peptide-O-fucosyltransferase activity			breast(1)	1			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	30838565	30838565	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30838565delT								POFUT1 (12099 upstream) : KIF3B (26902 downstream)																																			---	---	---	---
KIF3B	9371	broad.mit.edu	37	20	30871307	30871307	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30871307delA	uc002wxq.2	+						KIF3B_uc010ztv.1_Intron	NM_004798	NP_004789			kinesin family member 3B						anterograde axon cargo transport|blood coagulation|determination of left/right symmetry|mitotic centrosome separation|plus-end-directed vesicle transport along microtubule|spindle assembly involved in mitosis	centrosome|cytosol|kinesin II complex|plus-end kinesin complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|Rho GTPase binding			central_nervous_system(3)|ovary(2)	5			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
KIF3B	9371	broad.mit.edu	37	20	30884404	30884404	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30884404delA	uc002wxq.2	+						KIF3B_uc010ztv.1_Intron	NM_004798	NP_004789			kinesin family member 3B						anterograde axon cargo transport|blood coagulation|determination of left/right symmetry|mitotic centrosome separation|plus-end-directed vesicle transport along microtubule|spindle assembly involved in mitosis	centrosome|cytosol|kinesin II complex|plus-end kinesin complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|Rho GTPase binding			central_nervous_system(3)|ovary(2)	5			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	30932359	30932359	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30932359delA								KIF3B (9550 upstream) : ASXL1 (13794 downstream)																																			---	---	---	---
ASXL1	171023	broad.mit.edu	37	20	30963252	30963252	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30963252delA	uc002wxs.2	+						ASXL1_uc002wxr.1_Intron|ASXL1_uc010geb.2_Intron	NM_015338	NP_056153			additional sex combs like 1 isoform 1						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248								F|N|Mis		MDS|CMML								---	---	---	---
C20orf203	284805	broad.mit.edu	37	20	31241119	31241119	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31241119delT	uc002wxz.2	-							NR_026959				Homo sapiens cDNA FLJ33706 fis, clone BRAWH2007808.							cytoplasm					0																OREG0025864	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C20orf203	284805	broad.mit.edu	37	20	31262834	31262834	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31262834delA	uc002wxz.2	-							NR_026959				Homo sapiens cDNA FLJ33706 fis, clone BRAWH2007808.							cytoplasm					0																		---	---	---	---
COMMD7	149951	broad.mit.edu	37	20	31291449	31291449	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31291449delA	uc002wya.3	-						COMMD7_uc010ged.2_Intron|COMMD7_uc002wyb.2_3'UTR	NM_053041	NP_444269			COMM domain containing 7 isoform 1						negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent|tumor necrosis factor-mediated signaling pathway		NF-kappaB binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	31397728	31397729	+	IGR	INS	-	A	A	rs143553612		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31397728_31397729insA								DNMT3B (567 upstream) : MAPRE1 (9970 downstream)																																			---	---	---	---
SUN5	140732	broad.mit.edu	37	20	31577498	31577498	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31577498delT	uc002wyi.2	-	9	634	c.541delA	c.(541-543)ATGfs	p.M181fs		NM_080675	NP_542406	Q8TC36	SUN5_HUMAN	sperm associated antigen 4-like	181	Potential.				spermatogenesis					skin(1)	1																		---	---	---	---
SNTA1	6640	broad.mit.edu	37	20	32017746	32017746	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32017746delT	uc002wzd.1	-						SNTA1_uc010zuf.1_Intron	NM_003098	NP_003089			acidic alpha 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|sarcolemma	actin binding|calmodulin binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	32034744	32034744	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32034744delA								SNTA1 (3046 upstream) : CBFA2T2 (43184 downstream)																																			---	---	---	---
CBFA2T2	9139	broad.mit.edu	37	20	32166922	32166924	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32166922_32166924delTTT	uc002wzg.1	+						CBFA2T2_uc010zug.1_Intron|CBFA2T2_uc002wze.1_Intron|CBFA2T2_uc002wzf.1_Intron|CBFA2T2_uc002wzh.1_Intron|CBFA2T2_uc002wzi.1_Intron	NM_005093	NP_005084			core-binding factor, runt domain, alpha subunit							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2																		---	---	---	---
CBFA2T2	9139	broad.mit.edu	37	20	32176826	32176826	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32176826delA	uc002wzg.1	+						CBFA2T2_uc010zug.1_Intron|CBFA2T2_uc002wze.1_Intron|CBFA2T2_uc002wzf.1_Intron|CBFA2T2_uc002wzh.1_Intron|CBFA2T2_uc002wzi.1_Intron	NM_005093	NP_005084			core-binding factor, runt domain, alpha subunit							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2																		---	---	---	---
CBFA2T2	9139	broad.mit.edu	37	20	32189616	32189616	+	Intron	DEL	T	-	-	rs66932167		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32189616delT	uc002wzg.1	+						CBFA2T2_uc010zug.1_Intron|CBFA2T2_uc002wze.1_Intron|CBFA2T2_uc002wzf.1_Intron|CBFA2T2_uc002wzh.1_Intron|CBFA2T2_uc002wzi.1_Intron|CBFA2T2_uc002wzj.1_Intron	NM_005093	NP_005084			core-binding factor, runt domain, alpha subunit							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2																		---	---	---	---
PXMP4	11264	broad.mit.edu	37	20	32293411	32293411	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32293411delA	uc002wzv.2	-	4					PXMP4_uc002wzw.2_3'UTR|PXMP4_uc010zuh.1_3'UTR	NM_007238	NP_009169			peroxisomal membrane protein 4 isoform a							integral to membrane|membrane fraction|mitochondrial inner membrane|peroxisomal membrane	protein transporter activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	32501243	32501243	+	IGR	DEL	C	-	-	rs143767841		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32501243delC								CHMP4B (59074 upstream) : RALY (80489 downstream)																																			---	---	---	---
RALY	22913	broad.mit.edu	37	20	32645826	32645826	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32645826delT	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																		---	---	---	---
EIF2S2	8894	broad.mit.edu	37	20	32694234	32694235	+	Intron	DEL	TT	-	-	rs71992109		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32694234_32694235delTT	uc002xaf.2	-						EIF2S2_uc002xag.2_Intron|EIF2S2_uc010ges.2_Intron	NM_003908	NP_003899			eukaryotic translation initiation factor 2 beta							cytosol|eukaryotic translation initiation factor 2 complex	metal ion binding|protein binding|translation initiation factor activity			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	32749034	32749034	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32749034delT								EIF2S2 (48949 upstream) : ASIP (99137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	32766299	32766299	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32766299delC								EIF2S2 (66214 upstream) : ASIP (81872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	32801222	32801222	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32801222delA								EIF2S2 (101137 upstream) : ASIP (46949 downstream)																																			---	---	---	---
ITCH	83737	broad.mit.edu	37	20	33052522	33052522	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33052522delT	uc010geu.1	+						ITCH_uc002xak.2_Intron|ITCH_uc010zuj.1_Intron|MIR644_hsa-mir-644|MI0003659_5'Flank	NM_031483	NP_113671			itchy homolog E3 ubiquitin protein ligase						apoptosis|entry of virus into host cell|inflammatory response|innate immune response|negative regulation of apoptosis|negative regulation of defense response to virus|negative regulation of JNK cascade|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cell growth|regulation of protein deubiquitination|response to virus	cytosol|nucleus|plasma membrane	CXCR chemokine receptor binding|ribonucleoprotein binding|ubiquitin-protein ligase activity			breast(4)|lung(1)|central_nervous_system(1)	6																		---	---	---	---
ITCH	83737	broad.mit.edu	37	20	33086782	33086782	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33086782delT	uc010geu.1	+						ITCH_uc002xak.2_Intron|ITCH_uc010zuj.1_Intron	NM_031483	NP_113671			itchy homolog E3 ubiquitin protein ligase						apoptosis|entry of virus into host cell|inflammatory response|innate immune response|negative regulation of apoptosis|negative regulation of defense response to virus|negative regulation of JNK cascade|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cell growth|regulation of protein deubiquitination|response to virus	cytosol|nucleus|plasma membrane	CXCR chemokine receptor binding|ribonucleoprotein binding|ubiquitin-protein ligase activity			breast(4)|lung(1)|central_nervous_system(1)	6																		---	---	---	---
PIGU	128869	broad.mit.edu	37	20	33170490	33170490	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33170490delA	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron	NM_080476	NP_536724			phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0																		---	---	---	---
PIGU	128869	broad.mit.edu	37	20	33188384	33188384	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33188384delA	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron|PIGU_uc010gev.1_Intron	NM_080476	NP_536724			phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0																		---	---	---	---
PIGU	128869	broad.mit.edu	37	20	33188896	33188896	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33188896delA	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron|PIGU_uc010gev.1_Intron	NM_080476	NP_536724			phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0																		---	---	---	---
PIGU	128869	broad.mit.edu	37	20	33220729	33220731	+	Intron	DEL	AAA	-	-	rs74908424		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33220729_33220731delAAA	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron|PIGU_uc010gev.1_Intron	NM_080476	NP_536724			phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	33275803	33275803	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33275803delA								PIGU (10714 upstream) : TP53INP2 (16345 downstream)																																			---	---	---	---
NCOA6	23054	broad.mit.edu	37	20	33363109	33363110	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33363109_33363110delGT	uc002xav.2	-						NCOA6_uc002xaw.2_Intron|NCOA6_uc010gew.1_Intron	NM_014071	NP_054790			nuclear receptor coactivator 6						brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding			ovary(3)|breast(3)|central_nervous_system(1)	7																		---	---	---	---
NCOA6	23054	broad.mit.edu	37	20	33371085	33371085	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33371085delA	uc002xav.2	-						NCOA6_uc002xaw.2_Intron|NCOA6_uc010gew.1_Intron	NM_014071	NP_054790			nuclear receptor coactivator 6						brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding			ovary(3)|breast(3)|central_nervous_system(1)	7																		---	---	---	---
GSS	2937	broad.mit.edu	37	20	33527044	33527044	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33527044delA	uc002xbg.2	-						GSS_uc010zun.1_Intron|GSS_uc010zuo.1_Intron|GSS_uc010zup.1_Intron|GSS_uc002xbh.2_Intron|GSS_uc010gez.1_Intron	NM_000178	NP_000169			glutathione synthetase						nervous system development|response to oxidative stress|xenobiotic metabolic process	cytosol	ATP binding|glutathione binding|glutathione synthase activity|magnesium ion binding|protein homodimerization activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(18;0.035)		Glutathione(DB00143)|Glycine(DB00145)|L-Cysteine(DB00151)													---	---	---	---
TRPC4AP	26133	broad.mit.edu	37	20	33604435	33604435	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33604435delA	uc002xbk.2	-						TRPC4AP_uc010zuq.1_Intron|TRPC4AP_uc002xbl.2_Intron|TRPC4AP_uc010zur.1_Intron|TRPC4AP_uc002xbm.1_Intron	NM_015638	NP_056453			TRPC4-associated protein isoform a						protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
TRPC4AP	26133	broad.mit.edu	37	20	33647588	33647590	+	Intron	DEL	GAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33647588_33647590delGAA	uc002xbk.2	-						TRPC4AP_uc002xbl.2_Intron|TRPC4AP_uc010zur.1_Intron|TRPC4AP_uc002xbm.1_Intron	NM_015638	NP_056453			TRPC4-associated protein isoform a						protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
EDEM2	55741	broad.mit.edu	37	20	33736028	33736028	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33736028delT	uc002xbo.2	-						EDEM2_uc010zuv.1_Intron|EDEM2_uc002xbq.2_5'Flank|EDEM2_uc010zut.1_5'Flank|EDEM2_uc002xbp.2_5'Flank|EDEM2_uc002xbn.2_5'Flank|EDEM2_uc002xbr.2_5'Flank|EDEM2_uc010zuu.1_5'Flank	NM_018217	NP_060687			ER degradation enhancer, mannosidase alpha-like						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33925835	33925835	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33925835delA	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron	NM_000557	NP_000548			growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)															---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33969913	33969913	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33969913delT	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron|UQCC_uc002xci.1_Intron|UQCC_uc010gfd.1_Intron	NM_000557	NP_000548			growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)															---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33975318	33975318	+	Intron	DEL	T	-	-	rs75048205		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33975318delT	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	34096147	34096147	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34096147delT	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)															---	---	---	---
NFS1	9054	broad.mit.edu	37	20	34284587	34284587	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34284587delT	uc002xdw.1	-						NFS1_uc002xdt.1_Intron|NFS1_uc002xdu.1_Intron|NFS1_uc002xdv.1_Intron|NFS1_uc010zvk.1_Intron|NFS1_uc010zvl.1_Intron|NFS1_uc002xdx.2_Intron|ROMO1_uc002xdy.2_5'Flank|ROMO1_uc010gfm.2_5'Flank	NM_021100	NP_066923			NFS1 nitrogen fixation 1 precursor						cysteine metabolic process|iron incorporation into metallo-sulfur cluster|Mo-molybdopterin cofactor biosynthetic process|protein complex assembly|water-soluble vitamin metabolic process	cytosol|mitochondrial matrix|nucleus	cysteine desulfurase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)													---	---	---	---
RBM39	9584	broad.mit.edu	37	20	34330989	34330989	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34330989delA	uc002xeb.2	-						RBM39_uc002xea.2_5'Flank|RBM39_uc010gfn.2_5'Flank|RBM39_uc010zvm.1_5'Flank|RBM39_uc002xeg.2_5'Flank|RBM39_uc002xec.2_5'Flank|RBM39_uc002xed.2_5'Flank|RBM39_uc002xee.2_5'Flank|RBM39_uc002xef.2_5'Flank|RBM39_uc010zvn.1_5'Flank	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	34583248	34583248	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34583248delT	uc002xes.1	+						C20orf152_uc002xer.1_Intron|C20orf152_uc010gfp.1_Intron					SubName: Full=C20orf152 protein;												0	Breast(12;0.00631)															OREG0025897	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	34721778	34721779	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34721778_34721779delAA	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)																	---	---	---	---
C20orf4	25980	broad.mit.edu	37	20	34849289	34849290	+	Intron	DEL	TC	-	-	rs58789130	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34849289_34849290delTC	uc002xfd.1	+							NM_015511	NP_056326			hypothetical protein LOC25980												0	Breast(12;0.0162)	Myeloproliferative disorder(115;0.0393)																---	---	---	---
DLGAP4	22839	broad.mit.edu	37	20	35006853	35006853	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35006853delT	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	35045766	35045771	+	Intron	DEL	TTTTGT	-	-	rs11469398	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35045766_35045771delTTTTGT	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	35110388	35110388	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35110388delA	uc002xff.2	+						DLGAP4_uc010zvp.1_Intron|DLGAP4_uc002xfg.2_Intron|DLGAP4_uc002xfh.2_Intron	NM_014902	NP_055717			disks large-associated protein 4 isoform a						cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
TGIF2	60436	broad.mit.edu	37	20	35209057	35209057	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35209057delA	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	35229137	35229137	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35229137delT	uc002xfo.2	+							NM_018840	NP_061328			RAB5-interacting protein isoform a								protein binding				0	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
NDRG3	57446	broad.mit.edu	37	20	35307908	35307910	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35307908_35307910delTTT	uc002xfw.2	-						NDRG3_uc002xfx.2_Intron|NDRG3_uc010zvq.1_Intron|NDRG3_uc010zvr.1_Intron	NM_032013	NP_114402			N-myc downstream regulated gene 3 isoform a						cell differentiation|negative regulation of cell growth|spermatogenesis	cytoplasm				ovary(1)	1		Myeloproliferative disorder(115;0.00878)																---	---	---	---
DSN1	79980	broad.mit.edu	37	20	35381584	35381584	+	Intron	DEL	A	-	-	rs76358531		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35381584delA	uc010gfr.2	-						DSN1_uc002xfz.2_Intron|DSN1_uc002xfy.3_Intron|DSN1_uc002xga.2_Intron|DSN1_uc010zvs.1_Intron|DSN1_uc002xgc.2_Intron|DSN1_uc002xgb.2_Intron	NM_001145316	NP_001138788			DSN1, MIND kinetochore complex component,						cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			ovary(2)	2		Myeloproliferative disorder(115;0.00874)																---	---	---	---
DSN1	79980	broad.mit.edu	37	20	35382752	35382752	+	Intron	DEL	A	-	-	rs78743674		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35382752delA	uc010gfr.2	-						DSN1_uc002xfz.2_Intron|DSN1_uc002xfy.3_Intron|DSN1_uc002xga.2_Intron|DSN1_uc010zvs.1_Intron|DSN1_uc002xgc.2_Intron|DSN1_uc002xgb.2_Intron	NM_001145316	NP_001138788			DSN1, MIND kinetochore complex component,						cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			ovary(2)	2		Myeloproliferative disorder(115;0.00874)																---	---	---	---
C20orf117	140710	broad.mit.edu	37	20	35426475	35426476	+	Intron	INS	-	T	T	rs113753332		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35426475_35426476insT	uc002xgd.1	-						C20orf117_uc002xge.1_Intron	NM_199181	NP_954650			hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
C20orf118	140711	broad.mit.edu	37	20	35503709	35503712	+	5'Flank	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35503709_35503712delTTTT	uc002xgg.1	+							NM_080628	NP_542195			hypothetical protein LOC140711												0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
C20orf118	140711	broad.mit.edu	37	20	35520098	35520098	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35520098delT	uc002xgg.1	+							NM_080628	NP_542195			hypothetical protein LOC140711												0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
SAMHD1	25939	broad.mit.edu	37	20	35578734	35578734	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35578734delA	uc002xgh.1	-							NM_015474	NP_056289			SAM domain- and HD domain-containing protein 1						defense response to virus|innate immune response|regulation of innate immune response	nucleus	metal ion binding|phosphoric diester hydrolase activity				0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35653620	35653621	+	Intron	INS	-	TT	TT	rs140314356	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35653620_35653621insTT	uc002xgi.2	-						RBL1_uc010zvt.1_Intron|RBL1_uc002xgj.1_Intron	NM_002895	NP_002886			retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35692232	35692232	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35692232delT	uc002xgi.2	-						RBL1_uc010zvt.1_Intron|RBL1_uc002xgj.1_Intron|RBL1_uc010gfv.1_Intron	NM_002895	NP_002886			retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35708866	35708866	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35708866delT	uc002xgi.2	-						RBL1_uc010zvt.1_Intron|RBL1_uc002xgj.1_Intron|RBL1_uc010gfv.1_Intron	NM_002895	NP_002886			retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	35878292	35878293	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35878292_35878293delTT								RPN2 (8269 upstream) : GHRH (1199 downstream)																																			---	---	---	---
GHRH	2691	broad.mit.edu	37	20	35888803	35888803	+	Intron	DEL	A	-	-	rs35780841		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35888803delA	uc002xgs.2	-						GHRH_uc002xgt.2_Intron	NM_021081	NP_066567			growth hormone releasing hormone preproprotein						activation of adenylate cyclase activity by G-protein signaling pathway|adenohypophysis development|growth hormone secretion|positive regulation of cAMP biosynthetic process|positive regulation of cell proliferation|positive regulation of circadian sleep/wake cycle, REM sleep|positive regulation of growth hormone secretion|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of multicellular organism growth|response to food	extracellular space|terminal button	growth hormone-releasing hormone activity|growth hormone-releasing hormone receptor binding			ovary(1)	1		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	36041772	36041772	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36041772delT								SRC (7953 upstream) : BLCAP (104048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	36102089	36102089	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36102089delT								SRC (68270 upstream) : BLCAP (43731 downstream)																																			---	---	---	---
BLCAP	10904	broad.mit.edu	37	20	36146380	36146381	+	3'UTR	INS	-	AC	AC	rs142142675	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36146380_36146381insAC	uc002xha.2	-	2					BLCAP_uc002xhb.2_3'UTR|BLCAP_uc002xhc.2_3'UTR	NM_006698	NP_006689			bladder cancer associated protein						apoptosis|cell cycle	integral to membrane					0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	36256740	36256741	+	IGR	INS	-	T	T	rs143029563		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36256740_36256741insT								BLCAP (100437 upstream) : CTNNBL1 (65693 downstream)																																			---	---	---	---
CTNNBL1	56259	broad.mit.edu	37	20	36332951	36332952	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36332951_36332952delAA	uc010zvw.1	+						CTNNBL1_uc010zvv.1_Intron	NM_030877	NP_110517			beta catenin-like 1						apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
KIAA1755	85449	broad.mit.edu	37	20	36887856	36887857	+	Intron	DEL	TA	-	-	rs67600464		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36887856_36887857delTA	uc002xhy.1	-						KIAA1755_uc002xhz.1_Intron|uc002xia.1_5'Flank	NM_001029864	NP_001025035			hypothetical protein LOC85449											ovary(4)|pancreas(1)	5		Myeloproliferative disorder(115;0.00874)																---	---	---	---
BPI	671	broad.mit.edu	37	20	36938382	36938383	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36938382_36938383insT	uc002xib.2	+							NM_001725	NP_001716			bactericidal/permeability-increasing protein						defense response to bacterium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of macrophage activation|negative regulation of tumor necrosis factor production	extracellular region|integral to plasma membrane	lipid binding|lipopolysaccharide binding			ovary(4)	4		Myeloproliferative disorder(115;0.00878)																---	---	---	---
LBP	3929	broad.mit.edu	37	20	36988253	36988253	+	Intron	DEL	A	-	-	rs111643275		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36988253delA	uc002xic.1	+							NM_004139	NP_004130			lipopolysaccharide-binding protein precursor						acute-phase response|cellular defense response|cellular response to lipoteichoic acid|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|detection of molecule of bacterial origin|innate immune response|lipid transport|lipopolysaccharide transport|lipopolysaccharide-mediated signaling pathway|macrophage activation involved in immune response|negative regulation of tumor necrosis factor production|opsonization|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of macrophage activation|positive regulation of respiratory burst involved in inflammatory response|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of tumor necrosis factor production|Toll signaling pathway	extracellular space	Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|lipid binding|lipopolysaccharide binding|lipoteichoic acid binding|receptor binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	37018097	37018097	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37018097delA								LBP (12444 upstream) : LOC388796 (31142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37039596	37039597	+	Intron	INS	-	T	T	rs77591316		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37039596_37039597insT	uc002xid.1	-											Homo sapiens cDNA FLJ33613 fis, clone BRAMY2017348.																														---	---	---	---
SNHG11	128439	broad.mit.edu	37	20	37072812	37072812	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37072812delT	uc002xiq.1	+						SNHG11_uc002xir.1_5'Flank|SNHG11_uc002xis.1_5'Flank|SNHG11_uc002xit.1_5'Flank|SNHG11_uc002xiu.1_5'Flank	NR_003239				Homo sapiens hypothetical protein mRNA, complete cds.												0																		---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37154320	37154320	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37154320delT	uc002xiw.2	+						RALGAPB_uc002xix.2_Intron|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.2_Intron|RALGAPB_uc002xja.1_Intron	NM_020336	NP_065069			Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2																		---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37169993	37169993	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37169993delT	uc002xiw.2	+						RALGAPB_uc002xix.2_Intron|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.2_Intron|RALGAPB_uc002xja.1_Intron	NM_020336	NP_065069			Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2																		---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37196906	37196906	+	Intron	DEL	A	-	-	rs113434181		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37196906delA	uc002xiw.2	+						RALGAPB_uc002xix.2_Intron|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.2_Intron	NM_020336	NP_065069			Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	37324406	37324406	+	IGR	DEL	A	-	-	rs112556357		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37324406delA								ADIG (107302 upstream) : SLC32A1 (28699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37365495	37365495	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37365495delA								SLC32A1 (7480 upstream) : ACTR5 (11602 downstream)																																			---	---	---	---
FAM83D	81610	broad.mit.edu	37	20	37571668	37571669	+	Intron	DEL	TT	-	-	rs112144207		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37571668_37571669delTT	uc002xjg.2	+						FAM83D_uc002xjf.2_3'UTR	NM_030919	NP_112181			hypothetical protein LOC81610						cell division|mitosis	cytoplasm|spindle pole				ovary(3)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	37925147	37925147	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37925147delT								LOC339568 (71756 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38126145	38126145	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38126145delA								LOC339568 (272754 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38539008	38539008	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38539008delA								LOC339568 (685617 upstream) : MAFB (775511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38884083	38884083	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38884083delA								None (None upstream) : MAFB (430436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39059652	39059652	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39059652delT								None (None upstream) : MAFB (254867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39106784	39106784	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39106784delT								None (None upstream) : MAFB (207735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39564313	39564313	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39564313delA								MAFB (246437 upstream) : TOP1 (93149 downstream)																																			---	---	---	---
ZHX3	23051	broad.mit.edu	37	20	39898525	39898527	+	Intron	DEL	AAA	-	-	rs77687785		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39898525_39898527delAAA	uc002xjs.1	-						ZHX3_uc002xjq.1_5'Flank|ZHX3_uc002xjr.1_Intron|ZHX3_uc002xjt.1_Intron|ZHX3_uc002xju.1_Intron|ZHX3_uc002xjv.1_Intron|ZHX3_uc002xjw.1_Intron	NM_015035	NP_055850			zinc fingers and homeoboxes 3						negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Myeloproliferative disorder(115;0.00425)																---	---	---	---
ZHX3	23051	broad.mit.edu	37	20	39912396	39912397	+	Intron	DEL	AA	-	-	rs11477013		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39912396_39912397delAA	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	40650404	40650405	+	IGR	INS	-	TGTG	TGTG	rs140162178	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40650404_40650405insTGTG								CHD6 (403271 upstream) : PTPRT (50988 downstream)																																			---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41306343	41306344	+	Intron	DEL	AC	-	-	rs2425514	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41306343_41306344delAC	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	41753803	41753803	+	Intron	DEL	T	-	-	rs72296738		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41753803delT	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	41813328	41813328	+	Intron	DEL	A	-	-	rs6030684		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41813328delA	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	42060083	42060110	+	IGR	DEL	AAACACACACACAAACACACACACACAT	-	-	rs71193689	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42060083_42060110delAAACACACACACAAACACACACACACAT								PTPRT (241526 upstream) : SFRS6 (26394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	42063257	42063258	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42063257_42063258delAG								PTPRT (244700 upstream) : SFRS6 (23246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	42102923	42102924	+	IGR	DEL	TA	-	-	rs11475162		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42102923_42102924delTA								SFRS6 (10681 upstream) : L3MBTL (33426 downstream)																																			---	---	---	---
MYBL2	4605	broad.mit.edu	37	20	42308553	42308554	+	Intron	DEL	AA	-	-	rs67835138		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42308553_42308554delAA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	42377563	42377564	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42377563_42377564delTT								GTSF1L (21921 upstream) : TOX2 (165928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	42726977	42726977	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42726977delA								TOX2 (28725 upstream) : JPH2 (13360 downstream)																																			---	---	---	---
GDAP1L1	78997	broad.mit.edu	37	20	42883030	42883031	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42883030_42883031insC	uc002xlq.2	+						GDAP1L1_uc002xlp.1_Intron|GDAP1L1_uc010zwl.1_Intron|GDAP1L1_uc010zwm.1_Intron|GDAP1L1_uc010zwn.1_Intron	NM_024034	NP_076939			ganglioside-induced differentiation-associated											large_intestine(1)	1		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	42918088	42918088	+	IGR	DEL	A	-	-	rs77327839		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42918088delA								GDAP1L1 (9077 upstream) : FITM2 (17109 downstream)																																			---	---	---	---
HNF4A	3172	broad.mit.edu	37	20	43012497	43012497	+	Intron	DEL	A	-	-	rs150029107	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43012497delA	uc002xlv.2	+						HNF4A_uc010zwo.1_Intron|HNF4A_uc002xlt.2_Intron|HNF4A_uc002xlu.2_Intron|uc002xlw.1_Intron|uc002xlx.2_Intron	NM_175914	NP_787110			hepatocyte nuclear factor 4 alpha isoform d						blood coagulation|endocrine pancreas development|glucose homeostasis|negative regulation of cell growth|negative regulation of cell proliferation|ornithine metabolic process|phospholipid homeostasis|positive regulation of cholesterol homeostasis|regulation of growth hormone receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to glucose stimulus|triglyceride homeostasis|xenobiotic metabolic process	cytoplasm	activating transcription factor binding|protein homodimerization activity|receptor binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
PKIG	11142	broad.mit.edu	37	20	43189978	43189978	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43189978delA	uc002xmg.2	+						PKIG_uc002xmh.2_Intron|PKIG_uc002xmi.2_Intron	NM_181805	NP_861521			cAMP-dependent protein kinase inhibitor gamma								cAMP-dependent protein kinase inhibitor activity|protein binding				0		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.001)|COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
PKIG	11142	broad.mit.edu	37	20	43218722	43218722	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43218722delT	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)															---	---	---	---
ADA	100	broad.mit.edu	37	20	43252556	43252556	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43252556delT	uc002xmj.2	-						ADA_uc010ggt.2_Intron	NM_000022	NP_000013			adenosine deaminase						adenosine catabolic process|cell adhesion|hypoxanthine salvage|inosine biosynthetic process|negative regulation of adenosine receptor signaling pathway|purine nucleotide salvage|purine ribonucleoside monophosphate biosynthetic process|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation	cell junction|cytoplasmic membrane-bounded vesicle lumen|cytosol|external side of plasma membrane|lysosome	adenosine deaminase activity|protein binding|zinc ion binding			pancreas(2)|ovary(1)	3		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Cladribine(DB00242)|Dipyridamole(DB00975)|Erythromycin(DB00199)|Fludarabine(DB01073)|Idoxuridine(DB00249)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)									Adenosine_Deaminase_Deficiency				---	---	---	---
ADA	100	broad.mit.edu	37	20	43282912	43282913	+	5'Flank	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43282912_43282913delAA	uc002xmj.2	-						ADA_uc010ggt.2_5'Flank	NM_000022	NP_000013			adenosine deaminase						adenosine catabolic process|cell adhesion|hypoxanthine salvage|inosine biosynthetic process|negative regulation of adenosine receptor signaling pathway|purine nucleotide salvage|purine ribonucleoside monophosphate biosynthetic process|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation	cell junction|cytoplasmic membrane-bounded vesicle lumen|cytosol|external side of plasma membrane|lysosome	adenosine deaminase activity|protein binding|zinc ion binding			pancreas(2)|ovary(1)	3		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Cladribine(DB00242)|Dipyridamole(DB00975)|Erythromycin(DB00199)|Fludarabine(DB01073)|Idoxuridine(DB00249)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)									Adenosine_Deaminase_Deficiency				---	---	---	---
Unknown	0	broad.mit.edu	37	20	43288448	43288448	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43288448delA	uc002xmk.3	-											Homo sapiens hypothetical protein MGC5566, mRNA (cDNA clone IMAGE:3458308).																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	43341989	43341989	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43341989delT	uc002xml.1	-						uc002xmm.1_Intron|WISP2_uc002xmn.2_5'Flank|WISP2_uc002xmo.1_5'Flank|WISP2_uc002xmp.2_5'Flank|WISP2_uc002xmq.2_5'Flank					Homo sapiens cDNA FLJ33523 fis, clone BRAMY2006411.																														---	---	---	---
STK4	6789	broad.mit.edu	37	20	43596784	43596784	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43596784delT	uc002xnb.2	+						STK4_uc010ggx.2_Intron|STK4_uc010ggy.2_Intron|uc002xna.1_5'Flank|STK4_uc010ggw.1_Intron	NM_006282	NP_006273			serine/threonine kinase 4						apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding			ovary(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
STK4	6789	broad.mit.edu	37	20	43607423	43607423	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43607423delT	uc002xnb.2	+						STK4_uc010ggx.2_Intron|STK4_uc010ggy.2_Intron|STK4_uc010ggw.1_Intron	NM_006282	NP_006273			serine/threonine kinase 4						apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding			ovary(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
WFDC5	149708	broad.mit.edu	37	20	43741209	43741210	+	Intron	INS	-	CA	CA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43741209_43741210insCA	uc002xne.1	-							NM_145652	NP_663627			WAP four-disulfide core domain 5 precursor							extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	44551713	44551714	+	IGR	DEL	AA	-	-	rs77595722		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44551713_44551714delAA								PLTP (10927 upstream) : PCIF1 (11603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	44615123	44615124	+	IGR	INS	-	CTTC	CTTC	rs148299377	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44615123_44615124insCTTC								ZNF335 (14290 upstream) : MMP9 (22423 downstream)																																			---	---	---	---
NCOA5	57727	broad.mit.edu	37	20	44696576	44696576	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44696576delT	uc002xrd.2	-						NCOA5_uc002xrc.2_Intron|NCOA5_uc002xre.2_Intron	NM_020967	NP_066018			nuclear receptor coactivator 5						regulation of transcription, DNA-dependent|transcription, DNA-dependent|translation	nucleus	aminoacyl-tRNA ligase activity|ATP binding			central_nervous_system(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
CDH22	64405	broad.mit.edu	37	20	44894669	44894670	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44894669_44894670delTC	uc010ghk.1	-							NM_021248	NP_067071			cadherin 22 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ELMO2	63916	broad.mit.edu	37	20	45038394	45038394	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45038394delA	uc010zxs.1	-											SubName: Full=ELMO2 protein; SubName: Full=Engulfment and cell motility 2;						apoptosis|cell chemotaxis|phagocytosis	cytoskeleton|cytosol|membrane	lyase activity|receptor tyrosine kinase binding|SH3 domain binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
C20orf123	128506	broad.mit.edu	37	20	45181081	45181081	+	5'Flank	DEL	T	-	-	rs34775080		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45181081delT	uc010zxu.1	-							NM_080721	NP_542452			hypothetical protein LOC128506							integral to membrane					0																		---	---	---	---
SLC13A3	64849	broad.mit.edu	37	20	45190299	45190300	+	Intron	INS	-	T	T	rs112643992		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45190299_45190300insT	uc002xsf.1	-						SLC13A3_uc010ghn.1_Intron|SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc002xse.1_Intron|SLC13A3_uc010ghm.1_Intron|SLC13A3_uc010zxv.1_Intron	NM_022829	NP_073740			solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	45325999	45325999	+	IGR	DEL	T	-	-	rs113967747		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45325999delT								TP53RK (7723 upstream) : SLC2A10 (12280 downstream)																																			---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45608109	45608109	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45608109delT	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_5'Flank|EYA2_uc002xsp.2_5'Flank	NM_005244	NP_005235			eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)																---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45765501	45765501	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45765501delC	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235			eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)																---	---	---	---
ZMYND8	23613	broad.mit.edu	37	20	45970747	45970748	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45970747_45970748delAA	uc002xta.1	-						ZMYND8_uc010ghr.1_Intron|ZMYND8_uc002xst.1_Intron|ZMYND8_uc002xsu.1_Intron|ZMYND8_uc002xsv.1_Intron|ZMYND8_uc002xsw.1_Intron|ZMYND8_uc002xsx.1_Intron|ZMYND8_uc002xsy.1_Intron|ZMYND8_uc002xsz.1_Intron|ZMYND8_uc010zxy.1_Intron|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_Intron|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_Intron|ZMYND8_uc002xtf.1_Intron|ZMYND8_uc010ghs.1_Intron|ZMYND8_uc002xth.2_Intron	NM_012408	NP_036540			zinc finger, MYND-type containing 8 isoform b								protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	46013974	46013974	+	IGR	DEL	T	-	-	rs33922250		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46013974delT								ZMYND8 (28500 upstream) : NCOA3 (116683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46019821	46019821	+	IGR	DEL	T	-	-	rs11408741		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46019821delT								ZMYND8 (34347 upstream) : NCOA3 (110836 downstream)																																			---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46150092	46150092	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46150092delT	uc002xtk.2	+						NCOA3_uc010ght.1_Intron|NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron	NM_181659	NP_858045			nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5																		---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46164260	46164260	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46164260delT	uc002xtk.2	+						NCOA3_uc010ght.1_Intron|NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron	NM_181659	NP_858045			nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5																		---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46251243	46251243	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46251243delT	uc002xtk.2	+						NCOA3_uc010ght.1_Intron|NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron	NM_181659	NP_858045			nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5																		---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46281062	46281062	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46281062delA	uc002xtk.2	+						NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron|NCOA3_uc010zyc.1_Intron	NM_181659	NP_858045			nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5																		---	---	---	---
SULF2	55959	broad.mit.edu	37	20	46316458	46316458	+	Intron	DEL	T	-	-	rs74178754		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46316458delT	uc002xto.2	-						SULF2_uc002xtr.2_Intron|SULF2_uc002xtq.2_Intron	NM_018837	NP_061325			sulfatase 2 isoform a precursor						bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	46856268	46856268	+	IGR	DEL	G	-	-	rs59158573		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46856268delG								SULF2 (440908 upstream) : LOC284749 (132386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	47019803	47019804	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47019803_47019804delGT								LOC284749 (20422 upstream) : PREX1 (220989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	47154754	47154754	+	IGR	DEL	A	-	-	rs111378696		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47154754delA								LOC284749 (155373 upstream) : PREX1 (86039 downstream)																																			---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47347765	47347766	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47347765_47347766delCT	uc002xtw.1	-							NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47428063	47428064	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47428063_47428064delAC	uc002xtw.1	-							NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	47516048	47516048	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47516048delT								PREX1 (71628 upstream) : ARFGEF2 (22227 downstream)																																			---	---	---	---
ARFGEF2	10564	broad.mit.edu	37	20	47545041	47545041	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47545041delT	uc002xtx.3	+							NM_006420	NP_006411			ADP-ribosylation factor guanine						exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)															---	---	---	---
ARFGEF2	10564	broad.mit.edu	37	20	47612993	47612993	+	Intron	DEL	A	-	-	rs72185696		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47612993delA	uc002xtx.3	+						ARFGEF2_uc010zyf.1_Intron	NM_006420	NP_006411			ADP-ribosylation factor guanine						exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)															---	---	---	---
DDX27	55661	broad.mit.edu	37	20	47840583	47840583	+	Intron	DEL	T	-	-	rs79452818		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47840583delT	uc002xuh.2	+							NM_017895	NP_060365			DEAD (Asp-Glu-Ala-Asp) box polypeptide 27							nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
ZNFX1	57169	broad.mit.edu	37	20	47885373	47885373	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47885373delA	uc002xui.2	-							NM_021035	NP_066363			zinc finger, NFX1-type containing 1								metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
PTGIS	5740	broad.mit.edu	37	20	48127617	48127617	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48127617delC	uc002xut.2	-	9	1360	c.1306delG	c.(1306-1308)GCGfs	p.A436fs	PTGIS_uc010zyi.1_Frame_Shift_Del_p.A297fs	NM_000961	NP_000952	Q16647	PTGIS_HUMAN	prostaglandin I2 synthase	436					hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|prostaglandin-I synthase activity			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Phenylbutazone(DB00812)													---	---	---	---
PTGIS	5740	broad.mit.edu	37	20	48132425	48132425	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48132425delT	uc002xut.2	-						PTGIS_uc010zyi.1_Intron	NM_000961	NP_000952			prostaglandin I2 synthase						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|prostaglandin-I synthase activity			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Phenylbutazone(DB00812)													---	---	---	---
B4GALT5	9334	broad.mit.edu	37	20	48279379	48279379	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48279379delA	uc002xuu.3	-							NM_004776	NP_004767			UDP-Gal:betaGlcNAc beta 1,4-						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	galactosyltransferase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	48613796	48613797	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48613796_48613797delTT								SNAI1 (8378 upstream) : TMEM189-UBE2V1 (83866 downstream)																																			---	---	---	---
TMEM189	387521	broad.mit.edu	37	20	48741400	48741400	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48741400delA	uc002xvg.2	-	6					TMEM189-UBE2V1_uc002xvf.2_Intron|TMEM189_uc010zyq.1_RNA|TMEM189_uc010gif.2_3'UTR|TMEM189_uc010zyp.1_3'UTR	NM_199129	NP_954580			transmembrane protein 189 isoform 1							endoplasmic reticulum membrane|integral to membrane					0			BRCA - Breast invasive adenocarcinoma(9;3.02e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	48958372	48958372	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48958372delT								CEBPB (149160 upstream) : PTPN1 (168519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49026052	49026053	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49026052_49026053delAA								CEBPB (216840 upstream) : PTPN1 (100838 downstream)																																			---	---	---	---
FAM65C	140876	broad.mit.edu	37	20	49286399	49286399	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49286399delA	uc010zyt.1	-						FAM65C_uc010zyu.1_Intron	NM_080829	NP_543019			hypothetical protein LOC140876											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	49311242	49311242	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49311242delA								FAM65C (3326 upstream) : PARD6B (36839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49324291	49324295	+	IGR	DEL	GATAA	-	-	rs142372150		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49324291_49324295delGATAA								FAM65C (16375 upstream) : PARD6B (23786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49333401	49333401	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49333401delT								FAM65C (25485 upstream) : PARD6B (14680 downstream)																																			---	---	---	---
ADNP	23394	broad.mit.edu	37	20	49546255	49546255	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49546255delT	uc002xvt.1	-						ADNP_uc002xvu.1_Intron	NM_015339	NP_056154			activity-dependent neuroprotector							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2																OREG0026034	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DPM1	8813	broad.mit.edu	37	20	49556166	49556166	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49556166delT	uc002xvw.1	-						DPM1_uc002xvv.1_Intron|DPM1_uc002xvx.1_Intron	NM_003859	NP_003850			dolichyl-phosphate mannosyltransferase 1						C-terminal protein lipidation|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|protein N-linked glycosylation via asparagine|protein O-linked mannosylation	dolichol-phosphate-mannose synthase complex|endoplasmic reticulum membrane|membrane fraction	dolichyl-phosphate beta-D-mannosyltransferase activity|dolichyl-phosphate-mannose-protein mannosyltransferase activity|protein binding			ovary(1)	1																		---	---	---	---
DPM1	8813	broad.mit.edu	37	20	49562054	49562054	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49562054delT	uc002xvw.1	-						DPM1_uc002xvv.1_Intron|DPM1_uc002xvx.1_Intron	NM_003859	NP_003850			dolichyl-phosphate mannosyltransferase 1						C-terminal protein lipidation|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|protein N-linked glycosylation via asparagine|protein O-linked mannosylation	dolichol-phosphate-mannose synthase complex|endoplasmic reticulum membrane|membrane fraction	dolichyl-phosphate beta-D-mannosyltransferase activity|dolichyl-phosphate-mannose-protein mannosyltransferase activity|protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	49786124	49786124	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49786124delT								KCNG1 (146449 upstream) : NFATC2 (221642 downstream)																																			---	---	---	---
NFATC2	4773	broad.mit.edu	37	20	50025049	50025050	+	Intron	DEL	TA	-	-	rs6021186	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50025049_50025050delTA	uc002xwd.2	-						NFATC2_uc002xwc.2_Intron|NFATC2_uc010zyv.1_Intron|NFATC2_uc010zyw.1_Intron|NFATC2_uc010zyx.1_Intron|NFATC2_uc010zyy.1_Intron|NFATC2_uc010zyz.1_Intron|NFATC2_uc002xwe.2_Intron	NM_173091	NP_775114			nuclear factor of activated T-cells,						B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)																	---	---	---	---
NFATC2	4773	broad.mit.edu	37	20	50177265	50177266	+	Intron	INS	-	AC	AC	rs141552238	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50177265_50177266insAC	uc002xwe.2	-						NFATC2_uc010zyx.1_Intron|NFATC2_uc010zyy.1_Intron|NFATC2_uc010zyz.1_Intron	NM_001136021	NP_001129493			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	50240995	50240995	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50240995delT	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																OREG0026042	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50248321	50248321	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50248321delG	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-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50310051	50310051	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50310051delT	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	50327860	50327860	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50327860delT	uc002xwg.1	-						ATP9A_uc010gih.1_Intron	NM_006045	NP_006036			ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																		---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50349919	50349919	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50349919delT	uc002xwg.1	-						ATP9A_uc010gih.1_Intron	NM_006045	NP_006036			ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																		---	---	---	---
SALL4	57167	broad.mit.edu	37	20	50402191	50402191	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50402191delT	uc002xwh.3	-						SALL4_uc010gii.2_Intron|SALL4_uc002xwi.3_Intron	NM_020436	NP_065169			sal-like 4						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	50452730	50452730	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50452730delT								SALL4 (33682 upstream) : ZFP64 (247821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50518100	50518103	+	IGR	DEL	TGTG	-	-	rs72204888		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50518100_50518103delTGTG								SALL4 (99052 upstream) : ZFP64 (182448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50857286	50857286	+	IGR	DEL	A	-	-	rs11448808		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50857286delA								ZFP64 (48762 upstream) : TSHZ2 (731591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50894691	50894691	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50894691delT								ZFP64 (86167 upstream) : TSHZ2 (694186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51185532	51185532	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51185532delT								ZFP64 (377008 upstream) : TSHZ2 (403345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51260912	51260912	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51260912delA								ZFP64 (452388 upstream) : TSHZ2 (327965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51541878	51541878	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51541878delT								ZFP64 (733354 upstream) : TSHZ2 (46999 downstream)																																			---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51690298	51690298	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51690298delA	uc002xwo.2	+							NM_173485	NP_775756			teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51838233	51838233	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51838233delT	uc002xwo.2	+							NM_173485	NP_775756			teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	52148647	52148648	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52148647_52148648delTT								TSHZ2 (44682 upstream) : ZNF217 (34964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52149722	52149723	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52149722_52149723delAA								TSHZ2 (45757 upstream) : ZNF217 (33889 downstream)																																			---	---	---	---
ZNF217	7764	broad.mit.edu	37	20	52190609	52190609	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52190609delA	uc002xwq.3	-							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	52291757	52291759	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52291757_52291759delTTT								ZNF217 (80956 upstream) : SUMO1P1 (199283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52311317	52311318	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52311317_52311318delTT								ZNF217 (100516 upstream) : SUMO1P1 (179724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52311606	52311606	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52311606delA								ZNF217 (100805 upstream) : SUMO1P1 (179436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52314145	52314145	+	IGR	DEL	G	-	-	rs6068631		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52314145delG								ZNF217 (103344 upstream) : SUMO1P1 (176897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52354025	52354025	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52354025delT								ZNF217 (143224 upstream) : SUMO1P1 (137017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52451589	52451589	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52451589delT								ZNF217 (240788 upstream) : SUMO1P1 (39453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52480954	52480954	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52480954delT								ZNF217 (270153 upstream) : SUMO1P1 (10088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52808980	52808981	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52808980_52808981insC								CYP24A1 (18464 upstream) : PFDN4 (15521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52849158	52849159	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52849158_52849159delCT								PFDN4 (12667 upstream) : DOK5 (243098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52896774	52896774	+	IGR	DEL	A	-	-	rs79366178		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52896774delA								PFDN4 (60283 upstream) : DOK5 (195483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	53048908	53048909	+	IGR	INS	-	TG	TG	rs147726024	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53048908_53048909insTG								PFDN4 (212417 upstream) : DOK5 (43348 downstream)																																			---	---	---	---
DOK5	55816	broad.mit.edu	37	20	53264241	53264241	+	Intron	DEL	T	-	-	rs11086458		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53264241delT	uc002xwy.2	+						DOK5_uc010gin.2_Intron|DOK5_uc002xwz.2_Intron	NM_018431	NP_060901			docking protein 5								insulin receptor binding			ovary(1)	1			Colorectal(105;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	53351286	53351287	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53351286_53351287delGT								DOK5 (83577 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54185766	54185766	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54185766delA								DOK5 (918057 upstream) : CBLN4 (386731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54245997	54245997	+	IGR	DEL	T	-	-	rs143443998		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54245997delT								DOK5 (978288 upstream) : CBLN4 (326500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54594689	54594690	+	IGR	INS	-	T	T	rs140772545	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54594689_54594690insT								CBLN4 (14677 upstream) : MC3R (229098 downstream)																																			---	---	---	---
MC3R	4159	broad.mit.edu	37	20	54820948	54820948	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54820948delA	uc002xxb.2	+							NM_019888	NP_063941			melanocortin 3 receptor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|protein binding			ovary(2)|breast(2)	4			Colorectal(105;0.202)															---	---	---	---
AURKA	6790	broad.mit.edu	37	20	54957230	54957231	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54957230_54957231delAG	uc002xxd.1	-						AURKA_uc002xxe.1_Intron|AURKA_uc002xxf.1_Intron|AURKA_uc002xxg.1_Intron|AURKA_uc002xxh.1_Intron|AURKA_uc002xxi.1_Intron|AURKA_uc002xxj.1_Intron|AURKA_uc002xxk.1_Intron|AURKA_uc010zzd.1_Intron	NM_198433	NP_940835			serine/threonine protein kinase 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|phosphatidylinositol-mediated signaling|regulation of protein stability|spindle organization	cytosol|nucleus|perinuclear region of cytoplasm|spindle microtubule|spindle pole centrosome	ATP binding|protein kinase binding|protein serine/threonine kinase activity			lung(3)|ovary(2)|breast(1)|large_intestine(1)|skin(1)	8			Colorectal(105;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	55132808	55132809	+	IGR	DEL	AA	-	-	rs74177910		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55132808_55132809delAA								C20orf107 (21234 upstream) : TFAP2C (71549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55544488	55544491	+	IGR	DEL	TTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55544488_55544491delTTTT								TFAP2C (330152 upstream) : BMP7 (199318 downstream)																																			---	---	---	---
SPO11	23626	broad.mit.edu	37	20	55906732	55906733	+	Intron	INS	-	T	T	rs67108426		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55906732_55906733insT	uc002xye.2	+						SPO11_uc002xyf.2_Intron	NM_012444	NP_036576			meiotic recombination protein SPO11 isoform a						female gamete generation|reciprocal meiotic recombination	chromosome|nucleus	ATP binding|DNA binding|hydrolase activity			breast(2)|skin(1)	3	Lung NSC(12;0.0066)|all_lung(29;0.0188)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.73e-14)|Epithelial(14;9.02e-10)|all cancers(14;9.31e-09)										Editing_and_processing_nucleases					---	---	---	---
PMEPA1	56937	broad.mit.edu	37	20	56288102	56288102	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56288102delA	uc002xys.2	-						PMEPA1_uc002xyr.2_5'Flank|PMEPA1_uc002xyt.2_5'Flank	NM_199169	NP_954638			transmembrane prostate androgen-induced protein						androgen receptor signaling pathway	integral to membrane|plasma membrane	WW domain binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	56417539	56417539	+	IGR	DEL	G	-	-	rs35952456		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56417539delG								PMEPA1 (130998 upstream) : C20orf85 (308444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	56461890	56461890	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56461890delT								PMEPA1 (175349 upstream) : C20orf85 (264093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	56710803	56710803	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56710803delA								PMEPA1 (424262 upstream) : C20orf85 (15180 downstream)																																			---	---	---	---
RAB22A	57403	broad.mit.edu	37	20	56923849	56923849	+	Intron	DEL	A	-	-	rs71697053		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56923849delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	57034413	57034414	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57034413_57034414delTT								VAPB (12452 upstream) : APCDD1L (12 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	57518892	57518892	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57518892delA								GNAS (32643 upstream) : TH1L (37419 downstream)																																			---	---	---	---
ZNF831	128611	broad.mit.edu	37	20	57825781	57825781	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57825781delA	uc002yan.2	+							NM_178457	NP_848552			zinc finger protein 831							intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	57952791	57952791	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57952791delT								EDN3 (51745 upstream) : PHACTR3 (199773 downstream)																																			---	---	---	---
PHACTR3	116154	broad.mit.edu	37	20	58288801	58288801	+	Intron	DEL	T	-	-	rs80230376		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58288801delT	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron	NM_080672	NP_542403			phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)															---	---	---	---
SYCP2	10388	broad.mit.edu	37	20	58455614	58455614	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58455614delA	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)															---	---	---	---
SYCP2	10388	broad.mit.edu	37	20	58456449	58456449	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58456449delA	uc002yaz.2	-							NM_014258	NP_055073			synaptonemal complex protein 2						cell division|meiotic prophase I|synaptonemal complex assembly		DNA binding			ovary(3)|lung(2)	5	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)															---	---	---	---
SYCP2	10388	broad.mit.edu	37	20	58483336	58483336	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58483336delA	uc002yaz.2	-						SYCP2_uc010gju.1_Intron	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)															---	---	---	---
CDH26	60437	broad.mit.edu	37	20	58567357	58567357	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58567357delT	uc002ybe.2	+						CDH26_uc002ybf.1_Intron|CDH26_uc010zzy.1_Intron|CDH26_uc002ybg.2_5'Flank	NM_177980	NP_817089			cadherin-like 26 isoform a						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)															---	---	---	---
CDH26	60437	broad.mit.edu	37	20	58608829	58608832	+	3'UTR	DEL	TGTG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58608829_58608832delTGTG	uc002ybf.1	+	9						NM_177980	NP_817089			cadherin-like 26 isoform a						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	58751799	58751800	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58751799_58751800delGA	uc002ybl.2	+						uc010gjw.1_Intron					Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	58913262	58913263	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58913262_58913263delTG	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59027274	59027276	+	Intron	DEL	AAA	-	-	rs35277864		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59027274_59027276delAAA	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59050234	59050234	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59050234delT	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59112337	59112338	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59112337_59112338delAA	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59146663	59146664	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59146663_59146664insT	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59173189	59173189	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59173189delA	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59439514	59439515	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59439514_59439515delAC								MIR646 (555889 upstream) : CDH4 (388044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59584449	59584449	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59584449delT								MIR646 (700824 upstream) : CDH4 (243110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59658263	59658264	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59658263_59658264insC								MIR646 (774638 upstream) : CDH4 (169295 downstream)																																			---	---	---	---
CDH4	1002	broad.mit.edu	37	20	59871319	59871320	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59871319_59871320delGT	uc002ybn.1	+							NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	59872455	59872455	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59872455delA	uc002ybn.1	+							NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60140393	60140395	+	Intron	DEL	GTA	-	-	rs6121437		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60140393_60140395delGTA	uc002ybn.1	+							NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
TAF4	6874	broad.mit.edu	37	20	60557612	60557612	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60557612delC	uc002ybs.2	-							NM_003185	NP_003176			TBP-associated factor 4						interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)															---	---	---	---
TAF4	6874	broad.mit.edu	37	20	60589099	60589102	+	Intron	DEL	TGTA	-	-	rs150781044	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60589099_60589102delTGTA	uc002ybs.2	-							NM_003185	NP_003176			TBP-associated factor 4						interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)															---	---	---	---
TAF4	6874	broad.mit.edu	37	20	60604532	60604533	+	Intron	DEL	GC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60604532_60604533delGC	uc002ybs.2	-							NM_003185	NP_003176			TBP-associated factor 4						interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	60689219	60689219	+	IGR	DEL	A	-	-	rs5842374		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60689219delA								TAF4 (48353 upstream) : LSM14B (8298 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	60804681	60804682	+	5'Flank	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60804681_60804682delCA	uc002ycj.1	+											Homo sapiens cDNA FLJ44790 fis, clone BRACE3039288.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	61190250	61190251	+	IGR	INS	-	TG	TG	rs137918555	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61190250_61190251insTG								C20orf166 (22280 upstream) : SLCO4A1 (83546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	61330547	61330547	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61330547delC								SLCO4A1 (13421 upstream) : NTSR1 (9642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	61507110	61507110	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61507110delA								TCFL5 (13995 upstream) : DIDO1 (1980 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	61643631	61643631	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61643631delT	uc002yec.1	+											Homo sapiens cDNA FLJ46471 fis, clone THYMU3023394.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	61823830	61823830	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61823830delT								MIR124-3 (13892 upstream) : YTHDF1 (2954 downstream)																																			---	---	---	---
ARFGAP1	55738	broad.mit.edu	37	20	61908192	61908192	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61908192delG	uc002yem.2	+						ARFGAP1_uc011aas.1_Intron|ARFGAP1_uc011aat.1_Intron|ARFGAP1_uc002yel.2_Intron|ARFGAP1_uc002yen.2_Intron	NM_018209	NP_060679			ADP-ribosylation factor GTPase activating						COPI coating of Golgi vesicle|protein transport|regulation of ARF GTPase activity|retrograde vesicle-mediated transport, Golgi to ER	cytosol|Golgi-associated vesicle membrane	ARF GTPase activator activity|zinc ion binding			pancreas(1)	1	all_cancers(38;1.59e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	62156238	62156239	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62156238_62156239delAA								PPDPF (2715 upstream) : PTK6 (3539 downstream)																																			---	---	---	---
C20orf195	79025	broad.mit.edu	37	20	62184216	62184216	+	5'Flank	DEL	A	-	-	rs68061227		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62184216delA	uc002yfj.2	+						C20orf195_uc002yfk.2_5'Flank	NM_024059	NP_076964			hypothetical protein LOC79025												0	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)															---	---	---	---
ZBTB46	140685	broad.mit.edu	37	20	62455051	62455051	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62455051delA	uc002ygu.2	-							NM_025224				zinc finger and BTB domain containing 46						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)																	---	---	---	---
RGS19	10287	broad.mit.edu	37	20	62705783	62705783	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62705783delC	uc002yhy.2	-						RGS19_uc002yhz.2_Intron|RGS19_uc002yia.2_Intron|RGS19_uc002yib.2_Intron	NM_005873	NP_005864			G protein signalling regulator 19						autophagy|G-protein coupled receptor protein signaling pathway|negative regulation of signal transduction|small GTPase mediated signal transduction	Golgi apparatus|membrane fraction|plasma membrane	GTPase activator activity|protein binding|signal transducer activity			skin(1)	1	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	62881188	62881188	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62881188delT								MYT1 (7584 upstream) : PCMTD2 (5860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9652852	9652852	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9652852delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9864021	9864021	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9864021delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9866868	9866869	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9866868_9866869delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10435925	10435925	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10435925delT								None (None upstream) : TPTE (470818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10498470	10498470	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10498470delA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10503272	10503273	+	Intron	DEL	AA	-	-	rs71255876		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10503272_10503273delAA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10588349	10588349	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10588349delT	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10758392	10758392	+	IGR	DEL	C	-	-	rs71225086		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10758392delC								None (None upstream) : TPTE (148351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10771895	10771895	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10771895delT								None (None upstream) : TPTE (134848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10787223	10787242	+	IGR	DEL	AATGGAATGGAATGGAATGG	-	-	rs72353060		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10787223_10787242delAATGGAATGGAATGGAATGG								None (None upstream) : TPTE (119501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10812737	10812741	+	IGR	DEL	GAATG	-	-	rs142367413		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10812737_10812741delGAATG								None (None upstream) : TPTE (94002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	11111726	11111726	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11111726delT								BAGE (12789 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	11179613	11179613	+	IGR	DEL	T	-	-	rs71639665		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11179613delT								BAGE (80676 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14631345	14631346	+	IGR	DEL	TT	-	-	rs75080853		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14631345_14631346delTT								C21orf99 (140776 upstream) : POTED (351152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14846983	14846984	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14846983_14846984insA								C21orf99 (356414 upstream) : POTED (135514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16212153	16212154	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16212153_16212154insA	uc002yjw.1	-											full-length cDNA clone CS0DI053YO09 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	16249380	16249380	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16249380delA								SAMSN1 (293657 upstream) : NRIP1 (84176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16498808	16498808	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16498808delT								NRIP1 (61682 upstream) : USP25 (603688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16655815	16655815	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16655815delA								NRIP1 (218689 upstream) : USP25 (446681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16933226	16933226	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16933226delT								NRIP1 (496100 upstream) : USP25 (169270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16939978	16939978	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16939978delA								NRIP1 (502852 upstream) : USP25 (162518 downstream)																																			---	---	---	---
USP25	29761	broad.mit.edu	37	21	17238573	17238573	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17238573delT	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528			ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	17985392	17985392	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17985392delT								C21orf34 (3298 upstream) : CXADR (899938 downstream)																																			---	---	---	---
CXADR	1525	broad.mit.edu	37	21	18924021	18924022	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18924021_18924022delTG	uc002yki.2	+						CXADR_uc002ykh.1_Intron|CXADR_uc010gld.1_Intron|CXADR_uc010gle.1_Intron|CXADR_uc002ykj.1_Intron	NM_001338	NP_001329			coxsackie virus and adenovirus receptor						blood coagulation|cell adhesion|interspecies interaction between organisms|leukocyte migration|regulation of immune response	adherens junction|basolateral plasma membrane|extracellular region|integral to plasma membrane|nucleus|tight junction	receptor activity			ovary(1)	1				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)														---	---	---	---
C21orf91	54149	broad.mit.edu	37	21	19186391	19186391	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19186391delA	uc002yko.3	-						C21orf91_uc002ykq.3_Intron|C21orf91_uc002ykp.3_Intron	NM_001100420	NP_001093890			early undifferentiated retina and lens isoform											ovary(1)	1				Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)														---	---	---	---
C21orf91	54149	broad.mit.edu	37	21	19187982	19187983	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19187982_19187983delTT	uc002yko.3	-						C21orf91_uc002ykq.3_Intron|C21orf91_uc002ykp.3_Intron	NM_001100420	NP_001093890			early undifferentiated retina and lens isoform											ovary(1)	1				Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	20004840	20004843	+	Intron	DEL	GTGT	-	-	rs150275846		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20004840_20004843delGTGT	uc010glf.1	-						uc002ykx.2_Intron					Homo sapiens, clone IMAGE:5392784, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	20318029	20318029	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20318029delT								TMPRSS15 (542059 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21429495	21429495	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21429495delA								None (None upstream) : C21orf131 (685419 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	22059347	22059348	+	IGR	DEL	TC	-	-	rs77695927		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22059347_22059348delTC								None (None upstream) : C21orf131 (55566 downstream)																																			---	---	---	---
NCAM2	4685	broad.mit.edu	37	21	22490650	22490651	+	Intron	INS	-	G	G	rs145557274	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22490650_22490651insG	uc002yld.1	+						NCAM2_uc011acb.1_Intron	NM_004540	NP_004531			neural cell adhesion molecule 2 precursor						neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	22942087	22942088	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22942087_22942088delAC								NCAM2 (30873 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23018314	23018314	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23018314delT								NCAM2 (107100 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26036996	26036996	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26036996delA								None (None upstream) : NCRNA00158 (721138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26219329	26219329	+	IGR	DEL	T	-	-	rs113210184		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26219329delT								None (None upstream) : NCRNA00158 (538805 downstream)																																			---	---	---	---
ATP5J	522	broad.mit.edu	37	21	27097750	27097750	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27097750delT	uc002yls.2	-						ATP5J_uc002ylt.2_Intron|ATP5J_uc002ylu.2_Intron|ATP5J_uc002ylv.2_Intron|ATP5J_uc002ylw.2_Intron	NM_001685	NP_001676			ATP synthase, H+ transporting, mitochondrial F0						ATP catabolic process|respiratory electron transport chain		hydrogen ion transmembrane transporter activity				0																		---	---	---	---
GABPA	2551	broad.mit.edu	37	21	27124278	27124278	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27124278delT	uc002ylx.3	+						GABPA_uc002yly.3_Intron	NM_002040	NP_002031			GA binding protein transcription factor, alpha						positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
APP	351	broad.mit.edu	37	21	27354820	27354820	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27354820delA	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	NM_000484	NP_000475			amyloid beta A4 protein isoform a precursor						adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)																---	---	---	---
APP	351	broad.mit.edu	37	21	27394038	27394038	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27394038delA	uc002ylz.2	-						APP_uc010glk.2_Intron|APP_uc002yma.2_Intron|APP_uc011ach.1_Intron|APP_uc002ymb.2_Intron|APP_uc010glj.2_Intron|APP_uc011aci.1_Intron|APP_uc011acj.1_Intron	NM_000484	NP_000475			amyloid beta A4 protein isoform a precursor						adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)																---	---	---	---
APP	351	broad.mit.edu	37	21	27449379	27449381	+	Intron	DEL	AAA	-	-	rs145402551		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27449379_27449381delAAA	uc002ylz.2	-						APP_uc010glk.2_Intron|APP_uc002yma.2_Intron|APP_uc011ach.1_Intron|APP_uc002ymb.2_Intron|APP_uc010glj.2_Intron|APP_uc011aci.1_Intron|APP_uc011acj.1_Intron	NM_000484	NP_000475			amyloid beta A4 protein isoform a precursor						adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	27737691	27737691	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27737691delT								APP (194245 upstream) : CYYR1 (100838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	27754695	27754695	+	IGR	DEL	A	-	-	rs1478100	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27754695delA								APP (211249 upstream) : CYYR1 (83834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	27992614	27992614	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27992614delT								CYYR1 (47033 upstream) : ADAMTS1 (215994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28207520	28207521	+	IGR	INS	-	C	C	rs138068090	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28207520_28207521insC								CYYR1 (261939 upstream) : ADAMTS1 (1087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28261491	28261492	+	IGR	INS	-	GGGG	GGGG	rs146763349	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28261491_28261492insGGGG								ADAMTS1 (43763 upstream) : ADAMTS5 (28740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28686868	28686868	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28686868delT								ADAMTS5 (347429 upstream) : NCRNA00113 (407830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	29030826	29030826	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29030826delA								ADAMTS5 (691387 upstream) : NCRNA00113 (63872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	29441561	29441561	+	Intron	DEL	G	-	-	rs140003178		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29441561delG	uc002ymk.1	+											Homo sapiens cDNA FLJ35800 fis, clone TESTI2005933.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	30274390	30274390	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30274390delT								N6AMT1 (16697 upstream) : RNF160 (26076 downstream)																																			---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30340940	30340940	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30340940delT	uc002ymr.2	-						RNF160_uc010gll.1_Intron	NM_015565	NP_056380			zinc finger protein 294								ligase activity|zinc ion binding				0																		---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30354539	30354539	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30354539delA	uc002ymr.2	-						RNF160_uc010gll.1_Intron	NM_015565	NP_056380			zinc finger protein 294								ligase activity|zinc ion binding				0																		---	---	---	---
USP16	10600	broad.mit.edu	37	21	30410631	30410632	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30410631_30410632insT	uc002ymy.2	+						USP16_uc002ymx.2_Intron|USP16_uc002ymw.2_Intron|USP16_uc011acm.1_Intron|USP16_uc011acn.1_Intron|USP16_uc011aco.1_5'Flank	NM_006447	NP_006438			ubiquitin specific protease 16 isoform a						cell division|histone deubiquitination|mitosis|positive regulation of transcription, DNA-dependent|protein homotetramerization|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|histone binding|transcription coactivator activity|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(2)|breast(1)|pancreas(1)	4																		---	---	---	---
CCT8	10694	broad.mit.edu	37	21	30444332	30444332	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30444332delA	uc002ynb.2	-						CCT8_uc011acp.1_Intron|CCT8_uc002yna.2_Intron|CCT8_uc002ync.2_Intron|CCT8_uc010glm.2_Intron|CCT8_uc011acq.1_Intron	NM_006585	NP_006576			chaperonin containing TCP1, subunit 8 (theta)						'de novo' posttranslational protein folding	aggresome|cytosol|intermediate filament cytoskeleton|microtubule organizing center	ATP binding|ATPase activity, coupled|unfolded protein binding				0																		---	---	---	---
C21orf7	56911	broad.mit.edu	37	21	30478512	30478512	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30478512delT	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	30654625	30654625	+	Intron	DEL	T	-	-	rs75059541		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30654625delT	uc002ynh.2	+						NCRNA00189_uc002yni.2_Intron	NR_027072				Homo sapiens chromosome 21 open reading frame 109 (C21orf109) mRNA, complete cds.												0																		---	---	---	---
BACH1	571	broad.mit.edu	37	21	30719183	30719184	+	Intron	INS	-	G	G	rs72551929		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30719183_30719184insG	uc002ynl.2	+							NM_206866				BTB and CNC homology 1 transcription factor							nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|liver(1)	2																		---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	31163639	31163639	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31163639delA	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)													---	---	---	---
KRTAP25-1	100131902	broad.mit.edu	37	21	31661779	31661780	+	Frame_Shift_Ins	INS	-	AA	AA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31661779_31661780insAA	uc010glr.1	-	1	53_54	c.29_30insTT	c.(28-30)TTCfs	p.F10fs		NM_001128598	NP_001122070	Q3LHN0	KR251_HUMAN	keratin associated protein 25-1	10						intermediate filament					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	31736735	31736735	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31736735delT								KRTAP23-1 (15811 upstream) : KRTAP13-2 (6975 downstream)																																			---	---	---	---
KRTAP8-1	337879	broad.mit.edu	37	21	32186130	32186130	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32186130delT	uc002you.2	-							NM_175857	NP_787053			keratin associated protein 8-1							intermediate filament					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	32333010	32333010	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32333010delA								KRTAP11-1 (79136 upstream) : KRTAP19-8 (77469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	32342933	32342933	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32342933delT								KRTAP11-1 (89059 upstream) : KRTAP19-8 (67546 downstream)																																			---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32694764	32694764	+	Intron	DEL	G	-	-	rs71977227		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32694764delG	uc002yow.1	-						TIAM1_uc002yox.1_Intron	NM_003253	NP_003244			T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32713185	32713185	+	Intron	DEL	A	-	-	rs112495646		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32713185delA	uc002yow.1	-						TIAM1_uc002yox.1_Intron	NM_003253	NP_003244			T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	33028704	33028704	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33028704delA	uc002yoz.1	-											Homo sapiens, clone IMAGE:5171428, mRNA.																														---	---	---	---
SFRS15	57466	broad.mit.edu	37	21	33057695	33057695	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33057695delA	uc002ypd.2	-						SFRS15_uc002ype.2_Intron|SFRS15_uc010glu.2_Intron|SFRS15_uc002ypf.1_Intron	NM_020706	NP_065757			splicing factor, arginine/serine-rich 15 isoform							nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
NCRNA00159	54070	broad.mit.edu	37	21	33467348	33467355	+	Intron	DEL	GCTGCCAG	-	-	rs11269887		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33467348_33467355delGCTGCCAG	uc011adm.1	+							NR_024352				Homo sapiens non-protein coding RNA 159 (NCRNA00159), non-coding RNA.												0																		---	---	---	---
MRAP	56246	broad.mit.edu	37	21	33682649	33682649	+	Intron	DEL	G	-	-	rs113685676		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33682649delG	uc002ypj.2	+						MRAP_uc002ypk.2_Intron|MRAP_uc011ado.1_Intron|MRAP_uc002ypl.2_Intron|uc002ypm.2_5'Flank	NM_178817	NP_848932			melanocortin 2 receptor accessory protein						positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|integral to membrane|perinuclear region of cytoplasm|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding				0																		---	---	---	---
GCFC1	94104	broad.mit.edu	37	21	34116927	34116927	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34116927delA	uc002yqn.2	-						GCFC1_uc002yql.2_Intron|GCFC1_uc002yqm.2_Intron|GCFC1_uc002yqo.2_Intron|GCFC1_uc002yqp.2_Intron	NM_016631	NP_057715			GC-rich sequence DNA-binding factor candidate							cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	34299361	34299362	+	IGR	DEL	GT	-	-	rs72034272		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34299361_34299362delGT								C21orf62 (113308 upstream) : OLIG2 (98877 downstream)																																			---	---	---	---
IL10RB	3588	broad.mit.edu	37	21	34642690	34642690	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34642690delT	uc002yrk.1	+						IL10RB_uc002yrh.1_Intron|IL10RB_uc002yri.1_Intron|IL10RB_uc002yrl.1_Intron	NM_000628	NP_000619			interleukin 10 receptor, beta precursor						immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0																		---	---	---	---
IFNGR2	3460	broad.mit.edu	37	21	34809434	34809434	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34809434delT	uc002yrp.3	+	7					IFNGR2_uc002yrq.3_3'UTR|IFNGR2_uc010gma.2_3'UTR|IFNGR2_uc002yrr.3_3'UTR|TMEM50B_uc002yrs.1_Intron	NM_005534	NP_005525			interferon gamma receptor 2 precursor						regulation of interferon-gamma-mediated signaling pathway|response to virus	endoplasmic reticulum|integral to plasma membrane	interferon-gamma receptor activity				0					Interferon gamma-1b(DB00033)													---	---	---	---
SON	6651	broad.mit.edu	37	21	34929320	34929320	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34929320delT	uc002yse.1	+						SON_uc002ysb.1_Intron|SON_uc002ysc.2_Intron|SON_uc002ysd.2_Intron|SON_uc002ysf.1_Intron|SON_uc002ysg.2_Intron	NM_138927	NP_620305			SON DNA-binding protein isoform F						anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6																		---	---	---	---
RCAN1	1827	broad.mit.edu	37	21	35979954	35979954	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35979954delC	uc002yue.2	-						RCAN1_uc002yuc.2_Intron|RCAN1_uc002yud.2_Intron	NM_004414	NP_004405			calcipressin 1 isoform a						blood circulation|calcium-mediated signaling|central nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36383475	36383475	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36383475delA	uc010gmu.2	-						RUNX1_uc002yut.1_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron	NM_001754	NP_001745			runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36604756	36604757	+	Intron	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36604756_36604757delTG	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	37149735	37149735	+	Intron	DEL	T	-	-	rs72008408		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37149735delT	uc002yut.1	-											Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
Unknown	0	broad.mit.edu	37	21	37368477	37368477	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37368477delC								RUNX1 (11430 upstream) : SETD4 (38363 downstream)																																			---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37576957	37576957	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37576957delT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119			pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37577654	37577654	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37577654delT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119			pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37599842	37599843	+	Intron	INS	-	A	A	rs141141432	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37599842_37599843insA	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119			pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CHAF1B	8208	broad.mit.edu	37	21	37782973	37782973	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37782973delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	38016558	38016559	+	IGR	INS	-	T	T	rs143952449	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38016558_38016559insT								CLDN14 (67691 upstream) : SIM2 (55432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	38718304	38718304	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38718304delA								DSCR3 (78471 upstream) : DYRK1A (21555 downstream)																																			---	---	---	---
ERG	2078	broad.mit.edu	37	21	39900071	39900073	+	Intron	DEL	CTT	-	-	rs72057889		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39900071_39900073delCTT	uc010gnw.2	-						ERG_uc010gnv.2_Intron|ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc002yxc.3_Intron|ERG_uc010gnz.2_Intron	NM_001136155	NP_001129627			ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)																---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40558989	40558989	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40558989delA	uc002yxk.1	-	42	7065	c.6926delT	c.(6925-6927)TTAfs	p.L2309fs	BRWD1_uc010goc.1_Frame_Shift_Del_p.L952fs	NM_018963	NP_061836	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2309					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	40713204	40713204	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40713204delT								BRWD1 (27648 upstream) : HMGN1 (1043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	41069388	41069388	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41069388delT								B3GALT5 (34573 upstream) : IGSF5 (47946 downstream)																																			---	---	---	---
IGSF5	150084	broad.mit.edu	37	21	41142770	41142770	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41142770delA	uc002yyo.2	+							NM_001080444	NP_001073913			immunoglobulin superfamily 5 like							integral to membrane|tight junction					0		Prostate(19;5.35e-06)																---	---	---	---
IGSF5	150084	broad.mit.edu	37	21	41171430	41171430	+	Intron	DEL	T	-	-	rs76562952		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41171430delT	uc002yyo.2	+							NM_001080444	NP_001073913			immunoglobulin superfamily 5 like							integral to membrane|tight junction					0		Prostate(19;5.35e-06)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	41207459	41207459	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41207459delT								IGSF5 (33438 upstream) : PCP4 (31888 downstream)																																			---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41547738	41547739	+	Intron	INS	-	CG	CG	rs148927701	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41547738_41547739insCG	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	41564846	41564846	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41564846delT	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	42383554	42383554	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42383554delT								DSCAM (164515 upstream) : C21orf130 (129873 downstream)																																			---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43224441	43224441	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43224441delT	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398			PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43258311	43258311	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43258311delA	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398			PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
C2CD2	25966	broad.mit.edu	37	21	43338699	43338699	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43338699delT	uc002yzw.2	-						C2CD2_uc002yzu.2_Intron|C2CD2_uc002yzv.2_Intron|C2CD2_uc002yzx.1_Intron	NM_015500	NP_056315			C2 calcium-dependent domain containing 2 isoform							cytosol|extracellular region|nucleus				ovary(1)	1																		---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43512504	43512504	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43512504delT	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zag.1_Intron|UMODL1_uc010gow.1_Intron|UMODL1_uc002zai.1_Intron|UMODL1_uc010gox.1_Intron|UMODL1_uc010goy.1_Intron|UMODL1_uc002zaj.1_Intron|UMODL1_uc010goz.1_Intron	NM_001004416	NP_001004416			uromodulin-like 1 isoform 1 precursor							cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
TMPRSS3	64699	broad.mit.edu	37	21	43807481	43807482	+	Intron	DEL	GT	-	-	rs72303220		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43807481_43807482delGT	uc002zbb.2	-						TMPRSS3_uc002zaz.2_Intron|TMPRSS3_uc002zba.2_Intron|TMPRSS3_uc002zbc.2_Intron|TMPRSS3_uc002zbd.2_Intron	NM_024022	NP_076927			transmembrane protease, serine 3 isoform 1						cellular sodium ion homeostasis|proteolysis	endoplasmic reticulum membrane|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity|sodium channel regulator activity			ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	44040655	44040655	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44040655delA								SLC37A1 (39106 upstream) : PDE9A (33207 downstream)																																			---	---	---	---
WDR4	10785	broad.mit.edu	37	21	44270472	44270472	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44270472delG	uc002zci.2	-						WDR4_uc002zck.1_Intron|WDR4_uc002zcl.1_Intron|WDR4_uc010gpg.1_Intron|WDR4_uc011aew.1_Intron|WDR4_uc010gph.1_Intron	NM_033661	NP_387510			WD repeat domain 4 protein						tRNA modification	cytoplasm|nucleoplasm	protein binding			ovary(1)	1				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)														---	---	---	---
WDR4	10785	broad.mit.edu	37	21	44289778	44289778	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44289778delA	uc002zci.2	-						WDR4_uc002zck.1_Intron|WDR4_uc002zcl.1_Intron|WDR4_uc010gpg.1_Intron|WDR4_uc011aew.1_Intron|WDR4_uc010gph.1_Intron	NM_033661	NP_387510			WD repeat domain 4 protein						tRNA modification	cytoplasm|nucleoplasm	protein binding			ovary(1)	1				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	44386185	44386186	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44386185_44386186delAA								NDUFV3 (56413 upstream) : PKNOX1 (8457 downstream)																																			---	---	---	---
CBS	875	broad.mit.edu	37	21	44476001	44476001	+	Intron	DEL	T	-	-	rs79861734		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44476001delT	uc002zcu.2	-						CBS_uc002zcs.1_Intron|CBS_uc002zct.2_Intron|CBS_uc002zcw.3_Intron|CBS_uc002zcv.2_Intron|CBS_uc002zcx.2_3'UTR	NM_000071	NP_000062			cystathionine-beta-synthase						cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process	cytosol|nucleolus	cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding				0					L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	44577555	44577555	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44577555delA								U2AF1 (49867 upstream) : CRYAA (11586 downstream)																																			---	---	---	---
SIK1	150094	broad.mit.edu	37	21	44842069	44842069	+	Intron	DEL	A	-	-	rs111590464		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44842069delA	uc002zdf.2	-							NM_173354	NP_775490			salt-inducible kinase 1						anoikis|cell cycle|cell differentiation|intracellular protein kinase cascade|multicellular organismal development|regulation of cell differentiation|regulation of mitotic cell cycle	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(2)|testis(2)|ovary(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	45277799	45277799	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45277799delA								LOC284837 (45351 upstream) : AGPAT3 (7317 downstream)																																			---	---	---	---
AGPAT3	56894	broad.mit.edu	37	21	45355592	45355593	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45355592_45355593delTT	uc002zdv.2	+						AGPAT3_uc002zdw.2_Intron	NM_020132	NP_064517			1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)														---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45489114	45489114	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45489114delA	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron	NM_003274	NP_003265			trafficking protein particle complex 10						vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45513345	45513345	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45513345delA	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron|TRAPPC10_uc011afa.1_Intron|TRAPPC10_uc011afb.1_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																		---	---	---	---
ITGB2	3689	broad.mit.edu	37	21	46336787	46336789	+	Intron	DEL	AAA	-	-	rs67894019		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46336787_46336789delAAA	uc002zgf.3	-						ITGB2_uc011afl.1_Intron|ITGB2_uc010gpw.2_Intron|ITGB2_uc002zgg.2_Intron	NM_000211	NP_000202			integrin, beta 2 precursor						apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(4)|central_nervous_system(3)|breast(2)	9				Colorectal(79;0.0669)	Simvastatin(DB00641)													---	---	---	---
ADARB1	104	broad.mit.edu	37	21	46511117	46511117	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46511117delC	uc002zgy.2	+						ADARB1_uc002zgp.2_Intron|ADARB1_uc002zgr.2_Intron|ADARB1_uc002zgs.2_Intron|ADARB1_uc002zgw.2_Intron|ADARB1_uc002zgv.2_Intron|ADARB1_uc002zgt.2_Intron|ADARB1_uc010gpx.2_Intron|ADARB1_uc002zgq.2_Intron|ADARB1_uc002zgu.2_Intron	NM_015833	NP_056648			RNA-specific adenosine deaminase B1 isoform 2						adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	46774442	46774442	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46774442delA								LOC642852 (57174 upstream) : COL18A1 (50655 downstream)																																			---	---	---	---
PCBP3	54039	broad.mit.edu	37	21	47066977	47066977	+	Intron	DEL	A	-	-	rs111742933		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47066977delA	uc010gqb.2	+							NM_020528	NP_065389			poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)														---	---	---	---
PCBP3	54039	broad.mit.edu	37	21	47218048	47218049	+	Intron	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47218048_47218049delAG	uc010gqb.2	+							NM_020528	NP_065389			poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)														---	---	---	---
PCBP3	54039	broad.mit.edu	37	21	47228347	47228347	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47228347delA	uc010gqb.2	+							NM_020528	NP_065389			poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	47474810	47474811	+	IGR	DEL	CC	-	-	rs72208689		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47474810_47474811delCC								COL6A1 (49847 upstream) : COL6A2 (43222 downstream)																																			---	---	---	---
PCNT	5116	broad.mit.edu	37	21	47768704	47768704	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47768704delT	uc002zji.3	+						PCNT_uc002zjj.2_Intron|PCNT_uc010gqk.1_Intron	NM_006031	NP_006022			pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)																	---	---	---	---
PCNT	5116	broad.mit.edu	37	21	47817430	47817430	+	Intron	DEL	T	-	-	rs78975140		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47817430delT	uc002zji.3	+						PCNT_uc002zjj.2_Intron	NM_006031	NP_006022			pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	16052167	16052168	+	IGR	INS	-	AAAC	AAAC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16052167_16052168insAAAC								None (None upstream) : POTEH (204164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	16140023	16140026	+	Intron	DEL	AAGG	-	-	rs8141782		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16140023_16140026delAAGG	uc002zkr.3	-											Homo sapiens cDNA FLJ12852 fis, clone NT2RP2003445.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	17375692	17375692	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17375692delA								HSFYL1 (65467 upstream) : GAB4 (67137 downstream)																																			---	---	---	---
CECR1	51816	broad.mit.edu	37	22	17668217	17668217	+	Intron	DEL	T	-	-	rs112568426		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17668217delT	uc002zmk.1	-						CECR1_uc010gqu.1_Intron|CECR1_uc011agi.1_Intron|CECR1_uc002zmj.1_Intron	NM_017424	NP_059120			cat eye syndrome critical region protein 1						adenosine catabolic process|hypoxanthine salvage|inosine biosynthetic process|multicellular organismal development|purine ribonucleoside monophosphate biosynthetic process	extracellular space|Golgi apparatus	adenosine deaminase activity|adenosine receptor binding|growth factor activity|heparin binding|protein homodimerization activity|proteoglycan binding|zinc ion binding			ovary(1)	1		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)																---	---	---	---
CECR1	51816	broad.mit.edu	37	22	17673720	17673721	+	Intron	DEL	AA	-	-	rs35262317		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17673720_17673721delAA	uc002zmk.1	-						CECR1_uc010gqu.1_Intron|CECR1_uc011agi.1_Intron|CECR1_uc011agj.1_Intron|CECR1_uc002zmj.1_Intron	NM_017424	NP_059120			cat eye syndrome critical region protein 1						adenosine catabolic process|hypoxanthine salvage|inosine biosynthetic process|multicellular organismal development|purine ribonucleoside monophosphate biosynthetic process	extracellular space|Golgi apparatus	adenosine deaminase activity|adenosine receptor binding|growth factor activity|heparin binding|protein homodimerization activity|proteoglycan binding|zinc ion binding			ovary(1)	1		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)																---	---	---	---
CECR2	27443	broad.mit.edu	37	22	17903294	17903294	+	Intron	DEL	T	-	-	rs113256014		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17903294delT	uc010gqv.1	+							NM_031413	NP_113601			cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)														---	---	---	---
CECR2	27443	broad.mit.edu	37	22	17989500	17989500	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17989500delA	uc010gqw.1	+						CECR2_uc010gqv.1_Intron|CECR2_uc002zml.2_Intron|CECR2_uc002zmm.1_Intron	NM_031413	NP_113601			cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)														---	---	---	---
MICAL3	57553	broad.mit.edu	37	22	18382021	18382021	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18382021delT	uc002zng.3	-						MICAL3_uc011agl.1_Intron|MICAL3_uc002znh.2_Intron|MICAL3_uc002znj.1_Intron|MICAL3_uc002znk.1_Intron|MICAL3_uc002znl.1_Intron|MICAL3_uc010grf.2_Intron|MICAL3_uc011agm.1_3'UTR	NM_015241	NP_056056			microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	18537959	18537959	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18537959delT								FLJ41941 (17225 upstream) : TUBA8 (22727 downstream)																																			---	---	---	---
TUBA8	51807	broad.mit.edu	37	22	18602849	18602850	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18602849_18602850delCA	uc002znv.1	+						TUBA8_uc002znr.2_Intron|TUBA8_uc002znw.1_5'Flank|TUBA8_uc002znu.1_Intron	NM_018943	NP_061816			tubulin, alpha 8						microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0																		---	---	---	---
DGCR5	26220	broad.mit.edu	37	22	19009853	19009853	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19009853delT	uc002zon.1	+						DGCR10_uc011agq.1_5'Flank					Homo sapiens mRNA for KIAA1647 protein, partial cds.												0																		---	---	---	---
CDC45	8318	broad.mit.edu	37	22	19483435	19483435	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19483435delT	uc002zpr.2	+						CDC45_uc011agz.1_Intron|CDC45_uc011aha.1_Intron|CDC45_uc002zps.2_Intron|CDC45_uc002zpt.2_Intron	NM_003504	NP_003495			CDC45-like						DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	centrosome|nucleoplasm	protein binding			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	19623162	19623163	+	IGR	DEL	AA	-	-	rs112795899		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19623162_19623163delAA								LOC150185 (68800 upstream) : SEPT5 (78824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	20447540	20447541	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20447540_20447541insA								PI4KAP1 (19692 upstream) : RIMBP3 (8462 downstream)																																			---	---	---	---
KLHL22	84861	broad.mit.edu	37	22	20820090	20820090	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20820090delT	uc002zsl.1	-						KLHL22_uc011ahr.1_Intron|KLHL22_uc002zsm.1_Intron	NM_032775	NP_116164			kelch-like						cell division	Cul3-RING ubiquitin ligase complex				lung(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)															---	---	---	---
Unknown	0	broad.mit.edu	37	22	20979806	20979806	+	Intron	DEL	T	-	-	rs112952651		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20979806delT	uc002zsv.2	-											Homo sapiens, clone IMAGE:5171202, mRNA.																														---	---	---	---
PI4KA	5297	broad.mit.edu	37	22	21139938	21139938	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21139938delA	uc002zsz.3	-						SERPIND1_uc002ztb.1_Intron|SERPIND1_uc002ztc.2_Intron	NM_058004	NP_477352			phosphatidylinositol 4-kinase type 3 alpha						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)															---	---	---	---
Unknown	0	broad.mit.edu	37	22	21316407	21316407	+	Intron	DEL	T	-	-	rs78800285		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21316407delT	uc002zti.1	+											Homo sapiens cDNA clone IMAGE:40134315.																														---	---	---	---
P2RX6	9127	broad.mit.edu	37	22	21377597	21377597	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21377597delT	uc010gsu.1	+	7	672	c.672delT	c.(670-672)TATfs	p.Y224fs	P2RX6_uc002ztz.2_Frame_Shift_Del_p.Y198fs|P2RX6_uc002zua.2_RNA|P2RX6_uc002zuc.1_RNA	NM_005446	NP_005437	O15547	P2RX6_HUMAN	purinergic receptor P2X6 isoform 1	224	Extracellular (Potential).				muscle contraction|protein homooligomerization	cell junction|cytoplasm|integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|identical protein binding|purinergic nucleotide receptor activity				0																		---	---	---	---
HIC2	23119	broad.mit.edu	37	22	21797102	21797102	+	5'UTR	DEL	G	-	-	rs66532305		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21797102delG	uc002zur.3	+	2					HIC2_uc002zus.3_5'UTR	NM_015094	NP_055909			hypermethylated in cancer 2						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	focal adhesion|nucleus	DNA binding|protein C-terminus binding|zinc ion binding			skin(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00438)|Colorectal(54;0.0968)	Lung SC(17;0.0262)|all_lung(157;0.205)																---	---	---	---
PPIL2	23759	broad.mit.edu	37	22	22032477	22032477	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22032477delT	uc010gtj.1	+						PPIL2_uc002zvh.3_Intron|PPIL2_uc002zvi.3_Intron|PPIL2_uc002zvg.3_Intron|PPIL2_uc011aij.1_Intron	NM_148175	NP_680480			peptidylprolyl isomerase-like 2 isoform a						blood coagulation|leukocyte migration|protein folding|protein polyubiquitination	Golgi lumen|nucleus|ubiquitin ligase complex	peptidyl-prolyl cis-trans isomerase activity|ubiquitin-ubiquitin ligase activity			ovary(2)	2	Colorectal(54;0.105)																	---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22554617	22554618	+	Intron	DEL	TT	-	-	rs34093423		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22554617_22554618delTT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22780862	22780862	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22780862delA	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23001633	23001633	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23001633delA	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23025262	23025263	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23025262_23025263delGA	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
RTDR1	27156	broad.mit.edu	37	22	23486877	23486877	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23486877delA	uc002zwt.2	-						RTDR1_uc010gtv.1_5'Flank|RAB36_uc002zwv.1_5'Flank|RAB36_uc010gtw.1_5'Flank	NM_014433	NP_055248			rhabdoid tumor deletion region protein 1								binding			ovary(1)	1	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)														---	---	---	---
LOC91316	91316	broad.mit.edu	37	22	23983806	23983806	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23983806delT	uc002zxh.3	-						LOC91316_uc002zxi.3_Intron|LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron					Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0																		---	---	---	---
LOC91316	91316	broad.mit.edu	37	22	24058107	24058108	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24058107_24058108delAA	uc011aiz.1	-						LOC91316_uc010gub.1_Intron	NR_024448				Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0																		---	---	---	---
MMP11	4320	broad.mit.edu	37	22	24124456	24124456	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24124456delC	uc002zxx.2	+	7	1141	c.1119delC	c.(1117-1119)GGCfs	p.G373fs	MMP11_uc002zxy.2_Intron|MMP11_uc002zxz.2_RNA	NM_005940	NP_005931	P24347	MMP11_HUMAN	matrix metalloproteinase 11 preproprotein	373	Hemopexin-like 2.				collagen catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(2)|large_intestine(1)	3		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)																---	---	---	---
KIAA1671	85379	broad.mit.edu	37	22	25532213	25532214	+	Intron	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25532213_25532214delCT	uc003abn.2	+						KIAA1671_uc003abl.2_Intron	NM_001145206	NP_001138678			hypothetical protein LOC85379											lung(1)	1																		---	---	---	---
LRP5L	91355	broad.mit.edu	37	22	25754888	25754888	+	Intron	DEL	G	-	-	rs72617263	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25754888delG	uc003abs.2	-						LRP5L_uc011ajz.1_Intron|LRP5L_uc010guw.1_Intron	NM_182492	NP_872298			low density lipoprotein receptor-related protein												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	25953501	25953501	+	IGR	DEL	A	-	-	rs111810780		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25953501delA								LRP5L (175957 upstream) : ADRBK2 (7360 downstream)																																			---	---	---	---
HPS4	89781	broad.mit.edu	37	22	26854625	26854625	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26854625delA	uc003acl.2	-						HPS4_uc003aci.2_Intron|HPS4_uc003acj.2_Intron|HPS4_uc003ack.2_Intron|HPS4_uc003acn.2_Intron|HPS4_uc003ach.2_Intron	NM_022081	NP_071364			light ear protein isoform a						lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0														Hermansky-Pudlak_syndrome				---	---	---	---
TFIP11	24144	broad.mit.edu	37	22	26888509	26888509	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26888509delA	uc003acr.2	-						TFIP11_uc003acq.2_Intron|TFIP11_uc003acs.2_Intron|TFIP11_uc003act.2_Intron|uc003acu.1_RNA	NM_012143	NP_036275			tuftelin interacting protein 11						biomineral tissue development	catalytic step 2 spliceosome|cytoplasm|nuclear speck	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	27290729	27290731	+	IGR	DEL	AAG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27290729_27290731delAAG								MIAT (175780 upstream) : MN1 (853535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27366004	27366004	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27366004delT								MIAT (251055 upstream) : MN1 (778262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27439840	27439843	+	IGR	DEL	CTCC	-	-	rs142247464		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27439840_27439843delCTCC								MIAT (324891 upstream) : MN1 (704423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27486227	27486227	+	IGR	DEL	T	-	-	rs34617906		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27486227delT								MIAT (371278 upstream) : MN1 (658039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27662162	27662162	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27662162delA								MIAT (547213 upstream) : MN1 (482104 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27776789	27776789	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27776789delA								MIAT (661840 upstream) : MN1 (367477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27791752	27791753	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27791752_27791753delCA								MIAT (676803 upstream) : MN1 (352513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27824591	27824592	+	IGR	DEL	CC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27824591_27824592delCC								MIAT (709642 upstream) : MN1 (319674 downstream)																																			---	---	---	---
TTC28	23331	broad.mit.edu	37	22	28623693	28623693	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28623693delA	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
CHEK2	11200	broad.mit.edu	37	22	29120926	29120926	+	Intron	DEL	A	-	-	rs17880603		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29120926delA	uc003adu.1	-						CHEK2_uc003ads.1_Intron|CHEK2_uc010gvh.1_Intron|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_Intron|CHEK2_uc010gvk.1_Intron|CHEK2_uc003adt.1_Intron|CHEK2_uc003adv.1_Intron|CHEK2_uc003adw.1_Intron|CHEK2_uc003adx.1_Intron|CHEK2_uc003ady.1_Intron|CHEK2_uc003adz.1_Intron	NM_007194	NP_009125			protein kinase CHK2 isoform a						cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20								F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				---	---	---	---
HSCB	150274	broad.mit.edu	37	22	29139159	29139159	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29139159delA	uc003aea.2	+						CHEK2_uc003adt.1_5'Flank|CHEK2_uc003adu.1_5'Flank|CHEK2_uc003adv.1_5'Flank|CHEK2_uc003adw.1_5'Flank|CHEK2_uc003adx.1_5'Flank|CHEK2_uc003ady.1_5'Flank|CHEK2_uc003adz.1_5'Flank	NM_172002	NP_741999			J-type co-chaperone HSC20 precursor						iron-sulfur cluster assembly|protein folding	mitochondrion	chaperone binding|heat shock protein binding|metal ion binding			kidney(1)	1																		---	---	---	---
ZNRF3	84133	broad.mit.edu	37	22	29286755	29286755	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29286755delT	uc003aeg.2	+							NM_032173	NP_115549			zinc and ring finger 3							integral to membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
ZNRF3	84133	broad.mit.edu	37	22	29443074	29443074	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29443074delT	uc003aeg.2	+						ZNRF3_uc003aeh.1_Intron	NM_032173	NP_115549			zinc and ring finger 3							integral to membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	29818798	29818799	+	IGR	DEL	AC	-	-	rs150349877		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29818798_29818799delAC								AP1B1 (34229 upstream) : RFPL1S (14207 downstream)																																			---	---	---	---
NF2	4771	broad.mit.edu	37	22	29997192	29997192	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29997192delT	uc003age.3	+						NF2_uc003afy.3_5'Flank|NF2_uc003afz.3_5'Flank|NF2_uc003agf.3_5'Flank|NF2_uc003agb.3_5'Flank|NF2_uc003agc.3_5'Flank|NF2_uc003agd.3_5'Flank|NF2_uc003agg.3_5'Flank|NF2_uc003aga.3_5'Flank|NF2_uc003agh.3_5'Flank|NF2_uc003agi.3_5'Flank|NF2_uc003agj.3_5'Flank	NM_000268	NP_000259			neurofibromin 2 isoform 1						actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.?(1)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728								D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				---	---	---	---
Unknown	0	broad.mit.edu	37	22	30624100	30624100	+	IGR	DEL	A	-	-	rs112242513		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30624100delA								HORMAD2 (51042 upstream) : LIF (12342 downstream)																																			---	---	---	---
SEC14L2	23541	broad.mit.edu	37	22	30818069	30818069	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30818069delT	uc003ahr.2	+						SEC14L2_uc011akx.1_Intron|SEC14L2_uc003ahs.2_Intron|SEC14L2_uc011aky.1_Intron|SEC14L2_uc003aht.2_Intron|SEC14L2_uc003ahu.3_Intron|SEC14L2_uc010gvv.2_Intron|SEC14L2_uc010gvw.1_Intron|MTP18_uc010gvx.1_Intron|MTP18_uc003ahv.1_Intron|MTP18_uc010gvy.1_Intron	NM_012429	NP_036561			SEC14-like 2 isoform 1						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	phospholipid binding|transporter activity|vitamin E binding				0					Vitamin E(DB00163)													---	---	---	---
SEC14L4	284904	broad.mit.edu	37	22	30900639	30900640	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30900639_30900640insA	uc003aid.2	-						SEC14L4_uc011akz.1_Intron|SEC14L4_uc003aie.2_Intron|SEC14L4_uc003aif.2_Intron	NM_174977	NP_777637			SEC14p-like protein TAP3 isoform a							integral to membrane|intracellular	lipid binding|transporter activity			skin(1)	1					Vitamin E(DB00163)													---	---	---	---
Unknown	0	broad.mit.edu	37	22	30914530	30914530	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30914530delT								SEC14L4 (12832 upstream) : GAL3ST1 (36094 downstream)																																			---	---	---	---
OSBP2	23762	broad.mit.edu	37	22	31298098	31298099	+	Intron	DEL	AA	-	-	rs113921257		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31298098_31298099delAA	uc003aiy.1	+						OSBP2_uc011ala.1_Intron|OSBP2_uc010gwc.1_Intron|OSBP2_uc011alb.1_Intron|OSBP2_uc003aiz.1_Intron|OSBP2_uc003aja.1_Intron|OSBP2_uc011alc.1_Intron|OSBP2_uc003ajb.2_Intron|OSBP2_uc011ald.1_Intron|OSBP2_uc010gwd.1_Intron	NM_030758	NP_110385			oxysterol binding protein 2 isoform a						lipid transport	membrane	lipid binding			breast(1)|skin(1)	2																		---	---	---	---
INPP5J	27124	broad.mit.edu	37	22	31509421	31509422	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31509421_31509422delAA	uc010gwf.2	+						SELM_uc011alj.1_Intron					RecName: Full=Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A;          EC=3.1.3.56; AltName: Full=Inositol polyphosphate 5-phosphatase J;							cytoplasm|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|SH3 domain binding			skin(1)	1																		---	---	---	---
PLA2G3	50487	broad.mit.edu	37	22	31535796	31535796	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31535796delC	uc003aka.2	-							NM_015715	NP_056530			phospholipase A2, group III precursor						cilium morphogenesis|lipid catabolic process|phospholipid metabolic process	centriole|extracellular space|plasma membrane	calcium ion binding|calcium-dependent phospholipase A2 activity				0																		---	---	---	---
RNF185	91445	broad.mit.edu	37	22	31593111	31593111	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31593111delA	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	31703029	31703030	+	IGR	INS	-	T	T	rs142172603		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31703029_31703030insT								PIK3IP1 (14509 upstream) : PATZ1 (18761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	31715352	31715352	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31715352delC								PIK3IP1 (26832 upstream) : PATZ1 (6439 downstream)																																			---	---	---	---
EIF4ENIF1	56478	broad.mit.edu	37	22	31850085	31850085	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31850085delA	uc003akz.1	-						EIF4ENIF1_uc003akx.1_Intron|EIF4ENIF1_uc003aky.1_Intron|EIF4ENIF1_uc003ala.1_Intron|EIF4ENIF1_uc003alb.1_Intron|EIF4ENIF1_uc003akw.1_5'Flank	NM_019843	NP_062817			eukaryotic translation initiation factor 4E							nucleus	protein binding|protein transporter activity			ovary(1)	1																		---	---	---	---
EIF4ENIF1	56478	broad.mit.edu	37	22	31870051	31870051	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31870051delT	uc003akz.1	-						EIF4ENIF1_uc003ala.1_Intron|EIF4ENIF1_uc003alb.1_Intron|EIF4ENIF1_uc003alc.1_Intron	NM_019843	NP_062817			eukaryotic translation initiation factor 4E							nucleus	protein binding|protein transporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	32061604	32061604	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32061604delA								PISD (3403 upstream) : C22orf30 (10638 downstream)																																			---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32157500	32157500	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32157500delA	uc003als.2	+						DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alr.1_Intron|DEPDC5_uc011alt.1_Intron	NM_014662	NP_055477			DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	32381021	32381022	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32381021_32381022delAA								YWHAH (27432 upstream) : SLC5A1 (58015 downstream)																																			---	---	---	---
SLC5A1	6523	broad.mit.edu	37	22	32456002	32456003	+	Intron	DEL	AC	-	-	rs36058777		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32456002_32456003delAC	uc003amc.2	+						SLC5A1_uc011alz.1_Intron	NM_000343	NP_000334			solute carrier family 5 (sodium/glucose						carbohydrate metabolic process	integral to plasma membrane	glucose:sodium symporter activity|protein binding			skin(1)	1																		---	---	---	---
SLC5A4	6527	broad.mit.edu	37	22	32627877	32627877	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32627877delT	uc003ami.2	-							NM_014227	NP_055042			solute carrier family 5 (low affinity glucose						carbohydrate transport|sodium ion transport	integral to membrane	symporter activity				0																		---	---	---	---
C22orf28	51493	broad.mit.edu	37	22	32784367	32784367	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32784367delA	uc003amm.2	-							NM_014306	NP_055121			hypothetical protein LOC51493						cell-matrix adhesion|substrate adhesion-dependent cell spreading|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|tRNA-splicing ligase complex	ATP binding|metal ion binding|RNA ligase (ATP) activity|vinculin binding				0																		---	---	---	---
C22orf28	51493	broad.mit.edu	37	22	32788433	32788433	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32788433delA	uc003amm.2	-							NM_014306	NP_055121			hypothetical protein LOC51493						cell-matrix adhesion|substrate adhesion-dependent cell spreading|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|tRNA-splicing ligase complex	ATP binding|metal ion binding|RNA ligase (ATP) activity|vinculin binding				0																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	32938638	32938641	+	Intron	DEL	GTGC	-	-	rs3838157		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32938638_32938641delGTGC	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481			synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	33658753	33658757	+	IGR	DEL	CCTTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33658753_33658757delCCTTT								SYN3 (204376 upstream) : LARGE (10306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	34431808	34431809	+	IGR	DEL	CT	-	-	rs143908371		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34431808_34431809delCT								LARGE (113224 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	34541690	34541690	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34541690delC								LARGE (223106 upstream) : ISX (920439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	34965552	34965552	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34965552delT								LARGE (646968 upstream) : ISX (496577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35314249	35314250	+	IGR	INS	-	G	G	rs144893091	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35314249_35314250insG								LARGE (995665 upstream) : ISX (147879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35498361	35498362	+	IGR	INS	-	AC	AC	rs144886817	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35498361_35498362insAC								ISX (14983 upstream) : HMGXB4 (155083 downstream)																																			---	---	---	---
TOM1	10043	broad.mit.edu	37	22	35727881	35727881	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35727881delA	uc003ann.2	+						TOM1_uc011ami.1_Intron|TOM1_uc011amj.1_Intron|TOM1_uc003ans.2_Intron|TOM1_uc011amk.1_Intron|TOM1_uc003anp.2_Intron|TOM1_uc011aml.1_Intron|TOM1_uc003ano.2_Intron|TOM1_uc003anq.2_Intron|TOM1_uc003anr.2_Intron	NM_005488	NP_005479			target of myb1 isoform 1						endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	35834552	35834553	+	IGR	INS	-	CATCCATC	CATCCATC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35834552_35834553insCATCCATC								MCM5 (14058 upstream) : RASD2 (102799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35906134	35906135	+	IGR	DEL	TG	-	-	rs71660362	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35906134_35906135delTG								MCM5 (85640 upstream) : RASD2 (31217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35980877	35980878	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35980877_35980878delGT								RASD2 (30834 upstream) : MB (21934 downstream)																																			---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36330215	36330215	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36330215delA	uc003aon.3	-						RBM9_uc010gwu.2_Intron|RBM9_uc003aoo.3_Intron	NM_001082578	NP_001076047			RNA binding motif protein 9 isoform 5						estrogen receptor signaling pathway|mRNA processing|negative regulation of transcription, DNA-dependent|regulation of cell proliferation|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding|transcription corepressor activity|transcription factor binding				0																		---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36756758	36756758	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36756758delA	uc003apg.2	-						MYH9_uc003api.1_Intron	NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
Unknown	0	broad.mit.edu	37	22	37276994	37276994	+	IGR	DEL	T	-	-	rs3076360		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37276994delT								NCF4 (2936 upstream) : CSF2RB (32681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	37436490	37436491	+	IGR	INS	-	GT	GT	rs137969502	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37436490_37436491insGT								MPST (10628 upstream) : KCTD17 (11288 downstream)																																			---	---	---	---
CARD10	29775	broad.mit.edu	37	22	37909724	37909724	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37909724delA	uc003asx.1	-						CARD10_uc003ast.1_Intron|CARD10_uc003asy.1_Intron	NM_014550	NP_055365			caspase recruitment domain protein 10						activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1)	6	Melanoma(58;0.0574)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	37944643	37944643	+	IGR	DEL	T	-	-	rs68114690		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37944643delT								CARD10 (29265 upstream) : CDC42EP1 (11828 downstream)																																			---	---	---	---
GGA1	26088	broad.mit.edu	37	22	38006923	38006923	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38006923delG	uc003atc.2	+						GGA1_uc003atb.2_Intron|GGA1_uc003atd.2_Intron|GGA1_uc003ate.2_Intron|GGA1_uc003atf.2_Intron	NM_013365	NP_037497			golgi associated, gamma adaptin ear containing,						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|endosome membrane|Golgi apparatus part	protein binding			breast(2)|ovary(1)	3	Melanoma(58;0.0574)																	---	---	---	---
TRIOBP	11078	broad.mit.edu	37	22	38164039	38164039	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38164039delC	uc003atr.2	+						TRIOBP_uc003atu.2_Intron|TRIOBP_uc003atw.2_Intron|TRIOBP_uc003atx.1_Intron|TRIOBP_uc010gxh.2_Intron	NM_001039141	NP_001034230			TRIO and F-actin binding protein isoform 6						actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)																	---	---	---	---
GCAT	23464	broad.mit.edu	37	22	38209775	38209776	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38209775_38209776delTT	uc003atz.2	+						GCAT_uc003aua.1_Intron	NM_014291	NP_055106			glycine C-acetyltransferase precursor						biosynthetic process|cellular amino acid metabolic process		glycine C-acetyltransferase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups				0	Melanoma(58;0.045)				Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
PLA2G6	8398	broad.mit.edu	37	22	38548976	38548976	+	Intron	DEL	A	-	-	rs112507836		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38548976delA	uc003auy.1	-						PLA2G6_uc003auz.1_Intron|PLA2G6_uc003ava.1_Intron|PLA2G6_uc003avb.2_Intron|PLA2G6_uc010gxk.1_Intron|PLA2G6_uc011ano.1_Intron	NM_003560	NP_003551			phospholipase A2, group VI isoform a						cardiolipin biosynthetic process|cell death|lipid catabolic process	centrosome|membrane				ovary(1)	1	Melanoma(58;0.045)				Quinacrine(DB01103)													---	---	---	---
TMEM184B	25829	broad.mit.edu	37	22	38657872	38657872	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38657872delC	uc003avf.1	-						TMEM184B_uc003avg.1_Intron|TMEM184B_uc003avh.1_Intron|TMEM184B_uc010gxl.1_Intron	NM_012264	NP_036396			transmembrane protein 184B							integral to membrane					0	Melanoma(58;0.045)																	---	---	---	---
KCNJ4	3761	broad.mit.edu	37	22	38850078	38850079	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38850078_38850079delAC	uc003avt.1	-							NM_152868	NP_690607			potassium inwardly-rectifying channel J4						synaptic transmission	basolateral plasma membrane|voltage-gated potassium channel complex	inward rectifier potassium channel activity|PDZ domain binding				0	Melanoma(58;0.0286)																	---	---	---	---
DMC1	11144	broad.mit.edu	37	22	38931011	38931011	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38931011delA	uc003avz.1	-						DMC1_uc011anv.1_Intron	NM_007068	NP_008999			DMC1 dosage suppressor of mck1 homolog						reciprocal meiotic recombination	condensed nuclear chromosome	ATP binding|DNA binding|DNA-dependent ATPase activity|protein binding			ovary(1)	1	Melanoma(58;0.0286)												Homologous_recombination					---	---	---	---
CACNA1I	8911	broad.mit.edu	37	22	40023700	40023700	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40023700delG	uc003ayc.2	+						CACNA1I_uc003ayd.2_Intron|CACNA1I_uc003aye.2_Intron|CACNA1I_uc003ayf.2_Intron	NM_021096	NP_066919			calcium channel, voltage-dependent, T type,						axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)													---	---	---	---
CACNA1I	8911	broad.mit.edu	37	22	40052466	40052466	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40052466delC	uc003ayc.2	+						CACNA1I_uc003ayd.2_Intron|CACNA1I_uc003aye.2_Intron|CACNA1I_uc003ayf.2_Intron	NM_021096	NP_066919			calcium channel, voltage-dependent, T type,						axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)													---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40708460	40708460	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40708460delT	uc011aor.1	+						TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Intron|TNRC6B_uc003ayo.2_Intron	NM_001162501	NP_001155973			trinucleotide repeat containing 6B isoform 1						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
MKL1	57591	broad.mit.edu	37	22	40946857	40946857	+	Intron	DEL	T	-	-	rs111531159		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40946857delT	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								---	---	---	---
RBX1	9978	broad.mit.edu	37	22	41349507	41349508	+	Intron	INS	-	TG	TG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41349507_41349508insTG	uc003azk.2	+						XPNPEP3_uc011aoy.1_Intron	NM_014248	NP_055063			ring-box 1						DNA repair|interspecies interaction between organisms|protein neddylation|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|viral reproduction	Cul3-RING ubiquitin ligase complex|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytosol|nucleus|SCF ubiquitin ligase complex	NEDD8 ligase activity|protein binding|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	41432028	41432029	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41432028_41432029delCT								RBX1 (63362 upstream) : MIR1281 (56488 downstream)																																			---	---	---	---
EP300	2033	broad.mit.edu	37	22	41565470	41565470	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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				---	---	---	---
ZC3H7B	23264	broad.mit.edu	37	22	41720075	41720075	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41720075delA	uc003azw.2	+						ZC3H7B_uc003azv.1_Intron|ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060			zinc finger CCCH-type containing 7B						interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	41829152	41829154	+	IGR	DEL	CTC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41829152_41829154delCTC								TEF (33824 upstream) : TOB2 (338 downstream)																																			---	---	---	---
POLR3H	171568	broad.mit.edu	37	22	41938095	41938095	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41938095delT	uc003baf.2	-						POLR3H_uc003bae.2_Intron|POLR3H_uc003bag.2_Intron|POLR3H_uc003bai.2_Intron|POLR3H_uc003baj.1_Intron	NM_138338	NP_612211			polymerase (RNA) III (DNA directed) polypeptide						innate immune response|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	41945390	41945390	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41945390delA								POLR3H (4911 upstream) : CSDC2 (11624 downstream)																																			---	---	---	---
SREBF2	6721	broad.mit.edu	37	22	42256353	42256353	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42256353delA	uc003bbi.2	+						WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron	NM_004599	NP_004590			sterol regulatory element-binding transcription						cholesterol metabolic process	ER to Golgi transport vesicle membrane|Golgi membrane|nucleus|SREBP-SCAP-Insig complex	protein C-terminus binding			breast(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
NAGA	4668	broad.mit.edu	37	22	42458950	42458950	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42458950delG	uc003bbx.2	-	8	975	c.838delC	c.(838-840)CTCfs	p.L280fs	NAGA_uc003bby.2_Frame_Shift_Del_p.L280fs|NAGA_uc003bbw.3_Frame_Shift_Del_p.L280fs	NM_000262	NP_000253	P17050	NAGAB_HUMAN	alpha-N-acetylgalactosaminidase precursor	280					glycoside catabolic process|glycosylceramide catabolic process|oligosaccharide metabolic process	lysosome	alpha-galactosidase activity|alpha-N-acetylgalactosaminidase activity|cation binding|protein homodimerization activity			central_nervous_system(1)	1																		---	---	---	---
NFAM1	150372	broad.mit.edu	37	22	42778803	42778805	+	3'UTR	DEL	CTC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42778803_42778805delCTC	uc003bcn.3	-	6						NM_145912	NP_666017			NFAT activation molecule 1 precursor						B cell differentiation|inflammatory response|intracellular signal transduction|positive regulation of B cell receptor signaling pathway|positive regulation of cytokine production|positive regulation of sequence-specific DNA binding transcription factor activity	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	42843691	42843691	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42843691delT								NFAM1 (15290 upstream) : SERHL (52894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	42872507	42872508	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42872507_42872508insT								NFAM1 (44106 upstream) : SERHL (24077 downstream)																																			---	---	---	---
SERHL	94009	broad.mit.edu	37	22	42898666	42898666	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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																		---	---	---	---
ARFGAP3	26286	broad.mit.edu	37	22	43216376	43216377	+	Intron	DEL	TA	-	-	rs10585135		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43216376_43216377delTA	uc003bdd.2	-						ARFGAP3_uc010gzf.2_Intron|ARFGAP3_uc011apu.1_Intron	NM_014570	NP_055385			ADP-ribosylation factor GTPase activating						intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding			breast(1)	1																OREG0026610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EFCAB6	64800	broad.mit.edu	37	22	44158928	44158928	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44158928delT	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Intron|EFCAB6_uc003beb.3_Intron	NM_022785	NP_073622			CAP-binding protein complex interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)																---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44561997	44561997	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44561997delT	uc003ben.2	+						PARVB_uc003bem.2_Intron|PARVB_uc010gzn.2_Intron|PARVB_uc003beo.2_Intron	NM_013327	NP_037459			parvin, beta isoform b						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	44876010	44876011	+	IGR	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44876010_44876011delAG								KIAA1644 (167279 upstream) : LDOC1L (12439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	45003308	45003309	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45003308_45003309insG								NCRNA00207 (34979 upstream) : PRR5 (61284 downstream)																																			---	---	---	---
NUP50	10762	broad.mit.edu	37	22	45563924	45563924	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45563924delT	uc003bfr.2	+						NUP50_uc003bfs.2_Intron|NUP50_uc011aqn.1_Intron|NUP50_uc003bft.2_Intron	NM_007172	NP_009103			nucleoporin 50kDa isoform b						carbohydrate metabolic process|glucose transport|intracellular transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore|nucleoplasm	protein binding				0		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)														---	---	---	---
NUP50	10762	broad.mit.edu	37	22	45578836	45578836	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45578836delA	uc003bfr.2	+						NUP50_uc003bfs.2_Intron|NUP50_uc011aqn.1_Intron|NUP50_uc003bft.2_Intron|NUP50_uc011aqo.1_Intron	NM_007172	NP_009103			nucleoporin 50kDa isoform b						carbohydrate metabolic process|glucose transport|intracellular transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore|nucleoplasm	protein binding				0		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)														---	---	---	---
FBLN1	2192	broad.mit.edu	37	22	45937984	45937984	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45937984delA	uc003bgj.1	+						FBLN1_uc003bgg.1_Intron|FBLN1_uc003bgh.2_Intron|FBLN1_uc010gzz.2_Intron|FBLN1_uc003bgi.1_Intron	NM_006486	NP_006477			fibulin 1 isoform D						interspecies interaction between organisms	extracellular space|soluble fraction	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)														---	---	---	---
ATXN10	25814	broad.mit.edu	37	22	46123904	46123904	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46123904delT	uc003bgm.1	+						ATXN10_uc011aqt.1_Intron|ATXN10_uc003bgn.1_Intron	NM_013236	NP_037368			ataxin 10						cell death|neuron projection development	dendrite|neuronal cell body|perinuclear region of cytoplasm				ovary(1)|kidney(1)	2		Ovarian(80;0.00973)|all_neural(38;0.0417)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0223)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	46259460	46259460	+	IGR	DEL	A	-	-	rs68075444		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46259460delA								ATXN10 (18631 upstream) : WNT7B (56788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	46427897	46427897	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46427897delT								LOC730668 (21240 upstream) : LOC100271722 (7892 downstream)																																			---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46784246	46784246	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46784246delA	uc003bhw.1	-						CELSR1_uc011arc.1_Intron	NM_014246	NP_055061			cadherin EGF LAG seven-pass G-type receptor 1						central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46812365	46812366	+	Intron	INS	-	C	C	rs138351965	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46812365_46812366insC	uc003bhw.1	-							NM_014246	NP_055061			cadherin EGF LAG seven-pass G-type receptor 1						central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
GRAMD4	23151	broad.mit.edu	37	22	47066510	47066510	+	Intron	DEL	T	-	-	rs76902089		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47066510delT	uc003bhx.2	+						GRAMD4_uc010had.2_Intron	NM_015124	NP_055939			death-inducing-protein						apoptosis	integral to membrane|mitochondrial membrane				ovary(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)														---	---	---	---
TBC1D22A	25771	broad.mit.edu	37	22	47356163	47356163	+	Intron	DEL	T	-	-	rs77783350		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47356163delT	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	48480848	48480854	+	IGR	DEL	GGAGCCA	-	-	rs5845830		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48480848_48480854delGGAGCCA								TBC1D22A (911126 upstream) : FAM19A5 (404434 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49403748	49403748	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49403748delA								FAM19A5 (256006 upstream) : C22orf34 (404428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49472255	49472255	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49472255delA								FAM19A5 (324513 upstream) : C22orf34 (335921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	50094810	50094812	+	IGR	DEL	GAG	-	-	rs67888567		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50094810_50094812delGAG								C22orf34 (43620 upstream) : BRD1 (72126 downstream)																																			---	---	---	---
TRABD	80305	broad.mit.edu	37	22	50636199	50636199	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50636199delC	uc003bjq.1	+						TRABD_uc003bjr.1_Intron|TRABD_uc003bjs.1_Intron|TRABD_uc003bjt.1_Intron|TRABD_uc003bju.1_Intron|TRABD_uc003bjv.2_Intron|TRABD_uc003bjw.1_Intron	NM_025204	NP_079480			TraB domain containing												0		all_cancers(38;1.07e-07)|all_epithelial(38;9.6e-07)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		LUAD - Lung adenocarcinoma(64;0.105)														---	---	---	---
SAPS2	9701	broad.mit.edu	37	22	50796056	50796056	+	Intron	DEL	T	-	-	rs35526525		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50796056delT	uc003blc.2	+						SAPS2_uc003bky.1_Intron|SAPS2_uc003bkz.1_Intron|SAPS2_uc003bla.1_Intron	NM_014678	NP_055493			SAPS domain family, member 2							cytoplasm|intracellular membrane-bounded organelle	protein binding				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.222)														---	---	---	---
ARSA	410	broad.mit.edu	37	22	51063978	51063978	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51063978delG	uc003bnb.3	-						ARSA_uc003bna.3_Intron|ARSA_uc003bnc.3_Intron|ARSA_uc003bnd.3_Intron|ARSA_uc003bmz.3_Intron	NM_001085426	NP_001078895			arylsulfatase A isoform a precursor							lysosome	arylsulfatase activity|calcium ion binding|cerebroside-sulfatase activity			pancreas(1)|skin(1)	2		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)													---	---	---	---
SHANK3	85358	broad.mit.edu	37	22	51117521	51117521	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51117521delG	uc003bne.1	+	6	675	c.675delG	c.(673-675)CTGfs	p.L225fs		NM_001080420	NP_001073889	F2Z3L0	F2Z3L0_HUMAN	SH3 and multiple ankyrin repeat domains 3	225										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)														---	---	---	---
ACR	49	broad.mit.edu	37	22	51182226	51182226	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51182226delC	uc003bnh.3	+							NM_001097	NP_001088			acrosin precursor						acrosome matrix dispersal|activation of adenylate cyclase activity	acrosomal matrix|protein complex	amidase activity|copper ion binding|DNA binding|drug binding|fucose binding|mannose binding|protein binding|serine-type endopeptidase activity|zinc ion binding				0		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
Unknown	0	broad.mit.edu	37	X	424783	424783	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:424783delA								PPP2R3B (77156 upstream) : SHOX (160296 downstream)																																			---	---	---	---
SHOX	6473	broad.mit.edu	37	X	584193	584194	+	5'Flank	DEL	AG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:584193_584194delAG	uc004cph.1	+						SHOX_uc004cpi.2_5'Flank	NM_000451	NP_000442			short stature homeobox isoform SHOXa						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	1536439	1536440	+	Intron	INS	-	ACAC	ACAC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1536439_1536440insACAC	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183			acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
P2RY8	286530	broad.mit.edu	37	X	1582064	1582064	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1582064delT	uc004cpz.2	-	2						NM_178129	NP_835230			G-protein coupled purinergic receptor P2Y8							integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(5)	5		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)						T	CRLF2	B-ALL|Downs associated ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	X	1999795	1999802	+	IGR	DEL	AAGAAAGC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1999795_1999802delAAGAAAGC								ASMT (237822 upstream) : DHRSX (137755 downstream)																																			---	---	---	---
DHRSX	207063	broad.mit.edu	37	X	2142941	2142942	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2142941_2142942delCA	uc004cqf.3	-							NM_145177	NP_660160			dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)																---	---	---	---
DHRSX	207063	broad.mit.edu	37	X	2190177	2190177	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2190177delA	uc004cqf.3	-							NM_145177	NP_660160			dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)																---	---	---	---
DHRSX	207063	broad.mit.edu	37	X	2246121	2246121	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2246121delA	uc004cqf.3	-							NM_145177	NP_660160			dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)																---	---	---	---
DHRSX	207063	broad.mit.edu	37	X	2326918	2326919	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2326918_2326919delAA	uc004cqf.3	-							NM_145177	NP_660160			dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)																---	---	---	---
ARSD	414	broad.mit.edu	37	X	2826672	2826675	+	Intron	DEL	CATC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2826672_2826675delCATC	uc004cqy.2	-						ARSD_uc004cqz.1_Intron	NM_001669	NP_001660			arylsulfatase D isoform a precursor							lysosome	arylsulfatase activity|metal ion binding				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
ARSD	414	broad.mit.edu	37	X	2848389	2848389	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2848389delT	uc004cqy.2	-						ARSD_uc004cqz.1_5'Flank|ARSD_uc004cra.1_5'Flank|ARSD_uc004crb.3_5'Flank	NM_001669	NP_001660			arylsulfatase D isoform a precursor							lysosome	arylsulfatase activity|metal ion binding				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	3117311	3117311	+	IGR	DEL	A	-	-	rs149829018		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3117311delA								ARSF (86564 upstream) : MXRA5 (109300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	3226105	3226105	+	IGR	DEL	A	-	-	rs72244506		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3226105delA								ARSF (195358 upstream) : MXRA5 (506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	3750602	3750602	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3750602delA	uc011mhk.1	-						uc004crk.2_Intron					Homo sapiens similar to Serine/threonine-protein kinase PRKX (Protein kinase PKX1), mRNA (cDNA clone IMAGE:4124593), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	4062467	4062468	+	IGR	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:4062467_4062468delGA								PRKX (430806 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	5342025	5342025	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5342025delT								None (None upstream) : NLGN4X (466059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	5460069	5460069	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5460069delA								None (None upstream) : NLGN4X (348015 downstream)																																			---	---	---	---
NLGN4X	57502	broad.mit.edu	37	X	6026725	6026725	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6026725delA	uc010ndh.2	-						NLGN4X_uc004crp.2_Intron|NLGN4X_uc004crq.2_Intron|NLGN4X_uc010ndi.2_Intron|NLGN4X_uc004crr.2_Intron|NLGN4X_uc010ndj.2_Intron	NM_181332	NP_851849			X-linked neuroligin 4 precursor						brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	chloride ion binding|neurexin binding|protein homodimerization activity|receptor activity			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
NLGN4X	57502	broad.mit.edu	37	X	6087866	6087866	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6087866delA	uc010ndh.2	-						NLGN4X_uc004crq.2_Intron|NLGN4X_uc010ndi.2_Intron|NLGN4X_uc004crr.2_Intron|NLGN4X_uc010ndj.2_Intron	NM_181332	NP_851849			X-linked neuroligin 4 precursor						brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	chloride ion binding|neurexin binding|protein homodimerization activity|receptor activity			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	6405746	6405747	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6405746_6405747delAC								NLGN4X (259040 upstream) : VCX3A (45913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	7606590	7606590	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7606590delC								STS (333910 upstream) : VCX (203713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	7967888	7967889	+	IGR	DEL	TT	-	-	rs34546441		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7967888_7967889delTT								PNPLA4 (72108 upstream) : MIR651 (127117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	7988817	7988817	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7988817delT								PNPLA4 (93037 upstream) : MIR651 (106189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	8335830	8335830	+	IGR	DEL	A	-	-	rs113047595		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8335830delA								VCX2 (196522 upstream) : VCX3B (97041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	8854799	8854800	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8854799_8854800delAA								FAM9A (85375 upstream) : FAM9B (138239 downstream)																																			---	---	---	---
FAM9B	171483	broad.mit.edu	37	X	9079697	9079698	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9079697_9079698delCA	uc011mhv.1	-											Homo sapiens family with sequence similarity 9, member B (FAM9B) mRNA, complete cds.							nucleus					0		Hepatocellular(5;0.219)																---	---	---	---
SHROOM2	357	broad.mit.edu	37	X	9804525	9804526	+	Intron	DEL	TC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9804525_9804526delTC	uc004csu.1	+							NM_001649	NP_001640			apical protein of Xenopus-like						apical protein localization|brain development|cell migration|cell morphogenesis|cellular pigment accumulation|ear development|establishment of melanosome localization|eye pigment granule organization|lens morphogenesis in camera-type eye|melanosome organization	apical plasma membrane|cell-cell adherens junction|microtubule|tight junction	actin filament binding|beta-catenin binding|ligand-gated sodium channel activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8		Hepatocellular(5;0.000888)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	9926891	9926891	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9926891delT								SHROOM2 (9410 upstream) : WWC3 (56904 downstream)																																			---	---	---	---
WWC3	55841	broad.mit.edu	37	X	10060669	10060670	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10060669_10060670delTT	uc004csx.3	+						WWC3_uc010nds.2_Intron|WWC3_uc010ndt.2_Intron	NM_015691	NP_056506			WWC family member 3											ovary(4)	4																		---	---	---	---
MID1	4281	broad.mit.edu	37	X	10661402	10661402	+	Intron	DEL	T	-	-	rs75200912		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10661402delT	uc004cti.3	-						MID1_uc004ctj.3_Intron	NM_033290	NP_150632			midline 1						microtubule cytoskeleton organization|pattern specification process|positive regulation of stress-activated MAPK cascade	cytoplasm|microtubule|microtubule associated complex|spindle	ligase activity|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	12085547	12085547	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12085547delT								MSL3 (291677 upstream) : FRMPD4 (71038 downstream)																																			---	---	---	---
FRMPD4	9758	broad.mit.edu	37	X	12701580	12701580	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12701580delA	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	13286978	13286979	+	IGR	DEL	CA	-	-	rs111353790		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13286978_13286979delCA								FAM9C (224178 upstream) : ATXN3L (49791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	13496927	13496928	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13496927_13496928insG								ATXN3L (158409 upstream) : EGFL6 (90813 downstream)																																			---	---	---	---
RAB9A	9367	broad.mit.edu	37	X	13712296	13712296	+	Intron	DEL	A	-	-	rs6653643	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13712296delA	uc004cvm.2	+						RAB9A_uc010neh.2_Intron	NM_004251	NP_004242			RAB9A, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome|lysosome|plasma membrane	GDP binding|GTP binding|GTPase activity|protein binding			ovary(1)	1																		---	---	---	---
OFD1	8481	broad.mit.edu	37	X	13787350	13787350	+	3'UTR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13787350delT	uc004cvp.3	+	23					OFD1_uc004cvr.3_3'UTR|OFD1_uc011mil.1_3'UTR|OFD1_uc004cvq.3_3'UTR|OFD1_uc010nen.2_3'UTR|OFD1_uc004cvs.3_RNA|OFD1_uc004cvu.3_3'UTR|OFD1_uc004cvv.3_3'UTR	NM_003611	NP_003602			oral-facial-digital syndrome 1						cilium movement involved in determination of left/right asymmetry|G2/M transition of mitotic cell cycle	centriole|cilium|cytosol|microtubule basal body|nuclear membrane	alpha-tubulin binding|gamma-tubulin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	14071374	14071374	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14071374delT								GEMIN8 (23339 upstream) : GLRA2 (476046 downstream)																																			---	---	---	---
MOSPD2	158747	broad.mit.edu	37	X	14901317	14901317	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14901317delA	uc004cwi.2	+						MOSPD2_uc004cwj.2_5'Flank	NM_152581	NP_689794			motile sperm domain containing 2							integral to membrane	structural molecule activity			lung(1)	1	Hepatocellular(33;0.183)																	---	---	---	---
PIR	8544	broad.mit.edu	37	X	15440456	15440456	+	Intron	DEL	A	-	-	rs34503974		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15440456delA	uc004cwu.2	-						PIR_uc004cwv.2_Intron	NM_003662	NP_003653			pirin						transcription from RNA polymerase II promoter	cytoplasm|nucleus	metal ion binding|protein binding|quercetin 2,3-dioxygenase activity|transcription cofactor activity			ovary(1)	1	Hepatocellular(33;0.183)																	---	---	---	---
TMEM27	57393	broad.mit.edu	37	X	15658105	15658105	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15658105delC	uc004cxc.1	-							NM_020665	NP_065716			transmembrane protein 27 precursor						proteolysis	integral to membrane	metallopeptidase activity|peptidyl-dipeptidase activity			ovary(1)	1	Hepatocellular(33;0.183)																	---	---	---	---
CA5BP	340591	broad.mit.edu	37	X	15709999	15709999	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15709999delT	uc011mir.1	+							NR_026551				RecName: Full=Putative carbonic anhydrase 5B-like protein; AltName: Full=CA-VB-like protein;												0																		---	---	---	---
GRPR	2925	broad.mit.edu	37	X	16142707	16142707	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16142707delA	uc004cxj.2	+							NM_005314	NP_005305			gastrin-releasing peptide receptor						cell proliferation	integral to plasma membrane	bombesin receptor activity			ovary(3)|lung(1)	4	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	16220478	16220479	+	IGR	INS	-	T	T	rs34654827		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16220478_16220479insT								GRPR (48838 upstream) : CTPS2 (385645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	16385457	16385457	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16385457delT								GRPR (213817 upstream) : CTPS2 (220667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	16532413	16532413	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16532413delA								GRPR (360773 upstream) : CTPS2 (73711 downstream)																																			---	---	---	---
CTPS2	56474	broad.mit.edu	37	X	16631726	16631726	+	Intron	DEL	T	-	-	rs74657383		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16631726delT	uc004cxk.2	-						CTPS2_uc004cxl.2_Intron|CTPS2_uc004cxm.2_Intron	NM_001144002	NP_001137474			cytidine triphosphate synthase II						glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine nucleotide biosynthetic process	cytosol	ATP binding|CTP synthase activity			ovary(1)	1	Hepatocellular(33;0.0997)																	---	---	---	---
RBBP7	5931	broad.mit.edu	37	X	16871713	16871713	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16871713delA	uc004cxt.2	-						RBBP7_uc004cxs.1_Intron|RBBP7_uc004cxu.2_Intron|RBBP7_uc010nez.2_3'UTR	NM_002893	NP_002884			retinoblastoma binding protein 7						cell proliferation|cellular heat acclimation|CenH3-containing nucleosome assembly at centromere|DNA replication|multicellular organismal development|negative regulation of cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex|NuRD complex	protein binding			upper_aerodigestive_tract(1)|ovary(1)	2	Hepatocellular(33;0.0997)																	---	---	---	---
REPS2	9185	broad.mit.edu	37	X	17006113	17006113	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17006113delA	uc004cxv.1	+						REPS2_uc004cxw.1_Intron|REPS2_uc011miw.1_Intron	NM_004726	NP_004717			RALBP1 associated Eps domain containing 2						epidermal growth factor receptor signaling pathway|protein complex assembly	cytoplasm	calcium ion binding|protein binding			skin(2)|central_nervous_system(1)	3	Hepatocellular(33;0.183)																	---	---	---	---
REPS2	9185	broad.mit.edu	37	X	17054811	17054811	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17054811delA	uc004cxv.1	+						REPS2_uc004cxw.1_Intron|REPS2_uc011miw.1_Intron	NM_004726	NP_004717			RALBP1 associated Eps domain containing 2						epidermal growth factor receptor signaling pathway|protein complex assembly	cytoplasm	calcium ion binding|protein binding			skin(2)|central_nervous_system(1)	3	Hepatocellular(33;0.183)																	---	---	---	---
NHS	4810	broad.mit.edu	37	X	17413303	17413303	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17413303delA	uc004cxx.2	+						NHS_uc011mix.1_Intron	NM_198270	NP_938011			Nance-Horan syndrome protein isoform 1							nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)																	---	---	---	---
NHS	4810	broad.mit.edu	37	X	17633540	17633540	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17633540delT	uc004cxx.2	+						NHS_uc011mix.1_Intron	NM_198270	NP_938011			Nance-Horan syndrome protein isoform 1							nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	17885844	17885845	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17885844_17885845delCA								RAI2 (6387 upstream) : BEND2 (295208 downstream)																																			---	---	---	---
BEND2	139105	broad.mit.edu	37	X	18195983	18195983	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18195983delT	uc004cyj.3	-						BEND2_uc010nfb.2_Intron	NM_153346	NP_699177			BEN domain containing 2											ovary(3)|kidney(1)|central_nervous_system(1)	5																		---	---	---	---
BEND2	139105	broad.mit.edu	37	X	18221376	18221376	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18221376delA	uc004cyj.3	-						BEND2_uc010nfb.2_Intron	NM_153346	NP_699177			BEN domain containing 2											ovary(3)|kidney(1)|central_nervous_system(1)	5																		---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18490900	18490901	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18490900_18490901delTT	uc004cym.2	+						CDKL5_uc004cyn.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
RS1	6247	broad.mit.edu	37	X	18659978	18659979	+	3'UTR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18659978_18659979delAA	uc004cyo.2	-	6					CDKL5_uc004cym.2_Intron|CDKL5_uc004cyn.2_Intron	NM_000330	NP_000321			X-linked juvenile retinoschisis protein						cell adhesion|multicellular organismal development|response to stimulus|visual perception	extracellular space				ovary(2)	2	Hepatocellular(33;0.183)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18665265	18665265	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18665265delT	uc004cym.2	+						CDKL5_uc004cyn.2_Intron|RS1_uc004cyo.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	18878903	18878903	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18878903delA								PPEF1 (32871 upstream) : PHKA2 (31514 downstream)																																			---	---	---	---
GPR64	10149	broad.mit.edu	37	X	19039073	19039073	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19039073delA	uc004cyx.2	-						GPR64_uc004cyy.2_Intron|GPR64_uc004cyz.2_Intron|GPR64_uc004czb.2_Intron|GPR64_uc004czc.2_Intron|GPR64_uc004czd.2_Intron|GPR64_uc004cze.2_Intron|GPR64_uc004czf.2_Intron|GPR64_uc004cza.2_Intron|GPR64_uc004cyw.2_Intron|GPR64_uc010nfj.2_Intron	NM_001079858	NP_001073327			G protein-coupled receptor 64 isoform 1						neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	19358383	19358383	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19358383delG								GPR64 (217706 upstream) : PDHA1 (3628 downstream)																																			---	---	---	---
SH3KBP1	30011	broad.mit.edu	37	X	19569668	19569669	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19569668_19569669insT	uc004czm.2	-						SH3KBP1_uc011mje.1_Intron|SH3KBP1_uc011mjf.1_Intron|SH3KBP1_uc004czl.2_Intron|SH3KBP1_uc010nfm.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																		---	---	---	---
SH3KBP1	30011	broad.mit.edu	37	X	19808742	19808742	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19808742delT	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																		---	---	---	---
SH3KBP1	30011	broad.mit.edu	37	X	19908076	19908076	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19908076delT	uc004czm.2	-							NM_031892	NP_114098			SH3-domain kinase binding protein 1 isoform a						apoptosis|cell-cell signaling|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytoplasmic vesicle membrane|cytoskeleton|cytosol|focal adhesion|nucleus|synapse|synaptosome	SH3 domain binding				0																		---	---	---	---
MAP7D2	256714	broad.mit.edu	37	X	20037144	20037144	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20037144delT	uc004czr.1	-						MAP7D2_uc004czq.1_Intron|MAP7D2_uc011mji.1_Intron|MAP7D2_uc010nfo.1_Intron|MAP7D2_uc011mjj.1_Intron	NM_152780	NP_689993			MAP7 domain containing 2											ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	20447848	20447848	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20447848delT								RPS6KA3 (162325 upstream) : CNKSR2 (945132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	21059975	21059975	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21059975delT								RPS6KA3 (774452 upstream) : CNKSR2 (333005 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	21313638	21313638	+	IGR	DEL	T	-	-	rs77614660		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21313638delT								None (None upstream) : CNKSR2 (79342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	21384873	21384874	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21384873_21384874delAA								None (None upstream) : CNKSR2 (8106 downstream)																																			---	---	---	---
CNKSR2	22866	broad.mit.edu	37	X	21444882	21444882	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21444882delA	uc004czx.1	+						CNKSR2_uc004czw.2_Intron|CNKSR2_uc011mjn.1_Intron|CNKSR2_uc011mjo.1_Intron	NM_014927	NP_055742			connector enhancer of kinase suppressor of Ras						regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)|lung(1)	2																		---	---	---	---
CNKSR2	22866	broad.mit.edu	37	X	21571470	21571470	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21571470delT	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																		---	---	---	---
SMPX	23676	broad.mit.edu	37	X	21749681	21749688	+	Intron	DEL	TATGTGTA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21749681_21749688delTATGTGTA	uc004daa.2	-							NM_014332	NP_055147			small muscle protein, X-linked						striated muscle contraction						0																		---	---	---	---
SMPX	23676	broad.mit.edu	37	X	21772423	21772423	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21772423delA	uc004daa.2	-							NM_014332	NP_055147			small muscle protein, X-linked						striated muscle contraction						0																		---	---	---	---
SMS	6611	broad.mit.edu	37	X	21989957	21989957	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21989957delT	uc004dag.2	+						SMS_uc011mjq.1_Intron|SMS_uc004daf.1_Intron	NM_004595	NP_004586			spermine synthase						methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)													---	---	---	---
PHEX	5251	broad.mit.edu	37	X	22253951	22253951	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22253951delT	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	22621216	22621216	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22621216delT								ZNF645 (328642 upstream) : DDX53 (396871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	23285756	23285756	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23285756delA								DDX53 (265552 upstream) : PTCHD1 (67229 downstream)																																			---	---	---	---
PTCHD1	139411	broad.mit.edu	37	X	23390299	23390301	+	Intron	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23390299_23390301delTTT	uc004dal.3	+						PTCHD1_uc010nfu.1_Intron	NM_173495	NP_775766			patched domain containing 1						cognition|smoothened signaling pathway	integral to membrane|plasma membrane	hedgehog receptor activity			ovary(4)|kidney(1)|skin(1)	6																		---	---	---	---
PTCHD1	139411	broad.mit.edu	37	X	23397692	23397692	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23397692delT	uc004dal.3	+						PTCHD1_uc010nfu.1_Intron	NM_173495	NP_775766			patched domain containing 1						cognition|smoothened signaling pathway	integral to membrane|plasma membrane	hedgehog receptor activity			ovary(4)|kidney(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	23823857	23823857	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23823857delT								SAT1 (19532 upstream) : APOO (27624 downstream)																																			---	---	---	---
EIF2S3	1968	broad.mit.edu	37	X	24075730	24075730	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24075730delT	uc004dbc.2	+							NM_001415	NP_001406			eukaryotic translation initiation factor 2,							cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			lung(1)	1																		---	---	---	---
EIF2S3	1968	broad.mit.edu	37	X	24087494	24087496	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24087494_24087496delAAA	uc004dbc.2	+							NM_001415	NP_001406			eukaryotic translation initiation factor 2,							cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			lung(1)	1																		---	---	---	---
POLA1	5422	broad.mit.edu	37	X	24830852	24830853	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24830852_24830853insA	uc004dbl.2	+	29	3173_3174	c.3150_3151insA	c.(3148-3153)CTGAAAfs	p.L1050fs		NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1	1050_1051	Poly-Lys.				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	25035614	25035615	+	IGR	DEL	CT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25035614_25035615delCT								ARX (1549 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	25146304	25146304	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25146304delT								ARX (112239 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	25340989	25340989	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25340989delT								ARX (306924 upstream) : MAGEB18 (815474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	26627619	26627622	+	IGR	DEL	AAAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26627619_26627622delAAAA								VENTXP1 (48451 upstream) : SMEK3P (850706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	27248766	27248766	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27248766delT	uc004dbt.2	-											Homo sapiens cDNA clone IMAGE:4824334.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	27317742	27317742	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27317742delT	uc004dbt.2	-											Homo sapiens cDNA clone IMAGE:4824334.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	27465740	27465740	+	IGR	DEL	T	-	-	rs111416565		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27465740delT								VENTXP1 (886572 upstream) : SMEK3P (12588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	28472770	28472773	+	IGR	DEL	CTGA	-	-	rs66796974		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:28472770_28472773delCTGA								DCAF8L1 (473204 upstream) : IL1RAPL1 (132908 downstream)																																			---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	29062211	29062211	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29062211delT	uc004dby.2	+							NM_014271	NP_055086			interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5																		---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	29873837	29873837	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29873837delT	uc004dby.2	+							NM_014271	NP_055086			interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	30161235	30161235	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30161235delT								IL1RAPL1 (187218 upstream) : MAGEB2 (72440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	30349996	30349996	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30349996delA								NR0B1 (22501 upstream) : CXorf21 (226945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	30575906	30575906	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30575906delT								NR0B1 (248411 upstream) : CXorf21 (1035 downstream)																																			---	---	---	---
GK	2710	broad.mit.edu	37	X	30714853	30714853	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30714853delA	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																		---	---	---	---
DMD	1756	broad.mit.edu	37	X	31258320	31258320	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31258320delA	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	31280855	31280855	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31280855delT	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	32063200	32063200	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32063200delT	uc004dda.1	-						DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.1_Intron|DMD_uc010ngn.1_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	32475179	32475180	+	Intron	DEL	AA	-	-	rs112428143		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32475179_32475180delAA	uc004dda.1	-						DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.1_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	32826676	32826676	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32826676delA	uc004dda.1	-						DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.1_Intron|DMD_uc004ddf.2_Intron|DMD_uc010ngp.1_Intron|DMD_uc010ngq.1_Intron|DMD_uc010ngr.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	33222591	33222591	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:33222591delT	uc004dda.1	-						DMD_uc004ddb.1_Intron|DMD_uc010ngo.1_Intron|DMD_uc004ddf.2_Intron|DMD_uc010ngr.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	34415972	34415972	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34415972delT								FAM47A (265544 upstream) : TMEM47 (229211 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	35157040	35157041	+	IGR	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35157040_35157041insC								FAM47B (194006 upstream) : MAGEB16 (659418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	35243470	35243470	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35243470delA								FAM47B (280436 upstream) : MAGEB16 (572989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	35607408	35607408	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35607408delT								FAM47B (644374 upstream) : MAGEB16 (209051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	36535808	36535808	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36535808delT								CXorf30 (132375 upstream) : FAM47C (490662 downstream)																																			---	---	---	---
LANCL3	347404	broad.mit.edu	37	X	37497303	37497304	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37497303_37497304delGA	uc011mkd.1	+						LANCL3_uc004ddp.1_Intron	NM_198511	NP_940913			LanC lantibiotic synthetase component C-like 3								catalytic activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	37792659	37792659	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37792659delA								DYNLT3 (85770 upstream) : CXorf27 (57411 downstream)																																			---	---	---	---
RPGR	6103	broad.mit.edu	37	X	38144668	38144668	+	3'UTR	DEL	T	-	-	rs66997072		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38144668delT	uc004ded.1	-	15					RPGR_uc004deb.2_Intron|RPGR_uc004dea.2_Intron|RPGR_uc004dec.2_Intron	NM_001034853	NP_001030025			retinitis pigmentosa GTPase regulator isoform C						intracellular protein transport|response to stimulus|visual perception	Golgi apparatus|photoreceptor outer segment	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	38569406	38569406	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38569406delT								TSPAN7 (21235 upstream) : MID1IP1 (91279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	38612474	38612475	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38612474_38612475insA								TSPAN7 (64303 upstream) : MID1IP1 (48210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	38813202	38813203	+	IGR	INS	-	T	T	rs143292985		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38813202_38813203insT								MID1IP1 (147421 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	38832933	38832933	+	IGR	DEL	T	-	-	rs75145514		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38832933delT								MID1IP1 (167152 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	39069471	39069474	+	IGR	DEL	TAAC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39069471_39069474delTAAC								MID1IP1 (403690 upstream) : BCOR (841027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	39758962	39758962	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39758962delA								None (None upstream) : BCOR (151539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	39859326	39859326	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39859326delA								None (None upstream) : BCOR (51175 downstream)																																			---	---	---	---
BCOR	54880	broad.mit.edu	37	X	39930434	39930435	+	Intron	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39930434_39930435delAA	uc004den.3	-						BCOR_uc004dep.3_Intron|BCOR_uc004deo.3_Intron|BCOR_uc004dem.3_Intron	NM_001123385	NP_001116857			BCL-6 interacting corepressor isoform c						heart development|histone H2A monoubiquitination|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	40637393	40637394	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40637393_40637394delTT								MED14 (42257 upstream) : LOC100132831 (53076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	41182355	41182355	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41182355delG								USP9X (86525 upstream) : DDX3X (10296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	41252899	41252899	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41252899delT								DDX3X (29175 upstream) : NYX (53814 downstream)																																			---	---	---	---
NYX	60506	broad.mit.edu	37	X	41313574	41313574	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	41675063	41675063	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41675063delA	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	42662683	42662683	+	IGR	DEL	A	-	-	rs112304734		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42662683delA								PPP1R2P9 (25197 upstream) : MAOA (852726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	43013020	43013020	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43013020delA								PPP1R2P9 (375534 upstream) : MAOA (502389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	43035869	43035869	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43035869delT	uc004dfw.1	+											Homo sapiens cDNA FLJ31543 fis, clone NT2RI2000841.																														---	---	---	---
MAOA	4128	broad.mit.edu	37	X	43593380	43593381	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43593380_43593381delTT	uc004dfy.2	+						MAOA_uc011mkw.1_Intron	NM_000240	NP_000231			monoamine oxidase A						behavior|neurotransmitter biosynthetic process|neurotransmitter catabolic process|neurotransmitter secretion|xenobiotic metabolic process	integral to membrane|mitochondrial outer membrane	primary amine oxidase activity|protein binding			breast(2)|ovary(1)	3					Almotriptan(DB00918)|Carbidopa(DB00190)|Clonazepam(DB01068)|Dopamine(DB00988)|Fluvoxamine(DB00176)|Ginkgo biloba(DB01381)|Imipramine(DB00458)|Isocarboxazid(DB01247)|Levodopa(DB01235)|Linezolid(DB00601)|Lorazepam(DB00186)|Moclobemide(DB01171)|Nicotine(DB00184)|Norepinephrine(DB00368)|Phenelzine(DB00780)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pseudoephedrine(DB00852)|Rasagiline(DB01367)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	43617792	43617792	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43617792delT								MAOA (11725 upstream) : MAOB (8066 downstream)																																			---	---	---	---
EFHC2	80258	broad.mit.edu	37	X	44183814	44183815	+	Intron	DEL	AC	-	-	rs113984894	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44183814_44183815delAC	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																		---	---	---	---
EFHC2	80258	broad.mit.edu	37	X	44185143	44185143	+	Intron	DEL	T	-	-	rs113149319		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44185143delT	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																		---	---	---	---
FUNDC1	139341	broad.mit.edu	37	X	44386290	44386290	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44386290delA	uc004dgc.2	-							NM_173794	NP_776155			FUN14 domain containing 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	44476759	44476759	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44476759delA								FUNDC1 (74538 upstream) : DUSP21 (226490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	44679716	44679716	+	IGR	DEL	A	-	-	rs113431422		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44679716delA								FUNDC1 (277495 upstream) : DUSP21 (23533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	44711348	44711350	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44711348_44711350delTTT								DUSP21 (7216 upstream) : KDM6A (21073 downstream)																																			---	---	---	---
KDM6A	7403	broad.mit.edu	37	X	44938317	44938317	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44938317delA	uc004dge.3	+						KDM6A_uc010nhk.2_Intron|KDM6A_uc011mkz.1_Intron|KDM6A_uc011mla.1_Intron|KDM6A_uc011mlb.1_Intron|KDM6A_uc011mlc.1_Intron|KDM6A_uc011mld.1_Intron	NM_021140	NP_066963			ubiquitously transcribed tetratricopeptide						histone H3-K4 methylation		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84								D|N|F|S		renal|oesophageal SCC|MM								---	---	---	---
Unknown	0	broad.mit.edu	37	X	46027597	46027598	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46027597_46027598delTG								MIR222 (421067 upstream) : ZNF673 (279026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	46169527	46169527	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46169527delT								MIR222 (562997 upstream) : ZNF673 (137097 downstream)																																			---	---	---	---
PHF16	9767	broad.mit.edu	37	X	46866367	46866367	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46866367delT	uc004dgx.2	+						PHF16_uc004dgy.2_Intron	NM_001077445	NP_001070913			PHD finger protein 16						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0																		---	---	---	---
PHF16	9767	broad.mit.edu	37	X	46884358	46884358	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46884358delT	uc004dgx.2	+						PHF16_uc004dgy.2_Intron	NM_001077445	NP_001070913			PHD finger protein 16						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0																		---	---	---	---
PHF16	9767	broad.mit.edu	37	X	46898057	46898057	+	Intron	DEL	A	-	-	rs143579071		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46898057delA	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																		---	---	---	---
ZNF157	7712	broad.mit.edu	37	X	47227043	47227045	+	5'Flank	DEL	AAA	-	-	rs35308257		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47227043_47227045delAAA	uc004dhr.1	+							NM_003446	NP_003437			zinc finger protein 157						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
CFP	5199	broad.mit.edu	37	X	47489004	47489004	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47489004delC	uc004dig.3	-	2	272	c.146delG	c.(145-147)GGTfs	p.G49fs	CFP_uc004dih.2_Frame_Shift_Del_p.G49fs|CFP_uc004dii.1_5'UTR|CFP_uc010nhu.2_Frame_Shift_Del_p.G49fs	NM_001145252	NP_001138724	P27918	PROP_HUMAN	complement factor properdin precursor	49					complement activation, alternative pathway|defense response to bacterium	extracellular space				breast(2)|lung(1)	3																		---	---	---	---
UXT	8409	broad.mit.edu	37	X	47512680	47512680	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47512680delA	uc004din.2	-						ELK1_uc004dik.3_5'Flank|ELK1_uc010nhv.2_5'Flank|ELK1_uc010nhw.2_5'Flank|ELK1_uc004dil.3_5'Flank|UXT_uc004dim.2_Intron	NM_004182	NP_004173			ubiquitously-expressed transcript isoform 2						centrosome organization|mitochondrion transport along microtubule|protein folding	centrosome|nucleus|prefoldin complex	beta-tubulin binding|microtubule binding|unfolded protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	47578336	47578336	+	Intron	DEL	G	-	-	rs5953088	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47578336delG	uc004dio.1	+											Homo sapiens cDNA FLJ36789 fis, clone ADRGL2004459.																														---	---	---	---
ZNF81	347344	broad.mit.edu	37	X	47746001	47746002	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47746001_47746002delTT	uc010nhy.1	+							NM_007137	NP_009068			zinc finger protein 81							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(315;0.0973)																---	---	---	---
RBM3	5935	broad.mit.edu	37	X	48435397	48435397	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48435397delT	uc004dkf.1	+						RBM3_uc004dkd.1_Intron|RBM3_uc004dkg.2_Intron	NM_006743	NP_006734			RNA binding motif protein 3						positive regulation of translation	dendrite|nucleus	nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
WDR13	64743	broad.mit.edu	37	X	48462533	48462533	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48462533delA	uc004dkh.1	+						WDR13_uc004dki.1_Intron|WDR13_uc004dkj.1_Intron|WDR13_uc004dkk.1_Intron|WDR13_uc004dkl.3_Intron	NM_017883	NP_060353			WD repeat domain 13 protein							cytoplasm|nucleus				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	48721676	48721677	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48721676_48721677delTT								PCSK1N (27716 upstream) : TIMM17B (29055 downstream)																																			---	---	---	---
KCND1	3750	broad.mit.edu	37	X	48827408	48827408	+	5'UTR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48827408delG	uc004dlx.1	-	1					KCND1_uc004dlw.1_5'Flank	NM_004979	NP_004970			potassium voltage-gated channel, Shal-related							voltage-gated potassium channel complex	metal ion binding|voltage-gated potassium channel activity			ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	48878553	48878554	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48878553_48878554delAA								GRIPAP1 (19878 upstream) : TFE3 (7688 downstream)																																			---	---	---	---
PPP1R3F	89801	broad.mit.edu	37	X	49127514	49127514	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49127514delT	uc004dnh.1	+						PPP1R3F_uc011mnd.1_Intron|PPP1R3F_uc004dni.2_Intron	NM_033215	NP_149992			protein phosphatase 1, regulatory (inhibitor)							integral to membrane				ovary(2)|skin(1)	3	Ovarian(276;0.236)																	---	---	---	---
GAGE10	643832	broad.mit.edu	37	X	49158062	49158062	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49158062delT	uc010nir.1	+							NM_001098413	NP_001091883			G antigen 10												0	Ovarian(276;0.236)																	---	---	---	---
SHROOM4	57477	broad.mit.edu	37	X	50382313	50382314	+	Intron	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50382313_50382314delGA	uc004dpe.2	-						SHROOM4_uc004dpd.3_Intron|SHROOM4_uc004dpf.1_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	50985873	50985873	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50985873delT								BMP15 (326267 upstream) : NUDT10 (89210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	51110604	51110604	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51110604delT								NUDT10 (30235 upstream) : NUDT11 (122268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	51401979	51401981	+	IGR	DEL	TTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51401979_51401981delTTT								NUDT11 (162520 upstream) : GSPT2 (84516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	51663174	51663174	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51663174delG								MAGED1 (17726 upstream) : MAGED4 (141751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	52886649	52886649	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:52886649delA								XAGE5 (39327 upstream) : XAGE3 (4911 downstream)																																			---	---	---	---
KDM5C	8242	broad.mit.edu	37	X	53223980	53223980	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53223980delC	uc004drz.2	-						KDM5C_uc011moc.1_Intron|KDM5C_uc011mod.1_Intron|KDM5C_uc004dsa.2_Intron	NM_004187	NP_004178			jumonji, AT rich interactive domain 1C isoform						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18								N|F|S		clear cell renal carcinoma								---	---	---	---
KDM5C	8242	broad.mit.edu	37	X	53227508	53227509	+	Intron	INS	-	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53227508_53227509insC	uc004drz.2	-						KDM5C_uc011moc.1_Intron|KDM5C_uc011mod.1_Intron|KDM5C_uc004dsa.2_Intron	NM_004187	NP_004178			jumonji, AT rich interactive domain 1C isoform						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18								N|F|S		clear cell renal carcinoma								---	---	---	---
SMC1A	8243	broad.mit.edu	37	X	53418379	53418379	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53418379delA	uc004dsg.2	-						SMC1A_uc011moe.1_Intron	NM_006306	NP_006297			structural maintenance of chromosomes 1A						cell cycle checkpoint|cell division|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic sister chromatid cohesion|mitotic spindle organization|negative regulation of DNA endoreduplication|nuclear mRNA splicing, via spliceosome|response to radiation|signal transduction in response to DNA damage	cohesin core heterodimer|condensed chromosome kinetochore|condensed nuclear chromosome|cytoplasm|meiotic cohesin complex|nucleoplasm	ATP binding|chromatin binding|microtubule motor activity|protein heterodimerization activity			ovary(5)|central_nervous_system(1)	6																		---	---	---	---
HUWE1	10075	broad.mit.edu	37	X	53650325	53650325	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53650325delA	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																		---	---	---	---
FAM120C	54954	broad.mit.edu	37	X	54099268	54099270	+	3'UTR	DEL	CTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54099268_54099270delCTT	uc004dsz.3	-	16					FAM120C_uc011moh.1_3'UTR	NM_017848	NP_060318			hypothetical protein LOC54954											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	54747645	54747645	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54747645delT								GNL3L (155672 upstream) : ITIH5L (27687 downstream)																																			---	---	---	---
APEX2	27301	broad.mit.edu	37	X	55032913	55032914	+	Intron	INS	-	TC	TC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55032913_55032914insTC	uc004dtz.2	+						APEX2_uc011mom.1_Intron	NM_014481	NP_055296			apurinic/apyrimidinic endonuclease 2						cell cycle|DNA recombination|DNA repair	nucleus	DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|endonuclease activity|exonuclease activity|zinc ion binding			breast(1)	1													Other_BER_factors					---	---	---	---
ALAS2	212	broad.mit.edu	37	X	55040196	55040196	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55040196delT	uc004dua.3	-						ALAS2_uc004dub.3_Intron|ALAS2_uc004dud.3_Intron	NM_000032	NP_000023			5-aminolevulinate synthase 2 isoform a						cellular iron ion homeostasis|erythrocyte differentiation|heme biosynthetic process|hemoglobin biosynthetic process|oxygen homeostasis|response to hypoxia	mitochondrial inner membrane|mitochondrial matrix	5-aminolevulinate synthase activity|coenzyme binding|glycine binding|protein binding|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(1)	1					Glycine(DB00145)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	55689694	55689694	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55689694delG								FOXR2 (37937 upstream) : RRAGB (54416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	57221391	57221392	+	IGR	DEL	TG	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57221391_57221392delTG								SPIN2A (57333 upstream) : FAAH2 (91718 downstream)																																			---	---	---	---
FAAH2	158584	broad.mit.edu	37	X	57365333	57365333	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57365333delA	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	57703526	57703526	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57703526delT								ZXDB (79620 upstream) : ZXDA (230672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	58068955	58068957	+	IGR	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:58068955_58068957delAAA								ZXDA (131888 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61714751	61714751	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	61759297	61759297	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61759297delC								None (None upstream) : SPIN4 (807811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	63243165	63243165	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:63243165delC								MIR1468 (237198 upstream) : FAM123B (161833 downstream)														p.0?(2)																					---	---	---	---
MTMR8	55613	broad.mit.edu	37	X	63542050	63542050	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:63542050delT	uc004dvs.2	-						MTMR8_uc011mou.1_Intron	NM_017677	NP_060147			myotubularin related protein 8							nuclear envelope	protein tyrosine phosphatase activity			ovary(2)|breast(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	64352425	64352425	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64352425delA								ZC4H2 (97832 upstream) : ZC3H12B (356281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	64768038	64768038	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64768038delT								LAS1L (13371 upstream) : MSN (119473 downstream)																																			---	---	---	---
MSN	4478	broad.mit.edu	37	X	64952923	64952923	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64952923delA	uc004dwf.2	+							NM_002444	NP_002435			moesin						leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking	apical plasma membrane|cytoskeleton|extrinsic to membrane|microvillus membrane|nucleolus	cell adhesion molecule binding|receptor binding|structural constituent of cytoskeleton		MSN/ALK(6)	haematopoietic_and_lymphoid_tissue(6)|ovary(3)|lung(1)	10								T	ALK	ALCL								---	---	---	---
HEPH	9843	broad.mit.edu	37	X	65426913	65426913	+	Intron	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65426913delC	uc011moz.1	+						HEPH_uc004dwn.2_Intron|HEPH_uc004dwo.2_Intron|HEPH_uc010nkr.2_Intron|HEPH_uc011mpa.1_Intron|HEPH_uc010nks.2_Intron	NM_138737	NP_620074			hephaestin isoform a						cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9																		---	---	---	---
EDA2R	60401	broad.mit.edu	37	X	65854342	65854342	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65854342delT	uc004dws.2	-						EDA2R_uc011mpb.1_Intron|EDA2R_uc011mpc.1_Intron|EDA2R_uc010nkt.1_Intron	NM_021783	NP_068555			X-linked ectodysplasin receptor						cell differentiation|embryo development|epidermis development|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity	integral to plasma membrane	tumor necrosis factor receptor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	66086988	66086988	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66086988delG								EDA2R (227880 upstream) : AR (676886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	66099300	66099300	+	IGR	DEL	T	-	-	rs113187644		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66099300delT								EDA2R (240192 upstream) : AR (664574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	66286778	66286779	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66286778_66286779insT								EDA2R (427670 upstream) : AR (477095 downstream)																																			---	---	---	---
AR	367	broad.mit.edu	37	X	66892335	66892335	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66892335delT	uc004dwu.1	+						AR_uc011mpd.1_Intron|AR_uc011mpe.1_Intron|AR_uc011mpf.1_Intron|AR_uc004dwv.1_Intron	NM_000044	NP_000035			androgen receptor isoform 1						cell death|cell growth|cell proliferation|cell-cell signaling|negative regulation of apoptosis|negative regulation of integrin biosynthetic process|positive regulation of cell proliferation|positive regulation of integrin biosynthetic process|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|regulation of establishment of protein localization in plasma membrane|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transport	cytoplasm|nuclear chromatin|nucleoplasm	androgen binding|androgen receptor activity|beta-catenin binding|enzyme binding|ligand-regulated transcription factor activity|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(3)|lung(2)|breast(2)|central_nervous_system(1)	8	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone(DB04839)|Dromostanolone(DB00858)|Finasteride(DB01216)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Nandrolone(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Testosterone(DB00624)									Androgen_Insensitivity_Syndrome				---	---	---	---
AR	367	broad.mit.edu	37	X	66903718	66903720	+	Intron	DEL	AAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66903718_66903720delAAA	uc004dwu.1	+						AR_uc011mpd.1_Intron|AR_uc011mpe.1_Intron|AR_uc011mpf.1_Intron|AR_uc004dwv.1_Intron	NM_000044	NP_000035			androgen receptor isoform 1						cell death|cell growth|cell proliferation|cell-cell signaling|negative regulation of apoptosis|negative regulation of integrin biosynthetic process|positive regulation of cell proliferation|positive regulation of integrin biosynthetic process|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|regulation of establishment of protein localization in plasma membrane|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transport	cytoplasm|nuclear chromatin|nucleoplasm	androgen binding|androgen receptor activity|beta-catenin binding|enzyme binding|ligand-regulated transcription factor activity|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(3)|lung(2)|breast(2)|central_nervous_system(1)	8	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone(DB04839)|Dromostanolone(DB00858)|Finasteride(DB01216)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Nandrolone(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Testosterone(DB00624)									Androgen_Insensitivity_Syndrome				---	---	---	---
OPHN1	4983	broad.mit.edu	37	X	67552078	67552078	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67552078delT	uc004dww.3	-						OPHN1_uc011mpg.1_Intron|OPHN1_uc004dwx.2_Intron	NM_002547	NP_002538			oligophrenin 1						axon guidance|endocytosis|filopodium assembly|small GTPase mediated signal transduction|substrate-dependent cell migration, cell extension	axon|cell junction|cytosol|dendritic spine|synapse	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	67667568	67667569	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67667568_67667569delAA								OPHN1 (14269 upstream) : YIPF6 (51317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	67985848	67985848	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67985848delT								STARD8 (40171 upstream) : EFNB1 (62992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	68581533	68581533	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68581533delA								PJA1 (196193 upstream) : FAM155B (143545 downstream)																																			---	---	---	---
EDA	1896	broad.mit.edu	37	X	68979278	68979278	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68979278delA	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																		---	---	---	---
DGAT2L6	347516	broad.mit.edu	37	X	69422993	69422994	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69422993_69422994insT	uc004dxx.1	+							NM_198512	NP_940914			diacylglycerol O-acyltransferase 2-like 6						lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	69470797	69470797	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69470797delT								AWAT1 (10287 upstream) : P2RY4 (7219 downstream)																																			---	---	---	---
KIF4A	24137	broad.mit.edu	37	X	69521665	69521666	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69521665_69521666insT	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																		---	---	---	---
KIF4A	24137	broad.mit.edu	37	X	69600158	69600158	+	Intron	DEL	A	-	-	rs75758779		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69600158delA	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																		---	---	---	---
TEX11	56159	broad.mit.edu	37	X	69811475	69811475	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69811475delA	uc004dyl.2	-						TEX11_uc004dyk.2_Intron|TEX11_uc004dym.2_Intron	NM_001003811	NP_001003811			testis expressed sequence 11 isoform 1								protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	70309654	70309654	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70309654delG								SNX12 (21423 upstream) : FOXO4 (6372 downstream)																																			---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70596517	70596517	+	Intron	DEL	A	-	-	rs112839503		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70596517delA	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron	NM_138923	NP_620278			TBP-associated factor 1 isoform 2						G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)																---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70639873	70639874	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70639873_70639874delTT	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron|TAF1_uc004dzv.3_Intron|TAF1_uc010nld.1_Intron|TAF1_uc010nle.1_Intron|TAF1_uc010nlf.1_Intron|TAF1_uc004dzx.2_Intron|TAF1_uc004dzy.2_Intron	NM_138923	NP_620278			TBP-associated factor 1 isoform 2						G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)																---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70644161	70644162	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70644161_70644162insA	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron|TAF1_uc004dzv.3_Intron|TAF1_uc010nld.1_Intron|TAF1_uc010nle.1_Intron|TAF1_uc010nlf.1_Intron|TAF1_uc004dzx.2_Intron|TAF1_uc004dzy.2_Intron|TAF1_uc004dzw.1_Intron	NM_138923	NP_620278			TBP-associated factor 1 isoform 2						G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	71072936	71072936	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71072936delA								BCYRN1 (123974 upstream) : NHSL2 (58002 downstream)																																			---	---	---	---
ERCC6L	54821	broad.mit.edu	37	X	71454439	71454440	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71454439_71454440delTT	uc004eaq.1	-						PIN4_uc004eao.1_Intron|ERCC6L_uc004eap.1_Intron	NM_017669	NP_060139			excision repair protein ERCC6-like						cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol	ATP binding|DNA binding|helicase activity|protein binding			ovary(3)	3	Renal(35;0.156)																	---	---	---	---
HDAC8	55869	broad.mit.edu	37	X	71710648	71710648	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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)													---	---	---	---
CHIC1	53344	broad.mit.edu	37	X	72809971	72809972	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72809971_72809972insT	uc004ebk.3	+						CHIC1_uc010nlo.2_Intron|CHIC1_uc011mql.1_Intron|CHIC1_uc004ebl.3_Intron	NM_001039840	NP_001034929			cysteine-rich hydrophobic domain 1							cytoplasmic membrane-bounded vesicle|plasma membrane					0	Renal(35;0.156)																	---	---	---	---
TSIX	9383	broad.mit.edu	37	X	73037545	73037546	+	RNA	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73037545_73037546delAA	uc004ebn.2	+	1		c.25506_25507delAA				NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0																		---	---	---	---
XIST	7503	broad.mit.edu	37	X	73049071	73049071	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73049071delA	uc004ebm.1	-							NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	73629971	73629971	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73629971delA								ZCCHC13 (105103 upstream) : SLC16A2 (11114 downstream)																																			---	---	---	---
KIAA2022	340533	broad.mit.edu	37	X	74036939	74036939	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74036939delT	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	74441045	74441045	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74441045delT								ABCB7 (64913 upstream) : UPRT (52916 downstream)																																			---	---	---	---
UPRT	139596	broad.mit.edu	37	X	74504538	74504538	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74504538delG	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-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	75786464	75786464	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75786464delT								MAGEE1 (134720 upstream) : MIR384 (353234 downstream)																																			---	---	---	---
ATRX	546	broad.mit.edu	37	X	76819172	76819173	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76819172_76819173delGT	uc004ecp.3	-						ATRX_uc004ecq.3_Intron|ATRX_uc004eco.3_Intron	NM_000489	NP_000480			transcriptional regulator ATRX isoform 1						DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						---	---	---	---
Unknown	0	broad.mit.edu	37	X	79545335	79545335	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79545335delT	uc004edk.1	-											Homo sapiens cDNA FLJ26841 fis, clone PRS07619.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	79916096	79916096	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79916096delT								FAM46D (215286 upstream) : BRWD3 (15587 downstream)																																			---	---	---	---
BRWD3	254065	broad.mit.edu	37	X	79947491	79947491	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79947491delA	uc004edt.2	-						BRWD3_uc010nmi.1_Intron|BRWD3_uc004edo.2_Intron|BRWD3_uc004edp.2_Intron|BRWD3_uc004edq.2_Intron|BRWD3_uc010nmj.1_Intron|BRWD3_uc004edr.2_Intron|BRWD3_uc004eds.2_Intron|BRWD3_uc004edu.2_Intron|BRWD3_uc004edv.2_Intron|BRWD3_uc004edw.2_Intron|BRWD3_uc004edx.2_Intron|BRWD3_uc004edy.2_Intron|BRWD3_uc004edz.2_Intron|BRWD3_uc004eea.2_Intron|BRWD3_uc004eeb.2_Intron	NM_153252	NP_694984			bromodomain and WD repeat domain containing 3											ovary(4)	4																		---	---	---	---
BRWD3	254065	broad.mit.edu	37	X	80047491	80047491	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80047491delT	uc004edt.2	-						BRWD3_uc004edo.2_Intron|BRWD3_uc004edp.2_Intron|BRWD3_uc004edq.2_Intron|BRWD3_uc010nmj.1_Intron|BRWD3_uc004edr.2_Intron|BRWD3_uc004eds.2_Intron|BRWD3_uc004edu.2_Intron|BRWD3_uc004edv.2_Intron|BRWD3_uc004edw.2_Intron|BRWD3_uc004edx.2_Intron|BRWD3_uc004edy.2_Intron|BRWD3_uc004edz.2_Intron|BRWD3_uc004eea.2_Intron|BRWD3_uc004eeb.2_Intron	NM_153252	NP_694984			bromodomain and WD repeat domain containing 3											ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	80304754	80304754	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80304754delT								BRWD3 (239521 upstream) : HMGN5 (64446 downstream)																																			---	---	---	---
HMGN5	79366	broad.mit.edu	37	X	80395434	80395434	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80395434delT	uc004eee.1	-							NM_030763	NP_110390			high-mobility group nucleosome binding domain 5						chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleolus	chromatin binding|DNA binding			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	80587788	80587788	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80587788delT								SH3BGRL (33746 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	81962690	81962691	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:81962690_81962691delAA								None (None upstream) : POU3F4 (800578 downstream)																																			---	---	---	---
RPS6KA6	27330	broad.mit.edu	37	X	83403149	83403149	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83403149delA	uc004eej.1	-						RPS6KA6_uc011mqt.1_Intron|RPS6KA6_uc011mqu.1_Intron|RPS6KA6_uc010nmo.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	83564340	83564340	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83564340delA								MIR548I4 (83504 upstream) : HDX (11869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	83830238	83830239	+	IGR	INS	-	A	A	rs143663831		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83830238_83830239insA								HDX (72780 upstream) : UBE2DNL (358918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	84920669	84920670	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84920669_84920670delAC								POF1B (285921 upstream) : MIR1321 (170115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	85006481	85006481	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85006481delT								POF1B (371733 upstream) : MIR1321 (84304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87505081	87505081	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87505081delT								KLHL4 (580031 upstream) : CPXCR1 (497145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87672392	87672392	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87672392delA								KLHL4 (747342 upstream) : CPXCR1 (329834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87758527	87758527	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87758527delA								KLHL4 (833477 upstream) : CPXCR1 (243699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87787177	87787177	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87787177delA								KLHL4 (862127 upstream) : CPXCR1 (215049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	88256164	88256165	+	IGR	DEL	GT	-	-	rs112625027		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:88256164_88256165delGT								CPXCR1 (246381 upstream) : TGIF2LX (920775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	88380415	88380416	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:88380415_88380416insT								CPXCR1 (370632 upstream) : TGIF2LX (796524 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	89597189	89597189	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89597189delT								TGIF2LX (419309 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	89668317	89668317	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89668317delT								TGIF2LX (490437 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	89923489	89923490	+	IGR	DEL	AA	-	-	rs79594502		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89923489_89923490delAA								TGIF2LX (745609 upstream) : PABPC5 (766107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	90666707	90666707	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:90666707delA								None (None upstream) : PABPC5 (22890 downstream)																																			---	---	---	---
PCDH11X	27328	broad.mit.edu	37	X	91523300	91523300	+	Intron	DEL	T	-	-	rs67618334		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91523300delT	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	93167094	93167094	+	IGR	DEL	T	-	-	rs147338741	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:93167094delT								FAM133A (199833 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	93592246	93592246	+	IGR	DEL	T	-	-	rs79732511		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:93592246delT								FAM133A (624985 upstream) : MIR548M (725894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	93826851	93826852	+	IGR	INS	-	TA	TA			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:93826851_93826852insTA								FAM133A (859590 upstream) : MIR548M (491288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	93982638	93982638	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:93982638delA								None (None upstream) : MIR548M (335502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	94409200	94409200	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:94409200delA								MIR548M (90975 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	94537523	94537523	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:94537523delT								MIR548M (219298 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	95331644	95331644	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95331644delA								None (None upstream) : LOC643486 (260442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	95557567	95557568	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95557567_95557568delAA								None (None upstream) : LOC643486 (34518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	95578838	95578838	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95578838delA								None (None upstream) : LOC643486 (13248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	95713509	95713510	+	IGR	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95713509_95713510delCA								LOC643486 (120608 upstream) : DIAPH2 (226152 downstream)																																			---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96744393	96744393	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96744393delT	uc004efu.3	+							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	97026214	97026214	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:97026214delT								DIAPH2 (170618 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	97098939	97098939	+	IGR	DEL	C	-	-	rs72245667		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:97098939delC								DIAPH2 (243343 upstream) : None (None downstream)																																			---	---	---	---
PCDH19	57526	broad.mit.edu	37	X	99607004	99607004	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99607004delA	uc010nmz.2	-						PCDH19_uc004efw.3_Intron|PCDH19_uc004efx.3_Intron	NM_020766	NP_001098713			protocadherin 19 isoform b						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	100197872	100197872	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100197872delA								XKRX (13974 upstream) : ARL13A (26825 downstream)																																			---	---	---	---
TMEM35	59353	broad.mit.edu	37	X	100345159	100345159	+	Intron	DEL	T	-	-	rs72174233		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100345159delT	uc004egw.2	+							NM_021637	NP_067650			transmembrane protein 35							cytoplasmic membrane-bounded vesicle|integral to membrane|peroxisomal membrane					0																		---	---	---	---
ARMCX1	51309	broad.mit.edu	37	X	100806115	100806115	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100806115delT	uc004ehv.2	+						ARMCX1_uc004ehw.2_Intron	NM_016608	NP_057692			armadillo repeat containing, X-linked 1							integral to membrane	binding			ovary(3)|pancreas(1)	4																		---	---	---	---
NXF5	55998	broad.mit.edu	37	X	101093566	101093566	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101093566delG	uc011mrk.1	-						NXF5_uc004eih.1_Intron|NXF5_uc004eii.1_Intron|NXF5_uc004eij.1_Intron|NXF5_uc004eik.1_Intron|NXF5_uc004eil.1_Intron	NM_032946	NP_116564			nuclear RNA export factor 5						mRNA export from nucleus|multicellular organismal development	actin cytoskeleton|cytoplasm|nucleus	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1																		---	---	---	---
ZMAT1	84460	broad.mit.edu	37	X	101138347	101138347	+	3'UTR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101138347delA	uc004eim.2	-	2					ZMAT1_uc011mrl.1_3'UTR|ZMAT1_uc004ein.2_3'UTR|ZMAT1_uc011mrm.1_3'UTR	NM_032441	NP_115817			zinc finger, matrin type 1 isoform 3							nucleus	zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	102119870	102119871	+	Intron	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102119870_102119871delGT	uc004ejq.1	+						uc004ejr.2_Intron					Homo sapiens cDNA clone IMAGE:5576940.																														---	---	---	---
NGFRAP1	27018	broad.mit.edu	37	X	102632284	102632284	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102632284delA	uc004eki.2	+						NGFRAP1_uc004ekh.2_Intron|NGFRAP1_uc004ekj.1_5'UTR	NM_206915	NP_996798			nerve growth factor receptor (TNFRSF16)						apoptosis|multicellular organismal development|nerve growth factor receptor signaling pathway	cytosol|nucleus	caspase regulator activity|metal ion binding				0																		---	---	---	---
TMSB15B	286527	broad.mit.edu	37	X	103202429	103202429	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103202429delA	uc004elo.3	+											Homo sapiens cDNA FLJ33654 fis, clone BRAMY2024827.						actin cytoskeleton organization|sequestering of actin monomers	cytoplasm|cytoskeleton	actin binding			skin(1)	1																		---	---	---	---
TMSB15B	286527	broad.mit.edu	37	X	103219168	103219169	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103219168_103219169insA	uc010noz.2	+	2	187_188	c.73_74insA	c.(73-75)GAAfs	p.E25fs	TMSB15B_uc004elo.3_RNA|TMSB15B_uc004elq.3_RNA	NM_194324	NP_919305	P0CG34	TB15A_HUMAN	thymosin beta15b	25					actin cytoskeleton organization|sequestering of actin monomers	cytoplasm|cytoskeleton	actin binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	103242762	103242762	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103242762delT								H2BFXP (9977 upstream) : H2BFWT (22959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	103564130	103564130	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103564130delA								ESX1 (64542 upstream) : IL1RAPL2 (246866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	103578746	103578746	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103578746delT								ESX1 (79158 upstream) : IL1RAPL2 (232250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	103801786	103801786	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103801786delA								ESX1 (302198 upstream) : IL1RAPL2 (9210 downstream)																																			---	---	---	---
IL1RAPL2	26280	broad.mit.edu	37	X	104258801	104258802	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104258801_104258802insT	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	104673565	104673565	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104673565delT	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	105062066	105062066	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105062066delA								IL1RAPL2 (50244 upstream) : NRK (4470 downstream)																																			---	---	---	---
MORC4	79710	broad.mit.edu	37	X	106198749	106198750	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106198749_106198750delAC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	106277488	106277489	+	IGR	DEL	GA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106277488_106277489delGA								MORC4 (34046 upstream) : RBM41 (30161 downstream)																																			---	---	---	---
CXorf41	139212	broad.mit.edu	37	X	106459803	106459804	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106459803_106459804insT	uc004enc.2	+						CXorf41_uc004end.2_Intron	NM_173494	NP_775765			hypothetical protein LOC139212												0																		---	---	---	---
CXorf41	139212	broad.mit.edu	37	X	106472832	106472833	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106472832_106472833insT	uc004enc.2	+						CXorf41_uc004end.2_Intron	NM_173494	NP_775765			hypothetical protein LOC139212												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	106589047	106589047	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106589047delA								CXorf41 (101575 upstream) : PRPS1 (282607 downstream)																																			---	---	---	---
COL4A6	1288	broad.mit.edu	37	X	107676763	107676763	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107676763delT	uc004enw.3	-						COL4A6_uc004env.3_Intron|COL4A6_uc011msn.1_Intron|COL4A6_uc010npk.2_Intron|COL4A6_uc004enx.2_Intron|COL4A6_uc004eny.2_Intron	NM_001847	NP_001838			type IV alpha 6 collagen isoform A precursor						cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
Unknown	0	broad.mit.edu	37	X	108142625	108142625	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108142625delA								IRS4 (163018 upstream) : GUCY2F (473511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	108775211	108775212	+	IGR	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108775211_108775212delAC								GUCY2F (49926 upstream) : NXT2 (3798 downstream)																																			---	---	---	---
ACSL4	2182	broad.mit.edu	37	X	108967008	108967008	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108967008delA	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)													---	---	---	---
TMEM164	84187	broad.mit.edu	37	X	109275675	109275676	+	Intron	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109275675_109275676insT	uc004eom.2	+						TMEM164_uc004eol.2_Intron|TMEM164_uc010npq.2_Intron	NM_032227	NP_115603			transmembrane protein 164 isoform b							integral to membrane				large_intestine(1)|lung(1)|skin(1)	3																		---	---	---	---
CHRDL1	91851	broad.mit.edu	37	X	109943788	109943788	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109943788delT	uc004eou.3	-						CHRDL1_uc004eov.2_Intron|CHRDL1_uc004eow.2_Intron|CHRDL1_uc010nps.2_Intron|CHRDL1_uc004eot.2_Intron|CHRDL1_uc011mss.1_Intron	NM_001143981	NP_001137453			chordin-like 1 isoform 1 precursor						BMP signaling pathway|cell differentiation|nervous system development|ossification	extracellular region					0																		---	---	---	---
PAK3	5063	broad.mit.edu	37	X	110259962	110259963	+	Intron	INS	-	GAAG	GAAG	rs72257287		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110259962_110259963insGAAG	uc010npt.1	+						PAK3_uc010npu.1_Intron|PAK3_uc004eoy.1_Intron	NM_001128166	NP_001121638			p21-activated kinase 3 isoform a						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)			---	---	---	---
PAK3	5063	broad.mit.edu	37	X	110327861	110327861	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110327861delT	uc010npt.1	+						PAK3_uc010npu.1_Intron|PAK3_uc004eoy.1_Intron	NM_001128166	NP_001121638			p21-activated kinase 3 isoform a						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)			---	---	---	---
TRPC5	7224	broad.mit.edu	37	X	111143234	111143234	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111143234delA	uc004epl.1	-						TRPC5_uc004epm.1_Intron|uc004epn.2_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																		---	---	---	---
LHFPL1	340596	broad.mit.edu	37	X	111916602	111916602	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111916602delG	uc004epq.2	-						LHFPL1_uc004epp.2_5'Flank|LHFPL1_uc010nqa.2_Intron|LHFPL1_uc010nqb.2_Intron	NM_178175	NP_835469			lipoma HMGIC fusion partner-like 1 precursor							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	112003392	112003392	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112003392delT								LHFPL1 (80017 upstream) : AMOT (14714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	112580636	112580636	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112580636delT								AMOT (496593 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	113771691	113771692	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113771691_113771692insT								None (None upstream) : HTR2C (46859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	114669633	114669634	+	IGR	INS	-	ACA	ACA	rs150111707		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114669633_114669634insACA								LUZP4 (127514 upstream) : PLS3 (125572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	115358334	115358334	+	IGR	DEL	T	-	-	rs72262405		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115358334delT								AGTR2 (52111 upstream) : SLC6A14 (209440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	115434212	115434212	+	IGR	DEL	T	-	-	rs113111961		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115434212delT								AGTR2 (127989 upstream) : SLC6A14 (133562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	115516537	115516537	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115516537delA								AGTR2 (210314 upstream) : SLC6A14 (51237 downstream)																																			---	---	---	---
SLC6A14	11254	broad.mit.edu	37	X	115573843	115573843	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115573843delT	uc004eqi.2	+						SLC6A14_uc011mtm.1_Intron	NM_007231	NP_009162			solute carrier family 6 (amino acid						cellular amino acid metabolic process|response to toxin	integral to membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			ovary(2)|pancreas(1)	3					L-Proline(DB00172)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	116232390	116232390	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:116232390delC								CXorf61 (638253 upstream) : KLHL13 (799387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	116562492	116562492	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:116562492delA								CXorf61 (968355 upstream) : KLHL13 (469285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	116814769	116814769	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:116814769delA								None (None upstream) : KLHL13 (217008 downstream)																																			---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117752829	117752829	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117752829delT	uc004eqp.2	+						DOCK11_uc004eqq.2_Intron	NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	118337967	118337967	+	IGR	DEL	A	-	-	rs71948938		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118337967delA								KIAA1210 (53425 upstream) : PGRMC1 (32244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	118426869	118426870	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118426869_118426870insT								PGRMC1 (48441 upstream) : SLC25A43 (106153 downstream)																																			---	---	---	---
SEPT6	23157	broad.mit.edu	37	X	118811286	118811286	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118811286delG	uc004erv.2	-						SEPT6_uc010nqk.2_Intron|SEPT6_uc004ers.2_Intron|SEPT6_uc004ert.2_Intron|SEPT6_uc004eru.2_Intron|SEPT6_uc004erw.2_5'Flank|SEPT6_uc011mtv.1_Intron|SEPT6_uc011mtw.1_Intron	NM_015129	NP_055944			septin 6 isoform B						cell cycle|cytokinesis|interspecies interaction between organisms	cleavage furrow|condensed chromosome kinetochore|midbody|septin complex|spindle	GTP binding|protein binding			lung(1)|ovary(1)|prostate(1)|kidney(1)	4																		---	---	---	---
CUL4B	8450	broad.mit.edu	37	X	119694638	119694638	+	Intron	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119694638delG	uc004esw.2	-						CUL4B_uc004esv.2_5'UTR	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	119941214	119941214	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119941214delT								C1GALT1C1 (177273 upstream) : CT47B1 (65240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	120431860	120431862	+	IGR	DEL	AAA	-	-	rs68167336		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120431860_120431862delAAA								GLUD2 (248066 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	121000241	121000242	+	IGR	DEL	GT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:121000241_121000242delGT								GLUD2 (816447 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	121573970	121573970	+	IGR	DEL	C	-	-	rs72439979		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:121573970delC								None (None upstream) : GRIA3 (744126 downstream)																																			---	---	---	---
THOC2	57187	broad.mit.edu	37	X	122753870	122753870	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122753870delA	uc004etu.2	-						THOC2_uc010nqt.1_Intron|THOC2_uc004etw.1_Intron	NM_001081550	NP_001075019			THO complex 2						intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123646524	123646524	+	Intron	DEL	A	-	-	rs3216399		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123646524delA	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																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123875386	123875386	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123875386delA	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	124208110	124208110	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124208110delT								ODZ1 (110444 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	124292789	124292790	+	IGR	DEL	AA	-	-	rs66827552		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124292789_124292790delAA								ODZ1 (195123 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	124444225	124444225	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124444225delA								ODZ1 (346559 upstream) : DCAF12L2 (854289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	126110747	126110747	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:126110747delT								CXorf64 (154981 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	127240690	127240690	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127240690delT								ACTRT1 (54308 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	127322364	127322365	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127322364_127322365insA								ACTRT1 (135982 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	127818870	127818870	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127818870delT								ACTRT1 (632488 upstream) : SMARCA1 (761610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	128318930	128318930	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128318930delA								None (None upstream) : SMARCA1 (261550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	128433717	128433717	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128433717delT								None (None upstream) : SMARCA1 (146763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	128486829	128486829	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128486829delA								None (None upstream) : SMARCA1 (93651 downstream)																																			---	---	---	---
UTP14A	10813	broad.mit.edu	37	X	129038463	129038463	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129038463delA	uc004euz.2	+						UTP14A_uc011mup.1_5'Flank|UTP14A_uc011muq.1_5'Flank	NM_006649	NP_006640			UTP14, U3 small nucleolar ribonucleoprotein,						rRNA processing	nucleolus|small-subunit processome	protein binding			ovary(2)	2																		---	---	---	---
UTP14A	10813	broad.mit.edu	37	X	129054164	129054164	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129054164delA	uc004euz.2	+						UTP14A_uc011mup.1_Intron|UTP14A_uc011muq.1_Intron|UTP14A_uc004eva.1_5'Flank	NM_006649	NP_006640			UTP14, U3 small nucleolar ribonucleoprotein,						rRNA processing	nucleolus|small-subunit processome	protein binding			ovary(2)	2																		---	---	---	---
BCORL1	63035	broad.mit.edu	37	X	129147663	129147664	+	Frame_Shift_Ins	INS	-	TCAG	TCAG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129147663_129147664insTCAG	uc004evb.1	+	4	1029_1030	c.915_916insTCAG	c.(913-918)CTTTCAfs	p.L305fs	BCORL1_uc010nrd.1_Frame_Shift_Ins_p.L207fs	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	305_306	Pro-rich.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7																		---	---	---	---
AIFM1	9131	broad.mit.edu	37	X	129277822	129277822	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129277822delA	uc004evg.2	-						AIFM1_uc011mus.1_Intron|AIFM1_uc004evh.2_Intron|AIFM1_uc004evi.2_Intron|AIFM1_uc004evk.2_Intron	NM_004208	NP_004199			programmed cell death 8 isoform 1						activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm	DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			ovary(4)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	129426020	129426021	+	IGR	INS	-	AT	AT			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129426020_129426021insAT								ZNF280C (23147 upstream) : SLC25A14 (47889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	129640912	129640913	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129640912_129640913delTT	uc004evu.2	-											Homo sapiens cDNA clone IMAGE:5295457.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	130306039	130306039	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130306039delT								ARHGAP36 (82183 upstream) : IGSF1 (101444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	131106513	131106513	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131106513delG								LOC286467 (141842 upstream) : MST4 (50732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	131107904	131107904	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131107904delA								LOC286467 (143233 upstream) : MST4 (49341 downstream)																																			---	---	---	---
MST4	51765	broad.mit.edu	37	X	131175056	131175057	+	Intron	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131175056_131175057delTT	uc004ewk.1	+						MST4_uc004ewl.1_Intron|MST4_uc011mux.1_Intron|MST4_uc010nrj.1_Intron|MST4_uc004ewm.1_Intron	NM_016542	NP_057626			serine/threonine protein kinase MST4 isoform 1						cellular component disassembly involved in apoptosis|regulation of apoptosis	cytosol|Golgi membrane	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(3)|stomach(2)|upper_aerodigestive_tract(1)	9	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	131418136	131418136	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131418136delT	uc004ewr.1	+											Homo sapiens cDNA FLJ38120 fis, clone D3OST3000195.																														---	---	---	---
HS6ST2	90161	broad.mit.edu	37	X	131947772	131947772	+	Intron	DEL	T	-	-	rs57717522		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131947772delT	uc011mve.1	-						HS6ST2_uc011mvb.1_Intron|HS6ST2_uc011mvc.1_Intron|HS6ST2_uc011mvd.1_Intron	NM_147175	NP_671704			heparan sulfate 6-O-sulfotransferase 2 isoform							integral to membrane	sulfotransferase activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	132135261	132135261	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132135261delA								HS6ST2 (39838 upstream) : USP26 (23793 downstream)																																			---	---	---	---
GPC4	2239	broad.mit.edu	37	X	132469473	132469474	+	Intron	DEL	AC	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132469473_132469474delAC	uc004exc.1	-						GPC4_uc011mvg.1_Intron	NM_001448	NP_001439			glypican 4 precursor						anatomical structure morphogenesis|cell proliferation	anchored to membrane|external side of plasma membrane|extracellular space|insoluble fraction|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
GPC3	2719	broad.mit.edu	37	X	132777860	132777860	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132777860delT	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				---	---	---	---
MIR363	574031	broad.mit.edu	37	X	133304414	133304414	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133304414delA	hsa-mir-363|MI0000764	-						MIR92A2_hsa-mir-92a-2|MI0000094_5'Flank|uc004exf.2_5'Flank|uc011mvi.1_5'Flank|MIR19B2_hsa-mir-19b-2|MI0000075_5'Flank|MIR20B_hsa-mir-20b|MI0001519_5'Flank|MIR18B_hsa-mir-18b|MI0001518_5'Flank|uc004exg.1_5'Flank|MIR106A_hsa-mir-106a|MI0000113_5'Flank																	0																		---	---	---	---
CCDC160	347475	broad.mit.edu	37	X	133378875	133378875	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133378875delT	uc011mvj.1	+	2	366	c.45delT	c.(43-45)CCTfs	p.P15fs		NM_001101357	NP_001094827	A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	15										skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	133683009	133683009	+	5'Flank	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133683009delT	uc004exn.1	+						MGC16121_uc011mvm.1_5'Flank|MGC16121_uc004exm.2_5'Flank|MIR503_hsa-mir-503|MI0003188_5'Flank|uc011mvn.1_5'Flank|MGC16121_uc011mvo.1_5'Flank|MIR424_hsa-mir-424|MI0001446_5'Flank					Homo sapiens cDNA FLJ12932 fis, clone NT2RP2004897.																														---	---	---	---
PLAC1	10761	broad.mit.edu	37	X	133744710	133744710	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133744710delT	uc004exo.1	-						PLAC1_uc004exp.1_Intron	NM_021796	NP_068568			placenta-specific 1 precursor						placenta development	extracellular region				pancreas(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	133886279	133886279	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133886279delT								PLAC1 (93766 upstream) : FAM122B (17318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	134087369	134087369	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134087369delA								MOSPD1 (38072 upstream) : LOC644538 (37599 downstream)																																			---	---	---	---
ZNF75D	7626	broad.mit.edu	37	X	134383351	134383352	+	Intron	DEL	CA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134383351_134383352delCA	uc004eym.2	-											Homo sapiens mRNA; cDNA DKFZp451F083 (from clone DKFZp451F083); complete cds.						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
ZNF75D	7626	broad.mit.edu	37	X	134425372	134425373	+	Intron	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134425372_134425373insA	uc004eyp.2	-						ZNF75D_uc004eym.2_Intron|ZNF75D_uc004eyn.2_Intron|ZNF75D_uc004eyo.2_Intron	NM_007131	NP_009062			zinc finger protein 75						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	134614318	134614318	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134614318delT								NCRNA00086 (54094 upstream) : DDX26B (40237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	134841388	134841389	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134841388_134841389insG								DDX26B (124929 upstream) : CT45A1 (5796 downstream)																																			---	---	---	---
CT45A4	441520	broad.mit.edu	37	X	134934411	134934411	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134934411delT	uc004ezd.2	-							NM_001017436	NP_001017436			cancer/testis antigen family 45, member A4												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	135212704	135212704	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135212704delT								SLC9A6 (83278 upstream) : FHL1 (16157 downstream)																																			---	---	---	---
MAP7D3	79649	broad.mit.edu	37	X	135306559	135306559	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135306559delA	uc004ezt.2	-						MAP7D3_uc004ezs.2_Intron|MAP7D3_uc011mwc.1_Intron|MAP7D3_uc010nsa.1_Intron	NM_024597	NP_078873			MAP7 domain containing 3							cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MAP7D3	79649	broad.mit.edu	37	X	135322790	135322790	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135322790delT	uc004ezt.2	-						MAP7D3_uc004ezs.2_Intron|MAP7D3_uc011mwc.1_Intron|MAP7D3_uc010nsa.1_Intron	NM_024597	NP_078873			MAP7 domain containing 3							cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	135651206	135651207	+	IGR	INS	-	TG	TG			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135651206_135651207insTG								VGLL1 (12241 upstream) : CD40LG (79129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	136059145	136059145	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136059145delT	uc004fai.1	+											Homo sapiens cDNA FLJ31132 fis, clone IMR322000953.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	137470670	137470670	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137470670delA								ZIC3 (816413 upstream) : LOC158696 (226222 downstream)																																			---	---	---	---
FGF13	2258	broad.mit.edu	37	X	137816514	137816514	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137816514delT	uc004faq.2	-						FGF13_uc004fan.2_Intron|FGF13_uc011mwi.1_Intron|FGF13_uc004far.2_Intron|FGF13_uc011mwj.1_Intron|FGF13_uc011mwk.1_Intron	NM_001139502	NP_001132974			fibroblast growth factor 13 isoform 3						cell-cell signaling|MAPKKK cascade|nervous system development	cytoplasm|nucleus	growth factor activity|protein kinase activator activity			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	138466825	138466825	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138466825delA								FGF13 (179640 upstream) : F9 (146070 downstream)																																			---	---	---	---
ATP11C	286410	broad.mit.edu	37	X	138866027	138866027	+	Intron	DEL	A	-	-	rs71854240		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138866027delA	uc004faz.2	-						ATP11C_uc004fay.2_Intron|ATP11C_uc004fba.2_Intron	NM_173694	NP_775965			ATPase, class VI, type 11C isoform a						ATP biosynthetic process	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(5)|large_intestine(3)	8	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ATP11C	286410	broad.mit.edu	37	X	138871362	138871362	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138871362delA	uc004faz.2	-						ATP11C_uc004fay.2_Intron|ATP11C_uc004fba.2_Intron	NM_173694	NP_775965			ATPase, class VI, type 11C isoform a						ATP biosynthetic process	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(5)|large_intestine(3)	8	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	139088260	139088260	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139088260delA								CXorf66 (40583 upstream) : SOX3 (496892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	139201013	139201014	+	IGR	INS	-	T	T	rs76646592		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139201013_139201014insT								CXorf66 (153336 upstream) : SOX3 (384138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	139805682	139805685	+	IGR	DEL	ACAA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139805682_139805685delACAA								RP1-177G6.2 (8695 upstream) : CDR1 (59740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	140248923	140248924	+	IGR	DEL	AA	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140248923_140248924delAA								SPANXB2 (163053 upstream) : LDOC1 (21016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	141640109	141640109	+	IGR	DEL	A	-	-	rs78359341		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141640109delA								MAGEC2 (347033 upstream) : SPANXN4 (473595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	142757810	142757810	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142757810delT								SLITRK4 (34214 upstream) : SPANXN2 (37246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	144118505	144118506	+	IGR	INS	-	TC	TC			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144118505_144118506insTC								None (None upstream) : SPANXN1 (210601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	145289372	145289373	+	IGR	DEL	TT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145289372_145289373delTT								MIR891A (179982 upstream) : CXorf51 (601929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	145422402	145422405	+	IGR	DEL	CCTT	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145422402_145422405delCCTT								MIR891A (313012 upstream) : CXorf51 (468897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	145670540	145670541	+	IGR	INS	-	AC	AC	rs35991813		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145670540_145670541insAC								MIR891A (561150 upstream) : CXorf51 (220761 downstream)																																			---	---	---	---
MIR513C	100302114	broad.mit.edu	37	X	146272995	146272995	+	5'Flank	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146272995delA	hsa-mir-513c|MI0006649	-																							0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	146306738	146306738	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-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	146743380	146743383	+	IGR	DEL	ACAC	-	-	rs67673387		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146743380_146743383delACAC								MIR514-3 (377134 upstream) : ASFMR1 (247566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	146837912	146837912	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146837912delT								MIR514-3 (471666 upstream) : ASFMR1 (153037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	146882863	146882864	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146882863_146882864insA								MIR514-3 (516617 upstream) : ASFMR1 (108085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	146894305	146894305	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146894305delT								MIR514-3 (528059 upstream) : ASFMR1 (96644 downstream)																																			---	---	---	---
FMR1	2332	broad.mit.edu	37	X	147014135	147014135	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147014135delT	uc010nst.2	+						FMR1_uc011mwz.1_Intron|FMR1_uc004fcj.2_Intron|FMR1_uc004fck.3_Intron|FMR1_uc004fcl.3_Intron|FMR1_uc011mxa.1_Intron	NM_002024	NP_002015			fragile X mental retardation 1						mRNA transport|negative regulation of translational initiation	cytoplasm|mRNA cap binding complex|nucleolus|nucleoplasm|soluble fraction	mRNA binding|protein binding			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													Fragile_X_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	X	148269324	148269324	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148269324delA								AFF2 (187132 upstream) : IDS (290973 downstream)																																			---	---	---	---
LOC100272228	100272228	broad.mit.edu	37	X	149152655	149152655	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149152655delT	uc004feb.2	+						LOC100272228_uc004fea.2_Intron	NR_027456				Homo sapiens cDNA FLJ30251 fis, clone BRACE2002394.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	149516294	149516294	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149516294delA								MIR2114 (119976 upstream) : MAMLD1 (13542 downstream)																																			---	---	---	---
MTM1	4534	broad.mit.edu	37	X	149770604	149770604	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149770604delT	uc004fef.3	+						MTM1_uc011mxx.1_Intron|MTM1_uc011mxy.1_Intron|MTM1_uc011mxz.1_Intron|MTM1_uc010nte.2_Intron	NM_000252	NP_000243			myotubularin						endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|protein transport|regulation of vacuole organization	filopodium|late endosome|plasma membrane|ruffle	intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MTM1	4534	broad.mit.edu	37	X	149783252	149783252	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149783252delA	uc004fef.3	+						MTM1_uc011mxx.1_Intron|MTM1_uc011mxy.1_Intron|MTM1_uc011mxz.1_Intron|MTM1_uc010nte.2_Intron	NM_000252	NP_000243			myotubularin						endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|protein transport|regulation of vacuole organization	filopodium|late endosome|plasma membrane|ruffle	intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MTM1	4534	broad.mit.edu	37	X	149807261	149807261	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149807261delT	uc004fef.3	+						MTM1_uc011mxx.1_Intron|MTM1_uc011mxy.1_Intron|MTM1_uc011mxz.1_Intron|MTM1_uc010nte.2_Intron	NM_000252	NP_000243			myotubularin						endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|protein transport|regulation of vacuole organization	filopodium|late endosome|plasma membrane|ruffle	intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
CD99L2	83692	broad.mit.edu	37	X	149965669	149965669	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149965669delA	uc004fel.2	-						CD99L2_uc004fek.2_Intron|CD99L2_uc004fem.2_Intron|CD99L2_uc004fen.2_Intron|CD99L2_uc004feo.2_Intron|CD99L2_uc011myb.1_Intron	NM_031462	NP_113650			CD99 antigen-like 2 isoform E3'-E4'-E3-E4						cell adhesion	cell junction|integral to membrane				large_intestine(2)|ovary(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	150113060	150113061	+	IGR	INS	-	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150113060_150113061insG								CD99L2 (45881 upstream) : HMGB3 (38702 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	150221208	150221208	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150221208delT								HMGB3 (61962 upstream) : GPR50 (123851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	150398008	150398008	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150398008delT								GPR50 (48078 upstream) : VMA21 (167697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	150879832	150879832	+	IGR	DEL	C	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150879832delC								PRRG3 (9819 upstream) : FATE1 (4676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	151660609	151660609	+	IGR	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151660609delT								GABRA3 (40778 upstream) : GABRQ (146028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	151771907	151771908	+	IGR	INS	-	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151771907_151771908insT								GABRA3 (152076 upstream) : GABRQ (34729 downstream)																																			---	---	---	---
TEX28	1527	broad.mit.edu	37	X	153502876	153502876	+	Intron	DEL	T	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153502876delT	uc004fke.2	-						TEX28_uc004fkf.2_Intron	NM_001586	NP_001577			testis expressed 28							integral to membrane					0	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
MPP1	4354	broad.mit.edu	37	X	154018303	154018303	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154018303delA	uc004fmp.1	-						MPP1_uc010nvg.1_Intron|MPP1_uc011mzv.1_Intron|MPP1_uc004fmq.1_Intron|MPP1_uc011mzw.1_Intron|MPP1_uc010nvh.1_Intron	NM_002436	NP_002427			palmitoylated membrane protein 1						regulation of neutrophil chemotaxis|signal transduction	integral to plasma membrane|membrane fraction|stereocilium	guanylate kinase activity|protein binding			ovary(2)|central_nervous_system(1)	3	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)																	---	---	---	---
F8	2157	broad.mit.edu	37	X	154130484	154130484	+	Intron	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154130484delA	uc004fmt.2	-						F8_uc010nvi.1_Intron	NM_000132	NP_000123			coagulation factor VIII isoform a precursor						acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)													---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9954434	9954434	+	IGR	DEL	G	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9954434delG								TTTY22 (303580 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	10054312	10054312	+	IGR	DEL	A	-	-			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10054312delA								TTTY22 (403458 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13416348	13416349	+	IGR	DEL	GG	-	-	rs112119630		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13416348_13416349delGG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13451061	13451062	+	IGR	INS	-	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13451061_13451062insA								None (None upstream) : None (None downstream)																																			---	---	---	---
CDK11A	728642	broad.mit.edu	37	1	1638926	1638926	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1638926G>A	uc009vks.2	-	11	1275	c.1167C>T	c.(1165-1167)GGC>GGT	p.G389G	CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agv.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc001ahj.3_5'UTR|CDK11A_uc009vkp.2_Intron|CDK11A_uc009vkq.2_Intron|CDK11A_uc009vkr.2_Silent_p.G379G|CDK11A_uc010nys.1_Silent_p.G379G|CDK11A_uc010nyt.1_Silent_p.G389G|CDK11A_uc010nyu.1_RNA	NM_024011	NP_076916	Q9UQ88	CD11A_HUMAN	cell division cycle 2-like 2 isoform 1	392					apoptosis|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			stomach(1)	1																		---	---	---	---
MMEL1	79258	broad.mit.edu	37	1	2526293	2526293	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2526293G>A	uc001ajy.2	-	17	1838	c.1624C>T	c.(1624-1626)CAG>TAG	p.Q542*	MMEL1_uc009vlg.1_RNA	NM_033467	NP_258428	Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	542	Potential.|Lumenal (Potential).				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)														---	---	---	---
TP73	7161	broad.mit.edu	37	1	3638707	3638707	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3638707G>A	uc001akp.2	+	5	662	c.552G>A	c.(550-552)GCG>GCA	p.A184A	TP73_uc001akq.2_Silent_p.A184A|TP73_uc010nzj.1_Silent_p.A135A|TP73_uc001akr.2_Silent_p.A135A|TP73_uc009vlk.1_Silent_p.A135A|TP73_uc001aks.2_Silent_p.A135A|TP73_uc010nzk.1_Silent_p.A113A	NM_005427	NP_005418	O15350	P73_HUMAN	tumor protein p73 isoform a	184	DNA-binding (Potential).				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)														---	---	---	---
CHD5	26038	broad.mit.edu	37	1	6203990	6203990	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6203990C>A	uc001amb.1	-	13	2036	c.1936G>T	c.(1936-1938)GAG>TAG	p.E646*	CHD5_uc001ama.1_RNA|CHD5_uc001amc.1_RNA	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	646	Chromo 2.				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)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8424823	8424823	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8424823C>T	uc001ape.2	-	15	2333	c.1523G>A	c.(1522-1524)CGC>CAC	p.R508H	RERE_uc001apf.2_Missense_Mutation_p.R508H|RERE_uc010nzx.1_Missense_Mutation_p.R240H|RERE_uc001apd.2_5'UTR	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	508	GATA-type.				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)														---	---	---	---
PLOD1	5351	broad.mit.edu	37	1	12024809	12024809	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12024809C>A	uc001atm.2	+	13	1528	c.1437C>A	c.(1435-1437)CCC>CCA	p.P479P	PLOD1_uc010obb.1_Silent_p.P526P	NM_000302	NP_000293	Q02809	PLOD1_HUMAN	lysyl hydroxylase 1 precursor	479					epidermis development|hydroxylysine biosynthetic process|protein modification process|response to hypoxia	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein homodimerization activity			ovary(2)|breast(1)	3	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Minoxidil(DB00350)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
PRAMEF2	65122	broad.mit.edu	37	1	12920127	12920127	+	Splice_Site	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12920127G>A	uc001aum.1	+	3	953	c.866_splice	c.e3+1	p.R289_splice		NM_023014	NP_075390			PRAME family member 2												0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PRAMEF17	391004	broad.mit.edu	37	1	13716830	13716830	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13716830G>T	uc009vnz.1	+	2	347	c.317G>T	c.(316-318)CGG>CTG	p.R106L		NM_001099851	NP_001093321	Q5VTA0	PRA17_HUMAN	PRAME family member 17	106											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PRDM2	7799	broad.mit.edu	37	1	14149681	14149681	+	3'UTR	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14149681G>A	uc001avi.2	+	10					PRDM2_uc001avg.2_3'UTR|PRDM2_uc009voe.2_RNA|PRDM2_uc009vof.2_RNA|PRDM2_uc001avl.1_RNA	NM_012231	NP_036363			retinoblastoma protein-binding zinc finger							Golgi apparatus|nucleus	DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)														---	---	---	---
CELA2B	51032	broad.mit.edu	37	1	15813917	15813917	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15813917C>T	uc001awl.2	+	7	802	c.777C>T	c.(775-777)AAC>AAT	p.N259N		NM_015849	NP_056933	P08218	CEL2B_HUMAN	elastase 2B preproprotein	259	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
DNAJC16	23341	broad.mit.edu	37	1	15890807	15890807	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15890807T>C	uc001aws.2	+	11	1671	c.1551T>C	c.(1549-1551)GCT>GCC	p.A517A	DNAJC16_uc001awr.1_Silent_p.A517A|DNAJC16_uc001awt.2_Silent_p.A205A|DNAJC16_uc001awu.2_RNA	NM_015291	NP_056106	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	517	Cytoplasmic (Potential).				cell redox homeostasis|protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			urinary_tract(1)|lung(1)|kidney(1)	3		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)														---	---	---	---
RSC1A1	6248	broad.mit.edu	37	1	15986909	15986909	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15986909A>G	uc010obn.1	+	1	546	c.546A>G	c.(544-546)AAA>AAG	p.K182K		NM_006511	NP_006502	Q92681	RSCA1_HUMAN	regulatory solute carrier protein, family 1,	182					negative regulation of transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transport	cell junction|Golgi apparatus|nucleus	ion channel inhibitor activity			ovary(1)	1		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00276)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SPATA21	374955	broad.mit.edu	37	1	16725286	16725286	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16725286T>C	uc001ayn.2	-	13	1867	c.1384A>G	c.(1384-1386)AGC>GGC	p.S462G	SPATA21_uc001ayl.1_Intron|SPATA21_uc010occ.1_Missense_Mutation_p.S439G	NM_198546	NP_940948	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	462							calcium ion binding			ovary(2)|breast(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)														---	---	---	---
WNT4	54361	broad.mit.edu	37	1	22446648	22446648	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22446648C>A	uc001bfs.3	-	5	1055	c.951G>T	c.(949-951)ACG>ACT	p.T317T	WNT4_uc010odt.1_Silent_p.T254T	NM_030761	NP_110388	P56705	WNT4_HUMAN	wingless-type MMTV integration site family,	317					adrenal gland development|androgen biosynthetic process|anterior/posterior pattern formation|axis specification|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway|cellular response to transforming growth factor beta stimulus|dermatome development|endoderm development|epithelial to mesenchymal transition|establishment of protein localization in plasma membrane|female gonad development|female sex determination|liver development|male gonad development|mesonephric tubule development|metanephric mesenchymal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of male gonad development|negative regulation of testicular blood vessel morphogenesis|negative regulation of testosterone biosynthetic process|negative regulation of transcription, DNA-dependent|oocyte development|paramesonephric duct development|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of collagen biosynthetic process|positive regulation of cortisol biosynthetic process|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|protein palmitoylation|renal vesicle formation|smooth muscle cell differentiation|somatotropin secreting cell differentiation|tertiary branching involved in mammary gland duct morphogenesis|thyroid-stimulating hormone-secreting cell differentiation|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|extracellular space|Golgi apparatus|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|signal transducer activity|transcription corepressor activity			ovary(1)	1		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;9.02e-26)|Colorectal(126;1.71e-07)|COAD - Colon adenocarcinoma(152;1.17e-05)|GBM - Glioblastoma multiforme(114;2.01e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000568)|KIRC - Kidney renal clear cell carcinoma(1967;0.00277)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)														---	---	---	---
E2F2	1870	broad.mit.edu	37	1	23836471	23836471	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23836471T>C	uc001bhe.1	-	7	1643	c.1215A>G	c.(1213-1215)CCA>CCG	p.P405P		NM_004091	NP_004082	Q14209	E2F2_HUMAN	E2F transcription factor 2	405	Transactivation (Potential).				G1 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(2)|skin(2)	4		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.52e-24)|Colorectal(126;6.25e-08)|COAD - Colon adenocarcinoma(152;3.42e-06)|GBM - Glioblastoma multiforme(114;8.98e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00102)|KIRC - Kidney renal clear cell carcinoma(1967;0.00366)|STAD - Stomach adenocarcinoma(196;0.0132)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.0888)|LUSC - Lung squamous cell carcinoma(448;0.19)														---	---	---	---
TCEB3	6924	broad.mit.edu	37	1	24083515	24083515	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24083515T>C	uc001bho.2	+	10	2295	c.2235T>C	c.(2233-2235)CCT>CCC	p.P745P		NM_003198	NP_003189	Q14241	ELOA1_HUMAN	elongin A	745					positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|viral reproduction	integral to membrane	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)														---	---	---	---
GALE	2582	broad.mit.edu	37	1	24125170	24125170	+	Missense_Mutation	SNP	G	A	A	rs142821993	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24125170G>A	uc009vqo.1	-	3	382	c.172C>T	c.(172-174)CGC>TGC	p.R58C	GALE_uc001bhv.1_Missense_Mutation_p.R58C|GALE_uc001bhw.1_Missense_Mutation_p.R58C|GALE_uc001bhx.1_Missense_Mutation_p.R58C|GALE_uc009vqp.1_Missense_Mutation_p.R58C|GALE_uc001bhy.1_Missense_Mutation_p.R58C|GALE_uc001bhz.1_5'UTR|GALE_uc001bia.2_5'Flank|GALE_uc009vqq.1_Missense_Mutation_p.R58C	NM_001127621	NP_001121093	Q14376	GALE_HUMAN	UDP-galactose-4-epimerase	58					galactose catabolic process	cytosol	coenzyme binding|protein homodimerization activity|UDP-glucose 4-epimerase activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;1.79e-24)|Colorectal(126;4.8e-08)|COAD - Colon adenocarcinoma(152;2.83e-06)|GBM - Glioblastoma multiforme(114;4.22e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0827)|LUSC - Lung squamous cell carcinoma(448;0.184)														---	---	---	---
MYOM3	127294	broad.mit.edu	37	1	24408528	24408528	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24408528G>A	uc001bin.3	-	18	2406	c.2243C>T	c.(2242-2244)GCG>GTG	p.A748V	MYOM3_uc001bim.3_Missense_Mutation_p.A405V|MYOM3_uc001bio.2_Missense_Mutation_p.A748V|MYOM3_uc001bip.1_3'UTR	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3	748	Fibronectin type-III 4.									skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)														---	---	---	---
PDIK1L	149420	broad.mit.edu	37	1	26448694	26448694	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26448694G>T	uc010oew.1	+	3	925	c.652G>T	c.(652-654)GCA>TCA	p.A218S	PDIK1L_uc001blj.3_Missense_Mutation_p.A218S|PDIK1L_uc009vsb.2_Missense_Mutation_p.A218S	NM_152835	NP_690048	Q8N165	PDK1L_HUMAN	PDLIM1 interacting kinase 1 like	218	Protein kinase.					nucleus	ATP binding|protein serine/threonine kinase activity				0		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CCDC21	64793	broad.mit.edu	37	1	26582097	26582097	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26582097G>A	uc001bls.1	+	4	775	c.644G>A	c.(643-645)AGT>AAT	p.S215N	CCDC21_uc001blr.2_Missense_Mutation_p.S215N|CCDC21_uc010ofa.1_Missense_Mutation_p.S164N	NM_022778	NP_073615	Q6P2H3	CEP85_HUMAN	coiled-coil domain containing 21	215						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)														---	---	---	---
BAI2	576	broad.mit.edu	37	1	32210244	32210244	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32210244G>A	uc001btn.2	-						BAI2_uc010ogo.1_Intron|BAI2_uc010ogp.1_Intron|BAI2_uc010ogq.1_Intron|BAI2_uc001bto.2_Intron|BAI2_uc001btq.1_Intron|BAI2_uc010ogr.1_Intron	NM_001703	NP_001694			brain-specific angiogenesis inhibitor 2						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(5)|breast(4)|ovary(2)|central_nervous_system(1)|skin(1)	13		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)														---	---	---	---
ADC	113451	broad.mit.edu	37	1	33585749	33585749	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33585749T>C	uc001bwr.2	+	12	1936	c.1349T>C	c.(1348-1350)GTG>GCG	p.V450A	ADC_uc001bws.2_Missense_Mutation_p.V450A|ADC_uc009vue.2_Missense_Mutation_p.V450A|ADC_uc001bwt.1_3'UTR|ADC_uc001bwu.2_Missense_Mutation_p.V355A|ADC_uc001bwv.2_Missense_Mutation_p.V355A|ADC_uc001bww.2_Missense_Mutation_p.V355A|ADC_uc001bwx.1_3'UTR|ADC_uc009vug.2_Missense_Mutation_p.V470A	NM_052998	NP_443724	Q96A70	ADC_HUMAN	ODC antizyme inhibitor-2	450					polyamine biosynthetic process|spermatogenesis	cytosol	arginine decarboxylase activity			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)			L-Arginine(DB00125)|Pyridoxal Phosphate(DB00114)													---	---	---	---
PHC2	1912	broad.mit.edu	37	1	33841025	33841025	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33841025C>T	uc001bxg.1	-	1	170	c.116G>A	c.(115-117)CGC>CAC	p.R39H	PHC2_uc001bxh.1_Missense_Mutation_p.R39H|PHC2_uc009vuh.1_Missense_Mutation_p.R39H|PHC2_uc001bxi.1_Missense_Mutation_p.R39H	NM_198040	NP_932157	Q8IXK0	PHC2_HUMAN	polyhomeotic-like 2 isoform a	39					multicellular organismal development	PcG protein complex	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34006749	34006749	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34006749T>C	uc001bxn.1	-	58	9035	c.9006A>G	c.(9004-9006)GGA>GGG	p.G3002G	CSMD2_uc001bxm.1_Silent_p.G3146G	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3002	Extracellular (Potential).|Sushi 22.					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	34071015	34071015	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34071015C>A	uc001bxn.1	-	43	6434	c.6405G>T	c.(6403-6405)AGG>AGT	p.R2135S	CSMD2_uc001bxm.1_Missense_Mutation_p.R2133S|CSMD2_uc001bxo.1_Missense_Mutation_p.R1006S	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2135	Sushi 12.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
ZC3H12A	80149	broad.mit.edu	37	1	37948856	37948856	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37948856G>A	uc001cbb.3	+	6	1594	c.1444G>A	c.(1444-1446)GCA>ACA	p.A482T	ZC3H12A_uc001cbc.1_Missense_Mutation_p.A277T	NM_025079	NP_079355	Q5D1E8	ZC12A_HUMAN	zinc finger CCCH-type containing 12A	482	Pro-rich.				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)																---	---	---	---
BMP8B	656	broad.mit.edu	37	1	40230378	40230378	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40230378G>T	uc001cdz.1	-	4	1161	c.785C>A	c.(784-786)CCT>CAT	p.P262H	BMP8B_uc001cea.1_Missense_Mutation_p.P287H	NM_001720	NP_001711	P34820	BMP8B_HUMAN	bone morphogenetic protein 8B preproprotein	262					cartilage development|cell differentiation|growth|ossification	extracellular space	cytokine activity|growth factor activity				0	all_cancers(7;5.56e-14)|all_lung(5;3.88e-17)|all_epithelial(6;3.78e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;1.92e-17)|all cancers(16;4.03e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)															---	---	---	---
KIAA0467	23334	broad.mit.edu	37	1	43897958	43897958	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43897958C>A	uc001cjk.1	+	22	3055	c.2593C>A	c.(2593-2595)CAT>AAT	p.H865N		NM_015284	NP_056099	Q5T011	SZT2_HUMAN	hypothetical protein LOC23334	1764						peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
PTPRF	5792	broad.mit.edu	37	1	44064544	44064544	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44064544G>A	uc001cjr.2	+	13	2613	c.2273G>A	c.(2272-2274)GGA>GAA	p.G758E	PTPRF_uc001cjs.2_Missense_Mutation_p.G758E|PTPRF_uc001cju.2_Missense_Mutation_p.G329E|PTPRF_uc009vwt.2_Missense_Mutation_p.G329E|PTPRF_uc001cjv.2_Missense_Mutation_p.G227E|PTPRF_uc001cjw.2_5'UTR	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	758	Fibronectin type-III 5.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
B4GALT2	8704	broad.mit.edu	37	1	44447544	44447544	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44447544A>G	uc001clg.2	+	3	867	c.497A>G	c.(496-498)CAC>CGC	p.H166R	B4GALT2_uc001clh.2_Missense_Mutation_p.H100R|B4GALT2_uc010okl.1_Missense_Mutation_p.H195R|B4GALT2_uc001cli.2_Missense_Mutation_p.H166R	NM_003780	NP_003771	O60909	B4GT2_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	166	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
DMAP1	55929	broad.mit.edu	37	1	44684086	44684086	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44684086G>A	uc001clq.1	+	5	577	c.497G>A	c.(496-498)CGC>CAC	p.R166H	DMAP1_uc010okt.1_Missense_Mutation_p.A205T|DMAP1_uc001clr.1_Missense_Mutation_p.R166H|DMAP1_uc001cls.1_Missense_Mutation_p.R166H|DMAP1_uc010oku.1_Missense_Mutation_p.R156H	NM_001034024	NP_001029196	Q9NPF5	DMAP1_HUMAN	DNA methyltransferase 1 associated protein 1	166	SANT.				DNA methylation|histone H2A acetylation|histone H4 acetylation|negative regulation of transcription, DNA-dependent|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex	DNA binding|protein binding				0	Acute lymphoblastic leukemia(166;0.155)															OREG0013437	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	45287514	45287514	+	IGR	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45287514C>A								BTBD19 (7713 upstream) : PTCH2 (574 downstream)																																			---	---	---	---
ZSWIM5	57643	broad.mit.edu	37	1	45671791	45671791	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45671791C>T	uc001cnd.2	-	1	460	c.232G>A	c.(232-234)GCA>ACA	p.A78T		NM_020883	NP_065934	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM domain containing 5	78							zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
KIAA0494	9813	broad.mit.edu	37	1	47149030	47149030	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47149030T>C	uc001cqk.3	-	10	2231	c.1254A>G	c.(1252-1254)CCA>CCG	p.P418P	KIAA0494_uc010omh.1_Silent_p.P354P|KIAA0494_uc010omj.1_Silent_p.P210P	NM_014774	NP_055589	O75071	K0494_HUMAN	hypothetical protein LOC9813	418							calcium ion binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
STIL	6491	broad.mit.edu	37	1	47716975	47716975	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47716975C>A	uc001crc.1	-	17	3852	c.3697G>T	c.(3697-3699)GGG>TGG	p.G1233W	TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Missense_Mutation_p.G1187W|STIL_uc010omo.1_Missense_Mutation_p.G1216W|STIL_uc001crd.1_Missense_Mutation_p.G1234W|STIL_uc001cre.1_Missense_Mutation_p.G1233W	NM_003035	NP_003026	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus isoform 2	1233					cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)																---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52759355	52759355	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52759355T>C	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																		---	---	---	---
PPAP2B	8613	broad.mit.edu	37	1	56977735	56977735	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56977735C>A	uc001cyj.1	-	6	1224	c.723G>T	c.(721-723)ACG>ACT	p.T241T		NM_177414	NP_803133	O14495	LPP3_HUMAN	phosphatidic acid phosphatase type 2B	241	Helical; (Potential).				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																		---	---	---	---
FGGY	55277	broad.mit.edu	37	1	59811947	59811947	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59811947G>A	uc001czi.3	+	4	554	c.342G>A	c.(340-342)TGG>TGA	p.W114*	FGGY_uc001czg.2_Nonsense_Mutation_p.W2*|FGGY_uc001czh.2_RNA|FGGY_uc009wac.2_Nonsense_Mutation_p.W114*|FGGY_uc001czj.3_Nonsense_Mutation_p.W114*|FGGY_uc001czk.3_Nonsense_Mutation_p.W2*|FGGY_uc001czl.3_Intron	NM_018291	NP_060761	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	114					carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)																	---	---	---	---
KANK4	163782	broad.mit.edu	37	1	62718875	62718875	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62718875C>T	uc001dah.3	-	8	2923	c.2546G>A	c.(2545-2547)TGC>TAC	p.C849Y	KANK4_uc001dai.3_Missense_Mutation_p.C221Y|KANK4_uc001daf.3_5'UTR|KANK4_uc001dag.3_Missense_Mutation_p.C205Y	NM_181712	NP_859063	Q5T7N3	KANK4_HUMAN	ankyrin repeat domain 38	849	ANK 1.									ovary(3)|skin(2)|lung(1)	6																		---	---	---	---
TTLL7	79739	broad.mit.edu	37	1	84373183	84373183	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84373183G>T	uc001djc.2	-	16	2344	c.1948C>A	c.(1948-1950)CAT>AAT	p.H650N	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	650					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)														---	---	---	---
MCOLN2	255231	broad.mit.edu	37	1	85424271	85424271	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85424271T>G	uc001dkm.2	-	3	593	c.352A>C	c.(352-354)AGC>CGC	p.S118R	MCOLN2_uc001dkn.2_RNA	NM_153259	NP_694991	Q8IZK6	MCLN2_HUMAN	mucolipin 2	118						integral to membrane	ion channel activity			ovary(3)|upper_aerodigestive_tract(1)	4				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)														---	---	---	---
GBP2	2634	broad.mit.edu	37	1	89586917	89586917	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89586917T>C	uc001dmz.1	-	3	498	c.227A>G	c.(226-228)AAG>AGG	p.K76R	GBP2_uc001dmy.1_RNA	NM_004120	NP_004111	P32456	GBP2_HUMAN	guanylate binding protein 2,	76					interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)	1		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)														---	---	---	---
GLMN	11146	broad.mit.edu	37	1	92754658	92754658	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92754658T>C	uc001dor.2	-	6	560	c.445A>G	c.(445-447)ACC>GCC	p.T149A	GLMN_uc009wdg.2_RNA|GLMN_uc001dos.2_Missense_Mutation_p.T149A	NM_053274	NP_444504	Q92990	GLMN_HUMAN	glomulin	149					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				---	---	---	---
VCAM1	7412	broad.mit.edu	37	1	101186193	101186193	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101186193A>G	uc001dti.2	+	2	346	c.226A>G	c.(226-228)ACC>GCC	p.T76A	VCAM1_uc001dtj.2_Missense_Mutation_p.T76A|VCAM1_uc010ouj.1_Intron	NM_001078	NP_001069	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1 isoform a	76	Ig-like C2-type 1.|Extracellular (Potential).				heterophilic cell-cell adhesion|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|leukocyte tethering or rolling|membrane to membrane docking|positive regulation of T cell proliferation|regulation of immune response	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex|apical part of cell|external side of plasma membrane|extracellular space|filopodium|integral to membrane|microvillus|podosome	cell adhesion molecule binding|integrin binding			central_nervous_system(1)	1		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)													---	---	---	---
AHCYL1	10768	broad.mit.edu	37	1	110561191	110561191	+	Silent	SNP	G	T	T	rs147429632		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110561191G>T	uc001dyx.2	+	13	1603	c.1236G>T	c.(1234-1236)CCG>CCT	p.P412P	AHCYL1_uc010ovw.1_Silent_p.P365P|AHCYL1_uc001dyy.2_Silent_p.P365P|AHCYL1_uc010ovx.1_Silent_p.P365P	NM_006621	NP_006612	O43865	SAHH2_HUMAN	S-adenosylhomocysteine hydrolase-like 1	412	NAD binding (By similarity).				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)														---	---	---	---
C1orf103	55791	broad.mit.edu	37	1	111494604	111494604	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111494604G>A	uc001eaa.2	-	2	1158	c.902C>T	c.(901-903)ACG>ATG	p.T301M	C1orf103_uc001dzz.2_Intron|C1orf103_uc001eab.2_Intron|C1orf103_uc001eac.1_Intron	NM_018372	NP_060842	Q5T3J3	LRIF1_HUMAN	receptor-interacting factor 1 isoform 1	301					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix	protein binding				0		all_cancers(81;1.02e-05)|all_epithelial(167;1.87e-05)|all_lung(203;0.000234)|Lung NSC(277;0.000451)		Lung(183;0.0155)|Colorectal(144;0.0314)|all cancers(265;0.082)|LUSC - Lung squamous cell carcinoma(189;0.0826)|Epithelial(280;0.0891)|COAD - Colon adenocarcinoma(174;0.134)														---	---	---	---
MOV10	4343	broad.mit.edu	37	1	113237103	113237103	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113237103A>G	uc001eck.2	+	9	1594	c.1324A>G	c.(1324-1326)ACC>GCC	p.T442A	MOV10_uc001ecl.2_Missense_Mutation_p.T442A|MOV10_uc001ecn.2_Missense_Mutation_p.T442A|MOV10_uc001ecm.2_Missense_Mutation_p.T382A|MOV10_uc009wgj.1_Missense_Mutation_p.T382A	NM_001130079	NP_001123551	Q9HCE1	MOV10_HUMAN	Mov10, Moloney leukemia virus 10, homolog	442					mRNA cleavage involved in gene silencing by miRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body	ATP binding|helicase activity|protein binding|RNA binding			ovary(4)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)														---	---	---	---
PPM1J	333926	broad.mit.edu	37	1	113253964	113253964	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113253964G>T	uc001ect.1	-	6	997	c.970C>A	c.(970-972)CTT>ATT	p.L324I	PPM1J_uc009wgl.1_RNA|PPM1J_uc001ecs.1_Missense_Mutation_p.L118I	NM_005167	NP_005158	Q5JR12	PPM1J_HUMAN	protein phosphatase 1J (PP2C domain containing)	324	PP2C-like.									breast(2)|central_nervous_system(1)	3	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
PHTF1	10745	broad.mit.edu	37	1	114267375	114267375	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114267375T>C	uc009wgp.1	-						PHTF1_uc001edn.2_Intron|PHTF1_uc010own.1_Intron	NM_006608	NP_006599			putative homeodomain transcription factor 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
FAM72B	653820	broad.mit.edu	37	1	120846037	120846037	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120846037C>A	uc009whp.2	+	3	1102	c.273C>A	c.(271-273)TCC>TCA	p.S91S	FAM72B_uc001ein.3_Silent_p.S51S	NM_001100910	NP_001094380	Q86X60	FA72B_HUMAN	hypothetical protein LOC653820	91											0	all_neural(166;0.181)	all_lung(203;7.27e-05)|Lung NSC(69;0.000389)|all_epithelial(167;0.068)		Lung(183;0.0327)|LUSC - Lung squamous cell carcinoma(189;0.19)														---	---	---	---
OTUD7B	56957	broad.mit.edu	37	1	149916793	149916793	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149916793C>T	uc001etn.2	-	12	1851	c.1495G>A	c.(1495-1497)GCA>ACA	p.A499T		NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne	499					negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)															---	---	---	---
ZNF687	57592	broad.mit.edu	37	1	151259991	151259991	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151259991C>T	uc001exq.2	+	2	1322	c.1224C>T	c.(1222-1224)AAC>AAT	p.N408N	ZNF687_uc001exp.1_Silent_p.N417N|ZNF687_uc009wmo.2_Silent_p.N408N|ZNF687_uc009wmp.2_Silent_p.N408N	NM_020832	NP_065883	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	408					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding			central_nervous_system(3)|ovary(1)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
MIR554	693139	broad.mit.edu	37	1	151518351	151518351	+	RNA	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151518351T>C	hsa-mir-554|MI0003559	+			c.80T>C			TUFT1_uc001eyl.2_Intron|TUFT1_uc001eym.2_Intron|TUFT1_uc010pdf.1_Intron|TUFT1_uc010pdg.1_Intron																	0																		---	---	---	---
TCHH	7062	broad.mit.edu	37	1	152082434	152082434	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152082434G>A	uc001ezp.2	-	2	3259	c.3259C>T	c.(3259-3261)CAG>TAG	p.Q1087*	TCHH_uc009wne.1_Nonsense_Mutation_p.Q1087*	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1087	10 X 30 AA tandem repeats.|4-7.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
HRNR	388697	broad.mit.edu	37	1	152188549	152188549	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152188549G>A	uc001ezt.1	-	3	5632	c.5556C>T	c.(5554-5556)TCC>TCT	p.S1852S		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	1852	20.				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)															---	---	---	---
KCNN3	3782	broad.mit.edu	37	1	154698452	154698452	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154698452T>A	uc001ffp.2	-	5	1955	c.1641A>T	c.(1639-1641)GAA>GAT	p.E547D	KCNN3_uc001ffo.2_Missense_Mutation_p.E242D	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium	552						integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)															---	---	---	---
THBS3	7059	broad.mit.edu	37	1	155168382	155168382	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155168382C>A	uc001fix.2	-	17	1915	c.1892G>T	c.(1891-1893)GGG>GTG	p.G631V	RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Missense_Mutation_p.G622V|THBS3_uc001fiz.2_Missense_Mutation_p.G594V|THBS3_uc001fiy.2_Missense_Mutation_p.G160V|THBS3_uc010pfu.1_Missense_Mutation_p.G511V|THBS3_uc010pfv.1_RNA	NM_007112	NP_009043	P49746	TSP3_HUMAN	thrombospondin 3 precursor	631	TSP type-3 6.				cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
HCN3	57657	broad.mit.edu	37	1	155255714	155255714	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155255714G>A	uc001fjz.1	+	6	1444	c.1436G>A	c.(1435-1437)GGC>GAC	p.G479D	RAG1AP1_uc010pey.1_Intron|HCN3_uc010pfz.1_Missense_Mutation_p.G174D	NM_020897	NP_065948	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic	479	Cytoplasmic (Potential).|cAMP.					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)|breast(1)	2	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
HCN3	57657	broad.mit.edu	37	1	155257084	155257084	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155257084G>A	uc001fjz.1	+	7	1606	c.1598G>A	c.(1597-1599)CGC>CAC	p.R533H	RAG1AP1_uc010pey.1_Intron|HCN3_uc010pfz.1_Missense_Mutation_p.R228H	NM_020897	NP_065948	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic	533	Cytoplasmic (Potential).|cAMP.					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)|breast(1)	2	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
FCRL4	83417	broad.mit.edu	37	1	157557696	157557696	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157557696T>C	uc001fqw.2	-	4	657	c.521A>G	c.(520-522)AAT>AGT	p.N174S	FCRL4_uc010phy.1_Intron	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor	174	Extracellular (Potential).|Ig-like C2-type 2.					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)																---	---	---	---
CD5L	922	broad.mit.edu	37	1	157805724	157805724	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157805724A>G	uc001frk.3	-	3	420	c.277T>C	c.(277-279)TCA>CCA	p.S93P		NM_005894	NP_005885	O43866	CD5L_HUMAN	CD5 molecule-like precursor	93	SRCR 1.				apoptosis|cellular defense response	extracellular space|membrane	scavenger receptor activity			ovary(1)	1	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)															---	---	---	---
OR10T2	128360	broad.mit.edu	37	1	158368769	158368769	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158368769A>G	uc010pih.1	-	1	488	c.488T>C	c.(487-489)CTC>CCC	p.L163P		NM_001004475	NP_001004475	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T,	163	Extracellular (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)																	---	---	---	---
OR10T2	128360	broad.mit.edu	37	1	158368995	158368995	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158368995A>G	uc010pih.1	-	1	262	c.262T>C	c.(262-264)TCA>CCA	p.S88P		NM_001004475	NP_001004475	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T,	88	Extracellular (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)																	---	---	---	---
DARC	2532	broad.mit.edu	37	1	159176186	159176186	+	Silent	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159176186G>T	uc001fto.2	+	2	1197	c.957G>T	c.(955-957)CTG>CTT	p.L319L	DARC_uc001ftp.3_Silent_p.L321L	NM_002036	NP_002027	Q16570	DUFFY_HUMAN	Duffy blood group antigen isoform b	319	Cytoplasmic (Potential).				defense response	integral to membrane|plasma membrane	C-C chemokine binding|chemokine receptor activity			ovary(1)|lung(1)	2	all_hematologic(112;0.0429)																	---	---	---	---
FMO4	2329	broad.mit.edu	37	1	171310826	171310826	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171310826G>A	uc001gho.2	+	10	1742	c.1525G>A	c.(1525-1527)GCC>ACC	p.A509T		NM_002022	NP_002013	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	509					xenobiotic metabolic process	integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			kidney(2)|skin(1)	3	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
PIGC	5279	broad.mit.edu	37	1	172411772	172411772	+	5'UTR	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172411772A>G	uc001gil.2	-	2					PIGC_uc001gii.1_Intron|PIGC_uc001gij.1_Intron|C1orf105_uc001gik.2_Intron|PIGC_uc001gin.2_5'UTR|PIGC_uc001gio.2_5'UTR	NM_153747	NP_714969			phosphatidylinositol glycan, class C						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			lung(1)	1																		---	---	---	---
GAS5	60674	broad.mit.edu	37	1	173834756	173834756	+	Intron	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173834756A>C	uc001gji.2	-						GAS5_uc001gjj.2_Intron|GAS5_uc001gjk.2_Intron|SNORD81_uc009wwi.1_5'Flank|SNORD47_uc001gjl.2_5'Flank|SNORD80_uc009wwj.1_5'Flank|SNORD79_uc009wwk.1_5'Flank|ZBTB37_uc001gjp.1_5'Flank|ZBTB37_uc001gjq.3_5'Flank|ZBTB37_uc009wwp.1_5'Flank|ZBTB37_uc001gjr.2_5'Flank					Homo sapiens mRNA; cDNA DKFZp564D0164 (from clone DKFZp564D0164).												0																		---	---	---	---
TNN	63923	broad.mit.edu	37	1	175067511	175067511	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175067511G>C	uc001gkl.1	+	9	2012	c.1899G>C	c.(1897-1899)GAG>GAC	p.E633D	TNN_uc010pmx.1_Missense_Mutation_p.E544D	NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N precursor	633	Fibronectin type-III 5.				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)														---	---	---	---
FAM5B	57795	broad.mit.edu	37	1	177250122	177250122	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177250122C>T	uc001glf.2	+	8	2122	c.1810C>T	c.(1810-1812)CCT>TCT	p.P604S	FAM5B_uc001glg.2_Missense_Mutation_p.P499S	NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B	604						extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181680124	181680124	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181680124C>T	uc001gow.2	+	8	1255	c.1090C>T	c.(1090-1092)CGA>TGA	p.R364*	CACNA1E_uc009wxs.2_Nonsense_Mutation_p.R271*	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	364	Cytoplasmic (Potential).				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
RGS16	6004	broad.mit.edu	37	1	182572417	182572417	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182572417G>T	uc001gpl.3	-	2	256	c.102C>A	c.(100-102)TGC>TGA	p.C34*	RGS16_uc010pnv.1_Nonsense_Mutation_p.C34*	NM_002928	NP_002919	O15492	RGS16_HUMAN	regulator of G-protein signalling 16	34					negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception	cytoplasm|plasma membrane	calmodulin binding|GTPase activator activity|signal transducer activity			ovary(1)	1																		---	---	---	---
PRG4	10216	broad.mit.edu	37	1	186276875	186276875	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186276875A>G	uc001gru.3	+	7	2075	c.2024A>G	c.(2023-2025)AAC>AGC	p.N675S	PRG4_uc001grt.3_Missense_Mutation_p.N634S|PRG4_uc009wyl.2_Missense_Mutation_p.N582S|PRG4_uc009wym.2_Missense_Mutation_p.N541S|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	675	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
PTPRC	5788	broad.mit.edu	37	1	198711490	198711490	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198711490A>G	uc001gur.1	+	25	2865	c.2685A>G	c.(2683-2685)CAA>CAG	p.Q895Q	PTPRC_uc001gus.1_Silent_p.Q847Q|PTPRC_uc001gut.1_Silent_p.Q734Q	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	895	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1.	Substrate (By similarity).			axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12																		---	---	---	---
FMOD	2331	broad.mit.edu	37	1	203316677	203316677	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203316677C>A	uc001gzr.2	-	2	858	c.722G>T	c.(721-723)GGG>GTG	p.G241V	FMOD_uc010pqi.1_RNA	NM_002023	NP_002014	Q06828	FMOD_HUMAN	fibromodulin precursor	241	LRR 6.				transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)															---	---	---	---
GOLT1A	127845	broad.mit.edu	37	1	204168355	204168355	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204168355C>A	uc001has.1	-	4	514	c.328G>T	c.(328-330)GGC>TGC	p.G110C	KISS1_uc001har.2_5'Flank|GOLT1A_uc001hat.1_Missense_Mutation_p.G110C	NM_198447	NP_940849	Q6ZVE7	GOT1A_HUMAN	golgi transport 1 homolog A	110	Helical; Name=4; (Potential).				protein transport|vesicle-mediated transport	Golgi membrane|integral to membrane					0	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.244)															---	---	---	---
LRRN2	10446	broad.mit.edu	37	1	204588803	204588803	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204588803C>T	uc001hbe.1	-	3	706	c.318G>A	c.(316-318)TCG>TCA	p.S106S	MDM4_uc001hbd.1_Intron|LRRN2_uc001hbf.1_Silent_p.S106S|LRRN2_uc009xbf.1_Silent_p.S106S|MDM4_uc001hbc.2_Intron	NM_006338	NP_006329	O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2 precursor	106	LRR 2.|Extracellular (Potential).				cell adhesion	integral to membrane	receptor activity			central_nervous_system(2)	2	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)															---	---	---	---
TMCC2	9911	broad.mit.edu	37	1	205238824	205238824	+	Silent	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205238824T>G	uc001hbz.1	+	4	1938	c.1494T>G	c.(1492-1494)GGT>GGG	p.G498G	TMCC2_uc010prf.1_Silent_p.G420G|TMCC2_uc001hca.2_Silent_p.G273G|TMCC2_uc001hcb.1_Silent_p.G258G|TMCC2_uc001hcc.1_Silent_p.G119G|TMCC2_uc001hcd.2_Silent_p.G265G	NM_014858	NP_055673	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	498						integral to membrane	protein binding			pancreas(1)	1	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)															---	---	---	---
TMCC2	9911	broad.mit.edu	37	1	205241213	205241213	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205241213C>T	uc001hbz.1	+	6	2535	c.2091C>T	c.(2089-2091)TCC>TCT	p.S697S	TMCC2_uc010prf.1_Silent_p.S619S|TMCC2_uc001hca.2_Silent_p.S472S|TMCC2_uc001hcb.1_Silent_p.S457S|TMCC2_uc001hcc.1_Silent_p.S318S|TMCC2_uc001hcd.2_3'UTR	NM_014858	NP_055673	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	697	Helical; (Potential).					integral to membrane	protein binding			pancreas(1)	1	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)															---	---	---	---
CR1	1378	broad.mit.edu	37	1	207787753	207787753	+	Nonsense_Mutation	SNP	C	T	T	rs55749440		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207787753C>T	uc001hfy.2	+	32	5370	c.5230C>T	c.(5230-5232)CGA>TGA	p.R1744*	CR1_uc001hfx.2_Nonsense_Mutation_p.R2194*	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	1744	Extracellular (Potential).|Sushi 27.				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3																		---	---	---	---
CR1	1378	broad.mit.edu	37	1	207787831	207787831	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207787831G>T	uc001hfy.2	+	32	5448	c.5308G>T	c.(5308-5310)GAA>TAA	p.E1770*	CR1_uc001hfx.2_Nonsense_Mutation_p.E2220*	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	1770	Extracellular (Potential).|Sushi 27.				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3																		---	---	---	---
CENPF	1063	broad.mit.edu	37	1	214832209	214832209	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214832209G>A	uc001hkm.2	+	19	9153	c.8979G>A	c.(8977-8979)CCG>CCA	p.P2993P		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	3089	Sufficient for nuclear localization.|Sufficient for centromere localization.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)												OREG0014250	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215916618	215916618	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215916618T>G	uc001hku.1	-	59	11836	c.11449A>C	c.(11449-11451)ACA>CCA	p.T3817P		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3817	Fibronectin type-III 23.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216595572	216595572	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216595572A>C	uc001hku.1	-	2	494	c.107T>G	c.(106-108)CTT>CGT	p.L36R	USH2A_uc001hkv.2_Missense_Mutation_p.L36R	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	36	Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
LEFTY2	7044	broad.mit.edu	37	1	226125285	226125285	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226125285C>T	uc001hpt.1	-	4	1037	c.957G>A	c.(955-957)TCG>TCA	p.S319S	LEFTY2_uc010pvk.1_Silent_p.S285S|LEFTY2_uc009xek.1_3'UTR	NM_003240	NP_003231	O00292	LFTY2_HUMAN	endometrial bleeding associated factor	319					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)																	---	---	---	---
CABC1	56997	broad.mit.edu	37	1	227174190	227174190	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227174190C>A	uc001hqm.1	+	20	5115	c.1696C>A	c.(1696-1698)CTG>ATG	p.L566M	CABC1_uc001hqn.1_Missense_Mutation_p.L566M|CABC1_uc009xeq.1_Missense_Mutation_p.L514M|CABC1_uc010pvq.1_Missense_Mutation_p.L287M|CABC1_uc010pvr.1_Missense_Mutation_p.L240M|CABC1_uc001hqo.1_Missense_Mutation_p.L287M|CABC1_uc009xer.1_Missense_Mutation_p.L82M	NM_020247	NP_064632	Q8NI60	ADCK3_HUMAN	chaperone, ABC1 activity of bc1 complex like	566					cell death	mitochondrion	ATP binding|protein serine/threonine kinase activity				0		Prostate(94;0.0771)																---	---	---	---
JMJD4	65094	broad.mit.edu	37	1	227920624	227920624	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227920624G>A	uc001hrb.2	-	5	1065	c.1065C>T	c.(1063-1065)AGC>AGT	p.S355S	SNAP47_uc001hqz.2_Intron|SNAP47_uc001hra.2_Intron|SNAP47_uc001hrd.2_5'Flank|SNAP47_uc001hre.2_5'Flank|SNAP47_uc001hrf.2_5'Flank|LOC100130093_uc001hqx.3_RNA|LOC100130093_uc001hqy.3_RNA|JMJD4_uc001hrc.2_Intron	NM_023007	NP_075383	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4 isoform 1	355											0		Prostate(94;0.0885)																---	---	---	---
LYST	1130	broad.mit.edu	37	1	235914579	235914579	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235914579G>A	uc001hxj.2	-	28	7886	c.7711C>T	c.(7711-7713)CTC>TTC	p.L2571F	LYST_uc009xga.1_Missense_Mutation_p.L153F	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	2571					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				---	---	---	---
OR2L3	391192	broad.mit.edu	37	1	248224181	248224181	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248224181C>A	uc001idx.1	+	1	198	c.198C>A	c.(196-198)TCC>TCA	p.S66S	OR2L13_uc001ids.2_Intron	NM_001004687	NP_001004687	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L,	66	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)															---	---	---	---
OR2L13	284521	broad.mit.edu	37	1	248263381	248263381	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248263381A>G	uc001ids.2	+	3	1041	c.704A>G	c.(703-705)AAG>AGG	p.K235R		NM_175911	NP_787107	Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L,	235	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)															---	---	---	---
PXDN	7837	broad.mit.edu	37	2	1647304	1647304	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1647304G>C	uc002qxa.2	-	19	3852	c.3788C>G	c.(3787-3789)ACT>AGT	p.T1263S		NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	1263					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)														---	---	---	---
NOL10	79954	broad.mit.edu	37	2	10747419	10747419	+	Silent	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10747419G>T	uc002raq.2	-	14	1170	c.1045C>A	c.(1045-1047)CGG>AGG	p.R349R	NOL10_uc010yje.1_Silent_p.R323R|NOL10_uc010yjf.1_Silent_p.R299R|NOL10_uc002rap.2_Silent_p.R299R	NM_024894	NP_079170	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	349	WD 5.					nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)														---	---	---	---
GREB1	9687	broad.mit.edu	37	2	11755363	11755363	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11755363A>G	uc002rbk.1	+	20	3569	c.3269A>G	c.(3268-3270)GAT>GGT	p.D1090G	GREB1_uc002rbp.1_Missense_Mutation_p.D88G	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1090						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)														---	---	---	---
GEN1	348654	broad.mit.edu	37	2	17962826	17962826	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17962826A>G	uc002rct.2	+	14	2420	c.2347A>G	c.(2347-2349)ATG>GTG	p.M783V	SMC6_uc010exo.2_Intron|GEN1_uc010yjs.1_Missense_Mutation_p.M783V|GEN1_uc002rcu.2_Missense_Mutation_p.M783V	NM_182625	NP_872431	Q17RS7	GEN_HUMAN	Gen homolog 1, endonuclease	783					DNA repair	nucleus	DNA binding|endonuclease activity|metal ion binding			breast(5)|kidney(1)|central_nervous_system(1)|skin(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)												Homologous_recombination					---	---	---	---
HADHB	3032	broad.mit.edu	37	2	26505927	26505927	+	Intron	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26505927G>T	uc002rgz.2	+						HADHB_uc010ykv.1_Intron|HADHB_uc010ykw.1_Intron|HADHB_uc002rha.2_Intron|HADHB_uc010ykx.1_Intron	NM_000183	NP_000174			mitochondrial trifunctional protein, beta						fatty acid beta-oxidation	mitochondrial nucleoid	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acyltransferase activity|enoyl-CoA hydratase activity|protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
DPYSL5	56896	broad.mit.edu	37	2	27157527	27157527	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27157527C>T	uc002rhu.3	+	8	1030	c.872C>T	c.(871-873)GCG>GTG	p.A291V	DPYSL5_uc002rhv.3_Missense_Mutation_p.A291V	NM_020134	NP_064519	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	291					axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
ABHD1	84696	broad.mit.edu	37	2	27351926	27351926	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27351926G>T	uc002rit.2	+	3	549	c.389G>T	c.(388-390)GGC>GTC	p.G130V	ABHD1_uc002riu.2_RNA|ABHD1_uc002riv.2_RNA	NM_032604	NP_115993	Q96SE0	ABHD1_HUMAN	abhydrolase domain-containing protein 1	130						integral to membrane	carboxylesterase activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
WDR43	23160	broad.mit.edu	37	2	29135551	29135551	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29135551T>G	uc002rmo.2	+	4	613	c.581T>G	c.(580-582)GTT>GGT	p.V194G	SNORD92_uc002rmp.1_5'Flank	NM_015131	NP_055946	Q15061	WDR43_HUMAN	WD repeat domain 43	194	WD 4.					nucleolus				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
FAM179A	165186	broad.mit.edu	37	2	29237433	29237433	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29237433T>C	uc010ezl.2	+						FAM179A_uc010ymm.1_Intron|FAM179A_uc002rmr.3_Intron	NM_199280	NP_954974			hypothetical protein LOC165186								binding			ovary(3)|skin(1)	4																		---	---	---	---
C2orf71	388939	broad.mit.edu	37	2	29293519	29293519	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29293519C>T	uc002rmt.1	-	1	3609	c.3609G>A	c.(3607-3609)CCG>CCA	p.P1203P		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	1203					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1																		---	---	---	---
CEBPZ	10153	broad.mit.edu	37	2	37455474	37455474	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37455474T>C	uc002rpz.2	-	2	892	c.862A>G	c.(862-864)ACT>GCT	p.T288A		NM_005760	NP_005751	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein zeta	288					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding			pancreas(1)	1		all_hematologic(82;0.21)																---	---	---	---
SFRS7	6432	broad.mit.edu	37	2	38977264	38977264	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38977264T>C	uc002rqz.2	-	2	339	c.101A>G	c.(100-102)TAT>TGT	p.Y34C	SFRS7_uc002rra.2_RNA|SFRS7_uc010ynp.1_Missense_Mutation_p.Y34C|GEMIN6_uc002rrb.2_5'Flank	NM_001031684	NP_001026854	Q16629	SRSF7_HUMAN	splicing factor, arginine/serine-rich 7	34	RRM.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding|zinc ion binding				0		all_hematologic(82;0.248)																---	---	---	---
THUMPD2	80745	broad.mit.edu	37	2	39996850	39996850	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39996850C>A	uc002rru.2	-	3	709	c.672G>T	c.(670-672)CAG>CAT	p.Q224H	THUMPD2_uc002rrv.2_RNA|THUMPD2_uc010ynt.1_Intron|THUMPD2_uc010ynu.1_Missense_Mutation_p.Q224H	NM_025264	NP_079540	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	224	THUMP.						methyltransferase activity			skin(1)	1		all_hematologic(82;0.248)																---	---	---	---
PKDCC	91461	broad.mit.edu	37	2	42284800	42284800	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42284800A>G	uc002rsg.2	+	7	1633	c.1454A>G	c.(1453-1455)AAG>AGG	p.K485R		NM_138370	NP_612379	Q504Y2	PKDCC_HUMAN	protein kinase-like protein SgK493	485	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																		---	---	---	---
EML4	27436	broad.mit.edu	37	2	42513521	42513521	+	Splice_Site	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42513521T>C	uc002rsi.2	+	10	1384	c.1122_splice	c.e10+2	p.A374_splice	EML4_uc010fap.2_Splice_Site_p.A316_splice|EML4_uc002rsj.2_Splice_Site_p.A63_splice	NM_019063	NP_061936			echinoderm microtubule associated protein like 4						microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250								T	ALK	NSCLC								---	---	---	---
PAPOLG	64895	broad.mit.edu	37	2	61022147	61022147	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61022147C>T	uc002sai.2	+	21	2335	c.2104C>T	c.(2104-2106)CGC>TGC	p.R702C	PAPOLG_uc002saj.2_Missense_Mutation_p.R391C|PAPOLG_uc002sak.2_Missense_Mutation_p.R237C|PAPOLG_uc010fch.2_Missense_Mutation_p.R369C	NM_022894	NP_075045	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	702					mRNA processing|RNA polyadenylation|transcription, DNA-dependent	nucleus	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity|RNA binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)															---	---	---	---
XPO1	7514	broad.mit.edu	37	2	61721063	61721063	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61721063G>T	uc002sbj.2	-	12	1939	c.1211C>A	c.(1210-1212)CCC>CAC	p.P404H	XPO1_uc010fcl.2_Missense_Mutation_p.P400H|XPO1_uc010ypn.1_Missense_Mutation_p.P400H|XPO1_uc002sbk.2_5'UTR|XPO1_uc002sbh.2_Missense_Mutation_p.P51H	NM_003400	NP_003391	O14980	XPO1_HUMAN	exportin 1	404	HEAT 3.|Necessary for HTLV-1 Rex-mediated mRNA export.|Interaction with Ran and nuclear export complex formation.				intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)															---	---	---	---
PELI1	57162	broad.mit.edu	37	2	64327600	64327600	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64327600A>G	uc002scs.3	-	3	4274	c.235T>C	c.(235-237)TAT>CAT	p.Y79H	PELI1_uc002sct.3_Missense_Mutation_p.Y79H|PELI1_uc002scr.3_5'Flank	NM_020651	NP_065702	Q96FA3	PELI1_HUMAN	pellino protein	79					innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol				ovary(1)	1																		---	---	---	---
MPHOSPH10	10199	broad.mit.edu	37	2	71377061	71377061	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71377061A>G	uc002sht.1	+	11	2314	c.1962A>G	c.(1960-1962)GTA>GTG	p.V654V		NM_005791	NP_005782	O00566	MPP10_HUMAN	M-phase phosphoprotein 10	654	Potential.				RNA splicing, via transesterification reactions|rRNA processing	chromosome|nucleolus|small nucleolar ribonucleoprotein complex	protein binding			skin(2)|ovary(1)	3																		---	---	---	---
ALMS1	7840	broad.mit.edu	37	2	73678505	73678505	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73678505C>T	uc002sje.1	+	10	4965	c.4854C>T	c.(4852-4854)TCC>TCT	p.S1618S	ALMS1_uc002sjf.1_Silent_p.S1574S|ALMS1_uc002sjg.2_Silent_p.S1004S|ALMS1_uc002sjh.1_Silent_p.S1004S	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1616	23.|34 X 47 AA approximate tandem repeat.				G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9																		---	---	---	---
LOXL3	84695	broad.mit.edu	37	2	74776634	74776634	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74776634G>A	uc002smp.1	-	4	626	c.554C>T	c.(553-555)ACG>ATG	p.T185M	LOXL3_uc002smo.1_Translation_Start_Site|LOXL3_uc010ffm.1_Missense_Mutation_p.T185M|LOXL3_uc002smq.1_Intron|LOXL3_uc010ffn.1_Intron|DOK1_uc002smr.2_Intron	NM_032603	NP_115992	P58215	LOXL3_HUMAN	lysyl oxidase-like 3 precursor	185	SRCR 2.					extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity				0																		---	---	---	---
KCMF1	56888	broad.mit.edu	37	2	85280273	85280273	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85280273T>C	uc002sox.3	+	7	1231	c.887T>C	c.(886-888)TTG>TCG	p.L296S		NM_020122	NP_064507	Q9P0J7	KCMF1_HUMAN	potassium channel modulatory factor 1	296						intracellular	ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
POLR1A	25885	broad.mit.edu	37	2	86315957	86315957	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86315957C>A	uc002sqs.2	-	5	956	c.577G>T	c.(577-579)GCT>TCT	p.A193S	POLR1A_uc002sqv.2_Missense_Mutation_p.A193S	NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A	193					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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	89291996	89291996	+	RNA	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89291996G>T	uc010ytr.1	-	82		c.7210C>A			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
ARID5A	10865	broad.mit.edu	37	2	97217702	97217702	+	Silent	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97217702A>C	uc002swe.2	+	7	1537	c.1437A>C	c.(1435-1437)GCA>GCC	p.A479A	ARID5A_uc010yuq.1_Silent_p.A427A|ARID5A_uc002swf.2_Silent_p.A315A|ARID5A_uc002swg.2_Silent_p.A427A	NM_212481	NP_997646	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A	479					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding				0																		---	---	---	---
CHST10	9486	broad.mit.edu	37	2	101010201	101010201	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101010201C>T	uc002tam.2	-	7	936	c.577G>A	c.(577-579)GAA>AAA	p.E193K		NM_004854	NP_004845	O43529	CHSTA_HUMAN	HNK-1 sulfotransferase	193	PAPS (Probable).|Lumenal (Potential).				carbohydrate biosynthetic process|cell adhesion	Golgi membrane|integral to membrane|membrane fraction				ovary(1)	1																		---	---	---	---
TBC1D8	11138	broad.mit.edu	37	2	101656720	101656720	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101656720G>A	uc010fiv.2	-	6	1086	c.955C>T	c.(955-957)CGG>TGG	p.R319W	TBC1D8_uc010yvw.1_Missense_Mutation_p.R334W|TBC1D8_uc002tau.3_Missense_Mutation_p.R76W	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8	319	GRAM 2.				blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3																		---	---	---	---
RANBP2	5903	broad.mit.edu	37	2	109400209	109400209	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109400209T>C	uc002tem.3	+	29	9653	c.9527T>C	c.(9526-9528)CTG>CCG	p.L3176P		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	3176	PPIase cyclophilin-type.				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																		---	---	---	---
SEPT10	151011	broad.mit.edu	37	2	110332309	110332309	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110332309A>G	uc002tew.2	-	5	828	c.449T>C	c.(448-450)TTT>TCT	p.F150S	SEPT10_uc010ywu.1_Intron|SEPT10_uc002tex.2_Missense_Mutation_p.F127S|SEPT10_uc002tey.2_Missense_Mutation_p.F150S|SEPT10_uc010ywv.1_Missense_Mutation_p.F16S|SEPT10_uc002tev.1_5'UTR|SEPT10_uc010fjo.2_RNA	NM_144710	NP_653311	Q9P0V9	SEP10_HUMAN	septin 10 isoform 1	150					cell cycle|cell division	septin complex	GTP binding				0																		---	---	---	---
MAP3K2	10746	broad.mit.edu	37	2	128065338	128065338	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128065338C>T	uc002toj.1	-	16	1742	c.1677G>A	c.(1675-1677)CCG>CCA	p.P559P		NM_006609	NP_006600	Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase	559	Protein kinase.				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	128477098	128477098	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128477098C>T	uc002tpg.1	-	16	2684	c.2501G>A	c.(2500-2502)CGA>CAA	p.R834Q		NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1	834					postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)														---	---	---	---
POTEF	728378	broad.mit.edu	37	2	130832662	130832662	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130832662G>A	uc010fmh.2	-	17	2783	c.2383C>T	c.(2383-2385)CGT>TGT	p.R795C		NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on	795	Actin-like.					cell cortex	ATP binding			skin(3)|ovary(2)	5																		---	---	---	---
PLEKHB2	55041	broad.mit.edu	37	2	131890528	131890528	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131890528T>C	uc002tsg.3	+	6	947	c.387T>C	c.(385-387)CCT>CCC	p.P129P	PLEKHB2_uc002tsh.2_Silent_p.P129P|PLEKHB2_uc002tsj.3_Silent_p.P129P|PLEKHB2_uc002tsf.3_Silent_p.P129P|PLEKHB2_uc010zao.1_Silent_p.P79P|PLEKHB2_uc010zap.1_Silent_p.P129P|PLEKHB2_uc010zaq.1_Intron|PLEKHB2_uc002tsi.3_Silent_p.P170P	NM_001100623	NP_001094093	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B	129						membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0828)														---	---	---	---
GPR39	2863	broad.mit.edu	37	2	133174707	133174707	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133174707T>C	uc002ttl.2	+	1	561	c.92T>C	c.(91-93)ATC>ACC	p.I31T		NM_001508	NP_001499	O43194	GPR39_HUMAN	G protein-coupled receptor 39	31	Helical; Name=1; (Potential).					integral to plasma membrane	G-protein coupled receptor activity|metal ion binding				0																		---	---	---	---
SCN2A	6326	broad.mit.edu	37	2	166246213	166246213	+	Missense_Mutation	SNP	C	T	T	rs112098080		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166246213C>T	uc002udc.2	+	27	6187	c.5897C>T	c.(5896-5898)ACG>ATG	p.T1966M	SCN2A_uc002udd.2_Missense_Mutation_p.T1966M|SCN2A_uc002ude.2_Missense_Mutation_p.T1966M	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	1966					myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)													---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168108385	168108385	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168108385G>A	uc002udx.2	+	8	10501	c.10483G>A	c.(10483-10485)GGA>AGA	p.G3495R	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.G3320R|XIRP2_uc010fpq.2_Missense_Mutation_p.G3273R|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	3320					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
MYO3B	140469	broad.mit.edu	37	2	171242744	171242744	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171242744G>A	uc002ufy.2	+	13	1479	c.1336G>A	c.(1336-1338)GCC>ACC	p.A446T	MYO3B_uc002ufv.2_Missense_Mutation_p.A433T|MYO3B_uc010fqb.1_Missense_Mutation_p.A433T|MYO3B_uc002ufz.2_Missense_Mutation_p.A446T|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2	446	Myosin head-like.				response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19																		---	---	---	---
DYNC1I2	1781	broad.mit.edu	37	2	172546719	172546719	+	Silent	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172546719G>T	uc002uha.1	+	2	219	c.54G>T	c.(52-54)CTG>CTT	p.L18L	DYNC1I2_uc002uhc.2_Silent_p.L18L|DYNC1I2_uc002uhb.1_Silent_p.L18L|DYNC1I2_uc010zds.1_Silent_p.L18L|DYNC1I2_uc002uhd.1_Silent_p.L18L|DYNC1I2_uc002uhe.1_Silent_p.L18L|DYNC1I2_uc002uhf.1_Silent_p.L18L|DYNC1I2_uc010zdt.1_Silent_p.L18L	NM_001378	NP_001369	Q13409	DC1I2_HUMAN	dynein, cytoplasmic 1, intermediate chain 2	18					G2/M transition of mitotic cell cycle|interspecies interaction between organisms|microtubule-based movement|transport	centrosome|cytosol|dynein complex|microtubule|vesicle	microtubule motor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.198)															---	---	---	---
SLC25A12	8604	broad.mit.edu	37	2	172650186	172650186	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172650186A>T	uc002uhh.2	-	14	1486	c.1397T>A	c.(1396-1398)GTC>GAC	p.V466D	SLC25A12_uc010fqh.2_Missense_Mutation_p.V359D	NM_003705	NP_003696	O75746	CMC1_HUMAN	solute carrier family 25, member 12	466	Solcar 2.				gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)													---	---	---	---
MSTN	2660	broad.mit.edu	37	2	190925074	190925074	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190925074G>A	uc002urp.2	-	2	594	c.461C>T	c.(460-462)GCC>GTC	p.A154V		NM_005259	NP_005250	O14793	GDF8_HUMAN	myostatin precursor	154					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)															---	---	---	---
KCTD18	130535	broad.mit.edu	37	2	201355178	201355178	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201355178G>A	uc002uvs.2	-	7	1443	c.926C>T	c.(925-927)GCG>GTG	p.A309V	KCTD18_uc002uvt.2_Missense_Mutation_p.A309V	NM_152387	NP_689600	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain	309						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
CASP8	841	broad.mit.edu	37	2	202149988	202149988	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202149988G>T	uc002uxr.1	+	9	1461	c.1252G>T	c.(1252-1254)GGA>TGA	p.G418*	CASP8_uc002uxp.1_Nonsense_Mutation_p.G435*|CASP8_uc002uxq.1_Nonsense_Mutation_p.G403*|CASP8_uc002uxt.1_Nonsense_Mutation_p.G477*|CASP8_uc002uxu.1_RNA|CASP8_uc002uxw.1_Nonsense_Mutation_p.G403*|CASP8_uc002uxy.1_Intron|CASP8_uc002uxx.1_Intron|CASP8_uc010ftf.2_Nonsense_Mutation_p.G334*	NM_033355	NP_203519	Q14790	CASP8_HUMAN	caspase 8 isoform B precursor	418					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)			---	---	---	---
NRP2	8828	broad.mit.edu	37	2	206641015	206641015	+	Intron	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206641015C>A	uc002vaw.2	+						NRP2_uc002vau.2_Missense_Mutation_p.P829H|NRP2_uc002vav.2_Missense_Mutation_p.P824H|NRP2_uc002vax.2_Intron|NRP2_uc002vay.2_Intron	NM_201266	NP_957718			neuropilin 2 isoform 1 precursor						angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4																OREG0015157	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ZDBF2	57683	broad.mit.edu	37	2	207174987	207174987	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207174987C>T	uc002vbp.2	+	5	5985	c.5735C>T	c.(5734-5736)GCC>GTC	p.A1912V		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1912							nucleic acid binding|zinc ion binding			ovary(3)	3																		---	---	---	---
FAM119A	151194	broad.mit.edu	37	2	208477826	208477826	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208477826C>T	uc002vcf.2	-	4	761	c.601G>A	c.(601-603)GAA>AAA	p.E201K	FAM119A_uc002vce.2_Intron|FAM119A_uc010fuk.1_Missense_Mutation_p.E201K|FAM119A_uc002vcg.3_Missense_Mutation_p.E201K	NM_145280	NP_660323	Q8WXB1	MT21A_HUMAN	hypothetical protein LOC151194	201						integral to membrane	methyltransferase activity				0				LUSC - Lung squamous cell carcinoma(261;0.0705)|Epithelial(149;0.131)|Lung(261;0.135)														---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210558727	210558727	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210558727C>A	uc002vde.1	+	7	2081	c.1833C>A	c.(1831-1833)CCC>CCA	p.P611P	MAP2_uc002vdc.1_Silent_p.P611P|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Silent_p.P607P	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	611					central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
UNC80	285175	broad.mit.edu	37	2	210650864	210650864	+	Silent	SNP	A	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210650864A>T	uc010zjc.1	+	5	755	c.675A>T	c.(673-675)GGA>GGT	p.G225G	UNC80_uc002vdj.1_Silent_p.G225G	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1	225						integral to membrane					0																		---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212285296	212285296	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212285296T>C	uc002veg.1	-	25	3103	c.3005A>G	c.(3004-3006)AAG>AGG	p.K1002R	ERBB4_uc002veh.1_Missense_Mutation_p.K1002R|ERBB4_uc010zji.1_Missense_Mutation_p.K992R|ERBB4_uc010zjj.1_Missense_Mutation_p.K992R	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	1002	Cytoplasmic (Potential).				cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)											TSP Lung(8;0.080)			---	---	---	---
BARD1	580	broad.mit.edu	37	2	215645475	215645475	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215645475T>C	uc002veu.2	-	4	1258	c.1123A>G	c.(1123-1125)ACA>GCA	p.T375A	BARD1_uc010zjm.1_Missense_Mutation_p.T231A	NM_000465	NP_000456	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	375					cell cycle arrest|DNA repair|negative regulation of apoptosis|negative regulation of mRNA 3'-end processing|negative regulation of protein export from nucleus|positive regulation of apoptosis|positive regulation of protein catabolic process|protein K6-linked ubiquitination|regulation of phosphorylation|tissue homeostasis	BRCA1-A complex|BRCA1-BARD1 complex|cytoplasm	kinase binding|protein heterodimerization activity|protein homodimerization activity|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)										Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
MARCH4	57574	broad.mit.edu	37	2	217234942	217234942	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217234942G>C	uc002vgb.2	-	1	1809	c.42C>G	c.(40-42)TGC>TGG	p.C14W		NM_020814	NP_065865	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4	14						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)														---	---	---	---
TMEM198	130612	broad.mit.edu	37	2	220414535	220414535	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220414535G>T	uc002vme.2	+	6	1627	c.1042G>T	c.(1042-1044)GGA>TGA	p.G348*	TMEM198_uc002vmf.2_Nonsense_Mutation_p.G348*|hsa-mir-3132|MI0014152_5'Flank	NM_001005209	NP_001005209	Q66K66	TM198_HUMAN	transmembrane protein 198	348						integral to membrane				ovary(1)	1		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)														---	---	---	---
STK11IP	114790	broad.mit.edu	37	2	220474096	220474096	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220474096C>A	uc002vml.2	+	17	2014	c.1971C>A	c.(1969-1971)GCC>GCA	p.A657A	STK11IP_uc010zll.1_3'UTR|STK11IP_uc002vmm.1_Silent_p.A646A	NM_052902	NP_443134	Q8N1F8	S11IP_HUMAN	LKB1 interacting protein	657					protein localization	cytoplasm	protein kinase binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230652352	230652352	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230652352G>A	uc002vpw.1	-	32	4748	c.4639C>T	c.(4639-4641)CGG>TGG	p.R1547W	TRIP12_uc002vpx.1_Missense_Mutation_p.R1595W|TRIP12_uc002vpy.1_Missense_Mutation_p.R1277W	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1547	K-box.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)														---	---	---	---
CXCR7	57007	broad.mit.edu	37	2	237489246	237489246	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237489246G>A	uc010fyq.2	+	3	368	c.138G>A	c.(136-138)ACG>ACA	p.T46T	CXCR7_uc002vwd.2_Silent_p.T46T	NM_020311	NP_064707	P25106	CXCR7_HUMAN	chemokine orphan receptor 1	46	Helical; Name=1; (Potential).				interspecies interaction between organisms	integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			large_intestine(1)|central_nervous_system(1)|skin(1)	3		Breast(86;0.000182)|Renal(207;0.00339)|all_hematologic(139;0.0048)|Acute lymphoblastic leukemia(138;0.0775)|Ovarian(221;0.089)|all_lung(227;0.147)|all_neural(83;0.223)		Epithelial(121;8.35e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.09e-11)|Kidney(56;1.11e-07)|KIRC - Kidney renal clear cell carcinoma(57;3.03e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000176)|Lung(119;0.00468)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.118)														---	---	---	---
PER2	8864	broad.mit.edu	37	2	239159277	239159277	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239159277T>C	uc002vyc.2	-	21	3619	c.3382A>G	c.(3382-3384)ATT>GTT	p.I1128V	PER2_uc010znv.1_Missense_Mutation_p.I1128V	NM_022817	NP_073728	O15055	PER2_HUMAN	period 2	1128					circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			upper_aerodigestive_tract(1)|breast(1)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)														---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241700703	241700703	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241700703C>A	uc002vzy.2	-	23	2327	c.2181G>T	c.(2179-2181)TGG>TGT	p.W727C	KIF1A_uc010fzk.2_Missense_Mutation_p.W736C|KIF1A_uc002vzz.1_Missense_Mutation_p.W736C	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	727					anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)														---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241726673	241726673	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241726673C>T	uc002vzy.2	-	5	570	c.424G>A	c.(424-426)GTG>ATG	p.V142M	KIF1A_uc010fzk.2_Missense_Mutation_p.V142M|KIF1A_uc002vzz.1_Missense_Mutation_p.V142M	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	142	Kinesin-motor.				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)														---	---	---	---
CHL1	10752	broad.mit.edu	37	3	419520	419520	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:419520A>G	uc003bou.2	+	15	1994	c.1723A>G	c.(1723-1725)AAT>GAT	p.N575D	CHL1_uc003bot.2_Missense_Mutation_p.N591D|CHL1_uc003bow.1_Missense_Mutation_p.N575D|CHL1_uc011asi.1_Missense_Mutation_p.N591D|uc003box.1_Intron	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	575	Ig-like C2-type 6.|Extracellular (Potential).				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1)	12		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	3095601	3095601	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3095601A>G	uc003bpc.2	+	23	3143	c.2922A>G	c.(2920-2922)CCA>CCG	p.P974P	CNTN4_uc003bpe.2_Silent_p.P646P|CNTN4_uc003bpf.2_Silent_p.P645P|CNTN4_uc003bpg.2_Silent_p.P230P	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	974	Fibronectin type-III 4.				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)														---	---	---	---
IL17RE	132014	broad.mit.edu	37	3	9944618	9944618	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9944618T>C	uc003btu.2	+	2	119	c.2T>C	c.(1-3)ATG>ACG	p.M1T	CIDEC_uc003bto.2_Intron|IL17RE_uc003btv.2_Missense_Mutation_p.M1T|IL17RE_uc011atn.1_RNA|IL17RE_uc003btw.2_Missense_Mutation_p.M1T|IL17RE_uc003btx.2_5'UTR|IL17RE_uc010hcq.2_Missense_Mutation_p.M1T|IL17RE_uc003bty.2_RNA	NM_153483	NP_705616	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E isoform 1	1						cytoplasm|extracellular region|integral to membrane	receptor activity			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)														---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10370646	10370646	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10370646G>A	uc003bvt.2	-	23	4023	c.3584C>T	c.(3583-3585)GCG>GTG	p.A1195V	ATP2B2_uc003bvv.2_Missense_Mutation_p.A1150V|ATP2B2_uc003bvw.2_Missense_Mutation_p.A1150V|ATP2B2_uc003bvs.2_RNA|ATP2B2_uc010hdo.2_Missense_Mutation_p.A900V|hsa-mir-378b|MI0014154_5'Flank	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1	1195	Cytoplasmic (Potential).				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
MKRN2	23609	broad.mit.edu	37	3	12611711	12611711	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12611711C>T	uc003bxd.2	+	3	353	c.297C>T	c.(295-297)CCC>CCT	p.P99P	MKRN2_uc003bxe.2_Silent_p.P97P|MKRN2_uc011aus.1_Silent_p.P56P	NM_014160	NP_054879	Q9H000	MKRN2_HUMAN	makorin ring finger protein 2	99						intracellular	ligase activity|nucleic acid binding|zinc ion binding				0																		---	---	---	---
XPC	7508	broad.mit.edu	37	3	14187433	14187433	+	3'UTR	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14187433C>T	uc011ave.1	-	16					XPC_uc011avf.1_3'UTR|XPC_uc011avg.1_3'UTR	NM_004628	NP_004619			xeroderma pigmentosum, complementation group C						nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal	cytoplasm|nucleoplasm|XPC complex	bubble DNA binding|damaged DNA binding|loop DNA binding|protein binding|single-stranded DNA binding			ovary(2)|breast(1)	3								Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		NER	Xeroderma_Pigmentosum				---	---	---	---
NGLY1	55768	broad.mit.edu	37	3	25760980	25760980	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25760980C>A	uc003cdl.2	-	12	2044	c.1936G>T	c.(1936-1938)GAG>TAG	p.E646*	NGLY1_uc010hfg.2_Nonsense_Mutation_p.E628*|NGLY1_uc003cdm.2_3'UTR|NGLY1_uc011awo.1_Nonsense_Mutation_p.E604*|NGLY1_uc003cdk.2_RNA	NM_018297	NP_060767	Q96IV0	NGLY1_HUMAN	N-glycanase 1 isoform 1	646	PAW.				glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding			breast(1)	1																		---	---	---	---
GPD1L	23171	broad.mit.edu	37	3	32181769	32181769	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32181769G>A	uc003cew.2	+	4	476	c.416G>A	c.(415-417)CGT>CAT	p.R139H		NM_015141	NP_055956	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	139					glycerol-3-phosphate catabolic process	glycerol-3-phosphate dehydrogenase complex	glycerol-3-phosphate dehydrogenase|NAD binding|protein homodimerization activity				0																		---	---	---	---
ACVR2B	93	broad.mit.edu	37	3	38520654	38520654	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38520654C>T	uc003cif.2	+	6	726	c.702C>T	c.(700-702)TTC>TTT	p.F234F	ACVR2B_uc003cig.2_Silent_p.F25F	NM_001106	NP_001097	Q13705	AVR2B_HUMAN	activin A receptor, type IIB precursor	234	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|anterior/posterior pattern formation|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|regulation of transcription, DNA-dependent	cell surface|cytoplasm|integral to plasma membrane	activin receptor activity|ATP binding|growth factor binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)														---	---	---	---
CCR2	729230	broad.mit.edu	37	3	46399019	46399019	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46399019A>G	uc003cpn.3	+	2	486	c.1A>G	c.(1-3)ATG>GTG	p.M1V	CCR2_uc003cpm.3_Missense_Mutation_p.M1V	NM_001123041	NP_001116513	P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2 isoform A	1	Extracellular (Potential).				astrocyte cell migration|blood vessel remodeling|cellular defense response|chemokine-mediated signaling pathway|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|immune response|inflammatory response|interspecies interaction between organisms|JAK-STAT cascade|monocyte extravasation|negative regulation of adenylate cyclase activity|negative regulation of angiogenesis|negative regulation of eosinophil degranulation|negative regulation of type 2 immune response|positive regulation of alpha-beta T cell proliferation|positive regulation of immune complex clearance by monocytes and macrophages|positive regulation of inflammatory response|positive regulation of interferon-gamma production|positive regulation of interleukin-2 production|positive regulation of monocyte chemotaxis|positive regulation of T cell chemotaxis|positive regulation of T cell extravasation|positive regulation of T-helper 1 type immune response|positive regulation of tumor necrosis factor biosynthetic process|regulation of vascular endothelial growth factor production|T-helper 17 cell chemotaxis	cytosol|dendrite|integral to plasma membrane|perikaryon|perinuclear region of cytoplasm|soluble fraction	C-C chemokine receptor activity|CCR2 chemokine receptor binding|protein homodimerization activity			lung(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)														---	---	---	---
SMARCC1	6599	broad.mit.edu	37	3	47762174	47762174	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47762174C>A	uc003crq.2	-	7	816	c.698G>T	c.(697-699)TGG>TTG	p.W233L	SMARCC1_uc011bbd.1_Missense_Mutation_p.W124L	NM_003074	NP_003065	Q92922	SMRC1_HUMAN	SWI/SNF-related matrix-associated	233					chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity			skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)														---	---	---	---
P4HTM	54681	broad.mit.edu	37	3	49040002	49040002	+	Missense_Mutation	SNP	G	A	A	rs34281016		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49040002G>A	uc003cvg.2	+	4	1046	c.697G>A	c.(697-699)GCG>ACG	p.A233T	P4HTM_uc003cvh.2_Missense_Mutation_p.A233T|P4HTM_uc010hkm.1_Missense_Mutation_p.A119T	NM_177939	NP_808808	Q9NXG6	P4HTM_HUMAN	hypoxia-inducible factor prolyl 4-hydroxylase	233	Lumenal (Potential).|EF-hand 2.					endoplasmic reticulum membrane|integral to membrane	calcium ion binding|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			skin(1)|pancreas(1)	2					Vitamin C(DB00126)													---	---	---	---
AMIGO3	386724	broad.mit.edu	37	3	49755859	49755859	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49755859G>A	uc003cxj.2	-	1	1380	c.1040C>T	c.(1039-1041)GCG>GTG	p.A347V	RNF123_uc003cxh.2_Intron|RNF123_uc003cxi.2_Intron	NM_198722	NP_942015	Q86WK7	AMGO3_HUMAN	adhesion molecule with Ig-like domain 3	347	Extracellular (Potential).|Ig-like C2-type.				heterophilic cell-cell adhesion	integral to membrane				pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
CDHR4	389118	broad.mit.edu	37	3	49836267	49836267	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49836267C>A	uc010hkz.2	-	4	496	c.487G>T	c.(487-489)GGA>TGA	p.G163*	CDHR4_uc003cxp.2_Missense_Mutation_p.R188L|CDHR4_uc011bcw.1_Nonsense_Mutation_p.G163*	NM_001007540	NP_001007541	A6H8M9	CDHR4_HUMAN	cadherin-like 29 precursor	163	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0																		---	---	---	---
RBM6	10180	broad.mit.edu	37	3	50005493	50005493	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50005493G>A	uc003cyc.2	+	3	768	c.635G>A	c.(634-636)CGT>CAT	p.R212H	RBM6_uc011bdh.1_RNA|RBM6_uc010hlc.1_Intron|RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6	212					RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)														---	---	---	---
RBM6	10180	broad.mit.edu	37	3	50005514	50005514	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50005514A>G	uc003cyc.2	+	3	789	c.656A>G	c.(655-657)GAT>GGT	p.D219G	RBM6_uc011bdh.1_RNA|RBM6_uc010hlc.1_Intron|RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6	219					RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)														---	---	---	---
TLR9	54106	broad.mit.edu	37	3	52255367	52255367	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52255367G>A	uc003dda.1	-	2	3599	c.2965C>T	c.(2965-2967)CGC>TGC	p.R989C	TLR9_uc003ddb.2_Missense_Mutation_p.R1086C	NM_017442	NP_059138	Q9NR96	TLR9_HUMAN	toll-like receptor 9 isoform A precursor	989	TIR.|Cytoplasmic (Potential).				defense response to bacterium|fibroblast growth factor receptor signaling pathway|I-kappaB phosphorylation|inflammatory response|innate immune response|insulin receptor signaling pathway|maintenance of gastrointestinal epithelium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-beta production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|response to molecule of bacterial origin	apical plasma membrane|basolateral plasma membrane|early phagosome|endoplasmic reticulum membrane|endosome membrane|extracellular region|integral to membrane|lysosome	interleukin-1 receptor binding|siRNA binding|transmembrane receptor activity			large_intestine(2)|skin(2)	4				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)													---	---	---	---
GLYCTK	132158	broad.mit.edu	37	3	52325846	52325846	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52325846C>T	uc003ddo.2	+	4	709	c.613C>T	c.(613-615)CGT>TGT	p.R205C	GLYCTK_uc003ddq.2_Intron|GLYCTK_uc003ddm.2_RNA|GLYCTK_uc003ddn.2_Intron|GLYCTK_uc003ddp.1_Missense_Mutation_p.R205C|GLYCTK_uc003ddr.2_5'Flank	NM_145262	NP_660305	Q8IVS8	GLCTK_HUMAN	glycerate kinase isoform 1	205					protein phosphorylation	Golgi apparatus|mitochondrion	ATP binding|glycerate kinase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;3.56e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)|OV - Ovarian serous cystadenocarcinoma(275;0.235)												OREG0015611	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NISCH	11188	broad.mit.edu	37	3	52525384	52525384	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52525384G>T	uc011beg.1	+	21	3831	c.3759G>T	c.(3757-3759)CAG>CAT	p.Q1253H	NISCH_uc003ded.3_Missense_Mutation_p.Q1253H|NISCH_uc003dee.3_Missense_Mutation_p.Q742H|NISCH_uc003deg.1_RNA|NISCH_uc003deh.3_Missense_Mutation_p.Q2H	NM_007184	NP_009115	Q9Y2I1	NISCH_HUMAN	nischarin	1253					apoptosis|cell communication	cytosol|early endosome|plasma membrane|recycling endosome	phosphatidylinositol binding|receptor activity			ovary(3)|central_nervous_system(1)	4				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)														---	---	---	---
WNT5A	7474	broad.mit.edu	37	3	55508438	55508438	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55508438C>T	uc003dhn.2	-	4	929	c.611G>A	c.(610-612)CGC>CAC	p.R204H	WNT5A_uc003dhm.2_Missense_Mutation_p.R189H|WNT5A_uc010hmw.2_Missense_Mutation_p.R189H|WNT5A_uc010hmx.2_Missense_Mutation_p.R115H	NM_003392	NP_003383	P41221	WNT5A_HUMAN	wingless-type MMTV integration site family,	204					activation of JUN kinase activity|activation of protein kinase B activity|axon guidance|cartilage development|cellular protein localization|cellular response to calcium ion|cellular response to interferon-gamma|cellular response to lipopolysaccharide|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|cervix development|cochlea morphogenesis|convergent extension involved in organogenesis|dopaminergic neuron differentiation|dorsal/ventral axis specification|embryonic digit morphogenesis|embryonic skeletal system development|epithelial cell proliferation involved in mammary gland duct elongation|epithelial to mesenchymal transition|face development|genitalia development|heart looping|hemopoietic stem cell proliferation|keratinocyte differentiation|lateral sprouting involved in mammary gland duct morphogenesis|lens development in camera-type eye|male gonad development|mammary gland branching involved in thelarche|negative regulation of apoptosis|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of mesenchymal cell proliferation|negative regulation of transcription, DNA-dependent|neural tube closure|olfactory bulb interneuron development|optic cup formation involved in camera-type eye development|palate development|positive regulation of angiogenesis|positive regulation of cartilage development|positive regulation of cGMP metabolic process|positive regulation of chemokine biosynthetic process|positive regulation of cytokine secretion involved in immune response|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of macrophage activation|positive regulation of macrophage cytokine production|positive regulation of mesenchymal cell proliferation|positive regulation of neuron projection development|positive regulation of NF-kappaB transcription factor activity|positive regulation of ossification|positive regulation of protein catabolic process|positive regulation of protein kinase C signaling cascade|positive regulation of T cell chemotaxis|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|primitive streak formation|regulation of branching involved in mammary gland duct morphogenesis|somitogenesis|tail morphogenesis|type B pancreatic cell development|urinary bladder development|uterus development|vagina development|Wnt receptor signaling pathway, calcium modulating pathway|wound healing	extracellular space|membrane fraction|plasma membrane|proteinaceous extracellular matrix	frizzled binding|frizzled-2 binding|receptor tyrosine kinase-like orphan receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.00377)|Kidney(284;0.00408)|OV - Ovarian serous cystadenocarcinoma(275;0.204)														---	---	---	---
ACOX2	8309	broad.mit.edu	37	3	58516335	58516335	+	Missense_Mutation	SNP	C	T	T	rs143508132	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58516335C>T	uc003dkl.2	-	8	1025	c.850G>A	c.(850-852)GGT>AGT	p.G284S		NM_003500	NP_003491	Q99424	ACOX2_HUMAN	acyl-Coenzyme A oxidase 2	284					bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity|acyl-CoA dehydrogenase activity|pristanoyl-CoA oxidase activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)														---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	62204651	62204651	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62204651A>G	uc003dlb.2	+	13	3001	c.2282A>G	c.(2281-2283)TAC>TGC	p.Y761C	PTPRG_uc003dlc.2_Missense_Mutation_p.Y761C|PTPRG_uc011bfi.1_Missense_Mutation_p.Y36C	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	761	Helical; (Potential).				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)														---	---	---	---
SYNPR	132204	broad.mit.edu	37	3	63542315	63542315	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63542315C>T	uc003dlq.2	+	3	615	c.246C>T	c.(244-246)TTC>TTT	p.F82F	SYNPR_uc003dlp.2_Silent_p.F102F|SYNPR_uc011bfk.1_RNA|SYNPR_uc011bfl.1_Intron|SYNPR_uc010hnt.2_Silent_p.F91F|SYNPR_uc011bfm.1_Intron	NM_144642	NP_653243	Q8TBG9	SYNPR_HUMAN	synaptoporin isoform 2	82	MARVEL.|Helical; (Potential).					cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)														---	---	---	---
ATXN7	6314	broad.mit.edu	37	3	63981263	63981263	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63981263T>C	uc003dlw.3	+	12	2318	c.1765T>C	c.(1765-1767)TGT>CGT	p.C589R	ATXN7_uc003dlv.2_Missense_Mutation_p.C589R|ATXN7_uc010hnv.2_Missense_Mutation_p.C589R|ATXN7_uc011bfn.1_Missense_Mutation_p.C444R	NM_000333	NP_000324	O15265	ATX7_HUMAN	ataxin 7 isoform a	589					cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)														---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71027093	71027093	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71027093C>T	uc003dol.2	-	11	1557	c.1234G>A	c.(1234-1236)GCC>ACC	p.A412T	FOXP1_uc003dom.2_Missense_Mutation_p.A336T|FOXP1_uc003don.2_RNA|FOXP1_uc003doo.2_Missense_Mutation_p.A412T|FOXP1_uc003dop.2_Missense_Mutation_p.A412T|FOXP1_uc003doq.1_Missense_Mutation_p.A411T|FOXP1_uc003doi.2_Missense_Mutation_p.A312T|FOXP1_uc003doj.2_Missense_Mutation_p.A312T|FOXP1_uc003dok.2_Missense_Mutation_p.A225T|FOXP1_uc003dor.1_Missense_Mutation_p.A190T	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1	412					cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)				T	PAX5	ALL								---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71247410	71247410	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71247410C>T	uc003dol.2	-	2	446	c.123G>A	c.(121-123)ACG>ACA	p.T41T	FOXP1_uc003dom.2_Silent_p.T41T|FOXP1_uc003don.2_RNA|FOXP1_uc003doo.2_Silent_p.T41T|FOXP1_uc003dop.2_Silent_p.T41T|FOXP1_uc003doq.1_Silent_p.T41T|FOXP1_uc003dos.2_Silent_p.T41T	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1	41					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								---	---	---	---
NSUN3	63899	broad.mit.edu	37	3	93803180	93803180	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93803180G>C	uc003drl.1	+	3	468	c.352G>C	c.(352-354)GCT>CCT	p.A118P		NM_022072	NP_071355	Q9H649	NSUN3_HUMAN	NOL1/NOP2/Sun domain family, member 3	118							methyltransferase activity			skin(1)	1																		---	---	---	---
SENP7	57337	broad.mit.edu	37	3	101136515	101136515	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101136515A>G	uc003dut.2	-	5	515	c.404T>C	c.(403-405)TTG>TCG	p.L135S	SENP7_uc003duu.2_Missense_Mutation_p.L135S|SENP7_uc003duv.2_Missense_Mutation_p.L102S|SENP7_uc003duw.2_Intron|SENP7_uc003dux.2_Intron	NM_020654	NP_065705	Q9BQF6	SENP7_HUMAN	sentrin/SUMO-specific protease 7 isoform 1	135					proteolysis	nucleus	cysteine-type peptidase activity			ovary(3)|lung(2)	5																		---	---	---	---
DRD3	1814	broad.mit.edu	37	3	113847734	113847734	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113847734G>A	uc003ebd.2	-	8	1455	c.1032C>T	c.(1030-1032)CCC>CCT	p.P344P	DRD3_uc010hqn.1_Silent_p.P344P|DRD3_uc003ebb.1_Silent_p.P311P|DRD3_uc003ebc.1_Silent_p.P344P	NM_000796	NP_000787	P35462	DRD3_HUMAN	dopamine receptor D3 isoform a	344	Agonist binding.|Helical; Name=6.				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)													---	---	---	---
KLF15	28999	broad.mit.edu	37	3	126070902	126070902	+	Silent	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126070902G>T	uc011bkk.1	-	2	1046	c.864C>A	c.(862-864)GCC>GCA	p.A288A		NM_014079	NP_054798	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	288						nucleus	DNA binding|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(114;0.147)														---	---	---	---
PLXNA1	5361	broad.mit.edu	37	3	126710241	126710241	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126710241T>C	uc003ejg.2	+	2	1144	c.1140T>C	c.(1138-1140)GAT>GAC	p.D380D		NM_032242	NP_115618	Q9UIW2	PLXA1_HUMAN	plexin A1	403	Sema.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)|skin(1)	3				GBM - Glioblastoma multiforme(114;0.155)														---	---	---	---
NMNAT3	349565	broad.mit.edu	37	3	139280118	139280118	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139280118C>T	uc003etj.2	-	4	533	c.493G>A	c.(493-495)GTG>ATG	p.V165M	NMNAT3_uc003etk.2_Missense_Mutation_p.V128M|NMNAT3_uc003etl.2_RNA|NMNAT3_uc010hul.2_Missense_Mutation_p.V76M	NM_178177	NP_835471	Q96T66	NMNA3_HUMAN	nicotinamide mononucleotide adenylyltransferase	165					water-soluble vitamin metabolic process	cytosol|mitochondrion	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity				0																		---	---	---	---
HPS3	84343	broad.mit.edu	37	3	148872996	148872996	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148872996A>C	uc003ewu.1	+	8	1643	c.1503A>C	c.(1501-1503)AAA>AAC	p.K501N	HPS3_uc011bnq.1_Missense_Mutation_p.K336N	NM_032383	NP_115759	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3 protein	501						cytoplasm				ovary(5)|large_intestine(1)	6			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)											Hermansky-Pudlak_syndrome				---	---	---	---
FAM194A	131831	broad.mit.edu	37	3	150377912	150377912	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150377912G>A	uc003eyg.2	-	14	1816	c.1759C>T	c.(1759-1761)CGA>TGA	p.R587*	FAM194A_uc003eyh.2_Nonsense_Mutation_p.R441*	NM_152394	NP_689607	Q7L0X2	F194A_HUMAN	hypothetical protein LOC131831	587										skin(2)|ovary(1)	3																		---	---	---	---
SLC7A14	57709	broad.mit.edu	37	3	170244644	170244644	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170244644G>A	uc003fgz.2	-	2	398	c.82C>T	c.(82-84)CGC>TGC	p.R28C	CLDN11_uc011bpt.1_Intron|uc003fha.1_Intron	NM_020949	NP_066000	Q8TBB6	S7A14_HUMAN	solute carrier family 7 (cationic amino acid	28						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)															---	---	---	---
CCDC39	339829	broad.mit.edu	37	3	180365986	180365986	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180365986T>G	uc010hxe.2	-	10	1444	c.1329A>C	c.(1327-1329)GAA>GAC	p.E443D	CCDC39_uc003fkn.2_RNA	NM_181426	NP_852091	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	443	Potential.				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)															---	---	---	---
MCCC1	56922	broad.mit.edu	37	3	182790190	182790190	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182790190G>T	uc003fle.2	-	5	592	c.455C>A	c.(454-456)CCT>CAT	p.P152H	MCCC1_uc010hxi.2_RNA|MCCC1_uc011bqo.1_RNA|MCCC1_uc003flf.2_Intron|MCCC1_uc003flg.2_Missense_Mutation_p.P43H|MCCC1_uc011bqp.1_Missense_Mutation_p.P105H|MCCC1_uc011bqq.1_Missense_Mutation_p.P43H	NM_020166	NP_064551	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	152	Biotin carboxylation.				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)													---	---	---	---
ALG3	10195	broad.mit.edu	37	3	183963113	183963113	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183963113C>T	uc003fne.2	-	4	509	c.478G>A	c.(478-480)GCC>ACC	p.A160T	ALG3_uc011brc.1_Missense_Mutation_p.A125T|ALG3_uc011brd.1_Missense_Mutation_p.A104T|ALG3_uc011bre.1_Missense_Mutation_p.A112T|ALG3_uc003fnf.1_Missense_Mutation_p.A120T|ALG3_uc011brf.1_Missense_Mutation_p.A52T	NM_005787	NP_005778	Q92685	ALG3_HUMAN	alpha-1,3-mannosyltransferase ALG3 isoform a	160	Helical; (Potential).				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity				0	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
EIF4G1	1981	broad.mit.edu	37	3	184045694	184045694	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184045694C>T	uc003fnp.2	+	26	4055	c.3857C>T	c.(3856-3858)ACG>ATG	p.T1286M	EIF4G1_uc003fnt.2_Missense_Mutation_p.T997M|EIF4G1_uc003fnq.2_Missense_Mutation_p.T1199M|EIF4G1_uc003fnr.2_Missense_Mutation_p.T1122M|EIF4G1_uc010hxx.2_Missense_Mutation_p.T1293M|EIF4G1_uc003fns.2_Missense_Mutation_p.T1246M|EIF4G1_uc010hxy.2_Missense_Mutation_p.T1293M|EIF4G1_uc003fnv.3_Missense_Mutation_p.T1287M|EIF4G1_uc003fnu.3_Missense_Mutation_p.T1286M|EIF4G1_uc003fnw.2_Missense_Mutation_p.T1293M|EIF4G1_uc003fnx.2_Missense_Mutation_p.T1091M|EIF4G1_uc003fny.3_Missense_Mutation_p.T1090M|EIF4G1_uc003foa.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	1286	MI.				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
ATP13A3	79572	broad.mit.edu	37	3	194147839	194147839	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194147839C>T	uc003fty.3	-	28	3492	c.3090G>A	c.(3088-3090)CAG>CAA	p.Q1030Q	ATP13A3_uc003ftx.3_5'Flank	NM_024524	NP_078800	Q9H7F0	AT133_HUMAN	ATPase type 13A3	1030					ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(1)	1	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)														---	---	---	---
MFI2	4241	broad.mit.edu	37	3	196736658	196736658	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196736658G>A	uc003fxk.3	-	11	1469	c.1356C>T	c.(1354-1356)TAC>TAT	p.Y452Y		NM_005929	NP_005920	P08582	TRFM_HUMAN	melanoma-associated antigen p97 isoform 1	452	Transferrin-like 2.				cellular iron ion homeostasis|iron ion transport	anchored to membrane|extracellular region|integral to plasma membrane	ferric iron binding|protein binding				0	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)														---	---	---	---
TMEM129	92305	broad.mit.edu	37	4	1720065	1720065	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1720065A>G	uc003gdn.2	-	2	1014	c.494T>C	c.(493-495)ATT>ACT	p.I165T	TMEM129_uc010iby.2_RNA|TMEM129_uc003gdm.2_Missense_Mutation_p.I165T	NM_001127266	NP_001120738	A0AVI4	TM129_HUMAN	transmembrane protein 129 isoform a	165	Extracellular (Potential).					integral to membrane					0			OV - Ovarian serous cystadenocarcinoma(23;0.00765)															---	---	---	---
LETM1	3954	broad.mit.edu	37	4	1817414	1817414	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1817414C>T	uc003gdv.2	-	13	2344	c.2047G>A	c.(2047-2049)GTC>ATC	p.V683I		NM_012318	NP_036450	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane	683	Mitochondrial matrix (Potential).|EF-hand.|Potential.				cristae formation	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			central_nervous_system(1)	1			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)															---	---	---	---
FAM193A	8603	broad.mit.edu	37	4	2701621	2701621	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2701621T>C	uc010icl.2	+	17	3200	c.2849T>C	c.(2848-2850)ATG>ACG	p.M950T	FAM193A_uc010ick.2_Missense_Mutation_p.M1150T|FAM193A_uc003gfd.2_Missense_Mutation_p.M950T|FAM193A_uc011bvm.1_Missense_Mutation_p.M972T|FAM193A_uc011bvn.1_Missense_Mutation_p.M950T|FAM193A_uc011bvo.1_RNA|FAM193A_uc010icm.2_RNA|FAM193A_uc003gfe.2_Missense_Mutation_p.M804T	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	950										ovary(3)	3																		---	---	---	---
HTT	3064	broad.mit.edu	37	4	3158802	3158802	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3158802C>A	uc011bvq.1	+	29	3780	c.3635C>A	c.(3634-3636)TCT>TAT	p.S1212Y		NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin	1210					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)														---	---	---	---
CRMP1	1400	broad.mit.edu	37	4	5844899	5844899	+	Intron	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5844899A>C	uc003gip.2	-						CRMP1_uc003gin.1_Intron|CRMP1_uc003giq.2_Intron|CRMP1_uc003gir.2_Intron|CRMP1_uc003gis.2_Intron	NM_001313	NP_001304			collapsin response mediator protein 1 isoform 2						axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)														---	---	---	---
TADA2B	93624	broad.mit.edu	37	4	7056720	7056720	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7056720T>C	uc003gjw.3	+	2	1353	c.1202T>C	c.(1201-1203)CTA>CCA	p.L401P	TADA2B_uc010idi.2_Missense_Mutation_p.L326P	NM_152293	NP_689506	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2 (ADA2 homolog,	401					regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|zinc ion binding				0																		---	---	---	---
RAB28	9364	broad.mit.edu	37	4	13371528	13371528	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13371528G>A	uc003gmu.2	-						RAB28_uc003gmt.2_Missense_Mutation_p.T212I|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																		---	---	---	---
LCORL	254251	broad.mit.edu	37	4	17887775	17887775	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17887775A>G	uc003gpq.2	-	6	703	c.692T>C	c.(691-693)GTG>GCG	p.V231A	LCORL_uc011bxk.1_Intron	NM_153686	NP_710153	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor	231					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
PPARGC1A	10891	broad.mit.edu	37	4	23814436	23814436	+	Silent	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23814436G>C	uc003gqs.2	-	10	2073	c.1953C>G	c.(1951-1953)CGC>CGG	p.R651R	PPARGC1A_uc003gqt.2_RNA	NM_013261	NP_037393	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor	651					androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription cofactor activity|transcription factor binding			ovary(2)|lung(2)|kidney(2)|skin(2)	8		Breast(46;0.0503)																---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36115863	36115863	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36115863G>A	uc003gsq.1	-	26	4423	c.4085C>T	c.(4084-4086)GCG>GTG	p.A1362V		NM_015230	NP_056045	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	1362	Ras-associating.				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																		---	---	---	---
CORIN	10699	broad.mit.edu	37	4	47746539	47746539	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47746539G>T	uc003gxm.2	-	5	772	c.679C>A	c.(679-681)CTG>ATG	p.L227M	CORIN_uc011bzf.1_Missense_Mutation_p.L88M|CORIN_uc011bzg.1_Missense_Mutation_p.L160M|CORIN_uc011bzh.1_Missense_Mutation_p.L227M|CORIN_uc011bzi.1_Missense_Mutation_p.L227M|CORIN_uc003gxn.3_Missense_Mutation_p.L227M	NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin	227	Extracellular (Potential).|FZ 1.				peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
KIAA1211	57482	broad.mit.edu	37	4	57181919	57181919	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57181919C>T	uc003hbk.2	+	8	2642	c.2251C>T	c.(2251-2253)CTG>TTG	p.L751L	KIAA1211_uc010iha.2_Silent_p.L744L|KIAA1211_uc011bzz.1_Silent_p.L661L|KIAA1211_uc003hbm.1_Silent_p.L637L	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	751										ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
TMPRSS11F	389208	broad.mit.edu	37	4	68925166	68925166	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68925166G>A	uc003hdt.1	-	9	1085	c.1036C>T	c.(1036-1038)CGG>TGG	p.R346W	LOC550112_uc003hdl.3_Intron|uc011cak.1_Intron	NM_207407	NP_997290	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	346	Peptidase S1.|Extracellular (Potential).				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
GC	2638	broad.mit.edu	37	4	72649747	72649747	+	5'UTR	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72649747A>C	uc003hge.2	-	1					GC_uc010iie.2_5'UTR|GC_uc010iif.2_Missense_Mutation_p.S16A	NM_000583	NP_000574			vitamin D-binding protein precursor						hormone biosynthetic process|vitamin D metabolic process	cytosol|lysosomal lumen	actin binding|vitamin D binding|vitamin transporter activity			ovary(2)|upper_aerodigestive_tract(1)	3		all_hematologic(202;0.107)	Lung(101;0.148)		Cholecalciferol(DB00169)													---	---	---	---
AFM	173	broad.mit.edu	37	4	74364932	74364932	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74364932T>C	uc003hhb.2	+	11	1422	c.1391T>C	c.(1390-1392)CTA>CCA	p.L464P		NM_001133	NP_001124	P43652	AFAM_HUMAN	afamin precursor	464	Albumin 3.				vitamin transport		vitamin E binding			ovary(2)|central_nervous_system(1)	3	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
EREG	2069	broad.mit.edu	37	4	75246852	75246852	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75246852C>T	uc003hie.1	+	3	442	c.276C>T	c.(274-276)TGC>TGT	p.C92C	EREG_uc003hid.2_Silent_p.C86C	NM_001432	NP_001423	O14944	EREG_HUMAN	epiregulin preproprotein	92	Extracellular (Potential).|EGF-like.				angiogenesis|cell-cell signaling|cytokine-mediated signaling pathway|epidermal growth factor receptor signaling pathway|female meiosis|keratinocyte differentiation|keratinocyte proliferation|luteinizing hormone signaling pathway|mRNA transcription|negative regulation of epithelial cell proliferation|negative regulation of smooth muscle cell differentiation|negative regulation of transcription, DNA-dependent|oocyte maturation|organ morphogenesis|ovarian cumulus expansion|ovulation|positive regulation of cell division|positive regulation of cytokine production|positive regulation of DNA replication|positive regulation of epidermal growth factor receptor activity|positive regulation of fibroblast proliferation|positive regulation of innate immune response|positive regulation of interleukin-6 biosynthetic process|positive regulation of mitosis|positive regulation of phosphorylation|positive regulation of smooth muscle cell proliferation|primary follicle stage|wound healing	extracellular space|integral to plasma membrane	epidermal growth factor receptor binding|growth factor activity			breast(1)|skin(1)	2			Lung(101;0.196)															---	---	---	---
SDAD1	55153	broad.mit.edu	37	4	76895224	76895224	+	Intron	SNP	C	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76895224C>G	uc003hje.3	-						SDAD1_uc003hjf.3_Intron|SDAD1_uc011cbr.1_Intron	NM_018115	NP_060585			SDA1 domain containing 1						protein transport|ribosomal large subunit biogenesis	nucleolus	protein binding			ovary(1)	1			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
NUP54	53371	broad.mit.edu	37	4	77065399	77065399	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77065399A>G	uc003hjs.2	-	3	326	c.198T>C	c.(196-198)GGT>GGC	p.G66G	NUP54_uc010ije.2_5'UTR|NUP54_uc011cbs.1_5'UTR|NUP54_uc011cbt.1_Intron|NUP54_uc003hjt.2_5'UTR	NM_017426	NP_059122	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	66	Gly-rich.|Thr-rich.|9 X 2 AA repeats of F-G.				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																		---	---	---	---
HELQ	113510	broad.mit.edu	37	4	84374977	84374977	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84374977G>A	uc003hom.2	-	2	598	c.419C>T	c.(418-420)GCT>GTT	p.A140V	HELQ_uc010ikb.2_Missense_Mutation_p.A140V|HELQ_uc003hol.3_RNA|HELQ_uc010ikc.2_RNA|HELQ_uc003hon.1_Missense_Mutation_p.A34V|HELQ_uc003hoo.1_Missense_Mutation_p.A103V|HELQ_uc003hop.1_Missense_Mutation_p.A34V|HELQ_uc003hoq.1_Missense_Mutation_p.A140V|MRPS18C_uc003hor.3_5'Flank|MRPS18C_uc011ccu.1_5'Flank	NM_133636	NP_598375	Q8TDG4	HELQ_HUMAN	DNA helicase HEL308	140							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					---	---	---	---
NPNT	255743	broad.mit.edu	37	4	106819158	106819158	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106819158C>T	uc003hya.2	+	2	377	c.172C>T	c.(172-174)CCT>TCT	p.P58S	NPNT_uc011cfc.1_Missense_Mutation_p.P58S|NPNT_uc011cfd.1_Missense_Mutation_p.P58S|NPNT_uc011cfe.1_Missense_Mutation_p.P58S|NPNT_uc010ilt.1_Missense_Mutation_p.P58S|NPNT_uc011cff.1_Missense_Mutation_p.P58S|NPNT_uc010ilu.1_5'UTR	NM_001033047	NP_001028219	Q6UXI9	NPNT_HUMAN	nephronectin precursor	58	EGF-like 1.				cell differentiation	membrane	calcium ion binding			skin(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)														---	---	---	---
PAPSS1	9061	broad.mit.edu	37	4	108603286	108603286	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108603286A>G	uc003hyk.2	-	5	638	c.554T>C	c.(553-555)TTC>TCC	p.F185S	PAPSS1_uc011cfh.1_RNA	NM_005443	NP_005434	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase	185	Adenylyl-sulfate kinase.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|sulfate adenylyltransferase (ATP) activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)														---	---	---	---
SEC24B	10427	broad.mit.edu	37	4	110460714	110460714	+	Intron	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110460714C>T	uc003hzk.2	+						SEC24B_uc003hzl.2_Intron|SEC24B_uc011cfp.1_Intron|SEC24B_uc011cfq.1_Intron|SEC24B_uc011cfr.1_Intron	NM_006323	NP_006314			SEC24 (S. cerevisiae) homolog B isoform a						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)														---	---	---	---
BBS7	55212	broad.mit.edu	37	4	122756413	122756413	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122756413C>T	uc003ied.2	-	14	1571	c.1397G>A	c.(1396-1398)GGC>GAC	p.G466D	BBS7_uc003iee.1_Missense_Mutation_p.G466D	NM_176824	NP_789794	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7 protein isoform a	466					cilium morphogenesis|digestive tract morphogenesis|fat cell differentiation|heart looping|melanosome transport|pigment granule aggregation in cell center|response to stimulus|visual perception	BBSome|centrosome|cilium membrane	protein binding			ovary(1)	1														Bardet-Biedl_syndrome				---	---	---	---
ANKRD50	57182	broad.mit.edu	37	4	125631669	125631669	+	5'UTR	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125631669C>T	uc003ifg.3	-	1					ANKRD50_uc011cgo.1_Intron|ANKRD50_uc010inw.2_5'UTR	NM_020337	NP_065070			ankyrin repeat domain 50											central_nervous_system(1)	1																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126239199	126239199	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126239199G>A	uc003ifj.3	+	1	1633	c.1633G>A	c.(1633-1635)GCT>ACT	p.A545T		NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	545	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126370559	126370559	+	Silent	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126370559T>G	uc003ifj.3	+	9	8388	c.8388T>G	c.(8386-8388)ACT>ACG	p.T2796T	FAT4_uc011cgp.1_Silent_p.T1094T|FAT4_uc003ifi.1_Silent_p.T274T	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	2796	Cadherin 27.|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	126372301	126372301	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126372301A>T	uc003ifj.3	+	9	10130	c.10130A>T	c.(10129-10131)AAC>ATC	p.N3377I	FAT4_uc011cgp.1_Missense_Mutation_p.N1675I|FAT4_uc003ifi.1_Missense_Mutation_p.N855I	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	3377	Cadherin 32.|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	126411350	126411350	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126411350C>A	uc003ifj.3	+	17	13373	c.13373C>A	c.(13372-13374)ACG>AAG	p.T4458K	FAT4_uc011cgp.1_Missense_Mutation_p.T2699K|FAT4_uc003ifi.1_Missense_Mutation_p.T1935K	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4458	EGF-like 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143003205	143003205	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143003205C>A	uc003iix.3	-	26	3216	c.2621G>T	c.(2620-2622)CGA>CTA	p.R874L	INPP4B_uc003iiw.3_Missense_Mutation_p.R874L|INPP4B_uc011chm.1_RNA|INPP4B_uc011chn.1_Missense_Mutation_p.R689L|INPP4B_uc011cho.1_RNA	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,	874					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)																	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151773180	151773180	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151773180A>G	uc010ipj.2	-	23	4156	c.3682T>C	c.(3682-3684)TGT>CGT	p.C1228R	LRBA_uc003ilt.3_5'Flank|LRBA_uc003ilu.3_Missense_Mutation_p.C1228R	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	1228						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
KIAA0922	23240	broad.mit.edu	37	4	154519772	154519772	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154519772C>T	uc003inm.3	+	21	2203	c.2151C>T	c.(2149-2151)GGC>GGT	p.G717G	KIAA0922_uc010ipp.2_Silent_p.G718G|KIAA0922_uc010ipq.2_Silent_p.G486G	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2	717	Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
GUCY1A3	2982	broad.mit.edu	37	4	156631766	156631766	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156631766A>G	uc003iov.2	+	7	985	c.449A>G	c.(448-450)AAC>AGC	p.N150S	GUCY1A3_uc003iou.2_Missense_Mutation_p.N150S|GUCY1A3_uc010iqc.2_Missense_Mutation_p.N150S|GUCY1A3_uc003iow.2_Missense_Mutation_p.N150S|GUCY1A3_uc010iqd.2_Missense_Mutation_p.N149S|GUCY1A3_uc003iox.2_Missense_Mutation_p.N150S|GUCY1A3_uc003ioz.2_5'UTR|GUCY1A3_uc003ioy.2_Missense_Mutation_p.N150S|GUCY1A3_uc010iqe.2_Intron|GUCY1A3_uc003ipa.2_Intron|GUCY1A3_uc003ipb.2_Missense_Mutation_p.N150S	NM_000856	NP_000847	Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3 isoform A	150				VIKESLGEEVFKICYEEDENILGVVGGTLKDFLNSFSTLLK QSSHCQEAGKRGR -> LSKNLLVKRFLKYVTRKMKTSLGW LEAPLKIFKQLQYPSETEQPLPRSRKKGQ (in Ref. 1).	blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble	GTP binding|guanylate cyclase activity|heme binding|receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)														---	---	---	---
CTSO	1519	broad.mit.edu	37	4	156849508	156849508	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156849508T>G	uc003ipg.2	-	7	960	c.911A>C	c.(910-912)AAA>ACA	p.K304T		NM_001334	NP_001325	P43234	CATO_HUMAN	cathepsin O preproprotein	304					proteolysis	lysosome	cysteine-type endopeptidase activity				0	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.05)|Kidney(143;0.0627)|COAD - Colon adenocarcinoma(41;0.148)														---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	164506986	164506986	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164506986T>C	uc003iqs.1	-	6	1315	c.338A>G	c.(337-339)CAG>CGG	p.Q113R	MARCH1_uc003iqr.1_Missense_Mutation_p.Q96R	NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I	113	RING-CH-type.				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)																---	---	---	---
ENPP6	133121	broad.mit.edu	37	4	185038092	185038092	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185038092A>G	uc003iwc.2	-	5	914	c.772T>C	c.(772-774)TAC>CAC	p.Y258H		NM_153343	NP_699174	Q6UWR7	ENPP6_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	258	Extracellular (Potential).				lipid catabolic process	extracellular region|integral to membrane|plasma membrane				central_nervous_system(1)	1		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)														---	---	---	---
TRIML2	205860	broad.mit.edu	37	4	189013038	189013038	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189013038A>C	uc003izl.2	-	7	689	c.653T>G	c.(652-654)CTG>CGG	p.L218R	TRIML2_uc003izj.1_Missense_Mutation_p.L46R|TRIML2_uc003izk.1_Missense_Mutation_p.L26R|TRIML2_uc011cle.1_Missense_Mutation_p.L293R	NM_173553	NP_775824	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	218	B30.2/SPRY.						ligase activity			central_nervous_system(2)	2		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)														---	---	---	---
ADAMTS16	170690	broad.mit.edu	37	5	5303392	5303392	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5303392G>T	uc003jdl.2	+	19	2939	c.2801G>T	c.(2800-2802)GGG>GTG	p.G934V	ADAMTS16_uc003jdk.1_Missense_Mutation_p.G934V	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	934	TSP type-1 3.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11346569	11346569	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11346569G>A	uc003jfa.1	-	9	1688	c.1543C>T	c.(1543-1545)CCA>TCA	p.P515S	CTNND2_uc010itt.2_Missense_Mutation_p.P424S|CTNND2_uc011cmy.1_Missense_Mutation_p.P178S|CTNND2_uc011cmz.1_Missense_Mutation_p.P82S|CTNND2_uc010itu.1_RNA|CTNND2_uc011cmx.1_Missense_Mutation_p.P82S	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	515					multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13766090	13766090	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13766090A>C	uc003jfd.2	-	59	10138	c.10096T>G	c.(10096-10098)TTA>GTA	p.L3366V	DNAH5_uc003jfc.2_5'UTR	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3366	Stalk (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21802491	21802491	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21802491T>G	uc010iuc.2	-	7	1499	c.1041A>C	c.(1039-1041)AAA>AAC	p.K347N	CDH12_uc011cno.1_Missense_Mutation_p.K307N|CDH12_uc003jgk.2_Missense_Mutation_p.K347N	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	347	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24509890	24509890	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24509890T>C	uc003jgr.1	-	7	1373	c.1041A>G	c.(1039-1041)AAA>AAG	p.K347K	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	347	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)											HNSCC(23;0.051)			---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	32074648	32074648	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32074648A>G	uc003jhl.2	+	18	3824	c.3436A>G	c.(3436-3438)ACT>GCT	p.T1146A	PDZD2_uc003jhm.2_Missense_Mutation_p.T1146A|PDZD2_uc011cnx.1_Missense_Mutation_p.T972A	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	1146					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	32098700	32098700	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32098700T>C	uc003jhl.2	+	23	8566	c.8178T>C	c.(8176-8178)GGT>GGC	p.G2726G	PDZD2_uc003jhm.2_Silent_p.G2726G|PDZD2_uc003jhn.2_5'Flank	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	2726					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35641550	35641550	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35641550T>G	uc003jjo.2	+	3	290	c.179T>G	c.(178-180)CTT>CGT	p.L60R	SPEF2_uc003jjn.1_Missense_Mutation_p.L60R|SPEF2_uc003jjq.3_Missense_Mutation_p.L60R	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	60	CH.				nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35793420	35793420	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35793420A>G	uc003jjo.2	+	32	4825	c.4714A>G	c.(4714-4716)ATC>GTC	p.I1572V	SPEF2_uc003jjp.1_Missense_Mutation_p.I1058V|SPEF2_uc003jjr.2_Missense_Mutation_p.I627V	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	1572					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
NUP155	9631	broad.mit.edu	37	5	37299658	37299658	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37299658A>T	uc003jku.1	-	31	3692	c.3574T>A	c.(3574-3576)TTT>ATT	p.F1192I	NUP155_uc003jkt.1_Missense_Mutation_p.F1133I|NUP155_uc010iuz.1_Missense_Mutation_p.F1128I	NM_153485	NP_705618	O75694	NU155_HUMAN	nucleoporin 155kDa isoform 1	1192					carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
C6	729	broad.mit.edu	37	5	41149337	41149337	+	Intron	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41149337A>C	uc003jmk.2	-						C6_uc003jml.1_Intron	NM_000065	NP_000056			complement component 6 precursor						complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)																---	---	---	---
HCN1	348980	broad.mit.edu	37	5	45396642	45396642	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45396642G>A	uc003jok.2	-	4	1207	c.1182C>T	c.(1180-1182)ACC>ACT	p.T394T		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	394	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
SKIV2L2	23517	broad.mit.edu	37	5	54674186	54674186	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54674186A>G	uc003jpy.3	+	17	2121	c.1855A>G	c.(1855-1857)AAT>GAT	p.N619D	SKIV2L2_uc011cqi.1_Missense_Mutation_p.N518D	NM_015360	NP_056175	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2	619					maturation of 5.8S rRNA	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(1)|skin(1)	2		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)																---	---	---	---
MAP3K1	4214	broad.mit.edu	37	5	56181765	56181765	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56181765C>T	uc003jqw.3	+	17	4490	c.3989C>T	c.(3988-3990)TCG>TTG	p.S1330L		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase	1330	Protein kinase.				cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)														---	---	---	---
ISCA1P1	389293	broad.mit.edu	37	5	62072597	62072597	+	3'UTR	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62072597T>C	uc003jtf.2	-	2						NM_001080540	NP_001074009			iron-sulfur cluster assembly 1 homolog (S.												0																		---	---	---	---
RGS7BP	401190	broad.mit.edu	37	5	63871704	63871704	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63871704C>T	uc003jtj.2	+	3	436	c.436C>T	c.(436-438)CTG>TTG	p.L146L	RGS7BP_uc011cqu.1_Silent_p.L13L	NM_001029875	NP_001025046	Q6MZT1	R7BP_HUMAN	regulator of G-protein signaling 7 binding	146					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)														---	---	---	---
NLN	57486	broad.mit.edu	37	5	65088386	65088386	+	Silent	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65088386A>C	uc003juf.2	+	9	1547	c.1431A>C	c.(1429-1431)TCA>TCC	p.S477S	NLN_uc003jue.2_Silent_p.S477S|NLN_uc003jug.2_Silent_p.S306S|NLN_uc010iww.2_Silent_p.S172S	NM_020726	NP_065777	Q9BYT8	NEUL_HUMAN	neurolysin precursor	477					proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)														---	---	---	---
NLN	57486	broad.mit.edu	37	5	65105422	65105422	+	Silent	SNP	G	A	A	rs140799100	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65105422G>A	uc003juf.2	+	10	1724	c.1608G>A	c.(1606-1608)GTG>GTA	p.V536V	NLN_uc003jug.2_Silent_p.V365V|NLN_uc010iww.2_Silent_p.V213V	NM_020726	NP_065777	Q9BYT8	NEUL_HUMAN	neurolysin precursor	536					proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)														---	---	---	---
NLN	57486	broad.mit.edu	37	5	65105492	65105492	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65105492C>A	uc003juf.2	+	10	1794	c.1678C>A	c.(1678-1680)CTT>ATT	p.L560I	NLN_uc003jug.2_Missense_Mutation_p.L389I|NLN_uc010iww.2_Missense_Mutation_p.L237I	NM_020726	NP_065777	Q9BYT8	NEUL_HUMAN	neurolysin precursor	560					proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)														---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82816658	82816658	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82816658A>G	uc003kii.3	+	7	2889	c.2533A>G	c.(2533-2535)AGT>GGT	p.S845G	VCAN_uc003kij.3_Intron|VCAN_uc010jau.2_Missense_Mutation_p.S845G|VCAN_uc003kik.3_Intron	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	845	GAG-alpha (glucosaminoglycan attachment domain).				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)														---	---	---	---
GDF9	2661	broad.mit.edu	37	5	132197386	132197386	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132197386T>C	uc003kxz.1	-	2	1512	c.1260A>G	c.(1258-1260)GTA>GTG	p.V420V	GDF9_uc011cxj.1_Silent_p.V332V	NM_005260	NP_005251	O60383	GDF9_HUMAN	growth differentiation factor 9 precursor	420					female gamete generation|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			skin(1)	1		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
GDF9	2661	broad.mit.edu	37	5	132197483	132197483	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132197483C>A	uc003kxz.1	-	2	1415	c.1163G>T	c.(1162-1164)AGG>ATG	p.R388M	GDF9_uc011cxj.1_Missense_Mutation_p.R300M	NM_005260	NP_005251	O60383	GDF9_HUMAN	growth differentiation factor 9 precursor	388					female gamete generation|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			skin(1)	1		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
AFF4	27125	broad.mit.edu	37	5	132234075	132234075	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132234075T>C	uc003kyd.2	-	10	1644	c.1236A>G	c.(1234-1236)GAA>GAG	p.E412E	AFF4_uc011cxk.1_Silent_p.E90E|AFF4_uc003kye.1_Silent_p.E412E	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31	412	Ser-rich.				transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
KIF20A	10112	broad.mit.edu	37	5	137518981	137518981	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137518981C>T	uc003lcj.2	+	8	1452	c.956C>T	c.(955-957)CCG>CTG	p.P319L	KIF20A_uc011cyo.1_Missense_Mutation_p.P301L	NM_005733	NP_005724	O95235	KI20A_HUMAN	kinesin family member 20A	319	Kinesin-motor.				cytokinesis|M phase of mitotic cell cycle|microtubule-based movement|protein transport|vesicle-mediated transport	Golgi apparatus|microtubule|nucleoplasm	ATP binding|microtubule motor activity|protein binding|transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
PCDHA3	56145	broad.mit.edu	37	5	140181171	140181171	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140181171C>T	uc003lhf.2	+	1	389	c.389C>T	c.(388-390)GCG>GTG	p.A130V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.A130V	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	130	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHB8	56128	broad.mit.edu	37	5	140559946	140559946	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140559946C>T	uc011dai.1	+	1	2517	c.2331C>T	c.(2329-2331)GGC>GGT	p.G777G	PCDHB16_uc003liv.2_5'Flank|PCDHB16_uc010jfw.1_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	777	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB11	56125	broad.mit.edu	37	5	140581381	140581381	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140581381G>A	uc003liy.2	+	1	2034	c.2034G>A	c.(2032-2034)CCG>CCA	p.P678P	PCDHB11_uc011daj.1_Silent_p.P313P	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	678	Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHGA2	56113	broad.mit.edu	37	5	140719048	140719048	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140719048C>T	uc003ljk.1	+	1	695	c.510C>T	c.(508-510)TAC>TAT	p.Y170Y	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Silent_p.Y170Y	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	170	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PPARGC1B	133522	broad.mit.edu	37	5	149212845	149212845	+	Silent	SNP	C	T	T	rs141686848		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149212845C>T	uc003lrc.2	+	5	1251	c.1209C>T	c.(1207-1209)ACC>ACT	p.T403T	PPARGC1B_uc003lrb.1_Silent_p.T403T|PPARGC1B_uc003lrd.2_Silent_p.T364T|PPARGC1B_uc003lrf.2_Silent_p.T382T|PPARGC1B_uc003lre.1_Silent_p.T382T	NM_133263	NP_573570	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor	403					estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter	mediator complex	AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)															---	---	---	---
TCOF1	6949	broad.mit.edu	37	5	149769545	149769545	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149769545C>T	uc003lry.2	+	19	3250	c.3142C>T	c.(3142-3144)CGG>TGG	p.R1048W	TCOF1_uc011dch.1_Missense_Mutation_p.R1048W|TCOF1_uc003lrz.2_Missense_Mutation_p.R1048W|TCOF1_uc003lrx.2_Missense_Mutation_p.R971W|TCOF1_uc003lsa.2_Missense_Mutation_p.R971W	NM_001135243	NP_001128715	Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1048					skeletal system development	nucleolus	protein binding|transporter activity			ovary(2)|large_intestine(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
DCTN4	51164	broad.mit.edu	37	5	150095168	150095168	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150095168G>A	uc003lsv.2	-	12	1230	c.1128C>T	c.(1126-1128)TAC>TAT	p.Y376Y	DCTN4_uc003lsu.2_Silent_p.Y319Y|DCTN4_uc010jhi.2_Silent_p.Y383Y	NM_016221	NP_057305	Q9UJW0	DCTN4_HUMAN	dynactin 4 (p62) isoform b	376						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)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150917385	150917385	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150917385C>A	uc003lue.3	-	11	9175	c.9162G>T	c.(9160-9162)GGG>GGT	p.G3054G	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	3054	Extracellular (Potential).|Cadherin 27.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150928856	150928856	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150928856C>A	uc003lue.3	-	8	4802	c.4789G>T	c.(4789-4791)GGG>TGG	p.G1597W	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	1597	Extracellular (Potential).|Cadherin 14.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150933918	150933918	+	Intron	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150933918C>T	uc003lue.3	-						GM2A_uc011dcs.1_Intron	NM_001447	NP_001438			FAT tumor suppressor 2 precursor						epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
GALNT10	55568	broad.mit.edu	37	5	153760082	153760082	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153760082G>A	uc003lvh.2	+	6	961	c.829G>A	c.(829-831)GAG>AAG	p.E277K	GALNT10_uc003lvg.1_Missense_Mutation_p.E277K|GALNT10_uc010jic.2_RNA|GALNT10_uc010jid.2_Missense_Mutation_p.E118K	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a	277	Lumenal (Potential).					Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)															---	---	---	---
C5orf54	63920	broad.mit.edu	37	5	159821646	159821646	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159821646A>G	uc003lye.1	-	2	1316	c.852T>C	c.(850-852)CCT>CCC	p.P284P	C5orf54_uc003lyf.1_Silent_p.P284P	NM_022090	NP_071373	Q8IZ13	CE054_HUMAN	transposon-derived Buster3 transposase-like	284										pancreas(1)	1																		---	---	---	---
CCDC99	54908	broad.mit.edu	37	5	169031164	169031164	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169031164T>C	uc003mae.3	+	12	2050	c.1771T>C	c.(1771-1773)TAT>CAT	p.Y591H	CCDC99_uc011deq.1_Missense_Mutation_p.Y408H|CCDC99_uc010jjk.2_Missense_Mutation_p.Y317H	NM_017785	NP_060255	Q96EA4	SPDLY_HUMAN	coiled-coil domain containing 99	591					cell division|establishment of mitotic spindle orientation|mitotic metaphase plate congression|mitotic prometaphase|protein localization to kinetochore	condensed chromosome outer kinetochore|cytosol|microtubule organizing center|nucleus|spindle pole	kinetochore binding|protein binding			ovary(1)|liver(1)	2	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
CDHR2	54825	broad.mit.edu	37	5	176017621	176017621	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176017621G>T	uc003mem.1	+	28	3538	c.3472G>T	c.(3472-3474)GGA>TGA	p.G1158*	CDHR2_uc003men.1_Nonsense_Mutation_p.G1158*	NM_017675	NP_060145	Q9BYE9	CDHR2_HUMAN	protocadherin LKC precursor	1158	Helical; (Potential).				homophilic cell adhesion|negative regulation of cell growth	apical plasma membrane|cell junction|integral to membrane	calcium ion binding|protein binding			ovary(2)	2																		---	---	---	---
PROP1	5626	broad.mit.edu	37	5	177419842	177419842	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177419842G>A	uc003mif.1	-	3	858	c.549C>T	c.(547-549)GGC>GGT	p.G183G		NM_006261	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	183					central nervous system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
SQSTM1	8878	broad.mit.edu	37	5	179250912	179250912	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179250912G>A	uc003mkw.3	+	3	451	c.356G>A	c.(355-357)CGC>CAC	p.R119H	SQSTM1_uc011dgr.1_Missense_Mutation_p.R35H|SQSTM1_uc011dgs.1_Missense_Mutation_p.R35H|SQSTM1_uc003mkv.3_Missense_Mutation_p.R119H|SQSTM1_uc003mkx.2_Missense_Mutation_p.R35H	NM_003900	NP_003891	Q13501	SQSTM_HUMAN	sequestosome 1 isoform 1	119					anti-apoptosis|apoptosis|cell differentiation|endosome transport|induction of apoptosis by extracellular signals|intracellular signal transduction|macroautophagy|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein localization|regulation of I-kappaB kinase/NF-kappaB cascade|ubiquitin-dependent protein catabolic process	cytosol|late endosome|nucleoplasm	protein kinase C binding|receptor tyrosine kinase binding|SH2 domain binding|ubiquitin binding|zinc ion binding		SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(2)|ovary(1)	3	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											Paget_Disease_of_Bone				---	---	---	---
FLT4	2324	broad.mit.edu	37	5	180046728	180046728	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180046728C>T	uc003mma.3	-	18	2663	c.2584G>A	c.(2584-2586)GCC>ACC	p.A862T	FLT4_uc003mlz.3_Missense_Mutation_p.A862T|FLT4_uc003mmb.1_Missense_Mutation_p.A395T	NM_002020	NP_002011	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 2	862	Cytoplasmic (Potential).|Protein kinase.				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)									Congenital_Hereditary_Lymphedema				---	---	---	---
SERPINB9	5272	broad.mit.edu	37	6	2900854	2900854	+	5'UTR	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2900854G>A	uc003mug.2	-	2					uc003mue.2_RNA|SERPINB9_uc003muh.2_5'UTR	NM_004155	NP_004146			serpin peptidase inhibitor, clade B, member 9						anti-apoptosis|cellular response to estrogen stimulus|immune response|mast cell mediated immunity|regulation of proteolysis	cytosol|extracellular space|nucleus	caspase inhibitor activity|protease binding|serine-type endopeptidase inhibitor activity				0	Ovarian(93;0.0412)	all_hematologic(90;0.108)																---	---	---	---
F13A1	2162	broad.mit.edu	37	6	6196106	6196106	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6196106C>T	uc003mwv.2	-	10	1352	c.1229G>A	c.(1228-1230)TGT>TAT	p.C410Y	F13A1_uc011dib.1_Missense_Mutation_p.C347Y	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	410					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)													---	---	---	---
GCNT2	2651	broad.mit.edu	37	6	10557365	10557365	+	Intron	SNP	A	G	G	rs55736656		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10557365A>G	uc010joo.2	+						GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Intron|GCNT2_uc003mzd.2_Missense_Mutation_p.K237E	NM_145649	NP_663624			glucosaminyl (N-acetyl) transferase 2,							Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)														---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13283733	13283733	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13283733A>G	uc010jpc.2	+	13	1921	c.1589A>G	c.(1588-1590)GAC>GGC	p.D530G	PHACTR1_uc003nah.1_Missense_Mutation_p.D530G|TBC1D7_uc003naj.2_Intron|TBC1D7_uc011dis.1_Intron|uc003nak.1_Intron	NM_030948	NP_112210	Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	530						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)															---	---	---	---
CAP2	10486	broad.mit.edu	37	6	17507473	17507473	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17507473G>A	uc003ncb.2	+	5	617	c.374G>A	c.(373-375)CGG>CAG	p.R125Q	CAP2_uc010jpk.1_RNA|CAP2_uc011dja.1_Missense_Mutation_p.R99Q|CAP2_uc011djb.1_Missense_Mutation_p.R125Q|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357	P40123	CAP2_HUMAN	adenylyl cyclase-associated protein 2	125					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)															---	---	---	---
SLC17A1	6568	broad.mit.edu	37	6	25813374	25813374	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25813374T>C	uc003nfh.3	-	7	800	c.684A>G	c.(682-684)CCA>CCG	p.P228P	SLC17A1_uc011djy.1_Intron|SLC17A1_uc010jqb.1_Silent_p.P226P|SLC17A1_uc010jqc.1_Silent_p.P226P	NM_005074	NP_005065	Q14916	NPT1_HUMAN	solute carrier family 17 (sodium phosphate),	228					sodium ion transport|urate metabolic process	integral to plasma membrane|membrane fraction	sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(3)|pancreas(1)	4																		---	---	---	---
HLA-B	3106	broad.mit.edu	37	6	31324898	31324898	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31324898A>G	uc003nth.2	-	1	92	c.38T>C	c.(37-39)CTC>CCC	p.L13P	HLA-C_uc003ntb.2_5'Flank|HLA-C_uc003ntc.1_5'Flank|HLA-B_uc010jsm.1_5'Flank|HLA-B_uc011dnk.1_5'Flank|HLA-B_uc003ntf.2_Missense_Mutation_p.L13P|HLA-B_uc003ntg.1_5'Flank|HLA-B_uc003nti.1_5'Flank|HLA-B_uc010jsn.1_5'Flank|HLA-B_uc010jso.2_5'Flank	NM_005514	NP_005505	P01889	1B07_HUMAN	major histocompatibility complex, class I, B	13					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				---	---	---	---
AIF1	199	broad.mit.edu	37	6	31584639	31584639	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31584639G>T	uc003nuy.2	+	6	480	c.406G>T	c.(406-408)GGC>TGC	p.G136C	AIF1_uc010jsy.2_3'UTR|AIF1_uc003nva.2_Missense_Mutation_p.G82C	NM_001623	NP_001614	P55008	AIF1_HUMAN	allograft inflammatory factor 1 isoform 3	136				KEKPTGPPAKKAISELP -> RKTNTPPSQESPI (in Ref. 2; AAA92457).	actin filament bundle assembly|cell cycle arrest|inflammatory response|negative regulation of cell proliferation	nucleus|ruffle membrane	actin filament binding|calcium ion binding			ovary(1)	1																		---	---	---	---
VARS	7407	broad.mit.edu	37	6	31760167	31760167	+	Splice_Site	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31760167A>G	uc003nxe.2	-	5	1209	c.786_splice	c.e5+1	p.E262_splice	VARS_uc011doi.1_Splice_Site	NM_006295	NP_006286			valyl-tRNA synthetase						translational elongation|valyl-tRNA aminoacylation	cytosol	ATP binding|protein binding|valine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3					L-Valine(DB00161)													---	---	---	---
HSPA1L	3305	broad.mit.edu	37	6	31779676	31779676	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31779676T>C	uc003nxh.2	-	2	257	c.74A>G	c.(73-75)CAC>CGC	p.H25R	HSPA1L_uc010jte.2_Missense_Mutation_p.H25R	NM_005527	NP_005518	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	25					response to unfolded protein		ATP binding			ovary(3)|pleura(1)|kidney(1)|skin(1)	6																		---	---	---	---
PRRT1	80863	broad.mit.edu	37	6	32117114	32117114	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32117114C>T	uc003nzt.2	-	4	922	c.806G>A	c.(805-807)CGG>CAG	p.R269Q	PRRT1_uc003nzs.2_Missense_Mutation_p.R310Q|PRRT1_uc003nzu.2_Silent_p.P161P	NM_030651	NP_085154	Q99946	PRRT1_HUMAN	NG5 protein	269					response to biotic stimulus	integral to membrane				breast(1)	1																		---	---	---	---
MOCS1	4337	broad.mit.edu	37	6	39874630	39874630	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39874630G>T	uc003opb.2	-	10	1552	c.1414C>A	c.(1414-1416)CCC>ACC	p.P472T	MOCS1_uc003opa.2_3'UTR|MOCS1_uc003opc.2_Missense_Mutation_p.P456T|MOCS1_uc003opd.2_3'UTR|MOCS1_uc003ope.2_Missense_Mutation_p.P369T	NM_005942	NP_005933	Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis-step 1 protein	472	Molybdenum cofactor biosynthesis protein C.				Mo-molybdopterin cofactor biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding			ovary(1)|liver(1)|central_nervous_system(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)																	---	---	---	---
USP49	25862	broad.mit.edu	37	6	41767603	41767603	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41767603T>C	uc003ori.2	-	6	1857	c.1635A>G	c.(1633-1635)CTA>CTG	p.L545L		NM_018561	NP_061031	Q70CQ1	UBP49_HUMAN	ubiquitin thioesterase 49	545					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	42620242	42620242	+	Silent	SNP	G	T	T	rs146653824	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42620242G>T	uc011dur.1	+	25	2628	c.2628G>T	c.(2626-2628)CCG>CCT	p.P876P	UBR2_uc011dus.1_Silent_p.P521P|UBR2_uc003osh.2_RNA	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	876					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)															---	---	---	---
TTBK1	84630	broad.mit.edu	37	6	43252030	43252030	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43252030G>A	uc003ouq.1	+	14	3831	c.3552G>A	c.(3550-3552)TTG>TTA	p.L1184L		NM_032538	NP_115927	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	1184						cell junction|cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)															---	---	---	---
TMEM63B	55362	broad.mit.edu	37	6	44118039	44118039	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44118039A>G	uc003owr.2	+	17	1663	c.1599A>G	c.(1597-1599)GGA>GGG	p.G533G	TMEM63B_uc003ows.2_Silent_p.G436G|TMEM63B_uc010jyz.2_RNA	NM_018426	NP_060896	Q5T3F8	TM63B_HUMAN	transmembrane protein 63B	533	Helical; (Potential).					integral to membrane	nucleotide binding|protein binding			pancreas(2)|central_nervous_system(1)	3	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)															---	---	---	---
EFHC1	114327	broad.mit.edu	37	6	52334121	52334121	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52334121G>A	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)																	---	---	---	---
ICK	22858	broad.mit.edu	37	6	52869977	52869977	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52869977G>A	uc003pbh.2	-	15	2359	c.1869C>T	c.(1867-1869)GAC>GAT	p.D623D	ICK_uc003pbi.2_Silent_p.D623D	NM_016513	NP_057597	Q9UPZ9	ICK_HUMAN	intestinal cell kinase	623					intracellular protein kinase cascade|multicellular organismal development	cytosol|nucleus	ATP binding|cyclin-dependent protein kinase activity|magnesium ion binding			ovary(1)|large_intestine(1)|lung(1)|kidney(1)|central_nervous_system(1)	5	Lung NSC(77;0.103)																	---	---	---	---
EYS	346007	broad.mit.edu	37	6	66200483	66200483	+	Intron	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66200483T>G	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																		---	---	---	---
BAI3	577	broad.mit.edu	37	6	70070837	70070837	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70070837T>C	uc003pev.3	+	29	4120	c.3672T>C	c.(3670-3672)GAT>GAC	p.D1224D	BAI3_uc010kak.2_Silent_p.D1224D|BAI3_uc011dxx.1_Silent_p.D430D	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1224	Cytoplasmic (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)																---	---	---	---
CD109	135228	broad.mit.edu	37	6	74472143	74472143	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74472143G>A	uc003php.2	+	8	1220	c.795G>A	c.(793-795)ACG>ACA	p.T265T	CD109_uc010kaz.2_Silent_p.T265T|CD109_uc003phq.2_Silent_p.T265T|CD109_uc010kba.2_Silent_p.T188T	NM_133493	NP_598000	Q6YHK3	CD109_HUMAN	CD109 antigen isoform 1 precursor	265						anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75855832	75855832	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75855832T>C	uc003phs.2	-	24	4712	c.4546A>G	c.(4546-4548)ACA>GCA	p.T1516A	COL12A1_uc003pht.2_Missense_Mutation_p.T352A	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	1516	Fibronectin type-III 10.				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																		---	---	---	---
IBTK	25998	broad.mit.edu	37	6	82950021	82950021	+	Silent	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82950021G>T	uc003pjl.1	-	2	710	c.183C>A	c.(181-183)TCC>TCA	p.S61S	IBTK_uc011dyv.1_Silent_p.S61S|IBTK_uc011dyw.1_Silent_p.S61S|IBTK_uc010kbi.1_Translation_Start_Site|IBTK_uc003pjm.2_Silent_p.S61S	NM_015525	NP_056340	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton's tyrosine kinase	61	ANK 1.				negative regulation of protein phosphorylation|release of sequestered calcium ion into cytosol	cytoplasm|membrane|nucleus	protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(2)|central_nervous_system(2)	4		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)														---	---	---	---
SNAP91	9892	broad.mit.edu	37	6	84302947	84302947	+	Silent	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84302947T>G	uc011dze.1	-	18	2045	c.1728A>C	c.(1726-1728)GCA>GCC	p.A576A	SNAP91_uc011dzd.1_Silent_p.A79A|SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Silent_p.A574A|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Silent_p.A574A	NM_014841	NP_055656	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa homolog	576	Ala-rich.				clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90577062	90577062	+	Silent	SNP	C	T	T	rs147437828	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90577062C>T	uc003pnr.2	+	8	4249	c.4053C>T	c.(4051-4053)TGC>TGT	p.C1351C	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Silent_p.C1351C|CASP8AP2_uc011dzz.1_Silent_p.C1351C	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	1351					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)														---	---	---	---
SFRS18	25957	broad.mit.edu	37	6	99857075	99857075	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99857075G>T	uc003ppo.3	-	6	875	c.647C>A	c.(646-648)CCT>CAT	p.P216H	SFRS18_uc003ppp.3_Missense_Mutation_p.P216H|SFRS18_uc011eag.1_Missense_Mutation_p.P216H|SFRS18_uc003ppr.2_Missense_Mutation_p.P216H	NM_032870	NP_116259	Q8TF01	PNISR_HUMAN	splicing factor, arginine/serine-rich 130	216	Pro-rich.					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)														---	---	---	---
MAN1A1	4121	broad.mit.edu	37	6	119670101	119670101	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119670101G>A	uc003pym.1	-	2	572	c.130C>T	c.(130-132)CTG>TTG	p.L44L	MAN1A1_uc010kei.1_Silent_p.L44L	NM_005907	NP_005898	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	44	Helical; Signal-anchor for type II membrane protein; (Potential).			KGSGPAALRLTEKFVLLLV -> MNSNFITFDLKMSLLPSN L (in Ref. 2; CAA52831).	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)														---	---	---	---
TAAR1	134864	broad.mit.edu	37	6	132966361	132966361	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132966361A>G	uc003qdm.1	-	1	782	c.782T>C	c.(781-783)CTA>CCA	p.L261P		NM_138327	NP_612200	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	261	Helical; Name=6; (Potential).					plasma membrane					0	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)													---	---	---	---
TXLNB	167838	broad.mit.edu	37	6	139563701	139563701	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139563701G>A	uc011eds.1	-	10	2182	c.2017C>T	c.(2017-2019)CGC>TGC	p.R673C		NM_153235	NP_694967	Q8N3L3	TXLNB_HUMAN	taxilin beta	673						cytoplasm				large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146240594	146240594	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146240594G>A	uc003qlf.2	-	22	4441	c.4042C>T	c.(4042-4044)CGT>TGT	p.R1348C	SHPRH_uc003qld.2_Missense_Mutation_p.R1352C|SHPRH_uc003qle.2_Missense_Mutation_p.R1352C|SHPRH_uc003qlg.1_Missense_Mutation_p.R904C|SHPRH_uc003qlh.2_Missense_Mutation_p.R273C|SHPRH_uc003qli.1_Missense_Mutation_p.R273C	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1348					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)														---	---	---	---
TAB2	23118	broad.mit.edu	37	6	149700256	149700256	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149700256G>A	uc003qmj.2	+	3	1383	c.1205G>A	c.(1204-1206)CGG>CAG	p.R402Q	TAB2_uc011eec.1_Missense_Mutation_p.R370Q|TAB2_uc010kia.1_Missense_Mutation_p.R402Q|TAB2_uc010kib.1_Missense_Mutation_p.R402Q|TAB2_uc003qmk.3_RNA	NM_015093	NP_055908	Q9NYJ8	TAB2_HUMAN	mitogen-activated protein kinase kinase kinase 7	402					activation of MAPK activity|heart development|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	K63-linked polyubiquitin binding|zinc ion binding				0																		---	---	---	---
LATS1	9113	broad.mit.edu	37	6	149983013	149983013	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149983013C>T	uc003qmu.1	-	8	3793	c.3245G>A	c.(3244-3246)AGG>AAG	p.R1082K	LATS1_uc010kif.1_Missense_Mutation_p.R977K	NM_004690	NP_004681	O95835	LATS1_HUMAN	LATS homolog 1	1082	AGC-kinase C-terminal.				cell division|cytoplasmic sequestering of protein|G2/M transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|positive regulation of peptidyl-serine phosphorylation|regulation of actin filament polymerization|sister chromatid segregation	microtubule organizing center|spindle pole	ATP binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)														---	---	---	---
SUN1	23353	broad.mit.edu	37	7	895985	895985	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:895985T>C	uc011jvp.1	+						GET4_uc003sjj.1_Intron|SUN1_uc003sjf.2_Intron|SUN1_uc011jvq.1_Intron|SUN1_uc003sjg.2_Intron|SUN1_uc011jvr.1_Intron|SUN1_uc003sji.2_Intron|SUN1_uc003sjk.2_Intron	NM_001130965	NP_001124437			unc-84 homolog A isoform a						cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding				0																		---	---	---	---
FOXK1	221937	broad.mit.edu	37	7	4794168	4794168	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4794168C>T	uc003snc.1	+	3	835	c.825C>T	c.(823-825)GAC>GAT	p.D275D	FOXK1_uc003sna.1_Silent_p.D112D|FOXK1_uc003snb.1_Silent_p.D275D	NM_001037165	NP_001032242	P85037	FOXK1_HUMAN	forkhead box K1	275					cell differentiation|embryo development|muscle organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			upper_aerodigestive_tract(1)|skin(1)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)														---	---	---	---
COL28A1	340267	broad.mit.edu	37	7	7571324	7571324	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7571324C>A	uc003src.1	-	3	453	c.336G>T	c.(334-336)AAG>AAT	p.K112N	COL28A1_uc011jxe.1_Translation_Start_Site	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	collagen, type XXVIII precursor	112	VWFA 1.				cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity			skin(3)	3		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)														---	---	---	---
SNX13	23161	broad.mit.edu	37	7	17873707	17873707	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17873707G>T	uc003stw.1	-	15	1778	c.1565C>A	c.(1564-1566)CCT>CAT	p.P522H	SNX13_uc003stv.2_Missense_Mutation_p.P522H|SNX13_uc010kuc.2_Missense_Mutation_p.P319H			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;	522					cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)																	---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22184666	22184666	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22184666C>T	uc003svg.2	-	20	2036	c.1723G>A	c.(1723-1725)GCT>ACT	p.A575T	RAPGEF5_uc011jyl.1_Missense_Mutation_p.A256T	NM_012294	NP_036426	Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	425	Ras-GEF.				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																		---	---	---	---
EVX1	2128	broad.mit.edu	37	7	27282961	27282961	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27282961C>T	uc003szd.1	+	1	798	c.312C>T	c.(310-312)CTC>CTT	p.L104L	EVX1_uc011jzn.1_5'UTR|EVX1_uc010kuy.1_Silent_p.L104L	NM_001989	NP_001980	P49640	EVX1_HUMAN	even-skipped homeobox 1	104						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1																		---	---	---	---
ZNRF2	223082	broad.mit.edu	37	7	30395357	30395357	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30395357T>C	uc003tat.2	+	3	1630	c.579T>C	c.(577-579)AGT>AGC	p.S193S		NM_147128	NP_667339	Q8NHG8	ZNRF2_HUMAN	zinc finger/RING finger 2	193						cell junction|endosome membrane|lysosomal membrane|presynaptic membrane	ligase activity|zinc ion binding				0																		---	---	---	---
NPC1L1	29881	broad.mit.edu	37	7	44555476	44555476	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44555476C>T	uc003tlb.2	-	19	3859	c.3803G>A	c.(3802-3804)CGC>CAC	p.R1268H	NPC1L1_uc003tlc.2_Missense_Mutation_p.R1241H|NPC1L1_uc011kbw.1_Missense_Mutation_p.R1195H|NPC1L1_uc003tla.2_Intron	NM_013389	NP_037521	Q9UHC9	NPCL1_HUMAN	Niemann-Pick C1-like protein 1 isoform 1	1268	Cytoplasmic (Potential).				cholesterol biosynthetic process|intestinal cholesterol absorption|lipoprotein metabolic process	apical plasma membrane|cytoplasmic vesicle membrane|integral to membrane	hedgehog receptor activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5					Ezetimibe(DB00973)													---	---	---	---
ZMIZ2	83637	broad.mit.edu	37	7	44806214	44806214	+	Silent	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44806214G>C	uc003tlr.2	+	18	2730	c.2607G>C	c.(2605-2607)GGG>GGC	p.G869G	ZMIZ2_uc003tlq.2_Silent_p.G811G|ZMIZ2_uc003tls.2_Silent_p.G843G|ZMIZ2_uc003tlt.2_Silent_p.G492G|ZMIZ2_uc010kyj.2_Silent_p.G391G|ZMIZ2_uc003tlu.2_Silent_p.G150G|ZMIZ2_uc010kyk.1_5'Flank	NM_031449	NP_113637	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2 isoform 1	869	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																		---	---	---	---
TNS3	64759	broad.mit.edu	37	7	47467961	47467961	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47467961C>T	uc003tnv.2	-	9	705	c.338G>A	c.(337-339)CGC>CAC	p.R113H	TNS3_uc003tnw.2_Missense_Mutation_p.R113H|TNS3_uc010kyo.1_Missense_Mutation_p.R113H	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3	113	Phosphatase tensin-type.					focal adhesion	protein binding			ovary(4)	4																		---	---	---	---
PKD1L1	168507	broad.mit.edu	37	7	47851451	47851451	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47851451G>A	uc003tny.1	-	50	7545	c.7545C>T	c.(7543-7545)AGC>AGT	p.S2515S	C7orf69_uc003tnz.3_Intron|C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_Silent_p.S242S	NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	2515	Extracellular (Potential).				cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11																		---	---	---	---
GUSB	2990	broad.mit.edu	37	7	65444705	65444705	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65444705G>A	uc003tun.2	-						GUSB_uc011kdt.1_Intron|GUSB_uc010kzw.1_Intron	NM_000181	NP_000172			glucuronidase, beta precursor						glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0																		---	---	---	---
LAT2	7462	broad.mit.edu	37	7	73636008	73636008	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73636008C>A	uc003uag.2	+	10	924	c.374C>A	c.(373-375)TCG>TAG	p.S125*	RFC2_uc011kfa.1_Intron|LAT2_uc003uah.2_Nonsense_Mutation_p.S125*|LAT2_uc003uai.2_Nonsense_Mutation_p.S125*|LAT2_uc010lbo.2_Intron	NM_032464	NP_115853	Q9GZY6	NTAL_HUMAN	linker for activation of T cells family member	125	Cytoplasmic (Potential).				B cell activation|B cell receptor signaling pathway|calcium-mediated signaling|mast cell degranulation	integral to membrane|intracellular|membrane raft|plasma membrane	SH2 domain binding				0																		---	---	---	---
FGL2	10875	broad.mit.edu	37	7	76828797	76828797	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76828797T>C	uc003ugb.2	-	1	354	c.314A>G	c.(313-315)GAC>GGC	p.D105G	CCDC146_uc003ufz.1_Intron|CCDC146_uc003uga.2_Intron	NM_006682	NP_006673	Q14314	FGL2_HUMAN	fibrinogen-like 2 precursor	105	Potential.				signal transduction	fibrinogen complex	receptor binding			skin(2)	2																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82544043	82544043	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82544043A>C	uc003uhx.2	-	7	13548	c.13259T>G	c.(13258-13260)TTC>TGC	p.F4420C	PCLO_uc003uhv.2_Missense_Mutation_p.F4420C|PCLO_uc010lec.2_Missense_Mutation_p.F1385C	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4351					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	82580251	82580251	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82580251C>T	uc003uhx.2	-	6	9942	c.9653G>A	c.(9652-9654)CGT>CAT	p.R3218H	PCLO_uc003uhv.2_Missense_Mutation_p.R3218H|PCLO_uc010lec.2_Missense_Mutation_p.R183H	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3149	Gln-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
ABCB4	5244	broad.mit.edu	37	7	87032472	87032472	+	Silent	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87032472A>C	uc003uiv.1	-	27	3709	c.3633T>G	c.(3631-3633)GCT>GCG	p.A1211A	ABCB4_uc003uiw.1_Silent_p.A1204A|ABCB4_uc003uix.1_Silent_p.A1157A	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	1211	ABC transporter 2.|Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)																	---	---	---	---
STEAP2	261729	broad.mit.edu	37	7	89856641	89856641	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89856641T>C	uc003ujz.2	+	3	1242	c.849T>C	c.(847-849)TAT>TAC	p.Y283Y	STEAP2_uc003ujy.2_Silent_p.Y325Y|STEAP2_uc010len.2_Silent_p.Y283Y|STEAP2_uc003uka.2_Silent_p.Y283Y|STEAP2_uc003ukb.2_Silent_p.Y283Y|STEAP2_uc003ukc.2_Silent_p.Y283Y|STEAP2_uc003ukd.2_Silent_p.Y283Y	NM_152999	NP_694544	Q8NFT2	STEA2_HUMAN	six transmembrane epithelial antigen of the	283	Ferric oxidoreductase.				electron transport chain|endocytosis|Golgi to plasma membrane transport|ion transport|iron ion homeostasis|regulated secretory pathway|response to hormone stimulus	cytosol|early endosome|endosome membrane|integral to Golgi membrane|plasma membrane|trans-Golgi network transport vesicle|vesicular fraction	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity|transporter activity			ovary(2)	2	all_hematologic(106;0.112)																	---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91712572	91712572	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91712572T>C	uc003ulg.2	+	33	8474	c.8249T>C	c.(8248-8250)TTA>TCA	p.L2750S	AKAP9_uc003ulf.2_Missense_Mutation_p.L2742S|AKAP9_uc003uli.2_Missense_Mutation_p.L2373S|AKAP9_uc003ulj.2_Missense_Mutation_p.L520S|AKAP9_uc003ulk.2_Missense_Mutation_p.L25S	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	2762	Potential.|Glu-rich.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
COL1A2	1278	broad.mit.edu	37	7	94056940	94056940	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94056940G>A	uc003ung.1	+	49	3740	c.3269G>A	c.(3268-3270)GGC>GAC	p.G1090D	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	1090					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)										HNSCC(75;0.22)			---	---	---	---
DLX6	1750	broad.mit.edu	37	7	96639211	96639211	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96639211C>T	uc003uom.2	+	4	650	c.650C>T	c.(649-651)TCG>TTG	p.S217L	DLX6AS_uc003uol.2_Intron|DLX6AS_uc010lfo.1_Intron	NM_005222	NP_005213	P56179	DLX6_HUMAN	distal-less homeobox 6	127					nervous system development|skeletal system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)																	---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98567799	98567799	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98567799C>T	uc003upp.2	+	51	7765	c.7556C>T	c.(7555-7557)CCG>CTG	p.P2519L	TRRAP_uc011kis.1_Missense_Mutation_p.P2501L|TRRAP_uc003upr.2_Missense_Mutation_p.P2218L	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	2519					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ARPC1A	10552	broad.mit.edu	37	7	98957371	98957371	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98957371G>A	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)															---	---	---	---
LRRN3	54674	broad.mit.edu	37	7	110762919	110762919	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110762919C>A	uc003vft.3	+	4	1137	c.91C>A	c.(91-93)CGG>AGG	p.R31R	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Silent_p.R31R|LRRN3_uc003vfs.3_Silent_p.R31R	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	31	Extracellular (Potential).|LRRNT.					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)														---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	114269985	114269985	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114269985A>G	uc003vhb.2	+	5	896	c.522A>G	c.(520-522)CAA>CAG	p.Q174Q	FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_Silent_p.Q199Q|FOXP2_uc003vha.2_Silent_p.Q82Q|FOXP2_uc011kmu.1_Silent_p.Q191Q|FOXP2_uc011kmv.1_Silent_p.Q174Q|FOXP2_uc010ljz.1_Silent_p.Q82Q|FOXP2_uc003vgt.1_RNA|FOXP2_uc003vgv.1_Silent_p.Q174Q|FOXP2_uc003vgx.2_Silent_p.Q174Q|FOXP2_uc003vhd.2_Silent_p.Q174Q|FOXP2_uc003vhc.2_Silent_p.Q199Q	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I	174	Gln-rich.				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	p.Q174*(1)		ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8																		---	---	---	---
SPAM1	6677	broad.mit.edu	37	7	123594028	123594028	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123594028T>C	uc003vld.2	+	4	806	c.404T>C	c.(403-405)ATG>ACG	p.M135T	SPAM1_uc003vle.2_Missense_Mutation_p.M135T|SPAM1_uc011koa.1_5'Flank|SPAM1_uc003vlf.3_Missense_Mutation_p.M135T|SPAM1_uc010lku.2_Missense_Mutation_p.M135T	NM_153189	NP_694859	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 2	135					binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)													---	---	---	---
OPN1SW	611	broad.mit.edu	37	7	128415565	128415565	+	Missense_Mutation	SNP	C	T	T	rs144400933		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128415565C>T	uc003vnt.3	-	1	280	c.280G>A	c.(280-282)GCC>ACC	p.A94T		NM_001708	NP_001699	P03999	OPSB_HUMAN	opsin 1 (cone pigments), short-wave-sensitive	94	Helical; Name=2; (Potential).				phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity				0																		---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128489424	128489424	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128489424C>T	uc003vnz.3	+	30	5200	c.4991C>T	c.(4990-4992)ACG>ATG	p.T1664M	FLNC_uc003voa.3_Missense_Mutation_p.T1664M	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1664	Filamin 15.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
MEST	4232	broad.mit.edu	37	7	130144785	130144785	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130144785C>T	uc003vqg.2	+	12	1113	c.896C>T	c.(895-897)ACG>ATG	p.T299M	MEST_uc003vqc.2_Missense_Mutation_p.T290M|MEST_uc003vqd.2_Missense_Mutation_p.T256M|MEST_uc003vqf.2_Missense_Mutation_p.T290M|MEST_uc011kph.1_Missense_Mutation_p.T285M|MEST_uc010lmg.2_Missense_Mutation_p.R278C	NM_002402	NP_002393	Q5EB52	MEST_HUMAN	mesoderm specific transcript isoform a	299					mesoderm development	endoplasmic reticulum membrane|integral to membrane	hydrolase activity|protein binding			ovary(2)	2	Melanoma(18;0.0435)																	---	---	---	---
AKR1B15	441282	broad.mit.edu	37	7	134261802	134261802	+	Intron	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134261802A>C	uc011kpr.1	+						AKR1B15_uc011kps.1_Intron	NM_001080538	NP_001074007			aldo-keto reductase family 1, member B15								oxidoreductase activity			ovary(1)	1																		---	---	---	---
TRIM24	8805	broad.mit.edu	37	7	138189126	138189126	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138189126C>A	uc003vuc.2	+	2	671	c.456C>A	c.(454-456)CCC>CCA	p.P152P	TRIM24_uc003vub.2_Silent_p.P152P	NM_015905	NP_056989	O15164	TIF1A_HUMAN	transcriptional intermediary factor 1 alpha	152					cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter	cytoplasm	chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1)	8																		---	---	---	---
TAS2R40	259286	broad.mit.edu	37	7	142919775	142919775	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142919775A>G	uc011ksx.1	+	1	604	c.604A>G	c.(604-606)ATC>GTC	p.I202V		NM_176882	NP_795363	P59535	T2R40_HUMAN	taste receptor, type 2, member 40	202	Helical; Name=5; (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			ovary(1)	1	Melanoma(164;0.059)																	---	---	---	---
TAS2R60	338398	broad.mit.edu	37	7	143141266	143141266	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143141266G>A	uc011ktg.1	+	1	721	c.721G>A	c.(721-723)GCA>ACA	p.A241T	uc003wda.2_Intron	NM_177437	NP_803186	P59551	T2R60_HUMAN	taste receptor, type 2, member 60	241	Helical; Name=6; (Potential).				sensory perception of bitter taste	integral to membrane	G-protein coupled receptor activity			skin(6)	6	Melanoma(164;0.172)																	---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146536934	146536934	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146536934C>A	uc003weu.1	+	3	856	c.340C>A	c.(340-342)CGG>AGG	p.R114R		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	114	F5/8 type C.|Extracellular (Potential).		R -> Q.		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)			---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151871239	151871239	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151871239G>A	uc003wla.2	-	39	9570	c.9351C>T	c.(9349-9351)GGC>GGT	p.G3117G	MLL3_uc003wkz.2_Silent_p.G2178G|MLL3_uc003wky.2_Silent_p.G626G	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	3117	Gln-rich.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
Unknown	0	broad.mit.edu	37	7	152143302	152143302	+	IGR	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152143302C>T								FABP5L3 (3204 upstream) : LOC100128822 (17907 downstream)																																			---	---	---	---
HTR5A	3361	broad.mit.edu	37	7	154875885	154875885	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154875885G>T	uc003wlu.1	+	2	826	c.762G>T	c.(760-762)CAG>CAT	p.Q254H		NM_024012	NP_076917	P47898	5HT5A_HUMAN	5-hydroxytryptamine receptor 5A	254	Cytoplasmic (By similarity).					integral to plasma membrane	serotonin receptor activity			ovary(2)|large_intestine(1)	3	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)														---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9609294	9609294	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9609294C>T	uc003wss.2	+	19	3013	c.3008C>T	c.(3007-3009)GCC>GTC	p.A1003V	TNKS_uc011kww.1_Missense_Mutation_p.A766V|TNKS_uc010lrt.1_RNA	NM_003747	NP_003738	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related	1003					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)														---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10480562	10480562	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10480562G>A	uc003wtc.2	-	2	379	c.150C>T	c.(148-150)CGC>CGT	p.R50R		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	50					intracellular signal transduction			p.R50H(1)		ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
NEIL2	252969	broad.mit.edu	37	8	11643553	11643553	+	Missense_Mutation	SNP	G	A	A	rs8191664	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11643553G>A	uc003wug.2	+	5	1445	c.770G>A	c.(769-771)CGG>CAG	p.R257Q	NEIL2_uc003wue.2_Missense_Mutation_p.R257Q|NEIL2_uc003wuf.2_Missense_Mutation_p.R196Q|NEIL2_uc011kxd.1_Missense_Mutation_p.R141Q	NM_145043	NP_659480	Q969S2	NEIL2_HUMAN	nei like 2 isoform a	257					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					---	---	---	---
ADAM7	8756	broad.mit.edu	37	8	24304725	24304725	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24304725T>C	uc003xeb.2	+	3	296	c.183T>C	c.(181-183)TAT>TAC	p.Y61Y	ADAM7_uc003xea.1_Silent_p.Y61Y	NM_003817	NP_003808	Q9H2U9	ADAM7_HUMAN	a disintegrin and metalloproteinase domain 7	61	Extracellular (Potential).				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)														---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48848299	48848299	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48848299A>G	uc003xqi.2	-	13	1497	c.1440T>C	c.(1438-1440)AGT>AGC	p.S480S	PRKDC_uc003xqj.2_Silent_p.S480S|PRKDC_uc011ldh.1_Silent_p.S480S	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	480					cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)											NHEJ					---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56015465	56015465	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56015465C>T	uc003xsf.2	+	1	449	c.417C>T	c.(415-417)CGC>CGT	p.R139R		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	139						integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
VCPIP1	80124	broad.mit.edu	37	8	67577294	67577294	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67577294A>C	uc003xwn.2	-	1	2159	c.1900T>G	c.(1900-1902)TTT>GTT	p.F634V	SGK3_uc003xwp.2_5'Flank|C8orf44_uc003xwo.1_5'Flank	NM_025054	NP_079330	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex	634					protein ubiquitination	endoplasmic reticulum|Golgi stack	ubiquitin-specific protease activity			lung(2)|ovary(2)|central_nervous_system(1)|breast(1)|skin(1)|kidney(1)	8		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68111330	68111330	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68111330T>C	uc003xxo.1	-	39	5779	c.5389A>G	c.(5389-5391)AAA>GAA	p.K1797E	ARFGEF1_uc003xxl.1_Intron|ARFGEF1_uc003xxm.1_Missense_Mutation_p.K200E|ARFGEF1_uc003xxn.1_Missense_Mutation_p.K742E|ARFGEF1_uc003xxp.1_3'UTR	NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine	1797					exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69434189	69434189	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69434189C>T	uc010lyz.2	+	6	712	c.663C>T	c.(661-663)GGC>GGT	p.G221G	C8orf34_uc010lyy.1_Silent_p.G221G|C8orf34_uc003xyb.2_Silent_p.G196G	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	221					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)															---	---	---	---
EYA1	2138	broad.mit.edu	37	8	72123448	72123448	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72123448T>C	uc003xys.3	-	16	1928	c.1641A>G	c.(1639-1641)AGA>AGG	p.R547R	EYA1_uc003xyr.3_Silent_p.R512R|EYA1_uc003xyt.3_Silent_p.R514R|EYA1_uc010lzf.2_Silent_p.R474R|EYA1_uc003xyu.2_Silent_p.R547R|EYA1_uc011lfe.1_Silent_p.R541R|EYA1_uc003xyv.2_Silent_p.R425R	NM_172058	NP_742055	Q99502	EYA1_HUMAN	eyes absent 1 isoform b	547			R -> G (in anterior segment anomalies; with cataract).		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)															---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85774590	85774590	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85774590G>A	uc003ycq.3	+	7	889	c.473G>A	c.(472-474)CGT>CAT	p.R158H	RALYL_uc003ycr.3_Missense_Mutation_p.R158H|RALYL_uc003ycs.3_Missense_Mutation_p.R158H|RALYL_uc010lzy.2_Missense_Mutation_p.R147H|RALYL_uc003yct.3_Missense_Mutation_p.R171H|RALYL_uc003ycu.3_Missense_Mutation_p.R85H|RALYL_uc003ycv.3_Missense_Mutation_p.R70H	NM_001100392	NP_001093862	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like isoform 2	158							identical protein binding|nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
TMEM67	91147	broad.mit.edu	37	8	94793160	94793160	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94793160C>T	uc011lgk.1	+	9	999	c.928C>T	c.(928-930)CTC>TTC	p.L310F	TMEM67_uc010mat.1_Missense_Mutation_p.L225F|TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Missense_Mutation_p.L229F	NM_153704	NP_714915	Q5HYA8	MKS3_HUMAN	meckelin isoform 1	310					cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)															---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113318350	113318350	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113318350G>A	uc003ynu.2	-	51	8116	c.7957C>T	c.(7957-7959)CGA>TGA	p.R2653*	CSMD3_uc003yns.2_Nonsense_Mutation_p.R1855*|CSMD3_uc003ynt.2_Nonsense_Mutation_p.R2613*|CSMD3_uc011lhx.1_Nonsense_Mutation_p.R2549*	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2653	Extracellular (Potential).|Sushi 15.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118831966	118831966	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118831966C>A	uc003yok.1	-	6	2258	c.1485G>T	c.(1483-1485)CAG>CAT	p.Q495H		NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1	495	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)					Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				---	---	---	---
LRRC6	23639	broad.mit.edu	37	8	133584716	133584716	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133584716C>A	uc003ytk.2	-	12	1313	c.1239G>T	c.(1237-1239)ATG>ATT	p.M413I	LRRC6_uc003ytl.2_RNA	NM_012472	NP_036604	Q86X45	LRRC6_HUMAN	leucine rich repeat containing 6	413						cytoplasm				ovary(1)|kidney(1)	2	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)															---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139649029	139649029	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139649029C>T	uc003yvd.2	-	48	3958	c.3511G>A	c.(3511-3513)GGA>AGA	p.G1171R	COL22A1_uc011ljo.1_Missense_Mutation_p.G451R	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1171	Pro-rich.|Gly-rich.|Collagen-like 11.				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)			---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	141321405	141321405	+	Missense_Mutation	SNP	C	T	T	rs148453804	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141321405C>T	uc003yvj.2	-	10	1698	c.1564G>A	c.(1564-1566)GCC>ACC	p.A522T	TRAPPC9_uc003yvh.2_Missense_Mutation_p.A620T|TRAPPC9_uc003yvi.1_Missense_Mutation_p.A513T	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform	522					cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
DENND3	22898	broad.mit.edu	37	8	142160929	142160929	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142160929G>A	uc003yvy.2	+						DENND3_uc010mep.2_Intron	NM_014957	NP_055772			DENN/MADD domain containing 3											ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143427155	143427155	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143427155C>A	uc003ywk.2	-	3	305	c.187G>T	c.(187-189)GGT>TGT	p.G63C	TSNARE1_uc011lju.1_Missense_Mutation_p.G63C|TSNARE1_uc003ywj.2_Missense_Mutation_p.G63C|TSNARE1_uc003ywl.3_Intron	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	63					vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
BAI1	575	broad.mit.edu	37	8	143558823	143558823	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143558823C>T	uc003ywm.2	+	5	1483	c.1300C>T	c.(1300-1302)CGC>TGC	p.R434C		NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	434	Extracellular (Potential).|TSP type-1 3.				axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1)	8	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
ZC3H3	23144	broad.mit.edu	37	8	144550367	144550367	+	Intron	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144550367C>T	uc003yyd.2	-							NM_015117	NP_055932			zinc finger CCCH-type containing 3						mRNA polyadenylation|poly(A)+ mRNA export from nucleus|regulation of mRNA export from nucleus	nucleus	nucleic acid binding|zinc ion binding			skin(1)	1	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)															---	---	---	---
C8orf73	642475	broad.mit.edu	37	8	144652165	144652165	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144652165C>T	uc010mff.2	-	7	1158	c.1114G>A	c.(1114-1116)GCG>ACG	p.A372T	C8orf73_uc010mfg.1_Missense_Mutation_p.R384H	NM_001100878	NP_001094348	A6NGR9	CH073_HUMAN	hypothetical protein LOC642475	372	Leu-rich.						binding			ovary(1)	1	all_cancers(97;6.49e-11)|all_epithelial(106;4.73e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.014)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
NRBP2	340371	broad.mit.edu	37	8	144919329	144919329	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144919329A>G	uc011lkt.1	-	14	1285	c.1145T>C	c.(1144-1146)CTG>CCG	p.L382P	NRBP2_uc003yzv.2_Missense_Mutation_p.L139P|NRBP2_uc003yzz.1_5'UTR|NRBP2_uc003yzw.2_Missense_Mutation_p.L174P|NRBP2_uc010mfl.2_Missense_Mutation_p.L174P|NRBP2_uc010mfm.2_Missense_Mutation_p.L139P|NRBP2_uc011lks.1_Missense_Mutation_p.L139P|NRBP2_uc003yzy.2_Missense_Mutation_p.L139P	NM_178564	NP_848659	Q9NSY0	NRBP2_HUMAN	nuclear receptor binding protein 2	382					negative regulation of neuron apoptosis|neuron differentiation	cytoplasm	ATP binding|protein kinase activity			central_nervous_system(2)	2	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)															---	---	---	---
RANBP6	26953	broad.mit.edu	37	9	6013657	6013657	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6013657A>C	uc003zjr.2	-	1	1962	c.1951T>G	c.(1951-1953)TTA>GTA	p.L651V	RANBP6_uc011lmf.1_Missense_Mutation_p.L299V|RANBP6_uc003zjs.2_Missense_Mutation_p.L239V	NM_012416	NP_036548	O60518	RNBP6_HUMAN	RAN binding protein 6	651					protein transport	cytoplasm|nucleus	binding			ovary(3)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)														---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8484205	8484205	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8484205A>G	uc003zkk.2	-	29	4038	c.3327T>C	c.(3325-3327)CGT>CGC	p.R1109R	PTPRD_uc003zkp.2_Silent_p.R698R|PTPRD_uc003zkq.2_Silent_p.R698R|PTPRD_uc003zkr.2_Silent_p.R693R|PTPRD_uc003zks.2_Silent_p.R688R|PTPRD_uc003zkl.2_Silent_p.R1100R|PTPRD_uc003zkm.2_Silent_p.R1096R|PTPRD_uc003zkn.2_Silent_p.R698R|PTPRD_uc003zko.2_Silent_p.R695R	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1109	Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
BNC2	54796	broad.mit.edu	37	9	16435990	16435990	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16435990G>A	uc003zml.2	-	6	2342	c.2202C>T	c.(2200-2202)GGC>GGT	p.G734G	BNC2_uc011lmw.1_Silent_p.G639G|BNC2_uc003zmm.2_Silent_p.G692G|BNC2_uc003zmq.1_Silent_p.G748G|BNC2_uc003zmr.1_Silent_p.G771G|BNC2_uc003zmp.1_Silent_p.G762G|BNC2_uc010mij.1_Silent_p.G656G|BNC2_uc011lmv.1_Silent_p.G560G|BNC2_uc003zmo.1_Silent_p.G656G|BNC2_uc003zmj.2_Silent_p.G499G|BNC2_uc003zmk.2_RNA|BNC2_uc003zmi.2_Silent_p.G499G|BNC2_uc003zmn.1_Silent_p.G499G	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2	734					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)														---	---	---	---
CNTLN	54875	broad.mit.edu	37	9	17226276	17226276	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17226276A>C	uc003zmz.2	+	3	551	c.525A>C	c.(523-525)GAA>GAC	p.E175D	CNTLN_uc003zmx.3_Missense_Mutation_p.E175D|CNTLN_uc003zmy.2_Missense_Mutation_p.E175D	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1	175						centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18574264	18574264	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18574264A>G	uc003zne.3	+	4	601	c.474A>G	c.(472-474)CAA>CAG	p.Q158Q	ADAMTSL1_uc003znb.2_Silent_p.Q158Q|ADAMTSL1_uc003znc.3_Silent_p.Q158Q	NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	158						proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ACER2	340485	broad.mit.edu	37	9	19424786	19424786	+	Silent	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19424786T>G	uc003zny.1	+	3	470	c.312T>G	c.(310-312)GCT>GCG	p.A104A	ACER2_uc003znx.1_RNA|ACER2_uc003znz.1_Silent_p.A55A	NM_001010887	NP_001010887	Q5QJU3	ACER2_HUMAN	alkaline ceramidase 2	104	Helical; (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																		---	---	---	---
SLC24A2	25769	broad.mit.edu	37	9	19516258	19516258	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19516258G>A	uc003zoa.1	-	10	1941	c.1879C>T	c.(1879-1881)CGA>TGA	p.R627*	SLC24A2_uc003zob.1_Nonsense_Mutation_p.R610*	NM_020344	NP_065077	Q9UI40	NCKX2_HUMAN	solute carrier family 24	627	Extracellular (Potential).				visual perception	integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(3)	3				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)														---	---	---	---
IFT74	80173	broad.mit.edu	37	9	26984556	26984556	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26984556T>C	uc010mja.2	+	6	591	c.464T>C	c.(463-465)ATG>ACG	p.M155T	IFT74_uc010mjb.2_Missense_Mutation_p.M155T|IFT74_uc003zqf.3_Missense_Mutation_p.M155T|IFT74_uc003zqg.3_Missense_Mutation_p.M155T	NM_001099223	NP_001092693	Q96LB3	IFT74_HUMAN	coiled-coil domain containing 2 isoform a	155	Potential.					cytoplasmic membrane-bounded vesicle|intraflagellar transport particle B|microtubule-based flagellum				skin(1)	1		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)														---	---	---	---
C9orf72	203228	broad.mit.edu	37	9	27566788	27566788	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27566788C>T	uc003zqq.2	-	2	428	c.331G>A	c.(331-333)GGA>AGA	p.G111R	C9orf72_uc003zqr.1_Missense_Mutation_p.G111R	NM_018325	NP_060795	Q96LT7	CI072_HUMAN	hypothetical protein LOC203228 isoform a	111										ovary(3)|central_nervous_system(1)	4		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)														---	---	---	---
TAF1L	138474	broad.mit.edu	37	9	32635575	32635575	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32635575C>T	uc003zrg.1	-	1	93	c.3G>A	c.(1-3)ATG>ATA	p.M1I	uc003zrh.1_Intron	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1					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)														---	---	---	---
PRSS3	5646	broad.mit.edu	37	9	33797910	33797910	+	Missense_Mutation	SNP	G	A	A	rs146360076	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33797910G>A	uc003ztj.3	+	3	455	c.455G>A	c.(454-456)CGC>CAC	p.R152H	uc003ztk.1_Intron|PRSS3_uc003zti.3_Missense_Mutation_p.R109H|PRSS3_uc003ztl.3_Missense_Mutation_p.R95H	NM_007343	NP_031369	P35030	TRY3_HUMAN	mesotrypsin isoform 1 preproprotein	152	Peptidase S1.				digestion|endothelial cell migration|zymogen activation	extracellular space	calcium ion binding|protein binding|serine-type endopeptidase activity|serine-type peptidase activity				0			LUSC - Lung squamous cell carcinoma(29;0.0176)															---	---	---	---
PIGO	84720	broad.mit.edu	37	9	35091339	35091339	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35091339G>A	uc003zwd.2	-	7	2941	c.2545C>T	c.(2545-2547)CTG>TTG	p.L849L	PIGO_uc003zwc.1_3'UTR|PIGO_uc003zwe.2_Intron|PIGO_uc003zwf.2_Intron|PIGO_uc003zwg.1_Silent_p.L412L	NM_032634	NP_116023	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	849	Helical; (Potential).				C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	transferase activity			large_intestine(1)|ovary(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)															---	---	---	---
RUSC2	9853	broad.mit.edu	37	9	35558504	35558504	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35558504A>G	uc003zww.2	+	8	3536	c.3281A>G	c.(3280-3282)CAA>CGA	p.Q1094R	RUSC2_uc010mkq.2_RNA|RUSC2_uc003zwx.3_Missense_Mutation_p.Q1094R	NM_014806	NP_055621	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1094	RUN.					cytosol				ovary(1)	1			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
OR13J1	392309	broad.mit.edu	37	9	35869672	35869672	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35869672C>T	uc011lph.1	-	1	727	c.727G>A	c.(727-729)GCA>ACA	p.A243T		NM_001004487	NP_001004487	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J,	243	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
TMEM2	23670	broad.mit.edu	37	9	74360369	74360369	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74360369G>A	uc011lsa.1	-	4	1139	c.599C>T	c.(598-600)GCG>GTG	p.A200V	TMEM2_uc010mos.2_Missense_Mutation_p.A200V|TMEM2_uc011lsb.1_RNA	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a	200	G8.					integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)														---	---	---	---
GNAQ	2776	broad.mit.edu	37	9	80336240	80336240	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80336240T>C	uc004akw.2	-	7	1120	c.1079A>G	c.(1078-1080)TAA>TGA	p.*360*	GNAQ_uc011lso.1_Silent_p.*158*|GNAQ_uc004akv.1_5'Flank	NM_002072	NP_002063	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein),	360					activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity			eye(136)|skin(44)|meninges(11)|ovary(1)|kidney(1)	193								Mis		uveal melanoma								---	---	---	---
PHF2	5253	broad.mit.edu	37	9	96428055	96428055	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96428055T>C	uc004aub.2	+	15	2172	c.2025T>C	c.(2023-2025)GAT>GAC	p.D675D	PHF2_uc011lug.1_Silent_p.D558D|PHF2_uc004auc.2_Silent_p.D94D	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2	675					liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)														---	---	---	---
PTPDC1	138639	broad.mit.edu	37	9	96860859	96860859	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96860859C>T	uc004auf.1	+	7	2189	c.1849C>T	c.(1849-1851)CAG>TAG	p.Q617*	PTPDC1_uc004aug.1_Intron|PTPDC1_uc004auh.1_Nonsense_Mutation_p.Q669*|PTPDC1_uc010mrj.1_Nonsense_Mutation_p.Q671*|PTPDC1_uc010mri.1_Nonsense_Mutation_p.Q669*	NM_177995	NP_818931	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1	617							protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1																		---	---	---	---
TRIM14	9830	broad.mit.edu	37	9	100849622	100849622	+	Intron	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100849622G>T	uc004ayd.2	-						TRIM14_uc004ayf.1_Intron|TRIM14_uc011luz.1_3'UTR|TRIM14_uc011lva.1_3'UTR|TRIM14_uc004ayg.1_Intron|TRIM14_uc004ayh.1_3'UTR|TRIM14_uc004ayi.1_Missense_Mutation_p.P233Q|TRIM14_uc004ayj.1_3'UTR	NM_033220	NP_150089			tripartite motif protein TRIM14 isoform alpha							cytoplasm|intracellular	zinc ion binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
OR13C9	286362	broad.mit.edu	37	9	107379859	107379859	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107379859C>T	uc011lvr.1	-	1	627	c.627G>A	c.(625-627)ATG>ATA	p.M209I		NM_001001956	NP_001001956	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C,	209	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
MUSK	4593	broad.mit.edu	37	9	113530131	113530131	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113530131G>A	uc004bey.2	+	8	1050	c.952G>A	c.(952-954)GCC>ACC	p.A318T		NM_005592	NP_005583	O15146	MUSK_HUMAN	skeletal muscle receptor tyrosine kinase	318	FZ.|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																		---	---	---	---
SUSD1	64420	broad.mit.edu	37	9	114905868	114905868	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114905868G>A	uc004bfu.2	-	4	450	c.409C>T	c.(409-411)CAT>TAT	p.H137Y	SUSD1_uc010mui.2_Missense_Mutation_p.H137Y|SUSD1_uc010muj.2_Missense_Mutation_p.H137Y	NM_022486	NP_071931	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1 precursor	137	EGF-like 3; calcium-binding (Potential).|Extracellular (Potential).					integral to membrane	calcium ion binding				0																		---	---	---	---
RGS3	5998	broad.mit.edu	37	9	116353631	116353631	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116353631G>A	uc004bhq.2	+	22	3243	c.3034G>A	c.(3034-3036)GTT>ATT	p.V1012I	RGS3_uc004bhs.2_Missense_Mutation_p.V902I|RGS3_uc004bht.2_Missense_Mutation_p.V731I|RGS3_uc010muy.2_Missense_Mutation_p.V405I|RGS3_uc004bhv.2_Missense_Mutation_p.V333I|RGS3_uc010muz.1_Missense_Mutation_p.V351I|RGS3_uc004bhw.2_Intron|RGS3_uc011lxh.1_Missense_Mutation_p.V322I|RGS3_uc004bhx.2_Missense_Mutation_p.V333I|RGS3_uc004bhy.1_Missense_Mutation_p.V322I|RGS3_uc004bhz.2_Missense_Mutation_p.V354I|RGS3_uc004bia.2_5'Flank	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6	1012					inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
AKNA	80709	broad.mit.edu	37	9	117122197	117122197	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117122197A>T	uc004biq.3	-	9	2405	c.2270T>A	c.(2269-2271)GTT>GAT	p.V757D	AKNA_uc004bin.3_Missense_Mutation_p.V4D|AKNA_uc004bio.3_Missense_Mutation_p.V217D|AKNA_uc004bip.3_Missense_Mutation_p.V676D|AKNA_uc004bir.3_Missense_Mutation_p.V757D|AKNA_uc004bis.3_Missense_Mutation_p.V757D|AKNA_uc010mve.2_Missense_Mutation_p.V638D|AKNA_uc004biu.1_Missense_Mutation_p.V498D|AKNA_uc004biv.1_Missense_Mutation_p.V757D	NM_030767	NP_110394	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	757					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6																		---	---	---	---
C9orf91	203197	broad.mit.edu	37	9	117379548	117379548	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117379548C>A	uc004bjd.3	+	2	290	c.73C>A	c.(73-75)CTG>ATG	p.L25M	C9orf91_uc004bje.3_Translation_Start_Site	NM_153045	NP_694590	Q5VZI3	CI091_HUMAN	hypothetical protein LOC203197	25						integral to membrane				pancreas(1)	1																		---	---	---	---
TRIM32	22954	broad.mit.edu	37	9	119461306	119461306	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119461306C>A	uc004bjx.2	+	2	1443	c.1285C>A	c.(1285-1287)CTC>ATC	p.L429I	ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjs.1_Intron|ASTN2_uc004bjt.1_Intron|TRIM32_uc004bjw.2_Missense_Mutation_p.L429I	NM_001099679	NP_001093149	Q13049	TRI32_HUMAN	tripartite motif-containing 32	429	NHL 2.				fat cell differentiation|innate immune response|negative regulation of apoptosis|negative regulation of fibroblast proliferation|positive regulation of cell cycle|positive regulation of cell growth|positive regulation of cell migration|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein catabolic process|positive regulation of proteolysis|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to tumor necrosis factor|response to UV	nucleus	myosin binding|protein self-association|RNA binding|Tat protein binding|transcription coactivator activity|translation initiation factor binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(2)|kidney(1)	3														Bardet-Biedl_syndrome				---	---	---	---
OR1L3	26735	broad.mit.edu	37	9	125437522	125437522	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125437522T>C	uc011lzb.1	+	1	114	c.114T>C	c.(112-114)ACT>ACC	p.T38T		NM_001005234	NP_001005234	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L,	38	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1																		---	---	---	---
OR5C1	392391	broad.mit.edu	37	9	125551855	125551855	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125551855T>C	uc011lzd.1	+	1	644	c.644T>C	c.(643-645)GTG>GCG	p.V215A		NM_001001923	NP_001001923	Q8NGR4	OR5C1_HUMAN	olfactory receptor, family 5, subfamily C,	215	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1																		---	---	---	---
LMX1B	4010	broad.mit.edu	37	9	129455844	129455844	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129455844C>T	uc004bqj.2	+	5	764	c.714C>T	c.(712-714)CGC>CGT	p.R238R	LMX1B_uc004bqi.2_Silent_p.R238R|LMX1B_uc011maa.1_Silent_p.R238R	NM_002316	NP_002307	O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	238	Homeobox.				dorsal/ventral pattern formation|in utero embryonic development	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														Nail-Patella_Syndrome				---	---	---	---
RALGPS1	9649	broad.mit.edu	37	9	129961355	129961355	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129961355G>A	uc004bqo.1	+						RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron	NM_014636	NP_055451			Ral GEF with PH domain and SH3 binding motif 1						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1																OREG0019502	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DNM1	1759	broad.mit.edu	37	9	130980885	130980885	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130980885A>G	uc011mau.1	+	3	347	c.260A>G	c.(259-261)AAG>AGG	p.K87R	DNM1_uc010mxr.2_Missense_Mutation_p.K87R|DNM1_uc011mat.1_Missense_Mutation_p.K87R	NM_004408	NP_004399	Q05193	DYN1_HUMAN	dynamin 1 isoform 1	87					receptor-mediated endocytosis	microtubule	GTP binding|GTPase activity			ovary(2)	2																		---	---	---	---
TBC1D13	54662	broad.mit.edu	37	9	131570101	131570101	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131570101C>A	uc010myj.2	+	12	1269	c.1146C>A	c.(1144-1146)CCC>CCA	p.P382P	TBC1D13_uc010myk.2_Silent_p.P257P|TBC1D13_uc010myl.2_Silent_p.P201P	NM_018201	NP_060671	Q9NVG8	TBC13_HUMAN	TBC1 domain family, member 13	382						intracellular	Rab GTPase activator activity				0																		---	---	---	---
LAMC3	10319	broad.mit.edu	37	9	133901811	133901811	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133901811C>T	uc004caa.1	+	2	611	c.513C>T	c.(511-513)TAC>TAT	p.Y171Y		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	171	Laminin N-terminal.				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)														---	---	---	---
GTF3C5	9328	broad.mit.edu	37	9	135917576	135917576	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135917576C>A	uc004cci.3	+	2	593	c.256C>A	c.(256-258)CTC>ATC	p.L86I	GTF3C5_uc010mzz.2_Intron|GTF3C5_uc004ccj.3_Missense_Mutation_p.L86I	NM_012087	NP_036219	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5	86						transcription factor TFIIIC complex	DNA binding|protein binding				0				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)														---	---	---	---
RXRA	6256	broad.mit.edu	37	9	137328407	137328407	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137328407C>T	uc004cfb.2	+	10	1498	c.1336C>T	c.(1336-1338)CCC>TCC	p.P446S	RXRA_uc004cfc.1_Missense_Mutation_p.P349S	NM_002957	NP_002948	P19793	RXRA_HUMAN	retinoid X receptor, alpha	446	Ligand-binding.				cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process	nuclear chromatin|nucleoplasm	enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)													---	---	---	---
CAMSAP1	157922	broad.mit.edu	37	9	138703390	138703390	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138703390G>A	uc004cgr.3	-	17	4574	c.4574C>T	c.(4573-4575)GCG>GTG	p.A1525V	CAMSAP1_uc004cgq.3_Missense_Mutation_p.A1415V|CAMSAP1_uc010nbg.2_Missense_Mutation_p.A1247V	NM_015447	NP_056262	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein	1525	CKK.					cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)														---	---	---	---
NOTCH1	4851	broad.mit.edu	37	9	139409854	139409854	+	Splice_Site	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139409854T>C	uc004chz.2	-	12	1904	c.1904_splice	c.e12-1	p.G635_splice	NOTCH1_uc004cia.1_5'Flank	NM_017617	NP_060087			notch1 preproprotein						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)			---	---	---	---
C9orf172	389813	broad.mit.edu	37	9	139739752	139739752	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139739752G>A	uc011meh.1	+	1	886	c.886G>A	c.(886-888)GCC>ACC	p.A296T	PHPT1_uc004cjp.2_5'Flank	NM_001080482	NP_001073951	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	296	Pro-rich.										0																		---	---	---	---
NELF	26012	broad.mit.edu	37	9	140344138	140344138	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140344138G>A	uc004cna.2	-						C9orf167_uc011mew.1_Intron|NELF_uc011mex.1_Intron|NELF_uc010nci.2_Intron|NELF_uc011mey.1_Intron|NELF_uc011mez.1_Intron|NELF_uc004cmz.2_Intron|NELF_uc004cnc.2_Intron|NELF_uc004cnb.2_Intron	NM_001130969	NP_001124441			nasal embryonic LHRH factor isoform a							nucleus|plasma membrane					0	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000222)|Epithelial(140;0.000888)														---	---	---	---
C10orf18	54906	broad.mit.edu	37	10	5789072	5789072	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5789072A>G	uc001iij.2	+	15	4313	c.3688A>G	c.(3688-3690)ACA>GCA	p.T1230A	C10orf18_uc001iik.2_Missense_Mutation_p.T74A	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	1230										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
UPF2	26019	broad.mit.edu	37	10	12070793	12070793	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12070793G>A	uc001ila.2	-	2	1570	c.1096C>T	c.(1096-1098)CAC>TAC	p.H366Y	UPF2_uc001ilb.2_Missense_Mutation_p.H366Y|UPF2_uc001ilc.2_Missense_Mutation_p.H366Y|UPF2_uc009xiz.1_Missense_Mutation_p.H366Y	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	366	MIF4G 1.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)																---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12803039	12803039	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12803039C>T	uc001ilo.2	+	4	627	c.392C>T	c.(391-393)GCC>GTC	p.A131V	CAMK1D_uc001iln.2_Missense_Mutation_p.A131V	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	131	Protein kinase.					calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)														---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21074772	21074772	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21074772G>A	uc001iqi.2	-	28	3346	c.2949C>T	c.(2947-2949)AAC>AAT	p.N983N	NEBL_uc001iqj.2_RNA|NEBL_uc001iqk.2_Silent_p.N239N	NM_006393	NP_006384	O76041	NEBL_HUMAN	nebulette sarcomeric isoform	983	SH3.				regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28274045	28274045	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28274045C>G	uc009xky.2	-	4	576	c.478G>C	c.(478-480)GAT>CAT	p.D160H	ARMC4_uc010qdt.1_5'Flank|ARMC4_uc001itz.2_Missense_Mutation_p.D160H	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	160							binding			ovary(4)|skin(2)	6																		---	---	---	---
ZNF33B	7582	broad.mit.edu	37	10	43088670	43088670	+	Silent	SNP	C	A	A	rs140658159	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43088670C>A	uc001jaf.1	-	5	1843	c.1728G>T	c.(1726-1728)ACG>ACT	p.T576T	ZNF33B_uc009xmg.1_Intron|ZNF33B_uc001jae.1_Intron|ZNF33B_uc001jag.1_Silent_p.T464T|ZNF33B_uc001jad.2_Intron	NM_006955	NP_008886	Q06732	ZN33B_HUMAN	zinc finger protein 33B	576						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
ERCC6	2074	broad.mit.edu	37	10	50686483	50686483	+	Nonsense_Mutation	SNP	G	A	A	rs121917901		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50686483G>A	uc001jhs.3	-	11	2357	c.2203C>T	c.(2203-2205)CGA>TGA	p.R735*	ERCC6_uc009xod.2_5'Flank|ERCC6_uc010qgr.1_Nonsense_Mutation_p.R105*|ERCC6_uc001jhr.3_Nonsense_Mutation_p.R135*	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	735					base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding			lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1)	16													Direct_reversal_of_damage|NER					---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55581859	55581859	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55581859T>C	uc001jju.1	-	33	6022	c.5627A>G	c.(5626-5628)CAG>CGG	p.Q1876R	PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Missense_Mutation_p.Q730R|PCDH15_uc010qhv.1_Missense_Mutation_p.Q1873R|PCDH15_uc010qhw.1_Missense_Mutation_p.Q1836R|PCDH15_uc010qhx.1_Missense_Mutation_p.Q1807R|PCDH15_uc010qhy.1_Missense_Mutation_p.Q1883R|PCDH15_uc010qhz.1_Missense_Mutation_p.Q1878R|PCDH15_uc010qia.1_Missense_Mutation_p.Q1856R|PCDH15_uc010qib.1_Missense_Mutation_p.Q1853R	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1876	Cytoplasmic (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			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	55721625	55721625	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55721625T>C	uc001jju.1	-	22	3291	c.2896A>G	c.(2896-2898)AGA>GGA	p.R966G	PCDH15_uc010qhq.1_Missense_Mutation_p.R971G|PCDH15_uc010qhr.1_Missense_Mutation_p.R966G|PCDH15_uc010qhs.1_Missense_Mutation_p.R978G|PCDH15_uc010qht.1_Missense_Mutation_p.R973G|PCDH15_uc010qhu.1_Missense_Mutation_p.R966G|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.R966G|PCDH15_uc010qhw.1_Missense_Mutation_p.R929G|PCDH15_uc010qhx.1_Missense_Mutation_p.R895G|PCDH15_uc010qhy.1_Missense_Mutation_p.R971G|PCDH15_uc010qhz.1_Missense_Mutation_p.R966G|PCDH15_uc010qia.1_Missense_Mutation_p.R944G|PCDH15_uc010qib.1_Missense_Mutation_p.R944G	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	966	Extracellular (Potential).|Cadherin 9.				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)			---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68940246	68940246	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68940246A>G	uc009xpn.1	-	7	999	c.876T>C	c.(874-876)ACT>ACC	p.T292T	CTNNA3_uc001jmw.2_Silent_p.T292T|CTNNA3_uc001jmx.3_Silent_p.T292T|CTNNA3_uc009xpo.1_Silent_p.T152T|CTNNA3_uc001jna.2_Silent_p.T304T	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3	292					cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
ADAMTS14	140766	broad.mit.edu	37	10	72489928	72489928	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72489928A>G	uc001jrh.2	+	6	1025	c.1025A>G	c.(1024-1026)CAG>CGG	p.Q342R	ADAMTS14_uc001jrg.2_Missense_Mutation_p.Q342R	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1	342	Peptidase M12B.				collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6																		---	---	---	---
TTC18	118491	broad.mit.edu	37	10	75113397	75113397	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75113397G>C	uc009xrc.2	-	3	288	c.167C>G	c.(166-168)GCA>GGA	p.A56G	TTC18_uc001jty.2_Missense_Mutation_p.A56G|TTC18_uc009xrd.1_5'UTR	NM_145170	NP_660153	Q5T0N1	TTC18_HUMAN	tetratricopeptide repeat domain 18	56							binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)																	---	---	---	---
PTEN	5728	broad.mit.edu	37	10	89624305	89624305	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89624305T>G	uc001kfb.2	+	2	1110	c.79T>G	c.(79-81)TAT>GAT	p.Y27D	KILLIN_uc009xti.2_5'Flank	NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	27	Phosphatase tensin-type.		Y -> S (loss of phosphatase activity towards Ins(1,3,4,5)P4).		activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.?(13)|p.0?(12)|p.Y27fs*1(3)|p.Y27C(2)|p.Y27_N212>Y(2)|p.Y27S(1)|p.Y27fs*16(1)|p.Y27N(1)|p.Y27*(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)			31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			---	---	---	---
TNKS2	80351	broad.mit.edu	37	10	93596667	93596667	+	Intron	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93596667C>T	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)																---	---	---	---
COX15	1355	broad.mit.edu	37	10	101473179	101473179	+	3'UTR	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101473179T>G	uc001kqb.3	-	9					COX15_uc001kqc.3_Missense_Mutation_p.N387H|COX15_uc010qpj.1_3'UTR	NM_078470	NP_510870			COX15 homolog isoform 1						heme a biosynthetic process|respiratory chain complex IV assembly|respiratory gaseous exchange	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)														---	---	---	---
DNMBP	23268	broad.mit.edu	37	10	101731839	101731839	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101731839G>A	uc001kqj.2	-	2	135	c.43C>T	c.(43-45)CCT>TCT	p.P15S		NM_015221	NP_056036	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	15	SH3 1.				intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)|skin(1)	6		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)														---	---	---	---
SCD	6319	broad.mit.edu	37	10	102120550	102120550	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102120550C>T	uc001kqy.2	+	6	1430	c.940C>T	c.(940-942)CGC>TGC	p.R314C		NM_005063	NP_005054	O00767	ACOD_HUMAN	stearoyl-CoA desaturase 1	314	Cytoplasmic (Potential).				fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity				0		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)														---	---	---	---
GBF1	8729	broad.mit.edu	37	10	104103805	104103805	+	Intron	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104103805C>T	uc001kux.1	+						GBF1_uc001kuw.2_Intron|GBF1_uc001kuy.1_Intron|GBF1_uc001kuz.1_Intron	NM_004193	NP_004184			golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)														---	---	---	---
SFXN2	118980	broad.mit.edu	37	10	104489523	104489523	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104489523T>C	uc001kwb.2	+	6	717	c.551T>C	c.(550-552)GTG>GCG	p.V184A	SFXN2_uc001kwc.2_RNA|SFXN2_uc001kwd.2_Intron	NM_178858	NP_849189	Q96NB2	SFXN2_HUMAN	sideroflexin 2	184	Helical; (Potential).			QMALSYFTATTTAVATAVGMNMLTKKAPPLVGRWVPFAAVA AANCVNIPMMRQQELIKGI -> KRRPWWAAGCPLPLWLRL TVSISP (in Ref. 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)												OREG0020485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PDCD11	22984	broad.mit.edu	37	10	105174906	105174906	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105174906C>T	uc001kwy.1	+	12	1603	c.1516C>T	c.(1516-1518)CGG>TGG	p.R506W		NM_014976	NP_055791	Q14690	RRP5_HUMAN	programmed cell death 11	506	S1 motif 5.				mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)														---	---	---	---
COL17A1	1308	broad.mit.edu	37	10	105823514	105823514	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105823514A>G	uc001kxr.2	-	11	998	c.829T>C	c.(829-831)TCC>CCC	p.S277P	COL17A1_uc010qqv.1_Missense_Mutation_p.S261P|COL17A1_uc009xxp.1_Missense_Mutation_p.S277P	NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	277	Cytoplasmic (Potential).|Nonhelical region (NC16).				cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114925501	114925501	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114925501G>A	uc001lae.3	+	14	2086	c.1579G>A	c.(1579-1581)GCC>ACC	p.A527T	TCF7L2_uc001lac.3_Missense_Mutation_p.A521T|TCF7L2_uc010qrk.1_3'UTR|TCF7L2_uc010qrl.1_Missense_Mutation_p.A504T|TCF7L2_uc010qrm.1_3'UTR|TCF7L2_uc010qrn.1_3'UTR|TCF7L2_uc001lad.3_3'UTR|TCF7L2_uc001lag.3_3'UTR|TCF7L2_uc001laf.3_Missense_Mutation_p.A504T|TCF7L2_uc010qro.1_3'UTR|TCF7L2_uc001lah.2_3'UTR|TCF7L2_uc010qrp.1_3'UTR|TCF7L2_uc010qrq.1_3'UTR|TCF7L2_uc010qrr.1_Missense_Mutation_p.A459T|TCF7L2_uc010qrs.1_Missense_Mutation_p.A415T|TCF7L2_uc010qrt.1_Missense_Mutation_p.A415T|TCF7L2_uc010qru.1_3'UTR|TCF7L2_uc010qrv.1_3'UTR|TCF7L2_uc010qrw.1_3'UTR|TCF7L2_uc010qrx.1_3'UTR	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1	544					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)														---	---	---	---
GFRA1	2674	broad.mit.edu	37	10	118030461	118030461	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118030461C>A	uc001lcj.2	-	3	905	c.207G>T	c.(205-207)AAG>AAT	p.K69N	GFRA1_uc001lci.2_Missense_Mutation_p.K69N|GFRA1_uc009xyr.2_Missense_Mutation_p.K69N	NM_005264	NP_005255	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1 isoform a	69	1.				axon guidance	anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity			ovary(1)|pancreas(1)	2		Lung NSC(174;0.21)		all cancers(201;0.0337)														---	---	---	---
EMX2	2018	broad.mit.edu	37	10	119305139	119305139	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119305139G>A	uc001ldh.3	+						EMX2OS_uc001ldg.2_5'Flank|EMX2_uc001ldi.3_Intron	NM_004098	NP_004089			empty spiracles homeobox 2 isoform 1							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		Colorectal(252;0.109)|Lung NSC(174;0.179)|all_lung(145;0.22)		all cancers(201;0.0133)														---	---	---	---
PRLHR	2834	broad.mit.edu	37	10	120353797	120353797	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120353797G>A	uc001ldp.1	-	2	1099	c.960C>T	c.(958-960)TGC>TGT	p.C320C		NM_004248	NP_004239	P49683	PRLHR_HUMAN	G protein-coupled receptor 10	320	Helical; Name=7; (Potential).				female pregnancy	integral to plasma membrane	neuropeptide Y receptor activity				0		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)														---	---	---	---
SFXN4	119559	broad.mit.edu	37	10	120925115	120925115	+	Silent	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120925115T>G	uc001leb.2	-	1	90	c.45A>C	c.(43-45)CTA>CTC	p.L15L	SFXN4_uc001ldz.2_5'Flank|SFXN4_uc001lea.2_RNA	NM_213649	NP_998814	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	15					iron ion homeostasis	integral to membrane|mitochondrial membrane	cation transmembrane transporter activity			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)														---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123844834	123844834	+	Missense_Mutation	SNP	A	C	C	rs140606887	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123844834A>C	uc001lfv.2	+	4	3179	c.2819A>C	c.(2818-2820)AAG>ACG	p.K940T	TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Missense_Mutation_p.K940T|TACC2_uc010qtv.1_Missense_Mutation_p.K940T	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	940						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)																---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123903103	123903103	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123903103G>A	uc001lfv.2	+	7	6076	c.5716G>A	c.(5716-5718)GCC>ACC	p.A1906T	TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron|TACC2_uc001lfx.2_Intron|TACC2_uc001lfy.2_Intron	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	1906						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)														OREG0020589	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	129172450	129172450	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129172450A>C	uc001ljt.2	+	35	3648	c.3584A>C	c.(3583-3585)AAC>ACC	p.N1195T	DOCK1_uc010qun.1_Missense_Mutation_p.N1216T|DOCK1_uc009yaq.2_Missense_Mutation_p.N190T	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1195	DHR-2.				apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
MKI67	4288	broad.mit.edu	37	10	129905499	129905499	+	Silent	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129905499G>C	uc001lke.2	-	13	4800	c.4605C>G	c.(4603-4605)GGC>GGG	p.G1535G	MKI67_uc001lkf.2_Silent_p.G1175G|MKI67_uc009yav.1_Silent_p.G1110G|MKI67_uc009yaw.1_Silent_p.G685G	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	1535	5.|16 X 122 AA approximate repeats.				cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)																---	---	---	---
MKI67	4288	broad.mit.edu	37	10	129905503	129905503	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129905503G>A	uc001lke.2	-	13	4796	c.4601C>T	c.(4600-4602)GCA>GTA	p.A1534V	MKI67_uc001lkf.2_Missense_Mutation_p.A1174V|MKI67_uc009yav.1_Missense_Mutation_p.A1109V|MKI67_uc009yaw.1_Missense_Mutation_p.A684V	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	1534	5.|16 X 122 AA approximate repeats.				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)																---	---	---	---
DPYSL4	10570	broad.mit.edu	37	10	134014458	134014458	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134014458C>T	uc009ybb.2	+	10	1235	c.1081C>T	c.(1081-1083)CGC>TGC	p.R361C		NM_006426	NP_006417	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	361					axon guidance|pyrimidine base catabolic process	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			central_nervous_system(2)	2		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)														---	---	---	---
TRPM5	29850	broad.mit.edu	37	11	2438983	2438983	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2438983G>A	uc001lwm.3	-	7	992	c.983C>T	c.(982-984)ACG>ATG	p.T328M	TRPM5_uc010qxl.1_Missense_Mutation_p.T328M|TRPM5_uc009ydn.2_Missense_Mutation_p.T330M	NM_014555	NP_055370	Q9NZQ8	TRPM5_HUMAN	transient receptor potential cation channel,	328	Cytoplasmic (Potential).					integral to membrane|plasma membrane	receptor activity|voltage-gated ion channel activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)														---	---	---	---
UBQLN3	50613	broad.mit.edu	37	11	5528836	5528836	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5528836C>T	uc001may.1	-	2	2039	c.1953G>A	c.(1951-1953)AAG>AAA	p.K651K	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_5'Flank|OR51B5_uc001maq.1_5'Flank	NM_017481	NP_059509	Q9H347	UBQL3_HUMAN	ubiquilin 3	651	UBA.									ovary(3)	3		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
RRP8	23378	broad.mit.edu	37	11	6622451	6622451	+	Missense_Mutation	SNP	C	T	T	rs150955423		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6622451C>T	uc001med.2	-	3	924	c.845G>A	c.(844-846)CGC>CAC	p.R282H	ILK_uc001mee.2_5'Flank|ILK_uc001mef.2_5'Flank|ILK_uc010rap.1_5'Flank|ILK_uc010raq.1_5'Flank|ILK_uc001meg.2_5'Flank|ILK_uc001meh.2_5'Flank	NM_015324	NP_056139	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase,	282					chromatin modification|chromatin silencing at rDNA|rRNA processing|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	methylated histone residue binding|S-adenosylmethionine-dependent methyltransferase activity				0																		---	---	---	---
CTR9	9646	broad.mit.edu	37	11	10785739	10785739	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10785739T>C	uc001mja.2	+	10	1424	c.1275T>C	c.(1273-1275)ACT>ACC	p.T425T		NM_014633	NP_055448	Q6PD62	CTR9_HUMAN	SH2 domain binding protein 1	425	TPR 8.				histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)														---	---	---	---
MICALCL	84953	broad.mit.edu	37	11	12315225	12315225	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12315225C>T	uc001mkg.1	+	3	538	c.247C>T	c.(247-249)CCT>TCT	p.P83S		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	83	Interaction with MAPK1 (By similarity).				cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding			skin(1)	1				Epithelial(150;0.00177)														---	---	---	---
QSER1	79832	broad.mit.edu	37	11	32956709	32956709	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32956709C>A	uc001mty.2	+	4	3785	c.3518C>A	c.(3517-3519)CCT>CAT	p.P1173H	QSER1_uc001mtz.1_Missense_Mutation_p.P934H|QSER1_uc001mua.2_Missense_Mutation_p.P678H	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1173										ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)																	---	---	---	---
CHST1	8534	broad.mit.edu	37	11	45671618	45671618	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45671618C>A	uc001mys.1	-	4	1527	c.856G>T	c.(856-858)GGC>TGC	p.G286C		NM_003654	NP_003645	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6)	286	Lumenal (Potential).				galactose metabolic process|inflammatory response|keratan sulfate metabolic process	Golgi membrane|integral to membrane	keratan sulfotransferase activity			skin(4)|pancreas(1)	5				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)														---	---	---	---
PEX16	9409	broad.mit.edu	37	11	45935761	45935761	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45935761G>A	uc001nbu.2	-						PEX16_uc001nbt.2_Intron	NM_004813	NP_004804			peroxisomal biogenesis factor 16 isoform 1						ER-dependent peroxisome organization|peroxisome membrane biogenesis|protein import into peroxisome matrix|protein import into peroxisome membrane	endoplasmic reticulum membrane|integral to peroxisomal membrane	protein C-terminus binding			ovary(2)|skin(1)	3				GBM - Glioblastoma multiforme(35;0.223)														---	---	---	---
HARBI1	283254	broad.mit.edu	37	11	46625165	46625165	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46625165G>A	uc001ncy.2	-	3	1213	c.965C>T	c.(964-966)CCG>CTG	p.P322L		NM_173811	NP_776172	Q96MB7	HARB1_HUMAN	harbinger transposase derived 1	322						cytoplasm|nucleus	metal ion binding|nuclease activity				0																		---	---	---	---
ARHGAP1	392	broad.mit.edu	37	11	46701334	46701334	+	Intron	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46701334G>T	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)														---	---	---	---
LRP4	4038	broad.mit.edu	37	11	46910972	46910972	+	Silent	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46910972G>T	uc001ndn.3	-	16	2351	c.2205C>A	c.(2203-2205)GCC>GCA	p.A735A		NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	735	Extracellular (Potential).|EGF-like 3.				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4				Lung(87;0.159)												OREG0020948	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035844	55035844	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035844T>C	uc010rid.1	+	4	660	c.574T>C	c.(574-576)TAC>CAC	p.Y192H		NM_024114	NP_077019	Q8IWZ4	TRI48_HUMAN	tripartite motif-containing 48	176						intracellular	zinc ion binding				0																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035855	55035855	+	Intron	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035855A>G	uc010rid.1	+							NM_024114	NP_077019			tripartite motif-containing 48							intracellular	zinc ion binding				0																		---	---	---	---
OR4C16	219428	broad.mit.edu	37	11	55340531	55340531	+	Silent	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55340531A>C	uc010rih.1	+	1	928	c.928A>C	c.(928-930)AGA>CGA	p.R310R		NM_001004701	NP_001004701	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C,	310	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		all_epithelial(135;0.0748)																---	---	---	---
OR5D18	219438	broad.mit.edu	37	11	55587286	55587286	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55587286T>C	uc010rin.1	+	1	181	c.181T>C	c.(181-183)TAC>CAC	p.Y61H		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	61	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.208)																---	---	---	---
SLC43A1	8501	broad.mit.edu	37	11	57258808	57258808	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57258808G>A	uc001nkk.2	-	11	1200	c.1082C>T	c.(1081-1083)GCC>GTC	p.A361V	SLC43A1_uc001nkl.2_Missense_Mutation_p.A361V	NM_003627	NP_003618	O75387	LAT3_HUMAN	solute carrier family 43, member 1	361	Helical; (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	neutral amino acid transmembrane transporter activity				0																		---	---	---	---
INTS5	80789	broad.mit.edu	37	11	62416571	62416571	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62416571G>A	uc001nud.2	-	2	1034	c.981C>T	c.(979-981)GGC>GGT	p.G327G	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	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	327					snRNA processing	integral to membrane|integrator complex	protein binding			ovary(2)	2																		---	---	---	---
C11orf84	144097	broad.mit.edu	37	11	63585488	63585488	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63585488G>T	uc001nxt.2	+	2	575	c.339G>T	c.(337-339)CAG>CAT	p.Q113H		NM_138471	NP_612480	Q9BUA3	CK084_HUMAN	hypothetical protein LOC144097	113											0																		---	---	---	---
CDC42BPG	55561	broad.mit.edu	37	11	64606355	64606355	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64606355G>A	uc001obs.3	-	8	896	c.896C>T	c.(895-897)CCG>CTG	p.P299L		NM_017525	NP_059995	Q6DT37	MRCKG_HUMAN	CDC42 binding protein kinase gamma (DMPK-like)	299	Protein kinase.				actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|centrosome	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(3)|central_nervous_system(1)	4																		---	---	---	---
PPP2R5B	5526	broad.mit.edu	37	11	64698015	64698015	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64698015T>G	uc001oby.2	+	8	1430	c.845T>G	c.(844-846)CTG>CGG	p.L282R	PPP2R5B_uc001obz.2_Missense_Mutation_p.L282R	NM_006244	NP_006235	Q15173	2A5B_HUMAN	beta isoform of regulatory subunit B56, protein	282					signal transduction	cytoplasm|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(2)	2																		---	---	---	---
MALAT1	378938	broad.mit.edu	37	11	65269106	65269106	+	RNA	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65269106A>G	uc010roh.1	+	1		c.3874A>G			uc001ody.2_RNA|MALAT1_uc001odz.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0																		---	---	---	---
EHBP1L1	254102	broad.mit.edu	37	11	65349384	65349384	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65349384A>G	uc001oeo.3	+	9	1506	c.1241A>G	c.(1240-1242)GAG>GGG	p.E414G	EHBP1L1_uc001oep.1_Missense_Mutation_p.E34G	NM_001099409	NP_001092879	Q8N3D4	EH1L1_HUMAN	tangerin	414										central_nervous_system(1)	1																		---	---	---	---
PCNXL3	399909	broad.mit.edu	37	11	65386142	65386142	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65386142C>T	uc001oey.2	+	6	1309	c.1309C>T	c.(1309-1311)CGA>TGA	p.R437*		NM_032223	NP_115599	Q9H6A9	PCX3_HUMAN	pecanex-like 3	437	Ser-rich.					integral to membrane					0																		---	---	---	---
RNASEH2C	84153	broad.mit.edu	37	11	65486338	65486338	+	3'UTR	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65486338C>A	uc001ofn.2	-	4					KAT5_uc001ofi.2_Intron|KAT5_uc001ofj.2_Intron|KAT5_uc001ofk.2_Intron|KAT5_uc010roo.1_Intron|KAT5_uc001ofl.2_Intron|RNASEH2C_uc001ofm.2_RNA	NM_032193	NP_115569			ribonuclease H2, subunit C						RNA catabolic process	nucleus|ribonuclease H2 complex					0																		---	---	---	---
RBM4B	83759	broad.mit.edu	37	11	66436473	66436473	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66436473C>T	uc001oja.2	-	2	1371	c.702G>A	c.(700-702)GCG>GCA	p.A234A	RBM4B_uc001ojb.2_Silent_p.A234A	NM_031492	NP_113680	Q9BQ04	RBM4B_HUMAN	RNA binding motif protein 4B	234	Interaction with TNPO3 (By similarity).|Poly-Ala.				circadian regulation of gene expression|entrainment of circadian clock by photoperiod|mRNA processing|RNA splicing	nucleolus	nucleotide binding|RNA binding|zinc ion binding				0																		---	---	---	---
TBX10	347853	broad.mit.edu	37	11	67400514	67400514	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67400514G>A	uc001omp.2	-	5	698	c.610C>T	c.(610-612)CGC>TGC	p.R204C		NM_005995	NP_005986	O75333	TBX10_HUMAN	T-box 10	204	T-box.				anatomical structure morphogenesis|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
ALDH3B1	221	broad.mit.edu	37	11	67789015	67789015	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67789015C>T	uc010rpy.1	+	8	740	c.624C>T	c.(622-624)ACC>ACT	p.T208T	ALDH3B1_uc001omz.2_Silent_p.T208T|ALDH3B1_uc001ona.2_Silent_p.T171T|ALDH3B1_uc001onb.2_RNA	NM_001161473	NP_001154945	P43353	AL3B1_HUMAN	aldehyde dehydrogenase 3B1 isoform a	208					alcohol metabolic process|cellular aldehyde metabolic process|lipid metabolic process		3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase				0					NADH(DB00157)											OREG0021141	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GAL	51083	broad.mit.edu	37	11	68452421	68452421	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68452421C>A	uc001oob.2	+	2	248	c.30C>A	c.(28-30)GCC>GCA	p.A10A		NM_015973	NP_057057	P22466	GALA_HUMAN	galanin preproprotein	10					growth hormone secretion|insulin secretion|neuropeptide signaling pathway|smooth muscle contraction	extracellular region	neuropeptide hormone activity				0	Esophageal squamous(3;7.33e-10)	Melanoma(852;0.0749)	LUAD - Lung adenocarcinoma(13;0.0514)	Kidney(183;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.000152)|LUSC - Lung squamous cell carcinoma(976;0.00154)														---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71733444	71733444	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71733444G>T	uc001orl.1	-	7	485	c.313C>A	c.(313-315)CAC>AAC	p.H105N	NUMA1_uc001ork.1_Missense_Mutation_p.H105N|NUMA1_uc001orm.1_Missense_Mutation_p.H105N|NUMA1_uc009ysx.1_Missense_Mutation_p.H105N|NUMA1_uc001oro.1_Missense_Mutation_p.H105N|NUMA1_uc009ysy.1_Missense_Mutation_p.H105N|NUMA1_uc001orp.2_Missense_Mutation_p.H105N|NUMA1_uc001orq.2_Missense_Mutation_p.H105N	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	105					G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8								T	RARA	APL								---	---	---	---
FOLR2	2350	broad.mit.edu	37	11	71932697	71932697	+	Missense_Mutation	SNP	C	T	T	rs140546240		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71932697C>T	uc009ytd.2	+	5	828	c.659C>T	c.(658-660)GCG>GTG	p.A220V	FOLR2_uc009yte.2_Missense_Mutation_p.A220V|FOLR2_uc001ose.3_Missense_Mutation_p.A220V|FOLR2_uc009ytf.2_Missense_Mutation_p.A220V	NM_001113534	NP_001107006	P14207	FOLR2_HUMAN	folate receptor 2 precursor	220					folic acid transport	anchored to membrane|extracellular region|membrane fraction|plasma membrane	folic acid binding|receptor activity			breast(2)|ovary(1)	3					Folic Acid(DB00158)													---	---	---	---
CLPB	81570	broad.mit.edu	37	11	72006671	72006671	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72006671C>T	uc001osj.2	-	13	1491	c.1441G>A	c.(1441-1443)GGG>AGG	p.G481R	CLPB_uc010rqx.1_Missense_Mutation_p.G436R|CLPB_uc010rqy.1_Missense_Mutation_p.G422R|CLPB_uc001osk.2_Missense_Mutation_p.G451R|CLPB_uc009ytg.2_RNA|CLPB_uc010rqz.1_Missense_Mutation_p.G280R|CLPB_uc001osi.2_Missense_Mutation_p.G89R	NM_030813	NP_110440	Q9H078	CLPB_HUMAN	caseinolytic peptidase B	481					cellular response to heat		ATP binding|nucleoside-triphosphatase activity|protein binding			pancreas(1)	1																		---	---	---	---
MYO7A	4647	broad.mit.edu	37	11	76905421	76905421	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76905421C>T	uc001oyb.2	+	32	4447	c.4175C>T	c.(4174-4176)GCC>GTC	p.A1392V	MYO7A_uc010rsm.1_Missense_Mutation_p.A1381V|MYO7A_uc001oyc.2_Missense_Mutation_p.A1392V|MYO7A_uc009yus.1_RNA|MYO7A_uc009yut.1_Missense_Mutation_p.A603V	NM_000260	NP_000251	Q13402	MYO7A_HUMAN	myosin VIIA isoform 1	1392	FERM 1.				actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4																		---	---	---	---
ANKRD42	338699	broad.mit.edu	37	11	82951953	82951953	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82951953A>C	uc001ozz.1	+	9	1510	c.1088A>C	c.(1087-1089)GAC>GCC	p.D363A	ANKRD42_uc010rsv.1_Missense_Mutation_p.D391A|ANKRD42_uc001paa.2_Missense_Mutation_p.D391A|ANKRD42_uc001pab.1_Missense_Mutation_p.D390A	NM_182603	NP_872409	Q8N9B4	ANR42_HUMAN	ankyrin repeat domain 42	363										skin(1)	1																		---	---	---	---
TYR	7299	broad.mit.edu	37	11	89028414	89028414	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89028414C>A	uc001pcs.2	+	5	1552	c.1470C>A	c.(1468-1470)GCC>GCA	p.A490A		NM_000372	NP_000363	P14679	TYRO_HUMAN	tyrosinase precursor	490	Helical; (Potential).				eye pigment biosynthetic process|melanin biosynthetic process from tyrosine|visual perception	Golgi-associated vesicle|integral to membrane|lysosome|melanosome membrane|perinuclear region of cytoplasm	copper ion binding|monophenol monooxygenase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|NADH(DB00157)									Oculocutaneous_Albinism				---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92086551	92086551	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92086551C>T	uc001pdj.3	+	1	1290	c.1273C>T	c.(1273-1275)CGG>TGG	p.R425W		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	425	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	100211320	100211320	+	Silent	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100211320T>G	uc001pga.2	+	22	3195	c.2856T>G	c.(2854-2856)GCT>GCG	p.A952A	CNTN5_uc001pgb.2_Silent_p.A878A|CNTN5_uc010ruk.1_Silent_p.A223A	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	952	Fibronectin type-III 3.				cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	102987326	102987326	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102987326T>C	uc001pho.2	+	5	793	c.649T>C	c.(649-651)TTA>CTA	p.L217L	DYNC2H1_uc001phn.1_Silent_p.L217L|DYNC2H1_uc009yxe.1_Silent_p.L217L	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	217	Stem (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
KIAA1826	84437	broad.mit.edu	37	11	105880317	105880317	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105880317C>T	uc001piy.2	-	3	1156	c.983G>A	c.(982-984)CGC>CAC	p.R328H	KIAA1826_uc001piz.2_Missense_Mutation_p.R328H	NM_032424	NP_115800	Q8NCY6	K1826_HUMAN	hypothetical protein LOC84437	328	Potential.					nucleus				breast(1)	1		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.56e-05)|Epithelial(105;0.00432)|all cancers(92;0.0309)														---	---	---	---
KDELC2	143888	broad.mit.edu	37	11	108352801	108352801	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108352801A>C	uc001pkj.2	-	4	899	c.833T>G	c.(832-834)ATC>AGC	p.I278S	KDELC2_uc001pki.2_Missense_Mutation_p.I222S	NM_153705	NP_714916	Q7Z4H8	KDEL2_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 2 precursor	278						endoplasmic reticulum lumen				ovary(1)	1		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;6.93e-06)|BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|all cancers(92;0.00016)|OV - Ovarian serous cystadenocarcinoma(223;0.132)|Colorectal(284;0.14)														---	---	---	---
UBE4A	9354	broad.mit.edu	37	11	118244399	118244399	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118244399A>G	uc001psw.2	+	8	1244	c.1115A>G	c.(1114-1116)CAG>CGG	p.Q372R	UBE4A_uc001psv.2_Missense_Mutation_p.Q379R	NM_004788	NP_004779	Q14139	UBE4A_HUMAN	ubiquitination factor E4A	372					ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	5	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)														---	---	---	---
MCAM	4162	broad.mit.edu	37	11	119185613	119185613	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119185613G>A	uc001pwf.2	-	3	359	c.330C>T	c.(328-330)GAC>GAT	p.D110D		NM_006500	NP_006491	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	110	Extracellular (Potential).|Ig-like V-type 1.				anatomical structure morphogenesis|cell adhesion	integral to membrane|plasma membrane				ovary(2)|breast(1)|central_nervous_system(1)	4		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)														---	---	---	---
CRTAM	56253	broad.mit.edu	37	11	122720827	122720827	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122720827C>T	uc001pyj.2	+	2	98	c.98C>T	c.(97-99)ACG>ATG	p.T33M		NM_019604	NP_062550	O95727	CRTAM_HUMAN	class-I MHC-restricted T cell associated	33	Ig-like V-type.|Extracellular (Potential).				cell recognition|detection of tumor cell|positive regulation of cytokine secretion|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	integral to membrane|plasma membrane	receptor binding			ovary(1)	1		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)														---	---	---	---
OR10G4	390264	broad.mit.edu	37	11	123887010	123887010	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123887010C>T	uc010sac.1	+	1	729	c.729C>T	c.(727-729)CAC>CAT	p.H243H		NM_001004462	NP_001004462	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G,	243	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)														---	---	---	---
WNK1	65125	broad.mit.edu	37	12	992220	992220	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:992220A>G	uc001qio.3	+	15	3991	c.3484A>G	c.(3484-3486)ATT>GTT	p.I1162V	WNK1_uc001qip.3_Missense_Mutation_p.I915V|WNK1_uc001qir.3_Missense_Mutation_p.I335V	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1162					intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)															---	---	---	---
CACNA2D4	93589	broad.mit.edu	37	12	1904461	1904461	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1904461G>A	uc001qjp.2	-						CACNA2D4_uc001qjo.2_Intron	NM_172364	NP_758952			voltage-gated calcium channel alpha(2)delta-4							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)														---	---	---	---
ITFG2	55846	broad.mit.edu	37	12	2932087	2932087	+	Intron	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2932087G>T	uc001qlb.1	+						ITFG2_uc010seb.1_Intron|ITFG2_uc010sec.1_Intron	NM_018463	NP_060933			integrin alpha FG-GAP repeat containing 2												0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
KCNA6	3742	broad.mit.edu	37	12	4920572	4920572	+	Silent	SNP	C	T	T	rs140094246		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4920572C>T	uc001qng.2	+	1	2231	c.1365C>T	c.(1363-1365)CCC>CCT	p.P455P		NM_002235	NP_002226	P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related	455	Helical; Name=Segment S6; (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(2)|ovary(1)	3															HNSCC(72;0.22)			---	---	---	---
NCAPD2	9918	broad.mit.edu	37	12	6631158	6631158	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6631158G>A	uc001qoo.2	+	15	1955	c.1909G>A	c.(1909-1911)GCC>ACC	p.A637T	NCAPD2_uc009zen.1_Missense_Mutation_p.A509T|NCAPD2_uc010sfd.1_Missense_Mutation_p.A592T	NM_014865	NP_055680	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	637					cell division|mitotic chromosome condensation	condensin core heterodimer|cytoplasm	histone binding			ovary(2)|lung(1)|breast(1)|kidney(1)	5																		---	---	---	---
CLSTN3	9746	broad.mit.edu	37	12	7286179	7286179	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7286179C>T	uc001qsr.2	+	3	476	c.198C>T	c.(196-198)TGC>TGT	p.C66C	CLSTN3_uc001qss.2_Silent_p.C78C	NM_014718	NP_055533	Q9BQT9	CSTN3_HUMAN	calsyntenin 3 precursor	66	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1																		---	---	---	---
CD163L1	283316	broad.mit.edu	37	12	7531738	7531738	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7531738G>T	uc001qsy.2	-	9	2233	c.2207C>A	c.(2206-2208)GCA>GAA	p.A736E	CD163L1_uc010sge.1_Missense_Mutation_p.A746E	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	736	SRCR 7.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|skin(2)|central_nervous_system(1)	11																		---	---	---	---
CLEC4D	338339	broad.mit.edu	37	12	8673741	8673741	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8673741C>T	uc001qun.2	+	6	715	c.522C>T	c.(520-522)CCC>CCT	p.P174P		NM_080387	NP_525126	Q8WXI8	CLC4D_HUMAN	C-type lectin domain family 4, member D	174	C-type lectin.|Extracellular (Potential).				innate immune response	integral to membrane	sugar binding				0	Lung SC(5;0.184)																	---	---	---	---
TAS2R7	50837	broad.mit.edu	37	12	10954759	10954759	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10954759G>A	uc001qyv.2	-	1	468	c.411C>T	c.(409-411)TGC>TGT	p.C137C		NM_023919	NP_076408	Q9NYW3	TA2R7_HUMAN	taste receptor, type 2, member 7	137	Helical; Name=4; (Potential).				sensory perception of taste	integral to membrane	taste receptor activity			skin(1)	1																		---	---	---	---
PRB1	5542	broad.mit.edu	37	12	11506168	11506168	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11506168T>C	uc001qzw.1	-	4	906	c.869A>G	c.(868-870)AAC>AGC	p.N290S	PRB1_uc001qzu.1_Missense_Mutation_p.N157S|PRB1_uc001qzv.1_Missense_Mutation_p.N137S	NM_005039	NP_005030	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1 isoform 1	351	15.|15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].					extracellular region					0			OV - Ovarian serous cystadenocarcinoma(49;0.185)															---	---	---	---
ATF7IP	55729	broad.mit.edu	37	12	14628902	14628902	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14628902G>T	uc001rbw.2	+	11	3099	c.2941G>T	c.(2941-2943)GAC>TAC	p.D981Y	ATF7IP_uc001rbu.2_Missense_Mutation_p.G981C|ATF7IP_uc001rbv.1_Missense_Mutation_p.D980Y|ATF7IP_uc001rbx.2_Missense_Mutation_p.D980Y|ATF7IP_uc001rby.3_Missense_Mutation_p.D981Y|ATF7IP_uc001rca.2_Missense_Mutation_p.D981Y	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	981					DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5																		---	---	---	---
SLCO1B3	28234	broad.mit.edu	37	12	21033817	21033817	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21033817G>C	uc001rek.2	+	11	1486	c.1360G>C	c.(1360-1362)GTA>CTA	p.V454L	SLCO1B3_uc001rel.2_Missense_Mutation_p.V454L|SLCO1B3_uc010sil.1_Missense_Mutation_p.V454L|LST-3TM12_uc010sim.1_Intron|SLCO1B3_uc001reo.2_Missense_Mutation_p.V279L	NM_019844	NP_062818	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family,	454	Extracellular (Potential).|Kazal-like.				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)																	---	---	---	---
KRAS	3845	broad.mit.edu	37	12	25398281	25398281	+	Missense_Mutation	SNP	C	T	T	rs112445441		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25398281C>T	uc001rgp.1	-	2	219	c.38G>A	c.(37-39)GGC>GAC	p.G13D	KRAS_uc001rgq.1_Missense_Mutation_p.G13D|KRAS_uc001rgr.2_RNA	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	13	GTP.		G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway).|G -> D (in a breast carcinoma cell line and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.G13D(2647)|p.G13C(182)|p.G13S(58)|p.G13R(41)|p.G13V(27)|p.G13A(24)|p.G13G(11)|p.G13E(4)|p.G12_G13insG(4)|p.G13N(3)|p.G13I(1)|p.G13_V14>DI(1)		large_intestine(12391)|pancreas(3285)|lung(2847)|biliary_tract(521)|ovary(443)|endometrium(339)|haematopoietic_and_lymphoid_tissue(318)|stomach(203)|thyroid(149)|prostate(85)|soft_tissue(77)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|liver(31)|breast(28)|testis(17)|oesophagus(15)|central_nervous_system(9)|peritoneum(6)|salivary_gland(6)|kidney(5)|gastrointestinal_tract_(site_indeterminate)(5)|thymus(5)|eye(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	21052	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			G13D(NCIH647_LUNG)|G13D(MDAMB231_BREAST)|G13D(NCIH747_LARGE_INTESTINE)|G13D(T84_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT15_LARGE_INTESTINE)|G13D(HCT116_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			---	---	---	---
TMTC1	83857	broad.mit.edu	37	12	29669328	29669328	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29669328T>C	uc001rjb.2	-	15	2411	c.1937A>G	c.(1936-1938)TAT>TGT	p.Y646C	TMTC1_uc001riz.2_Missense_Mutation_p.Y403C|TMTC1_uc001rja.2_Missense_Mutation_p.Y490C|TMTC1_uc001riy.2_Missense_Mutation_p.Y99C	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat	754	TPR 8.					integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)																	---	---	---	---
CNTN1	1272	broad.mit.edu	37	12	41419075	41419075	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41419075G>A	uc001rmm.1	+	21	2760	c.2647G>A	c.(2647-2649)GCC>ACC	p.A883T	CNTN1_uc001rmn.1_Missense_Mutation_p.A872T	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor	883	Fibronectin type-III 3.				axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)																---	---	---	---
SENP1	29843	broad.mit.edu	37	12	48440804	48440804	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48440804T>G	uc001rqx.2	-	16	2179	c.1733A>C	c.(1732-1734)GAG>GCG	p.E578A	SENP1_uc001rqw.2_Missense_Mutation_p.E578A|SENP1_uc001rqy.2_Missense_Mutation_p.E379A|SENP1_uc001rqz.2_Missense_Mutation_p.E379A|SENP1_uc009zkx.2_Missense_Mutation_p.E578A	NM_014554	NP_055369	Q9P0U3	SENP1_HUMAN	sentrin/SUMO-specific protease 1	578	Protease.				activation of caspase activity|induction of apoptosis by extracellular signals|protein desumoylation|proteolysis	cytoplasm|nucleus	endopeptidase activity|SUMO-specific protease activity			pancreas(2)|lung(1)	3		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)																---	---	---	---
CACNB3	784	broad.mit.edu	37	12	49220203	49220203	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49220203C>T	uc001rsl.1	+	10	997	c.796C>T	c.(796-798)CTA>TTA	p.L266L	CACNB3_uc010sly.1_Silent_p.L253L|CACNB3_uc010slz.1_Silent_p.L265L|CACNB3_uc001rsk.1_Silent_p.L113L	NM_000725	NP_000716	P54284	CACB3_HUMAN	calcium channel, voltage-dependent, beta 3	266					axon guidance|membrane depolarization|synaptic transmission	cytosol|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0					Verapamil(DB00661)													---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49427944	49427944	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49427944G>A	uc001rta.3	-	38	10646	c.10646C>T	c.(10645-10647)GCC>GTC	p.A3549V		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	3549	Gln-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41								N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			---	---	---	---
GALNT6	11226	broad.mit.edu	37	12	51773084	51773084	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51773084C>T	uc001ryk.2	-	2	707	c.482G>A	c.(481-483)CGA>CAA	p.R161Q	GALNT6_uc009zma.1_RNA|GALNT6_uc001ryl.1_Missense_Mutation_p.R161Q|GALNT6_uc010snh.1_Missense_Mutation_p.R161Q	NM_007210	NP_009141	Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	161	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2																		---	---	---	---
KRT6A	3853	broad.mit.edu	37	12	52883807	52883807	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52883807G>A	uc001sam.2	-	6	1332	c.1123C>T	c.(1123-1125)CGC>TGC	p.R375C		NM_005554	NP_005545	P02538	K2C6A_HUMAN	keratin 6A	375	Rod.|Coil 2.				cell differentiation|ectoderm development|positive regulation of cell proliferation	keratin filament	protein binding|structural constituent of cytoskeleton			ovary(4)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
KRT6A	3853	broad.mit.edu	37	12	52885323	52885323	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52885323C>A	uc001sam.2	-	2	947	c.738G>T	c.(736-738)GTG>GTT	p.V246V		NM_005554	NP_005545	P02538	K2C6A_HUMAN	keratin 6A	246	Coil 1B.|Rod.				cell differentiation|ectoderm development|positive regulation of cell proliferation	keratin filament	protein binding|structural constituent of cytoskeleton			ovary(4)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
KRT78	196374	broad.mit.edu	37	12	53233614	53233614	+	Missense_Mutation	SNP	C	T	T	rs140505762	byFrequency;by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53233614C>T	uc001sbc.1	-	7	1266	c.1202G>A	c.(1201-1203)AGC>AAC	p.S401N		NM_173352	NP_775487	Q8N1N4	K2C78_HUMAN	keratin 5b	401	Coil 2.|Rod.					keratin filament	protein binding|structural molecule activity			ovary(2)	2																		---	---	---	---
TENC1	23371	broad.mit.edu	37	12	53454525	53454525	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53454525C>A	uc001sbp.2	+	20	2970	c.2835C>A	c.(2833-2835)GCC>GCA	p.A945A	TENC1_uc001sbl.2_Silent_p.A821A|TENC1_uc001sbn.2_Silent_p.A955A|TENC1_uc001sbq.2_Silent_p.A343A|TENC1_uc001sbr.2_RNA|TENC1_uc009zmr.2_Silent_p.A440A|TENC1_uc001sbs.2_5'Flank	NM_170754	NP_736610	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase	945	Pro-rich.				intracellular signal transduction|negative regulation of cell proliferation	focal adhesion	metal ion binding|phosphoprotein phosphatase activity|protein binding			ovary(1)|pancreas(1)	2																		---	---	---	---
SLC39A5	283375	broad.mit.edu	37	12	56625312	56625312	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56625312C>A	uc010sqj.1	+	4	511	c.254C>A	c.(253-255)GCT>GAT	p.A85D	SLC39A5_uc010sqi.1_Translation_Start_Site|SLC39A5_uc010sqk.1_Missense_Mutation_p.A85D	NM_173596	NP_775867	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (metal ion	85	Extracellular (By similarity).				zinc ion transport	basolateral plasma membrane|integral to membrane	metal ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
TIMELESS	8914	broad.mit.edu	37	12	56818681	56818681	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56818681A>G	uc001slf.2	-	15	1901	c.1733T>C	c.(1732-1734)ATG>ACG	p.M578T		NM_003920	NP_003911	Q9UNS1	TIM_HUMAN	timeless homolog	578					cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin				ovary(5)|breast(2)|pancreas(1)	8																		---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57579622	57579622	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57579622A>G	uc001snd.2	+	41	7238	c.6772A>G	c.(6772-6774)AGC>GGC	p.S2258G		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	2258	LDL-receptor class B 21.|Extracellular (Potential).				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)													---	---	---	---
BEST3	144453	broad.mit.edu	37	12	70049234	70049234	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70049234T>G	uc001svg.2	-	10	1687	c.1460A>C	c.(1459-1461)CAG>CCG	p.Q487P	BEST3_uc001svd.1_Intron|BEST3_uc001sve.1_Intron|BEST3_uc001svf.2_Missense_Mutation_p.Q274P|BEST3_uc010stm.1_Missense_Mutation_p.Q381P	NM_032735	NP_116124	Q8N1M1	BEST3_HUMAN	vitelliform macular dystrophy 2-like 3 isoform	487	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	chloride channel activity				0	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)															---	---	---	---
CNOT2	4848	broad.mit.edu	37	12	70704760	70704760	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70704760G>A	uc001svv.2	+	3	713	c.134G>A	c.(133-135)AGC>AAC	p.S45N	CNOT2_uc009zro.2_Missense_Mutation_p.S45N|CNOT2_uc009zrp.2_Missense_Mutation_p.S25N|CNOT2_uc009zrq.2_Missense_Mutation_p.S45N	NM_014515	NP_055330	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	45					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	protein binding|RNA polymerase II transcription cofactor activity				0	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)															---	---	---	---
KCNC2	3747	broad.mit.edu	37	12	75601370	75601370	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75601370G>A	uc001sxg.1	-	2	938	c.394C>T	c.(394-396)CCG>TCG	p.P132S	KCNC2_uc009zry.2_Missense_Mutation_p.P132S|KCNC2_uc001sxe.2_Missense_Mutation_p.P132S|KCNC2_uc001sxf.2_Missense_Mutation_p.P132S|KCNC2_uc010stw.1_Missense_Mutation_p.P132S	NM_139137	NP_631875	Q96PR1	KCNC2_HUMAN	Shaw-related voltage-gated potassium channel	132	Cytoplasmic (Potential).				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																		---	---	---	---
ALX1	8092	broad.mit.edu	37	12	85674056	85674056	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85674056A>G	uc001tae.3	+	1	21	c.17A>G	c.(16-18)GAG>GGG	p.E6G		NM_006982	NP_008913	Q15699	ALX1_HUMAN	cartilage paired-class homeoprotein 1	6					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)														---	---	---	---
C12orf29	91298	broad.mit.edu	37	12	88433914	88433914	+	Intron	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88433914C>T	uc001tao.2	+						C12orf29_uc001tap.2_Intron|C12orf29_uc009zsk.2_Intron	NM_001009894	NP_001009894			hypothetical protein LOC91298												0																		---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94769791	94769791	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94769791A>G	uc001tdd.2	-	8	1390	c.804T>C	c.(802-804)GCT>GCC	p.A268A	CCDC41_uc001tde.2_Silent_p.A268A|CCDC41_uc009zsw.1_RNA|CCDC41_uc001tdf.2_Silent_p.A268A	NM_016122	NP_057206	Q9Y592	CCD41_HUMAN	NY-REN-58 antigen	260	Potential.										0																		---	---	---	---
APAF1	317	broad.mit.edu	37	12	99121028	99121028	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99121028C>A	uc001tfz.2	+	26	4111	c.3534C>A	c.(3532-3534)GGC>GGA	p.G1178G	APAF1_uc001tfy.2_Silent_p.G1167G|APAF1_uc001tga.2_Silent_p.G1124G|APAF1_uc001tgb.2_Silent_p.G1135G|APAF1_uc001tgc.2_Intron|APAF1_uc009zto.2_Silent_p.G502G	NM_181861	NP_863651	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1 isoform	1178	WD 13.				activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)													---	---	---	---
GNPTAB	79158	broad.mit.edu	37	12	102154925	102154925	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102154925C>T	uc001tit.2	-	15	3294	c.3115G>A	c.(3115-3117)GAA>AAA	p.E1039K		NM_024312	NP_077288	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase	1039	EF-hand.				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	104123939	104123939	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104123939A>G	uc001tjw.2	+	49	5314	c.5128A>G	c.(5128-5130)ATC>GTC	p.I1710V	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	1710	Extracellular (Potential).|FAS1 5.				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	108013807	108013807	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108013807G>A	uc001tmk.1	+	11	3018	c.2497G>A	c.(2497-2499)GCC>ACC	p.A833T	BTBD11_uc009zut.1_Missense_Mutation_p.A714T|BTBD11_uc001tmj.2_Missense_Mutation_p.A833T|BTBD11_uc001tml.1_Missense_Mutation_p.A370T	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a	833	ANK 5.					integral to membrane	DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
MYO1H	283446	broad.mit.edu	37	12	109845646	109845646	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109845646A>G	uc010sxn.1	+	9	1035	c.1035A>G	c.(1033-1035)GCA>GCG	p.A345A		NM_001101421	NP_001094891	Q8N1T3	MYO1H_HUMAN	myosin 1H	Error:Variant_position_missing_in_B4DNW6_after_alignment						myosin complex	motor activity				0																		---	---	---	---
MVK	4598	broad.mit.edu	37	12	110023886	110023886	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110023886T>A	uc001toy.3	+	6	771	c.587T>A	c.(586-588)ATT>AAT	p.I196N	MVK_uc009zvk.2_Missense_Mutation_p.I196N|MVK_uc010sxr.1_Missense_Mutation_p.I144N|MVK_uc001toz.3_Missense_Mutation_p.I2N|MVK_uc001tpc.3_RNA	NM_001114185	NP_001107657	Q03426	KIME_HUMAN	mevalonate kinase	196					cholesterol biosynthetic process|isoprenoid biosynthetic process	cytosol|peroxisome	ATP binding|identical protein binding|mevalonate kinase activity				0																		---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	111953992	111953992	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111953992A>G	uc001tsj.2	-	10	1983	c.1821T>C	c.(1819-1821)CCT>CCC	p.P607P	ATXN2_uc001tsh.2_Silent_p.P342P|ATXN2_uc001tsi.2_Silent_p.P318P|ATXN2_uc001tsk.2_RNA|ATXN2_uc001tsm.1_Silent_p.P342P	NM_002973	NP_002964	Q99700	ATX2_HUMAN	ataxin 2	607	Pro-rich.				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																		---	---	---	---
DDX54	79039	broad.mit.edu	37	12	113617081	113617081	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113617081C>T	uc001tup.2	-	4	459	c.431G>A	c.(430-432)AGT>AAT	p.S144N	DDX54_uc001tuq.3_Missense_Mutation_p.S144N	NM_024072	NP_076977	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	144	ATP (By similarity).|Helicase ATP-binding.				estrogen receptor signaling pathway|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nucleolus	ATP binding|ATP-dependent RNA helicase activity|estrogen receptor binding|RNA binding|transcription corepressor activity			skin(2)|central_nervous_system(1)	3																		---	---	---	---
RNFT2	84900	broad.mit.edu	37	12	117217060	117217060	+	Silent	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117217060G>T	uc009zwn.2	+	7	1022	c.789G>T	c.(787-789)GTG>GTT	p.V263V	RNFT2_uc001twb.3_Silent_p.V263V|RNFT2_uc001twa.3_Silent_p.V173V|RNFT2_uc001twc.3_Silent_p.V11V	NM_001109903	NP_001103373	Q96EX2	RNFT2_HUMAN	transmembrane protein 118 isoform 1	263	Helical; (Potential).					integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)														---	---	---	---
GCN1L1	10985	broad.mit.edu	37	12	120599678	120599678	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120599678T>C	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)																	---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	121970842	121970842	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121970842G>A	uc001uat.2	-	8	904	c.800C>T	c.(799-801)ACG>ATG	p.T267M	KDM2B_uc001uas.2_Missense_Mutation_p.T236M|KDM2B_uc001uau.2_Missense_Mutation_p.T150M|KDM2B_uc001uav.3_Intron	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform	267	JmjC.				embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
VPS33A	65082	broad.mit.edu	37	12	122750948	122750948	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122750948G>A	uc001ucd.2	-	1	121	c.8C>T	c.(7-9)GCT>GTT	p.A3V	VPS33A_uc001ucc.2_RNA|VPS33A_uc001uce.2_Missense_Mutation_p.A3V	NM_022916	NP_075067	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33A	3					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)														---	---	---	---
PITPNM2	57605	broad.mit.edu	37	12	123489928	123489928	+	Missense_Mutation	SNP	C	T	T	rs138122520		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123489928C>T	uc001uej.1	-	6	950	c.811G>A	c.(811-813)GTC>ATC	p.V271I	PITPNM2_uc001uek.1_Missense_Mutation_p.V271I|PITPNM2_uc009zxu.1_Missense_Mutation_p.V271I	NM_020845	NP_065896	Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein,	271					metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124371810	124371810	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124371810A>G	uc001uft.3	+	51	8616	c.8591A>G	c.(8590-8592)CAT>CGT	p.H2864R		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2864	AAA 4 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
FZD10	11211	broad.mit.edu	37	12	130647844	130647844	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130647844G>A	uc001uii.2	+	1	813	c.357G>A	c.(355-357)CCG>CCA	p.P119P	uc001uig.1_5'Flank|uc001uih.1_5'Flank	NM_007197	NP_009128	Q9ULW2	FZD10_HUMAN	frizzled 10 precursor	119	FZ.|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)														---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133353615	133353615	+	Silent	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133353615G>T	uc001ukz.1	-	20	4343	c.3784C>A	c.(3784-3786)CGG>AGG	p.R1262R	GOLGA3_uc001ula.1_Silent_p.R1262R	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	1262	Potential.|Gln-rich.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)														---	---	---	---
ATP12A	479	broad.mit.edu	37	13	25283492	25283492	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25283492T>C	uc001upp.2	+						ATP12A_uc010aaa.2_Intron	NM_001676	NP_001667			hydrogen/potassium-exchanging ATPase 12A						ATP biosynthetic process	hydrogen:potassium-exchanging ATPase complex	ATP binding|hydrogen:potassium-exchanging ATPase activity|metal ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|breast(1)	6		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)	Esomeprazole(DB00736)|Pantoprazole(DB00213)													---	---	---	---
PDX1	3651	broad.mit.edu	37	13	28498612	28498612	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28498612G>A	uc001urt.2	+	2	734	c.626G>A	c.(625-627)CGC>CAC	p.R209H		NM_000209	NP_000200	P52945	PDX1_HUMAN	pancreatic and duodenal homeobox 1	209					detection of glucose|generation of precursor metabolites and energy|insulin secretion|nitric oxide mediated signal transduction|organ morphogenesis|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|type B pancreatic cell differentiation	nucleus	sequence-specific DNA binding transcription factor activity				0	all_cancers(110;0.175)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155)	Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0402)|all cancers(112;0.0404)|OV - Ovarian serous cystadenocarcinoma(117;0.197)														---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	30077239	30077239	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30077239G>T	uc001usl.3	+	14	4094	c.4036G>T	c.(4036-4038)GGG>TGG	p.G1346W	MTUS2_uc001usm.3_Missense_Mutation_p.G315W|MTUS2_uc010aau.2_Missense_Mutation_p.G225W|MTUS2_uc010tdq.1_Missense_Mutation_p.G98W	NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a	1336						cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
NBEA	26960	broad.mit.edu	37	13	36006531	36006531	+	Splice_Site	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36006531G>C	uc001uvb.2	+	39	6510	c.6304_splice	c.e39+1	p.G2102_splice	NBEA_uc010abi.2_Splice_Site_p.G758_splice	NM_015678	NP_056493			neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)														---	---	---	---
DCLK1	9201	broad.mit.edu	37	13	36385001	36385001	+	Silent	SNP	G	A	A	rs144489471	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36385001G>A	uc001uvf.2	-	12	1892	c.1659C>T	c.(1657-1659)TAC>TAT	p.Y553Y	DCLK1_uc001uve.3_Silent_p.Y246Y|DCLK1_uc010teh.1_Silent_p.Y246Y|DCLK1_uc010abk.2_Silent_p.Y73Y	NM_004734	NP_004725	O15075	DCLK1_HUMAN	doublecortin-like kinase 1	553	Protein kinase.				cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)														---	---	---	---
POSTN	10631	broad.mit.edu	37	13	38153362	38153362	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38153362T>C	uc001uwo.3	-						POSTN_uc010tet.1_Intron|POSTN_uc001uwp.3_Intron|POSTN_uc001uwr.2_Intron|POSTN_uc001uwq.2_Intron|POSTN_uc010teu.1_Intron|POSTN_uc010tev.1_Intron|POSTN_uc010tew.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)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39264788	39264788	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39264788T>A	uc001uwv.2	+	1	3616	c.3307T>A	c.(3307-3309)TTG>ATG	p.L1103M		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	1103	Extracellular (Potential).|CSPG 7.				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)														---	---	---	---
NHLRC3	387921	broad.mit.edu	37	13	39621842	39621842	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39621842G>A	uc001uxc.2	+	7	1145	c.823G>A	c.(823-825)GCC>ACC	p.A275T	NHLRC3_uc001uxd.2_Missense_Mutation_p.A208T|NHLRC3_uc001uxe.2_Missense_Mutation_p.A78T	NM_001012754	NP_001012772	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3 isoform a	275						extracellular region				skin(1)	1		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)														---	---	---	---
ELF1	1997	broad.mit.edu	37	13	41533046	41533046	+	Missense_Mutation	SNP	A	G	G	rs138470719	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41533046A>G	uc001uxs.2	-	3	552	c.179T>C	c.(178-180)ATG>ACG	p.M60T	ELF1_uc010tfc.1_Missense_Mutation_p.M60T|ELF1_uc010acd.2_5'UTR	NM_172373	NP_758961	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription	60					positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)														---	---	---	---
MTRF1	9617	broad.mit.edu	37	13	41797467	41797467	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41797467C>T	uc001uxx.2	-	11	1619	c.1149G>A	c.(1147-1149)GAG>GAA	p.E383E	MTRF1_uc001uxy.2_Silent_p.E383E|MTRF1_uc001uxz.2_Silent_p.E219E|MTRF1_uc010tff.1_Silent_p.E396E|uc001uxv.1_Intron	NM_004294	NP_004285	O75570	RF1M_HUMAN	mitochondrial translational release factor 1	383					regulation of translational termination	mitochondrion	translation release factor activity, codon specific				0		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)														---	---	---	---
SPERT	220082	broad.mit.edu	37	13	46287863	46287863	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46287863G>A	uc001van.1	+	3	783	c.703G>A	c.(703-705)GCC>ACC	p.A235T	SPERT_uc001vao.2_Missense_Mutation_p.A199T	NM_152719	NP_689932	Q8NA61	SPERT_HUMAN	spermatid associated	235						cytoplasmic membrane-bounded vesicle				central_nervous_system(1)|pancreas(1)	2		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)														---	---	---	---
KPNA3	3839	broad.mit.edu	37	13	50296149	50296149	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50296149A>G	uc001vdj.2	-	9	1083	c.668T>C	c.(667-669)GTC>GCC	p.V223A		NM_002267	NP_002258	O00505	IMA3_HUMAN	karyopherin alpha 3	223	NLS binding site (major) (By similarity).|ARM 4.				interspecies interaction between organisms|NLS-bearing substrate import into nucleus|protein complex assembly	cytoplasm|nuclear pore	nuclear localization sequence binding|protein transporter activity				0		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)														---	---	---	---
SERPINE3	647174	broad.mit.edu	37	13	51922396	51922396	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51922396C>T	uc001vfh.2	+	4	808	c.748C>T	c.(748-750)CCT>TCT	p.P250S	SERPINE3_uc010tgp.1_Missense_Mutation_p.P250S	NM_001101320	NP_001094790	A8MV23	SERP3_HUMAN	nexin-related serine protease inhibitor	250					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)	2																		---	---	---	---
SUGT1	10910	broad.mit.edu	37	13	53250454	53250454	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53250454A>G	uc001vhc.2	+	12	1038	c.813A>G	c.(811-813)GCA>GCG	p.A271A	SUGT1_uc001vha.2_RNA|SUGT1_uc001vhb.2_Silent_p.A239A|SUGT1_uc010thb.1_Silent_p.A183A|SUGT1_uc001vhd.2_Silent_p.A128A	NM_001130912	NP_001124384	Q9Y2Z0	SUGT1_HUMAN	suppressor of G2 allele of SKP1 isoform a	271					mitosis	kinetochore|ubiquitin ligase complex	binding				0		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)														---	---	---	---
PCDH17	27253	broad.mit.edu	37	13	58206969	58206969	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58206969C>T	uc001vhq.1	+	1	1181	c.289C>T	c.(289-291)CGC>TGC	p.R97C	PCDH17_uc010aec.1_Missense_Mutation_p.R97C	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	97	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)														---	---	---	---
EDNRB	1910	broad.mit.edu	37	13	78492678	78492678	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78492678C>T	uc001vko.2	-	1	289	c.31G>A	c.(31-33)GCC>ACC	p.A11T	uc001vks.2_5'Flank|EDNRB_uc001vkq.1_Missense_Mutation_p.A11T|EDNRB_uc010aez.1_Missense_Mutation_p.A11T|EDNRB_uc001vkp.1_Missense_Mutation_p.A94T|EDNRB_uc010afa.1_Missense_Mutation_p.A11T	NM_001122659	NP_001116131	P24530	EDNRB_HUMAN	endothelin receptor type B isoform 1 precursor	11					activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction	integral to plasma membrane	endothelin-B receptor activity|peptide hormone binding				0		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)											OREG0022452	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EDNRB	1910	broad.mit.edu	37	13	78493632	78493632	+	5'Flank	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78493632G>A	uc001vko.2	-						uc001vks.2_5'Flank|EDNRB_uc001vkq.1_Intron|EDNRB_uc010aez.1_5'Flank|EDNRB_uc001vkp.1_Missense_Mutation_p.A33V|EDNRB_uc010afa.1_5'Flank	NM_001122659	NP_001116131			endothelin receptor type B isoform 1 precursor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction	integral to plasma membrane	endothelin-B receptor activity|peptide hormone binding				0		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)											OREG0022452	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DOCK9	23348	broad.mit.edu	37	13	99505739	99505739	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99505739C>T	uc001vnt.2	-	35	3927	c.3872G>A	c.(3871-3873)CGC>CAC	p.R1291H	DOCK9_uc001vnw.2_Missense_Mutation_p.R1290H|DOCK9_uc001vnv.1_RNA|DOCK9_uc010tir.1_Missense_Mutation_p.R1291H|DOCK9_uc010tip.1_5'UTR|DOCK9_uc010tiq.1_Missense_Mutation_p.R269H	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a	1291					blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
UBAC2	337867	broad.mit.edu	37	13	99966475	99966475	+	Splice_Site	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99966475G>A	uc001voa.3	+	5	997	c.513_splice	c.e5+1	p.Q171_splice	UBAC2_uc010tiu.1_Splice_Site_p.Q193_splice|UBAC2_uc001vob.3_Splice_Site_p.Q144_splice|UBAC2_uc010tiv.1_Intron|UBAC2_uc001vod.2_Splice_Site_p.Q58_splice|UBAC2_uc001voc.2_Splice_Site_p.Q136_splice|UBAC2_uc010tiw.1_Intron|UBAC2_uc001voh.2_Splice_Site	NM_001144072	NP_001137544			UBA domain containing 2 isoform 1							integral to membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
TMTC4	84899	broad.mit.edu	37	13	101278337	101278337	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101278337C>T	uc001vou.2	-	12	1677	c.1517G>A	c.(1516-1518)CGG>CAG	p.R506Q	TMTC4_uc001vot.2_Missense_Mutation_p.R525Q|TMTC4_uc010tja.1_Missense_Mutation_p.R395Q|TMTC4_uc001vov.1_Missense_Mutation_p.R251Q|TMTC4_uc001vow.1_Missense_Mutation_p.R289Q	NM_001079669	NP_001073137	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat	506	TPR 2.					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	103443745	103443745	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103443745C>A	uc001vpq.3	-	5	1092	c.708G>T	c.(706-708)TTG>TTT	p.L236F	KDELC1_uc001vpr.3_Missense_Mutation_p.L17F	NM_024089	NP_076994	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1 precursor	236						endoplasmic reticulum lumen				ovary(1)	1	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)																	---	---	---	---
COL4A2	1284	broad.mit.edu	37	13	111083059	111083059	+	Intron	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111083059C>A	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)															---	---	---	---
MCF2L	23263	broad.mit.edu	37	13	113731509	113731509	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113731509G>A	uc001vsu.2	+	13	1837	c.1815G>A	c.(1813-1815)TCG>TCA	p.S605S	MCF2L_uc001vsq.2_Silent_p.S605S|MCF2L_uc010tjr.1_Silent_p.S548S|MCF2L_uc001vsr.2_Silent_p.S552S|MCF2L_uc001vss.3_Silent_p.S546S|MCF2L_uc010tjs.1_Silent_p.S546S|MCF2L_uc001vst.1_Silent_p.S510S	NM_001112732	NP_001106203	O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming	578					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)																---	---	---	---
OR11H12	440153	broad.mit.edu	37	14	19377709	19377709	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19377709A>C	uc010tkp.1	+	1	116	c.116A>C	c.(115-117)CAG>CCG	p.Q39P		NM_001013354	NP_001013372	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H,	39	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)														---	---	---	---
POTEG	404785	broad.mit.edu	37	14	19553565	19553565	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19553565A>G	uc001vuz.1	+	1	201	c.149A>G	c.(148-150)GAC>GGC	p.D50G	POTEG_uc001vva.1_RNA|POTEG_uc010ahc.1_RNA	NM_001005356	NP_001005356	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	50										ovary(1)	1																		---	---	---	---
OR4Q3	441669	broad.mit.edu	37	14	20215981	20215981	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20215981G>A	uc010tkt.1	+	1	395	c.395G>A	c.(394-396)CGC>CAC	p.R132H		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	132	Cytoplasmic (Potential).				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)														---	---	---	---
OR4M1	441670	broad.mit.edu	37	14	20248625	20248625	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20248625C>A	uc010tku.1	+	1	144	c.144C>A	c.(142-144)ACC>ACA	p.T48T		NM_001005500	NP_001005500	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M,	48	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)														---	---	---	---
OR4L1	122742	broad.mit.edu	37	14	20529031	20529031	+	Silent	SNP	A	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20529031A>T	uc001vwn.1	+	1	828	c.828A>T	c.(826-828)ACA>ACT	p.T276T		NM_001004717	NP_001004717	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L,	276	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)														---	---	---	---
ANG	283	broad.mit.edu	37	14	21162101	21162101	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21162101C>T	uc001vxw.3	+	2	978	c.378C>T	c.(376-378)AAC>AAT	p.N126N	RNASE4_uc001vxx.3_Intron|RNASE4_uc001vxy.3_Intron|ANG_uc001vxz.2_Silent_p.N126N|RNASE4_uc001vya.2_Intron	NM_001145	NP_001136	P03950	ANGI_HUMAN	angiogenin, ribonuclease, RNase A family, 5	126					actin filament polymerization|activation of phospholipase A2 activity|activation of phospholipase C activity|activation of protein kinase B activity|angiogenesis|cell communication|cell death|cell migration|diacylglycerol biosynthetic process|homeostatic process|negative regulation of smooth muscle cell proliferation|negative regulation of translation|oocyte maturation|ovarian follicle development|placenta development|positive regulation of endothelial cell proliferation|positive regulation of phosphorylation|positive regulation of protein secretion|response to hormone stimulus|response to hypoxia|rRNA transcription	angiogenin-PRI complex|basal lamina|extracellular space|growth cone|neuronal cell body|nucleolus	actin binding|copper ion binding|heparin binding|pancreatic ribonuclease activity|peptide binding|receptor binding|rRNA binding			ovary(1)	1	all_cancers(95;0.00387)	all_cancers(140;0.196)|all_epithelial(140;0.156)	Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	OV - Ovarian serous cystadenocarcinoma(311;3.25e-17)|GBM - Glioblastoma multiforme(265;5.56e-07)														---	---	---	---
RNASE1	6035	broad.mit.edu	37	14	21270141	21270141	+	Silent	SNP	C	T	T	rs150792279		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21270141C>T	uc001vyf.2	-	2	263	c.87G>A	c.(85-87)AAG>AAA	p.K29K	RNASE1_uc001vyg.2_Silent_p.K29K|RNASE1_uc001vyh.2_Silent_p.K29K|RNASE1_uc001vyi.2_Silent_p.K29K	NM_198232	NP_937875	P07998	RNAS1_HUMAN	pancreatic ribonuclease precursor	29						extracellular region	nucleic acid binding|pancreatic ribonuclease activity|protein binding				0	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)														---	---	---	---
NDRG2	57447	broad.mit.edu	37	14	21488953	21488953	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21488953G>A	uc001vyy.2	-	8	608	c.458C>T	c.(457-459)GCG>GTG	p.A153V	NDRG2_uc010tll.1_Missense_Mutation_p.A149V|NDRG2_uc001vyt.2_Missense_Mutation_p.A66V|NDRG2_uc001vyu.2_Missense_Mutation_p.A139V|NDRG2_uc001vyv.2_Missense_Mutation_p.A139V|NDRG2_uc001vyw.2_Missense_Mutation_p.A139V|NDRG2_uc001vzb.2_Missense_Mutation_p.A93V|NDRG2_uc001vyx.2_Missense_Mutation_p.A153V|NDRG2_uc001vza.2_Missense_Mutation_p.A139V|NDRG2_uc001vyz.2_Missense_Mutation_p.A139V|NDRG2_uc001vzc.2_Missense_Mutation_p.A139V|NDRG2_uc001vze.2_Missense_Mutation_p.A153V|NDRG2_uc001vzd.2_Missense_Mutation_p.A153V|NDRG2_uc001vzg.2_Missense_Mutation_p.A139V|NDRG2_uc001vzf.2_Missense_Mutation_p.A139V|NDRG2_uc010aig.2_Missense_Mutation_p.A153V	NM_201540	NP_963834	Q9UN36	NDRG2_HUMAN	N-myc downstream-regulated gene 2 isoform a	153					cell differentiation|nervous system development	centrosome|cytosol|Golgi apparatus|nucleus|perinuclear region of cytoplasm				ovary(1)|breast(1)	2	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22789057	22789057	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22789057G>A	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wdr.2_Silent_p.K90K					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
CDH24	64403	broad.mit.edu	37	14	23517497	23517497	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23517497C>T	uc001wil.2	-	13	2412	c.2152G>A	c.(2152-2154)GCG>ACG	p.A718T	CDH24_uc001wik.3_RNA|CDH24_uc010akf.2_Missense_Mutation_p.A680T	NM_022478	NP_071923	Q86UP0	CAD24_HUMAN	cadherin-like 24 isoform 1	718	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|cell-cell adhesion|homophilic cell adhesion	cell-cell junction|cell-cell junction|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|delta-catenin binding			central_nervous_system(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)														---	---	---	---
PABPN1	8106	broad.mit.edu	37	14	23777209	23777209	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23777209G>A	uc001wjh.3	+	3	421	c.233G>A	c.(232-234)CGC>CAC	p.R78H	BCL2L2_uc001wjg.3_Missense_Mutation_p.R78H|BCL2L2_uc001wji.3_Missense_Mutation_p.R78H	NM_004643	NP_004634	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1	Error:Variant_position_missing_in_Q86U42_after_alignment					modification by virus of host mRNA processing|mRNA 3'-end processing|muscle contraction|nuclear mRNA splicing, via spliceosome|poly(A)+ mRNA export from nucleus|termination of RNA polymerase II transcription|viral infectious cycle	cytoplasm|nucleoplasm|ribonucleoprotein complex	nucleotide binding|protein binding|RNA binding			ovary(2)	2	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)														---	---	---	---
MYH6	4624	broad.mit.edu	37	14	23855229	23855229	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23855229G>A	uc001wjv.2	-	34	5138	c.5071C>T	c.(5071-5073)CGT>TGT	p.R1691C		NM_002471	NP_002462	P13533	MYH6_HUMAN	myosin heavy chain 6	1691	Potential.				adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)														---	---	---	---
PCK2	5106	broad.mit.edu	37	14	24572069	24572069	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24572069G>A	uc001wlt.2	+	8	1474	c.1342G>A	c.(1342-1344)GCC>ACC	p.A448T	NRL_uc001wlq.2_Intron|PCK2_uc001wlr.1_Missense_Mutation_p.A460T|PCK2_uc010tnw.1_Missense_Mutation_p.A314T|PCK2_uc010tnx.1_Missense_Mutation_p.A314T|PCK2_uc001wlu.3_Missense_Mutation_p.A314T	NM_004563	NP_004554	Q16822	PCKGM_HUMAN	mitochondrial phosphoenolpyruvate carboxykinase	448					gluconeogenesis	mitochondrial matrix	GTP binding|metal ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.0184)														---	---	---	---
GMPR2	51292	broad.mit.edu	37	14	24707853	24707853	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24707853C>A	uc001wnr.2	+	10	1298	c.916C>A	c.(916-918)CGA>AGA	p.R306R	GMPR2_uc001wnv.2_Silent_p.R143R|GMPR2_uc001wns.2_Silent_p.R306R|GMPR2_uc001wnt.2_Silent_p.R273R|GMPR2_uc001wnu.2_Silent_p.R331R|GMPR2_uc001wnw.2_Silent_p.R306R|GMPR2_uc010all.2_Silent_p.R278R|GMPR2_uc001wnx.2_Silent_p.R324R|GMPR2_uc010tod.1_Silent_p.R273R|GMPR2_uc010alk.1_Silent_p.R367R|GMPR2_uc010toe.1_Silent_p.R367R	NM_001002001	NP_001002001	Q9P2T1	GMPR2_HUMAN	guanosine monophosphate reductase 2 isoform 2	306					nucleotide metabolic process|purine base metabolic process|purine-containing compound salvage	cytosol	GMP reductase activity|metal ion binding			ovary(3)	3				GBM - Glioblastoma multiforme(265;0.0181)														---	---	---	---
TGM1	7051	broad.mit.edu	37	14	24727798	24727798	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24727798T>C	uc001wod.2	-	8	1365	c.1241A>G	c.(1240-1242)GAC>GGC	p.D414G	TGM1_uc010tog.1_Intron	NM_000359	NP_000350	P22735	TGM1_HUMAN	transglutaminase 1	414					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)													---	---	---	---
PRKD1	5587	broad.mit.edu	37	14	30103733	30103733	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30103733T>G	uc001wqh.2	-	8	1386	c.1205A>C	c.(1204-1206)AAC>ACC	p.N402T		NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1	402					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)														---	---	---	---
SCFD1	23256	broad.mit.edu	37	14	31188570	31188570	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31188570C>T	uc001wqm.1	+	21	1747	c.1723C>T	c.(1723-1725)CGG>TGG	p.R575W	SCFD1_uc001wqn.1_Missense_Mutation_p.R508W|SCFD1_uc010tpg.1_Missense_Mutation_p.R516W|SCFD1_uc010tph.1_Missense_Mutation_p.R390W|SCFD1_uc010amf.1_Missense_Mutation_p.R390W|SCFD1_uc010tpi.1_Missense_Mutation_p.R483W|SCFD1_uc010ame.1_Missense_Mutation_p.R508W	NM_016106	NP_057190	Q8WVM8	SCFD1_HUMAN	vesicle transport-related protein isoform a	575					post-Golgi vesicle-mediated transport|protein transport|regulation of ER to Golgi vesicle-mediated transport|response to toxin|retrograde vesicle-mediated transport, Golgi to ER|vesicle docking involved in exocytosis	cis-Golgi network|endoplasmic reticulum membrane|Golgi cisterna membrane|Golgi-associated vesicle|plasma membrane	syntaxin-5 binding				0	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)														---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31638663	31638663	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31638663C>T	uc001wrc.1	-	9	1833	c.1344G>A	c.(1342-1344)CGG>CGA	p.R448R	HECTD1_uc001wrd.1_5'Flank	NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	448	ANK 2.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33015700	33015700	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33015700T>C	uc001wrq.2	+	4	2011	c.1841T>C	c.(1840-1842)GTC>GCC	p.V614A	AKAP6_uc010aml.2_Missense_Mutation_p.V611A	NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	614					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)														---	---	---	---
SEC23A	10484	broad.mit.edu	37	14	39514489	39514489	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39514489A>G	uc001wup.1	-	16	2000	c.1777T>C	c.(1777-1779)TTT>CTT	p.F593L	SEC23A_uc010tqa.1_Missense_Mutation_p.F479L|SEC23A_uc010tqb.1_Missense_Mutation_p.F564L	NM_006364	NP_006355	Q15436	SC23A_HUMAN	SEC23-related protein A	593					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)														---	---	---	---
C14orf182	283551	broad.mit.edu	37	14	50472448	50472448	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50472448T>C	uc001wxi.1	-	1	1791	c.70A>G	c.(70-72)ACC>GCC	p.T24A		NM_001012706	NP_001012724	A1A4T8	CN182_HUMAN	hypothetical protein LOC283551	24											0																		---	---	---	---
WDHD1	11169	broad.mit.edu	37	14	55457924	55457924	+	Intron	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55457924G>C	uc001xbm.1	-						WDHD1_uc010aom.1_Intron|WDHD1_uc001xbn.1_Intron	NM_007086	NP_009017			WD repeat and HMG-box DNA binding protein 1							cytoplasm|nucleoplasm	DNA binding			skin(1)	1																		---	---	---	---
TBPL2	387332	broad.mit.edu	37	14	55900349	55900349	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55900349T>C	uc001xby.2	-	4	787	c.787A>G	c.(787-789)AGT>GGT	p.S263G		NM_199047	NP_950248	Q6SJ96	TBPL2_HUMAN	TATA box binding protein like 2	263					multicellular organismal development|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding				0																		---	---	---	---
C14orf105	55195	broad.mit.edu	37	14	57938138	57938138	+	Missense_Mutation	SNP	G	C	C	rs144453893	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57938138G>C	uc001xcy.2	-	6	969	c.826C>G	c.(826-828)CGA>GGA	p.R276G	C14orf105_uc010trl.1_Missense_Mutation_p.R316G|C14orf105_uc010trm.1_Missense_Mutation_p.R187G|C14orf105_uc010trn.1_Missense_Mutation_p.R187G|C14orf105_uc001xcz.2_Missense_Mutation_p.R275G	NM_018168	NP_060638	Q9NVL8	CN105_HUMAN	hypothetical protein LOC55195	276											0																		---	---	---	---
WDR89	112840	broad.mit.edu	37	14	64065892	64065892	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64065892G>A	uc001xgh.2	-	3	1015	c.769C>T	c.(769-771)CGT>TGT	p.R257C	WDR89_uc001xgi.2_Missense_Mutation_p.R257C	NM_001008726	NP_001008726	Q96FK6	WDR89_HUMAN	WD repeat domain 89	257											0				OV - Ovarian serous cystadenocarcinoma(108;0.00543)|all cancers(60;0.0181)|BRCA - Breast invasive adenocarcinoma(234;0.101)														---	---	---	---
ACTN1	87	broad.mit.edu	37	14	69358881	69358881	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69358881C>T	uc001xkl.2	-	10	1285	c.975G>A	c.(973-975)CCG>CCA	p.P325P	ACTN1_uc010ttb.1_Silent_p.P260P|ACTN1_uc001xkm.2_Silent_p.P325P|ACTN1_uc001xkn.2_Silent_p.P325P|ACTN1_uc001xko.1_Silent_p.P260P|ACTN1_uc010ttd.1_Silent_p.P304P	NM_001102	NP_001093	P12814	ACTN1_HUMAN	actinin, alpha 1 isoform b	325	Spectrin 1.|Interaction with DDN.				focal adhesion assembly|negative regulation of cellular component movement|platelet activation|platelet degranulation|regulation of apoptosis	actin cytoskeleton|cytosol|extracellular region|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|sarcomere	actin binding|calcium ion binding|integrin binding|vinculin binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)														---	---	---	---
C14orf115	55237	broad.mit.edu	37	14	74824119	74824119	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74824119C>T	uc001xpw.3	+	2	824	c.633C>T	c.(631-633)TGC>TGT	p.C211C		NM_018228	NP_060698	Q9H8Y1	VRTN_HUMAN	hypothetical protein LOC55237	211					transposition, DNA-mediated		DNA binding|transposase activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00147)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	80319917	80319917	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80319917G>A	uc001xun.2	+						NRXN3_uc001xum.1_RNA|NRXN3_uc001xup.2_RNA|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)														---	---	---	---
PSMC1	5700	broad.mit.edu	37	14	90735804	90735804	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90735804G>C	uc001xyf.2	+	9	993	c.945G>C	c.(943-945)CAG>CAC	p.Q315H	PSMC1_uc001xyg.2_Missense_Mutation_p.Q242H|PSMC1_uc001xyh.2_Missense_Mutation_p.Q242H	NM_002802	NP_002793	P62191	PRS4_HUMAN	proteasome 26S ATPase subunit 1	315					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding				0		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)														---	---	---	---
ASB2	51676	broad.mit.edu	37	14	94413763	94413763	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94413763G>A	uc001ycc.1	-	5	1329	c.840C>T	c.(838-840)GCC>GCT	p.A280A	ASB2_uc001ycd.2_Silent_p.A328A|ASB2_uc001yce.1_Silent_p.A226A	NM_016150	NP_057234	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box-containing protein	280	ANK 7.				intracellular signal transduction					ovary(1)|pancreas(1)	2		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)														---	---	---	---
TMEM179	388021	broad.mit.edu	37	14	105061420	105061420	+	3'UTR	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105061420G>T	uc001yox.1	-	3						NM_207379	NP_997262			transmembrane protein 179							integral to membrane					0			all cancers(16;0.00276)|OV - Ovarian serous cystadenocarcinoma(23;0.0262)|Epithelial(46;0.058)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.129)														---	---	---	---
ADSSL1	122622	broad.mit.edu	37	14	105208323	105208323	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105208323C>A	uc001ypd.2	+	9	1006	c.932C>A	c.(931-933)CCC>CAC	p.P311H	INF2_uc010tyi.1_Intron|ADSSL1_uc001ype.2_Missense_Mutation_p.P354H|ADSSL1_uc001ypf.2_RNA	NM_152328	NP_689541	Q8N142	PURA1_HUMAN	adenylosuccinate synthase like 1 isoform 2	311					AMP biosynthetic process|immune system process|purine base metabolic process	cytosol	adenylosuccinate synthase activity|GTP binding|magnesium ion binding|phosphate binding			ovary(1)|central_nervous_system(1)	2		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.18)	L-Aspartic Acid(DB00128)													---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106090835	106090835	+	RNA	SNP	A	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106090835A>T	uc010tyt.1	-	3648		c.62576T>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106321609	106321609	+	RNA	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106321609T>C	uc010tyt.1	-	3599		c.55787A>G			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysj.2_Intron|uc001ysk.1_Intron|uc001ysl.1_Intron|uc001ysm.1_Intron|uc001ysn.1_Intron|uc001yso.1_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
MAGEL2	54551	broad.mit.edu	37	15	23890722	23890722	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23890722G>A	uc001ywj.3	-	1	454	c.359C>T	c.(358-360)GCC>GTC	p.A120V		NM_019066	NP_061939			MAGE-like protein 2												0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)														---	---	---	---
C15orf2	23742	broad.mit.edu	37	15	24923624	24923624	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24923624A>C	uc001ywo.2	+	1	3084	c.2610A>C	c.(2608-2610)CAA>CAC	p.Q870H		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	870					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	8		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)														---	---	---	---
SNORD116-4	100033416	broad.mit.edu	37	15	25299457	25299457	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25299457G>A	uc001yxh.1	+						SNORD116-4_uc001yxj.1_5'Flank|SNORD116-3_uc001yxk.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0																		---	---	---	---
OTUD7A	161725	broad.mit.edu	37	15	31776530	31776530	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31776530G>A	uc001zfq.2	-	11	1841	c.1748C>T	c.(1747-1749)CCG>CTG	p.P583L	OTUD7A_uc001zfr.2_Missense_Mutation_p.P590L	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A	583						cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)														---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33358802	33358802	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33358802C>T	uc001zhf.3	-	1	1284	c.1284G>A	c.(1282-1284)AAG>AAA	p.K428K	FMN1_uc001zhg.2_Silent_p.K428K	NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1	178	Microtubule-binding (By similarity).				actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)														---	---	---	---
TGM5	9333	broad.mit.edu	37	15	43545709	43545709	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43545709C>T	uc001zrd.1	-	5	687	c.679G>A	c.(679-681)GCC>ACC	p.A227T	TGM5_uc001zre.1_Missense_Mutation_p.A145T	NM_201631	NP_963925	O43548	TGM5_HUMAN	transglutaminase 5 isoform 1	227					epidermis development|peptide cross-linking	cytoplasm	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(1)	1		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)													---	---	---	---
RNF111	54778	broad.mit.edu	37	15	59359012	59359012	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59359012T>C	uc002afv.2	+	6	1695	c.1416T>C	c.(1414-1416)CCT>CCC	p.P472P	RNF111_uc002afs.2_Silent_p.P472P|RNF111_uc002aft.2_Silent_p.P472P|RNF111_uc002afu.2_Silent_p.P472P|RNF111_uc002afw.2_Silent_p.P472P|RNF111_uc002afx.2_5'UTR	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111	472					multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)														---	---	---	---
RNF111	54778	broad.mit.edu	37	15	59373146	59373146	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59373146A>G	uc002afv.2	+	8	2239	c.1960A>G	c.(1960-1962)ACA>GCA	p.T654A	RNF111_uc002afs.2_Missense_Mutation_p.T654A|RNF111_uc002aft.2_Missense_Mutation_p.T654A|RNF111_uc002afu.2_Missense_Mutation_p.T653A|RNF111_uc002afw.2_Missense_Mutation_p.T654A|RNF111_uc002afx.2_Missense_Mutation_p.T180A	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111	654	Pro-rich.				multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)														---	---	---	---
HERC1	8925	broad.mit.edu	37	15	63904497	63904497	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63904497T>C	uc002amp.2	-	77	14501	c.14353A>G	c.(14353-14355)AAC>GAC	p.N4785D	HERC1_uc002amo.2_5'Flank	NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	4785	HECT.				protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19																		---	---	---	---
FAM96A	84191	broad.mit.edu	37	15	64373351	64373351	+	Splice_Site	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64373351C>A	uc002amt.1	-	3	530	c.290_splice	c.e3-1	p.G97_splice	FAM96A_uc002amu.1_Intron|FAM96A_uc010uin.1_Intron	NM_032231	NP_115607			family with sequence similarity 96, member A						chromosome segregation						0																		---	---	---	---
CYP11A1	1583	broad.mit.edu	37	15	74640300	74640300	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74640300G>A	uc002axt.2	-	2	521	c.366C>T	c.(364-366)CTC>CTT	p.L122L	CYP11A1_uc002axs.2_5'UTR|CYP11A1_uc010bjm.1_Intron|CYP11A1_uc010bjn.1_RNA|CYP11A1_uc010bjo.1_Silent_p.L122L|CYP11A1_uc010ulj.1_5'UTR|CYP11A1_uc010bjq.2_Silent_p.L122L	NM_000781	NP_000772	P05108	CP11A_HUMAN	cytochrome P450, family 11, subfamily A,	122					C21-steroid hormone biosynthetic process|cholesterol metabolic process|vitamin D metabolic process|xenobiotic metabolic process	mitochondrial matrix	cholesterol monooxygenase (side-chain-cleaving) activity|electron carrier activity|heme binding			ovary(2)	2					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Clotrimazole(DB00257)|Digitoxin(DB01396)|Digoxin(DB00390)|Medroxyprogesterone(DB00603)|Ouabain(DB01092)|Progesterone(DB00396)|Testosterone(DB00624)|Trilostane(DB01108)													---	---	---	---
HMG20A	10363	broad.mit.edu	37	15	77759517	77759517	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77759517C>A	uc002bcr.2	+	5	519	c.318C>A	c.(316-318)CCC>CCA	p.P106P	HMG20A_uc002bcs.2_Silent_p.P106P	NM_018200	NP_060670	Q9NP66	HM20A_HUMAN	high-mobility group 20A	106	HMG box.				chromatin modification	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
KIAA1024	23251	broad.mit.edu	37	15	79755669	79755669	+	Intron	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79755669C>A	uc002bew.1	+						KIAA1024_uc010unk.1_Intron	NM_015206	NP_056021			hypothetical protein LOC23251							integral to membrane				pancreas(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
AP3B2	8120	broad.mit.edu	37	15	83333197	83333197	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83333197C>A	uc010uoh.1	-	18	2303	c.2126G>T	c.(2125-2127)AGC>ATC	p.S709I	AP3B2_uc010uoi.1_Missense_Mutation_p.S728I|AP3B2_uc010uoj.1_Missense_Mutation_p.S677I|AP3B2_uc010bmp.2_5'Flank|AP3B2_uc010uog.1_Missense_Mutation_p.S345I|AP3B2_uc002biy.1_5'Flank	NM_004644	NP_004635	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2	709	Glu/Ser-rich.				endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)															---	---	---	---
DET1	55070	broad.mit.edu	37	15	89060009	89060009	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89060009G>A	uc002bmr.2	-						DET1_uc002bmp.3_Intron|DET1_uc010bnk.2_Intron|DET1_uc002bmq.2_Intron	NM_001144074	NP_001137546			de-etiolated 1 isoform 2							nucleus				lung(1)|pancreas(1)	2	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)															---	---	---	---
BLM	641	broad.mit.edu	37	15	91295092	91295092	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91295092A>G	uc002bpr.2	+	4	972	c.875A>G	c.(874-876)GAT>GGT	p.D292G	BLM_uc010uqh.1_Missense_Mutation_p.D292G|BLM_uc010uqi.1_5'UTR|BLM_uc010bnx.2_Missense_Mutation_p.D292G	NM_000057	NP_000048	P54132	BLM_HUMAN	Bloom syndrome protein	292	Poly-Asp.				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				---	---	---	---
TMEM8A	58986	broad.mit.edu	37	16	424217	424217	+	Intron	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:424217C>A	uc002cgu.3	-						TMEM8A_uc002cgv.3_Intron	NM_021259	NP_067082			transmembrane protein 8 (five membrane-spanning						cell adhesion	integral to plasma membrane				central_nervous_system(2)|pancreas(1)	3																OREG0003702	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
SOLH	6650	broad.mit.edu	37	16	603483	603483	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:603483G>T	uc002chi.2	+	14	3591	c.3228G>T	c.(3226-3228)GAG>GAT	p.E1076D	SOLH_uc002chj.2_Missense_Mutation_p.E136D	NM_005632	NP_005623	O75808	CAN15_HUMAN	small optic lobes	1076					proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)	2		Hepatocellular(780;0.00335)																---	---	---	---
WDR90	197335	broad.mit.edu	37	16	705158	705158	+	Intron	SNP	C	T	T	rs149348093	by1000genomes	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:705158C>T	uc002cii.1	+						WDR90_uc002cig.1_Intron|WDR90_uc002cih.1_Intron|WDR90_uc002cij.1_Intron|WDR90_uc002cik.1_5'UTR|WDR90_uc002cil.1_5'Flank|WDR90_uc002cim.1_5'Flank	NM_145294	NP_660337			WD repeat domain 90											ovary(1)	1		Hepatocellular(780;0.0218)																---	---	---	---
TELO2	9894	broad.mit.edu	37	16	1556268	1556268	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1556268C>T	uc002cly.2	+	17	2355	c.2064C>T	c.(2062-2064)AGC>AGT	p.S688S		NM_016111	NP_057195	Q9Y4R8	TELO2_HUMAN	TEL2, telomere maintenance 2, homolog	688						chromosome, telomeric region|cytoplasm|membrane|nucleus	protein binding				0		Hepatocellular(780;0.219)																---	---	---	---
SEPX1	51734	broad.mit.edu	37	16	1991343	1991343	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1991343G>T	uc010uvs.1	-	2	256	c.119C>A	c.(118-120)TCG>TAG	p.S40*		NM_016332	NP_057416	Q9NZV6	MSRB1_HUMAN	selenoprotein X, 1	40					protein repair	cytoplasm|nucleus	peptide-methionine-(S)-S-oxide reductase activity|zinc ion binding			ovary(1)	1					L-Methionine(DB00134)													---	---	---	---
PKD1	5310	broad.mit.edu	37	16	2158763	2158763	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2158763C>T	uc002cos.1	-	15	6614	c.6405G>A	c.(6403-6405)GCG>GCA	p.A2135A	PKD1_uc002cot.1_Silent_p.A2135A	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	2135	PKD 17.|Extracellular (Potential).				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3																		---	---	---	---
SRRM2	23524	broad.mit.edu	37	16	2812054	2812054	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2812054C>A	uc002crk.2	+	11	2074	c.1525C>A	c.(1525-1527)CGA>AGA	p.R509R	SRRM2_uc002crj.1_Silent_p.R413R|SRRM2_uc002crl.1_Silent_p.R509R|SRRM2_uc010bsu.1_Silent_p.R413R	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	509	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																		---	---	---	---
ZSCAN10	84891	broad.mit.edu	37	16	3142748	3142748	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3142748C>T	uc002ctv.1	-	1	114	c.26G>A	c.(25-27)CGG>CAG	p.R9Q	ZSCAN10_uc002cty.1_Intron|ZSCAN10_uc002ctw.1_Silent_p.P16P|ZSCAN10_uc002ctx.1_5'UTR	NM_032805	NP_116194	Q96SZ4	ZSC10_HUMAN	zinc finger and SCAN domain containing 10	9	SCAN box.				negative regulation of transcription, DNA-dependent|viral reproduction	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
ZNF205	7755	broad.mit.edu	37	16	3170075	3170075	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3170075G>T	uc002cub.2	+	7	1549	c.1414G>T	c.(1414-1416)GGC>TGC	p.G472C	ZNF205_uc002cua.2_Missense_Mutation_p.G472C	NM_001042428	NP_001035893	O95201	ZN205_HUMAN	zinc finger protein 205	472					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding				0																		---	---	---	---
BTBD12	84464	broad.mit.edu	37	16	3645599	3645599	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3645599T>C	uc002cvp.2	-							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				---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	9934585	9934585	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9934585A>C	uc002czo.3	-	7	2118	c.1570T>G	c.(1570-1572)TTC>GTC	p.F524V	GRIN2A_uc010uym.1_Missense_Mutation_p.F524V|GRIN2A_uc010uyn.1_Missense_Mutation_p.F367V|GRIN2A_uc002czr.3_Missense_Mutation_p.F524V	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	524	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
ITPRIPL2	162073	broad.mit.edu	37	16	19127146	19127146	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19127146G>A	uc002dfu.3	+	1	1893	c.1363G>A	c.(1363-1365)GTC>ATC	p.V455I	ITPRIPL2_uc002dft.2_Missense_Mutation_p.V151I	NM_001034841	NP_001030013	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-triphosphate receptor interacting	455	Cytoplasmic (Potential).					integral to membrane				skin(2)	2																		---	---	---	---
PLK1	5347	broad.mit.edu	37	16	23695383	23695383	+	Missense_Mutation	SNP	C	T	T	rs150139246		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23695383C>T	uc002dlz.1	+	5	1062	c.1009C>T	c.(1009-1011)CGG>TGG	p.R337W		NM_005030	NP_005021	P53350	PLK1_HUMAN	polo-like kinase 1	337	D-box that targets the protein for proteasomal degradation in anaphase.			R->A: Interferes with ubiquitination and subsequent proteasomal degradation in anaphase; when associated with A-340.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G2/M transition DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic prophase|negative regulation of cyclin-dependent protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|protein localization to chromatin|protein ubiquitination|regulation of mitotic anaphase|regulation of protein binding	centrosome|condensed nuclear chromosome outer kinetochore|cytosol|nucleoplasm|spindle microtubule|spindle midzone|spindle pole	anaphase-promoting complex binding|ATP binding|polo kinase kinase activity|protein kinase binding			lung(1)|skin(1)	2				GBM - Glioblastoma multiforme(48;0.0156)														---	---	---	---
AQP8	343	broad.mit.edu	37	16	25228660	25228660	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25228660G>A	uc002doc.2	+	2	236	c.154G>A	c.(154-156)GGG>AGG	p.G52R		NM_001169	NP_001160	O94778	AQP8_HUMAN	aquaporin 8	52	Helical; (Potential).				cellular response to cAMP	integral to plasma membrane	water channel activity			upper_aerodigestive_tract(1)|breast(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(48;0.044)														---	---	---	---
KIAA0556	23247	broad.mit.edu	37	16	27709693	27709693	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27709693A>C	uc002dow.2	+	9	1009	c.985A>C	c.(985-987)ACT>CCT	p.T329P	KIAA0556_uc002dox.1_Missense_Mutation_p.T237P	NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	329										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8																		---	---	---	---
TAOK2	9344	broad.mit.edu	37	16	29997132	29997132	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29997132C>T	uc002dva.1	+	15	2725	c.1942C>T	c.(1942-1944)CGC>TGC	p.R648C	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TAOK2_uc002dvb.1_Missense_Mutation_p.R648C|TAOK2_uc002dvc.1_Missense_Mutation_p.R648C|TAOK2_uc010bzm.1_Missense_Mutation_p.R655C|TAOK2_uc002dvd.1_Missense_Mutation_p.R475C	NM_016151	NP_057235	Q9UL54	TAOK2_HUMAN	TAO kinase 2 isoform 2	648					actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress	cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus	ATP binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
ZNF768	79724	broad.mit.edu	37	16	30536832	30536832	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30536832A>G	uc002dyk.3	-	2	805	c.629T>C	c.(628-630)CTG>CCG	p.L210P	ZNF768_uc010vex.1_Missense_Mutation_p.L179P|uc002dyl.1_5'Flank|ZNF768_uc010vew.1_Missense_Mutation_p.L179P	NM_024671	NP_078947	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	210					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	DNA binding|zinc ion binding				0																		---	---	---	---
PHKG2	5261	broad.mit.edu	37	16	30768297	30768297	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30768297A>G	uc002dzk.1	+	10	1193	c.1100A>G	c.(1099-1101)CAG>CGG	p.Q367R	PHKG2_uc002dzi.1_Missense_Mutation_p.Q371R|PHKG2_uc002dzj.1_Missense_Mutation_p.Q265R	NM_000294	NP_000285	P15735	PHKG2_HUMAN	phosphorylase kinase, gamma 2 (testis)	367	Calmodulin-binding (domain-C) (By similarity).				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	ATP binding|calmodulin binding|phosphorylase kinase activity			ovary(1)	1			Colorectal(24;0.198)															---	---	---	---
ABCC11	85320	broad.mit.edu	37	16	48239399	48239399	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48239399A>G	uc002eff.1	-	12	2080	c.1730T>C	c.(1729-1731)GTC>GCC	p.V577A	ABCC11_uc002efg.1_Missense_Mutation_p.V577A|ABCC11_uc002efh.1_Missense_Mutation_p.V577A|ABCC11_uc010vgk.1_RNA	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	577	ABC transporter 1.|Cytoplasmic (Potential).					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)												Cerumen_Type				---	---	---	---
ADCY7	113	broad.mit.edu	37	16	50326687	50326687	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50326687T>C	uc002egd.1	+	4	906	c.638T>C	c.(637-639)GTG>GCG	p.V213A	ADCY7_uc002egb.1_Missense_Mutation_p.V213A|ADCY7_uc002egc.1_Missense_Mutation_p.V213A	NM_001114	NP_001105	P51828	ADCY7_HUMAN	adenylate cyclase 7	213	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to ethanol|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of cAMP biosynthetic process|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			skin(1)	1		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)	Bromocriptine(DB01200)													---	---	---	---
FTO	79068	broad.mit.edu	37	16	53922854	53922854	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53922854G>T	uc002ehr.2	+	7	1452	c.1230G>T	c.(1228-1230)ATG>ATT	p.M410I	FTO_uc010vha.1_Missense_Mutation_p.M114I|FTO_uc010cbz.2_Missense_Mutation_p.M11I	NM_001080432	NP_001073901	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	410					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																		---	---	---	---
IRX3	79191	broad.mit.edu	37	16	54318975	54318975	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54318975G>A	uc002eht.1	-	2	1234	c.818C>T	c.(817-819)GCG>GTG	p.A273V		NM_024336	NP_077312	P78415	IRX3_HUMAN	iroquois homeobox 3	273					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
LPCAT2	54947	broad.mit.edu	37	16	55583231	55583231	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55583231C>T	uc002eie.3	+	10	1159	c.978C>T	c.(976-978)TGC>TGT	p.C326C	LPCAT2_uc002eic.2_Silent_p.C56C	NM_017839	NP_060309	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2	326	Lumenal (Potential).				cellular membrane organization|platelet activating factor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|Golgi stack|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding				0																		---	---	---	---
LPCAT2	54947	broad.mit.edu	37	16	55584911	55584911	+	Missense_Mutation	SNP	C	T	T	rs139462449		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55584911C>T	uc002eie.3	+	11	1293	c.1112C>T	c.(1111-1113)GCG>GTG	p.A371V	LPCAT2_uc002eic.2_Missense_Mutation_p.A101V	NM_017839	NP_060309	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2	371	Lumenal (Potential).				cellular membrane organization|platelet activating factor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|Golgi stack|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding				0																		---	---	---	---
CES1	1066	broad.mit.edu	37	16	55850858	55850858	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55850858T>A	uc002eim.2	-	8	1028	c.920A>T	c.(919-921)GAC>GTC	p.D307V	CES1_uc010ccf.2_5'UTR|CES1_uc002eil.2_Missense_Mutation_p.D308V|CES1_uc002ein.2_Missense_Mutation_p.D307V	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor	307					response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)													---	---	---	---
RSPRY1	89970	broad.mit.edu	37	16	57246908	57246908	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57246908A>G	uc002elb.2	+	5	819	c.541A>G	c.(541-543)ATT>GTT	p.I181V	RSPRY1_uc002elc.2_Missense_Mutation_p.I181V|RSPRY1_uc002eld.2_Missense_Mutation_p.I181V	NM_133368	NP_588609	Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	181						extracellular region	zinc ion binding			ovary(1)	1																		---	---	---	---
CDH8	1006	broad.mit.edu	37	16	61935209	61935209	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61935209A>G	uc002eog.1	-	3	673	c.421T>C	c.(421-423)TGG>CGG	p.W141R		NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	141	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
PSKH1	5681	broad.mit.edu	37	16	67942865	67942865	+	Silent	SNP	G	A	A	rs146109328		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67942865G>A	uc002euv.2	+	2	383	c.213G>A	c.(211-213)ACG>ACA	p.T71T	PSKH1_uc010cet.2_Silent_p.T71T	NM_006742	NP_006733	P11801	KPSH1_HUMAN	protein serine kinase H1	71						endoplasmic reticulum membrane|Golgi apparatus|microtubule organizing center|nuclear speck|plasma membrane	ATP binding|protein serine/threonine kinase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0044)|Epithelial(162;0.0197)|all cancers(182;0.128)														---	---	---	---
SLC12A4	6560	broad.mit.edu	37	16	67986246	67986246	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67986246A>G	uc002euz.2	-	7	899	c.758T>C	c.(757-759)GTG>GCG	p.V253A	SLC12A4_uc010ceu.2_Missense_Mutation_p.V247A|SLC12A4_uc010vkh.1_Missense_Mutation_p.V222A|SLC12A4_uc010vki.1_Missense_Mutation_p.V253A|SLC12A4_uc010vkj.1_Missense_Mutation_p.V255A|SLC12A4_uc002eva.2_Missense_Mutation_p.V253A|SLC12A4_uc002evb.2_RNA|SLC12A4_uc010cew.1_3'UTR	NM_005072	NP_005063	Q9UP95	S12A4_HUMAN	solute carrier family 12, member 4 isoform a	253	Helical; (Potential).				cell volume homeostasis|potassium ion transport|sodium ion transport	integral to plasma membrane|membrane fraction	potassium:chloride symporter activity			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)													---	---	---	---
PLA2G15	23659	broad.mit.edu	37	16	68293549	68293549	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68293549C>A	uc002evr.2	+	6	1311	c.1228C>A	c.(1228-1230)CTT>ATT	p.L410I	PLA2G15_uc010vld.1_3'UTR|PLA2G15_uc010vle.1_Missense_Mutation_p.L316I|PLA2G15_uc010vlf.1_Missense_Mutation_p.L210I|PLA2G15_uc002evs.2_Missense_Mutation_p.L231I	NM_012320	NP_036452	Q8NCC3	PAG15_HUMAN	lysophospholipase 3 (lysosomal phospholipase A2)	410					fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding			ovary(1)	1																		---	---	---	---
ZFP90	146198	broad.mit.edu	37	16	68597409	68597409	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68597409C>A	uc010cff.2	+	5	1011	c.719C>A	c.(718-720)CCT>CAT	p.P240H	ZFP90_uc002ewb.2_Missense_Mutation_p.L46I|ZFP90_uc002ewc.2_Missense_Mutation_p.L46I|ZFP90_uc002ewd.2_Missense_Mutation_p.P240H|ZFP90_uc002ewe.2_Missense_Mutation_p.P240H	NM_133458	NP_597715	Q8TF47	ZFP90_HUMAN	zinc finger protein 90	240					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)														---	---	---	---
CLEC18A	348174	broad.mit.edu	37	16	69996892	69996892	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69996892G>A	uc010vlo.1	+	12	1345	c.1225G>A	c.(1225-1227)GTG>ATG	p.V409M	CLEC18C_uc002exy.2_Intron|CLEC18A_uc002exz.2_Missense_Mutation_p.V409M|CLEC18A_uc002eya.2_Missense_Mutation_p.V409M	NM_001136214	NP_001129686	A5D8T8	CL18A_HUMAN	secretory protein LOC348174 precursor	409	C-type lectin.					extracellular region	sugar binding				0																		---	---	---	---
DDX19A	55308	broad.mit.edu	37	16	70395364	70395364	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70395364C>A	uc002eyv.2	+	5	408	c.337C>A	c.(337-339)CGA>AGA	p.R113R	DDX19B_uc010vly.1_Intron|DDX19A_uc002eys.2_Silent_p.R114R|DDX19A_uc010cfq.1_5'UTR|DDX19A_uc010cfr.2_5'UTR|DDX19A_uc010cfs.2_5'UTR|DDX19A_uc010vlz.1_Intron|DDX19A_uc010vma.1_Silent_p.R23R	NM_018332	NP_060802	Q9NUU7	DD19A_HUMAN	DDX19-like protein	113	Q motif.				mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)																---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	70843797	70843797	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70843797C>T	uc002ezr.2	-	85	14897	c.14769G>A	c.(14767-14769)ACG>ACA	p.T4923T	HYDIN_uc010cfy.2_RNA	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	4924										ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
TAT	6898	broad.mit.edu	37	16	71610203	71610203	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71610203G>T	uc002fap.2	-	2	215	c.116C>A	c.(115-117)GCC>GAC	p.A39D	TAT_uc002faq.2_Missense_Mutation_p.A39D|TAT_uc002far.2_Missense_Mutation_p.A39D	NM_000353	NP_000344	P17735	ATTY_HUMAN	tyrosine aminotransferase	39					2-oxoglutarate metabolic process|glutamate metabolic process|L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	1-aminocyclopropane-1-carboxylate synthase activity|L-tyrosine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(2)	2		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Glutamic Acid(DB00142)|L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Pyridoxal Phosphate(DB00114)													---	---	---	---
ZNF821	55565	broad.mit.edu	37	16	71894307	71894307	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71894307G>A	uc010vmj.1	-	7	1229	c.853C>T	c.(853-855)CGG>TGG	p.R285W	ATXN1L_uc010vmi.1_Intron|ZNF821_uc002fbe.2_Missense_Mutation_p.R135W|ZNF821_uc002fbf.2_Missense_Mutation_p.R243W|ZNF821_uc002fbg.3_Missense_Mutation_p.R135W|ZNF821_uc002fbh.3_Missense_Mutation_p.R243W|ZNF821_uc002fbi.3_Missense_Mutation_p.R82W	NM_017530	NP_060000	O75541	ZN821_HUMAN	zinc finger protein 821	285	Potential.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
MLKL	197259	broad.mit.edu	37	16	74729294	74729294	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74729294C>T	uc002fdb.2	-	2	803	c.362G>A	c.(361-363)CGC>CAC	p.R121H	MLKL_uc002fdc.2_Missense_Mutation_p.R121H	NM_152649	NP_689862	Q8NB16	MLKL_HUMAN	mixed lineage kinase domain-like isoform 1	121							ATP binding|protein binding|protein kinase activity			stomach(2)	2																		---	---	---	---
WDR59	79726	broad.mit.edu	37	16	74908279	74908279	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74908279T>C	uc002fdh.1	-	26	2855	c.2753A>G	c.(2752-2754)AAA>AGA	p.K918R	WDR59_uc002fdf.1_Missense_Mutation_p.K363R|WDR59_uc002fdg.1_Missense_Mutation_p.K510R	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	918										ovary(1)|breast(1)	2																		---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77328919	77328919	+	Silent	SNP	T	G	G	rs140716153		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77328919T>G	uc002ffc.3	-	19	3326	c.2907A>C	c.(2905-2907)GCA>GCC	p.A969A	ADAMTS18_uc010chc.1_Silent_p.A557A	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	969	TSP type-1 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18																		---	---	---	---
GAN	8139	broad.mit.edu	37	16	81391541	81391541	+	Intron	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81391541C>T	uc002fgo.2	+							NM_022041	NP_071324			gigaxonin						cell death	cytoplasm|neurofilament	protein binding			ovary(2)	2		Colorectal(91;0.153)																---	---	---	---
KIAA0182	23199	broad.mit.edu	37	16	85688453	85688453	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85688453A>G	uc002fix.2	+	5	727	c.653A>G	c.(652-654)TAC>TGC	p.Y218C	KIAA0182_uc002fiw.2_Missense_Mutation_p.Y114C|KIAA0182_uc002fiy.2_Missense_Mutation_p.Y145C	NM_014615	NP_055430	Q14687	GSE1_HUMAN	genetic suppressor element 1 isoform 1	218							protein binding			large_intestine(3)|ovary(1)|skin(1)	5																		---	---	---	---
FBXO31	79791	broad.mit.edu	37	16	87367837	87367837	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87367837C>T	uc002fjw.2	-	8	1096	c.1052G>A	c.(1051-1053)CGG>CAG	p.R351Q	FBXO31_uc010vot.1_Missense_Mutation_p.R179Q|FBXO31_uc002fjv.2_Missense_Mutation_p.R243Q	NM_024735	NP_079011	Q5XUX0	FBX31_HUMAN	F-box protein 31	351					cell cycle|cyclin catabolic process|mitotic cell cycle G1/S transition DNA damage checkpoint|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	SCF ubiquitin ligase complex	cyclin binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0272)														---	---	---	---
CTU2	348180	broad.mit.edu	37	16	88781126	88781126	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88781126G>A	uc002flm.2	+	12	1381	c.1333G>A	c.(1333-1335)GGC>AGC	p.G445S	CTU2_uc002fln.2_Missense_Mutation_p.G445S|CTU2_uc010chz.2_Missense_Mutation_p.G516S|CTU2_uc010cia.2_Missense_Mutation_p.G358S	NM_001012759	NP_001012777	Q2VPK5	CTU2_HUMAN	cytoplasmic tRNA 2-thiolation protein 2 isoform	445					tRNA thio-modification|tRNA wobble uridine modification	cytoplasm|protein complex|soluble fraction	protein binding			skin(1)	1																		---	---	---	---
WDR81	124997	broad.mit.edu	37	17	1634162	1634162	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1634162A>G	uc002fti.2	+	3	469	c.208A>G	c.(208-210)AGC>GGC	p.S70G	WDR81_uc002fth.2_Missense_Mutation_p.S246G|WDR81_uc010vqp.1_Missense_Mutation_p.S94G|WDR81_uc002ftj.2_Missense_Mutation_p.S1297G|WDR81_uc010vqq.1_5'UTR	NM_001163811	NP_001157283	Q562E7	WDR81_HUMAN	WD repeat domain 81 isoform 4	70										skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)														---	---	---	---
VMO1	284013	broad.mit.edu	37	17	4689224	4689224	+	Intron	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4689224C>T	uc002fyx.2	-						VMO1_uc010vsh.1_Intron|VMO1_uc010vsi.1_Missense_Mutation_p.A107T|VMO1_uc002fyy.2_Intron	NM_182566	NP_872372			vitelline membrane outer layer 1 isoform 1						vitelline membrane formation	extracellular region				ovary(1)	1																		---	---	---	---
ENO3	2027	broad.mit.edu	37	17	4858519	4858519	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4858519C>A	uc002gab.3	+	7	688	c.594C>A	c.(592-594)GCC>GCA	p.A198A	ENO3_uc010vsr.1_Silent_p.A105A|ENO3_uc002gac.3_Silent_p.A198A|ENO3_uc010vss.1_Silent_p.A155A|ENO3_uc010vst.1_Silent_p.A34A	NM_053013	NP_443739	P13929	ENOB_HUMAN	enolase 3	198					gluconeogenesis|glycolysis	phosphopyruvate hydratase complex	magnesium ion binding|phosphopyruvate hydratase activity			ovary(1)	1																		---	---	---	---
SPAG7	9552	broad.mit.edu	37	17	4864074	4864074	+	Intron	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4864074T>G	uc002gae.2	-						SPAG7_uc002gad.2_Intron|SPAG7_uc002gaf.2_Intron	NM_004890	NP_004881			sperm associated antigen 7							nucleus	nucleic acid binding|protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
FAM64A	54478	broad.mit.edu	37	17	6348605	6348605	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6348605G>A	uc002gcw.1	+	2	224	c.175G>A	c.(175-177)GTC>ATC	p.V59I	FAM64A_uc002gct.1_Missense_Mutation_p.V59I|FAM64A_uc002gcu.1_Missense_Mutation_p.V59I|FAM64A_uc002gcv.1_Missense_Mutation_p.V59I|FAM64A_uc002gcx.1_Missense_Mutation_p.V59I|FAM64A_uc002gcy.1_RNA|FAM64A_uc002gcz.1_RNA|FAM64A_uc002gda.1_Missense_Mutation_p.V59I|FAM64A_uc002gdb.1_Missense_Mutation_p.V59I	NM_019013	NP_061886	Q9BSJ6	FA64A_HUMAN	family with sequence similarity 64, member A	59						nucleolus	protein binding				0				COAD - Colon adenocarcinoma(228;0.141)														---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8383818	8383818	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8383818G>A	uc002gll.2	-	37	5293	c.5197C>T	c.(5197-5199)CGT>TGT	p.R1733C	MYH10_uc002glm.2_Missense_Mutation_p.R1764C|MYH10_uc010cnx.2_Missense_Mutation_p.R1742C	NM_005964	NP_005955	P35580	MYH10_HUMAN	myosin, heavy polypeptide 10, non-muscle	1733	Potential.				actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
PIK3R6	146850	broad.mit.edu	37	17	8707380	8707380	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8707380C>T	uc002glq.1	-	20	2327	c.2087G>A	c.(2086-2088)CGC>CAC	p.R696H	PIK3R6_uc002glr.1_RNA|PIK3R6_uc002gls.1_RNA	NM_001010855	NP_001010855	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6	696					platelet activation	cytosol					0																		---	---	---	---
FLCN	201163	broad.mit.edu	37	17	17131329	17131329	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17131329C>A	uc002gra.3	-	4	627	c.123G>T	c.(121-123)CAG>CAT	p.Q41H	PLD6_uc010cpn.2_RNA|FLCN_uc002grb.3_Missense_Mutation_p.Q41H|FLCN_uc002grc.2_Missense_Mutation_p.Q41H	NM_144997	NP_659434	Q8NFG4	FLCN_HUMAN	folliculin isoform 1	41					regulation of protein phosphorylation	cytoplasm|nucleus|plasma membrane	protein binding			thyroid(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)	3														Birt-Hogg-Dub__syndrome|Familial_Non-VHL_Clear_Cell_Renal_Cancer				---	---	---	---
LRRC48	83450	broad.mit.edu	37	17	17898358	17898358	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17898358A>G	uc010vxd.1	+	9	1136	c.757A>G	c.(757-759)ATG>GTG	p.M253V	LRRC48_uc002gsa.2_Missense_Mutation_p.M253V|LRRC48_uc010vxc.1_Missense_Mutation_p.M253V|LRRC48_uc002gsb.2_Missense_Mutation_p.M253V|LRRC48_uc010vxe.1_5'Flank	NM_001130090	NP_001123562	Q9H069	LRC48_HUMAN	leucine rich repeat containing 48 isoform a	253						cytoplasm				pancreas(1)	1	all_neural(463;0.228)																	---	---	---	---
DRG2	1819	broad.mit.edu	37	17	18005286	18005286	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18005286C>T	uc002gsh.1	+	9	836	c.781C>T	c.(781-783)CGA>TGA	p.R261*	DRG2_uc002gsi.1_RNA|DRG2_uc002gsj.1_Nonsense_Mutation_p.R261*	NM_001388	NP_001379	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	261					signal transduction		GTP binding			ovary(1)	1	all_neural(463;0.228)																	---	---	---	---
FBXW10	10517	broad.mit.edu	37	17	18653319	18653319	+	Intron	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18653319C>T	uc002guk.2	+						FBXW10_uc002guj.2_Intron|FBXW10_uc002gul.2_Missense_Mutation_p.P319S|FBXW10_uc010cqh.1_Intron	NM_031456	NP_113644			F-box and WD-40 domain protein 10											ovary(1)	1																		---	---	---	---
USP22	23326	broad.mit.edu	37	17	20907606	20907606	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20907606T>G	uc002gym.3	-	12	1648	c.1444A>C	c.(1444-1446)AGC>CGC	p.S482R	USP22_uc002gyn.3_Missense_Mutation_p.S470R|USP22_uc002gyl.3_Missense_Mutation_p.S377R	NM_015276	NP_056091	Q9UPT9	UBP22_HUMAN	ubiquitin thiolesterase 22	482					cell cycle|embryo development|histone deubiquitination|histone H4 acetylation|histone ubiquitination|positive regulation of mitotic cell cycle|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	SAGA complex	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1																		---	---	---	---
MAP2K3	5606	broad.mit.edu	37	17	21208376	21208376	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21208376A>C	uc002gys.2	+	9	975	c.710A>C	c.(709-711)AAC>ACC	p.N237T	MAP2K3_uc002gyt.2_Missense_Mutation_p.N208T|MAP2K3_uc002gyu.2_Missense_Mutation_p.N208T	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	237	Protein kinase.				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)														---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25909717	25909717	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25909717G>A	uc010crg.2	+	5	600	c.155G>A	c.(154-156)CGG>CAG	p.R52Q	KSR1_uc002gzj.1_Intron	NM_014238	NP_055053	Q8IVT5	KSR1_HUMAN	kinase suppressor of ras	187					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)														---	---	---	---
SLC13A2	9058	broad.mit.edu	37	17	26821457	26821457	+	Missense_Mutation	SNP	C	T	T	rs141214124		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26821457C>T	uc002hbh.2	+	9	1302	c.1235C>T	c.(1234-1236)ACG>ATG	p.T412M	SLC13A2_uc010wam.1_Missense_Mutation_p.T368M|SLC13A2_uc010wan.1_Missense_Mutation_p.T461M|SLC13A2_uc010wao.1_Missense_Mutation_p.T369M|SLC13A2_uc002hbi.2_Missense_Mutation_p.T341M	NM_003984	NP_003975	Q13183	S13A2_HUMAN	solute carrier family 13, member 2 isoform b	412						integral to plasma membrane|membrane fraction	low affinity sodium:dicarboxylate symporter activity				0	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)											OREG0024276	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26970621	26970621	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26970621T>C	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)																	---	---	---	---
TAOK1	57551	broad.mit.edu	37	17	27869581	27869581	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27869581T>C	uc002hdz.1	+	20	2741	c.2547T>C	c.(2545-2547)ATT>ATC	p.I849I	TAOK1_uc010wbe.1_Silent_p.I701I|TAOK1_uc010wbf.1_Silent_p.I849I	NM_020791	NP_065842	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	849	Potential.				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)															---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	31087632	31087632	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31087632C>T	uc002hho.1	-	9	1061	c.1049G>A	c.(1048-1050)CGC>CAC	p.R350H	MYO1D_uc002hhp.1_Missense_Mutation_p.R350H|MYO1D_uc010wcb.1_Missense_Mutation_p.R350H	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID	350	Myosin head-like.					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)															---	---	---	---
TMEM98	26022	broad.mit.edu	37	17	31260227	31260227	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31260227A>G	uc002hhq.2	+	4	625	c.167A>G	c.(166-168)CAG>CGG	p.Q56R	TMEM98_uc002hhr.2_Missense_Mutation_p.Q56R	NM_015544	NP_056359	Q9Y2Y6	TMM98_HUMAN	transmembrane protein 98	56						endoplasmic reticulum|integral to membrane					0		Ovarian(249;0.182)|Breast(31;0.244)	BRCA - Breast invasive adenocarcinoma(9;0.0769)															---	---	---	---
SLFN11	91607	broad.mit.edu	37	17	33679651	33679651	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33679651A>G	uc010ctp.2	-	7	2872	c.2430T>C	c.(2428-2430)GCT>GCC	p.A810A	SLFN11_uc010ctq.2_Silent_p.A810A|SLFN11_uc002hjh.3_Silent_p.A810A|SLFN11_uc002hjg.3_Silent_p.A810A|SLFN11_uc010ctr.2_Silent_p.A810A	NM_001104588	NP_001098058	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	810						nucleus	ATP binding			large_intestine(1)|ovary(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
MYO19	80179	broad.mit.edu	37	17	34862834	34862834	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34862834A>G	uc010wcy.1	-	18	2604	c.1612T>C	c.(1612-1614)TAC>CAC	p.Y538H	MYO19_uc002hmw.2_Intron|MYO19_uc010cuu.2_RNA|MYO19_uc010wcz.1_RNA	NM_001163735	NP_001157207	Q96H55	MYO19_HUMAN	myosin XIX isoform 2	538	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)														---	---	---	---
LHX1	3975	broad.mit.edu	37	17	35298059	35298059	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35298059C>T	uc002hnh.1	+	3	1546	c.550C>T	c.(550-552)CGC>TGC	p.R184C	LHX1_uc010cux.1_Missense_Mutation_p.R92C	NM_005568	NP_005559	P48742	LHX1_HUMAN	LIM homeobox protein 1	184	Homeobox.			R -> G (in Ref. 1; AAA21644).	cerebellar Purkinje cell differentiation|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation|cervix development|comma-shaped body morphogenesis|dorsal/ventral pattern formation|ectoderm formation|embryonic pattern specification|embryonic retina morphogenesis in camera-type eye|embryonic viscerocranium morphogenesis|endoderm formation|forebrain regionalization|head development|motor axon guidance|negative regulation of transcription, DNA-dependent|nephric duct morphogenesis|nephron tubule epithelial cell differentiation|neuron migration|oviduct epithelium development|paramesonephric duct development|positive regulation of anterior head development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of embryonic development|positive regulation of gastrulation|positive regulation of transcription, DNA-dependent|post-embryonic development|primitive streak formation|renal vesicle morphogenesis|retina layer formation|S-shaped body morphogenesis|spinal cord association neuron differentiation|transcription from RNA polymerase II promoter|ureteric bud development|uterine epithelium development|vagina development	nucleus|protein complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(25;0.00607)																---	---	---	---
CWC25	54883	broad.mit.edu	37	17	36958376	36958376	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36958376A>G	uc002hqu.2	-	10	1400	c.1247T>C	c.(1246-1248)GTA>GCA	p.V416A	CWC25_uc010wdv.1_Missense_Mutation_p.V353A|PIP4K2B_uc002hqs.2_5'Flank|PIP4K2B_uc010wdt.1_5'Flank	NM_017748	NP_060218	Q9NXE8	CWC25_HUMAN	coiled-coil domain containing 49	416											0																		---	---	---	---
MED24	9862	broad.mit.edu	37	17	38188288	38188288	+	Intron	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38188288C>A	uc002htt.2	-						MED24_uc010wes.1_Intron|MED24_uc010wet.1_Intron|MED24_uc002hts.2_Intron|MED24_uc002htu.2_Intron|MED24_uc010cwn.2_Intron|MED24_uc010weu.1_Intron|MED24_uc010wev.1_Intron|MED24_uc010wew.1_Intron|MED24_uc010wex.1_Intron	NM_014815	NP_055630			mediator complex subunit 24 isoform 1						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1	Colorectal(19;0.000442)																	---	---	---	---
TNS4	84951	broad.mit.edu	37	17	38638411	38638411	+	Missense_Mutation	SNP	G	T	T	rs112122797		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38638411G>T	uc010cxb.2	-	8	1806	c.1642C>A	c.(1642-1644)CTG>ATG	p.L548M	TNS4_uc002huu.3_5'Flank	NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	tensin 4 precursor	548	Phosphatase tensin-type.|SH2.				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)															---	---	---	---
KRT10	3858	broad.mit.edu	37	17	38978786	38978786	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38978786C>A	uc002hvi.2	-	1	78	c.52G>T	c.(52-54)GGA>TGA	p.G18*	KRT10_uc010cxd.2_5'Flank|TMEM99_uc002hvj.1_Intron	NM_000421	NP_000412	P13645	K1C10_HUMAN	keratin 10	18	Head.|Gly-rich.				epidermis development		protein binding|structural constituent of epidermis				0		Breast(137;0.000301)																---	---	---	---
KRT39	390792	broad.mit.edu	37	17	39123064	39123064	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39123064T>C	uc002hvo.1	-	1	81	c.45A>G	c.(43-45)CCA>CCG	p.P15P	KRT39_uc010wfm.1_5'UTR	NM_213656	NP_998821	Q6A163	K1C39_HUMAN	type I hair keratin KA35	15	Head.					intermediate filament	structural molecule activity				0		Breast(137;0.00043)|Ovarian(249;0.15)																---	---	---	---
DNAJC7	7266	broad.mit.edu	37	17	40152526	40152526	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40152526G>A	uc002hyo.2	-	2	377	c.140C>T	c.(139-141)GCT>GTT	p.A47V	DNAJC7_uc010wgb.1_5'UTR|DNAJC7_uc010wgc.1_5'UTR|DNAJC7_uc002hyp.2_Intron|DNAJC7_uc010cxw.2_RNA	NM_003315	NP_003306	Q99615	DNJC7_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 7	47	TPR 1.				chaperone cofactor-dependent protein refolding	cytoplasm|cytoskeleton|nucleus	heat shock protein binding|unfolded protein binding			ovary(1)	1		all_cancers(22;0.00273)|Breast(137;0.00104)|all_epithelial(22;0.0305)																---	---	---	---
STAT5B	6777	broad.mit.edu	37	17	40375395	40375395	+	Intron	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40375395C>A	uc002hzh.2	-						STAT5B_uc002hzi.3_Intron	NM_012448	NP_036580			signal transducer and activator of transcription						2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|JAK-STAT cascade involved in growth hormone signaling pathway|oxaloacetate metabolic process|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|glucocorticoid receptor binding|sequence-specific DNA binding transcription factor activity			ovary(3)|lung(2)|skin(1)	6		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)													---	---	---	---
NBR1	4077	broad.mit.edu	37	17	41348612	41348612	+	Intron	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41348612A>G	uc010czd.2	+						NBR1_uc010diz.2_Intron|NBR1_uc010whu.1_Intron|NBR1_uc010whv.1_Intron|NBR1_uc010whw.1_Intron	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)														---	---	---	---
MEOX1	4222	broad.mit.edu	37	17	41719304	41719304	+	Missense_Mutation	SNP	A	C	C	rs78282512		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41719304A>C	uc002idz.2	-	3	768	c.739T>G	c.(739-741)TCC>GCC	p.S247A	MEOX1_uc002iea.2_3'UTR|MEOX1_uc002ieb.2_Missense_Mutation_p.S132A	NM_004527	NP_004518	P50221	MEOX1_HUMAN	mesenchyme homeobox 1 isoform 1	247						nucleus	sequence-specific DNA binding				0		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)														---	---	---	---
SOST	50964	broad.mit.edu	37	17	41835990	41835990	+	Silent	SNP	G	A	A	rs149814744		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41835990G>A	uc002iec.1	-	1	167	c.120C>T	c.(118-120)CTC>CTT	p.L40L		NM_025237	NP_079513	Q9BQB4	SOST_HUMAN	sclerostin precursor	40					negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of ossification|negative regulation of protein complex assembly|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway		heparin binding|protein binding				0		Breast(137;0.00725)		UCEC - Uterine corpus endometrioid carcinoma (308;0.177)|BRCA - Breast invasive adenocarcinoma(366;0.0741)														---	---	---	---
SLC4A1	6521	broad.mit.edu	37	17	42328633	42328633	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42328633A>G	uc002igf.3	-	19	2698	c.2549T>C	c.(2548-2550)GTG>GCG	p.V850A		NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member	850	Helical; (Potential).|Membrane (anion exchange).		Missing (in AR-dRTA).		bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)														---	---	---	---
GPATCH8	23131	broad.mit.edu	37	17	42483368	42483368	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42483368A>G	uc002igw.1	-	7	608	c.544T>C	c.(544-546)TCC>CCC	p.S182P	GPATCH8_uc002igv.1_Missense_Mutation_p.S104P|GPATCH8_uc010wiz.1_Missense_Mutation_p.S104P	NM_001002909	NP_001002909	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	182						intracellular	nucleic acid binding|zinc ion binding			ovary(2)|kidney(1)|skin(1)	4		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)														---	---	---	---
PLEKHM1	9842	broad.mit.edu	37	17	43555345	43555345	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43555345C>A	uc002ija.2	-	3	387	c.217G>T	c.(217-219)GGA>TGA	p.G73*	PLEKHM1_uc010wjm.1_Intron|PLEKHM1_uc002ijb.2_Translation_Start_Site|PLEKHM1_uc010wjn.1_Intron|hsa-mir-4315-1|MI0015844_5'Flank|PLEKHM1_uc002ijd.1_Nonsense_Mutation_p.G73*	NM_014798	NP_055613	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M	73	RUN.				intracellular signal transduction	cytoplasm	metal ion binding				0	Renal(3;0.0405)																	---	---	---	---
SGCA	6442	broad.mit.edu	37	17	48245314	48245314	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48245314G>A	uc002iqi.2	+	4	355	c.319G>A	c.(319-321)GCC>ACC	p.A107T	SGCA_uc010wmh.1_Missense_Mutation_p.A5T|SGCA_uc002iqj.2_Missense_Mutation_p.A107T|SGCA_uc010wmi.1_RNA	NM_000023	NP_000014	Q16586	SGCA_HUMAN	sarcoglycan, alpha isoform 1 precursor	107	Extracellular (Potential).				muscle contraction|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(2)	2																		---	---	---	---
LRRC59	55379	broad.mit.edu	37	17	48462519	48462519	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48462519C>T	uc002iqt.2	-	6	790	c.636G>A	c.(634-636)GAG>GAA	p.E212E		NM_018509	NP_060979	Q96AG4	LRC59_HUMAN	leucine rich repeat containing 59	212	Potential.|Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial nucleoid	protein binding			central_nervous_system(1)	1	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)															---	---	---	---
SPATA20	64847	broad.mit.edu	37	17	48631632	48631632	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48631632A>G	uc002irf.2	+	14	2071	c.1930A>G	c.(1930-1932)AGC>GGC	p.S644G	SPATA20_uc002irc.2_Missense_Mutation_p.S311G|SPATA20_uc002ire.2_Missense_Mutation_p.S600G|SPATA20_uc002ird.2_Missense_Mutation_p.S660G|SPATA20_uc002irg.2_RNA	NM_022827	NP_073738	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	644					cell differentiation|mannose metabolic process|multicellular organismal development|spermatogenesis	extracellular region	mannose-6-phosphate isomerase activity|protein binding				0	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)															---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48678110	48678110	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48678110G>A	uc002irk.1	+	18	4086	c.3714G>A	c.(3712-3714)GCG>GCA	p.A1238A	CACNA1G_uc002iri.1_Silent_p.A1238A|CACNA1G_uc002irj.1_Silent_p.A1215A|CACNA1G_uc002irl.1_Silent_p.A1215A|CACNA1G_uc002irm.1_Silent_p.A1215A|CACNA1G_uc002irn.1_Silent_p.A1215A|CACNA1G_uc002iro.1_Silent_p.A1215A|CACNA1G_uc002irp.1_Silent_p.A1238A|CACNA1G_uc002irq.1_Silent_p.A1215A|CACNA1G_uc002irr.1_Silent_p.A1238A|CACNA1G_uc002irs.1_Silent_p.A1238A|CACNA1G_uc002irt.1_Silent_p.A1238A|CACNA1G_uc002irv.1_Silent_p.A1238A|CACNA1G_uc002irw.1_Silent_p.A1215A|CACNA1G_uc002iru.1_Silent_p.A1215A|CACNA1G_uc002irx.1_Silent_p.A1151A|CACNA1G_uc002iry.1_Silent_p.A1151A|CACNA1G_uc002irz.1_Silent_p.A1151A|CACNA1G_uc002isa.1_Silent_p.A1151A|CACNA1G_uc002isb.1_Silent_p.A1151A|CACNA1G_uc002isc.1_Silent_p.A1151A|CACNA1G_uc002isd.1_Silent_p.A1151A|CACNA1G_uc002ise.1_Silent_p.A1151A|CACNA1G_uc002isf.1_Silent_p.A1151A|CACNA1G_uc002isg.1_Silent_p.A1151A|CACNA1G_uc002ish.1_Silent_p.A1151A|CACNA1G_uc002isi.1_Silent_p.A1128A|CACNA1G_uc002isj.2_Translation_Start_Site	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	1238	Cytoplasmic (Potential).				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
AKAP1	8165	broad.mit.edu	37	17	55189988	55189988	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55189988G>A	uc002iux.2	+						AKAP1_uc010wnl.1_Intron|AKAP1_uc002iuy.2_Intron|AKAP1_uc010dcm.2_Intron	NM_003488	NP_003479			A-kinase anchor protein 1 precursor						blood coagulation	cytosol|integral to membrane|mitochondrial outer membrane	protein binding|RNA binding			ovary(1)	1	Breast(9;5.46e-08)																	---	---	---	---
MPO	4353	broad.mit.edu	37	17	56355248	56355248	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56355248G>T	uc002ivu.1	-	7	1321	c.1144C>A	c.(1144-1146)CTG>ATG	p.L382M		NM_000250	NP_000241	P05164	PERM_HUMAN	myeloperoxidase	382					anti-apoptosis|hydrogen peroxide catabolic process|low-density lipoprotein particle remodeling	extracellular space|lysosome|nucleus|stored secretory granule	chromatin binding|heme binding|heparin binding|peroxidase activity			ovary(2)|large_intestine(1)|pancreas(1)	4					Cefdinir(DB00535)													---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61889307	61889307	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61889307A>G	uc002jbu.2	+	15	1671	c.1414A>G	c.(1414-1416)ACA>GCA	p.T472A	DDX42_uc002jbv.2_Missense_Mutation_p.T472A|DDX42_uc002jbw.1_Missense_Mutation_p.T208A|DDX42_uc002jbx.2_Missense_Mutation_p.T208A|DDX42_uc002jby.2_Missense_Mutation_p.T18A	NM_007372	NP_031398	Q86XP3	DDX42_HUMAN	DEAD box polypeptide 42 protein	472					protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5																		---	---	---	---
BPTF	2186	broad.mit.edu	37	17	65944394	65944394	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65944394T>C	uc002jgf.2	+	23	7959	c.7898T>C	c.(7897-7899)CTG>CCG	p.L2633P	BPTF_uc002jge.2_Missense_Mutation_p.L2616P|BPTF_uc002jgg.2_Missense_Mutation_p.L290P|BPTF_uc002jgh.2_Missense_Mutation_p.L92P	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2759					brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
OTOP3	347741	broad.mit.edu	37	17	72943232	72943232	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72943232G>T	uc010wrr.1	+	6	1282	c.1282G>T	c.(1282-1284)GGC>TGC	p.G428C	OTOP3_uc010wrq.1_Missense_Mutation_p.G410C	NM_178233	NP_839947	Q7RTS5	OTOP3_HUMAN	otopetrin 3	428	Helical; (Potential).					integral to membrane|intracellular	zinc ion binding			ovary(1)	1	all_lung(278;0.151)|Lung NSC(278;0.185)																	---	---	---	---
ITGB4	3691	broad.mit.edu	37	17	73748363	73748363	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73748363G>A	uc002jpg.2	+	31	4089	c.3902G>A	c.(3901-3903)CGC>CAC	p.R1301H	ITGB4_uc002jph.2_Missense_Mutation_p.R1301H|ITGB4_uc002jpi.3_Missense_Mutation_p.R1301H|ITGB4_uc002jpj.2_Missense_Mutation_p.R1301H|GALK1_uc010wsi.1_Intron	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor	1301	Fibronectin type-III 2.|Cytoplasmic (Potential).				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
ITGB4	3691	broad.mit.edu	37	17	73750720	73750720	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73750720T>C	uc002jpg.2	+	34	4569	c.4382T>C	c.(4381-4383)ATG>ACG	p.M1461T	ITGB4_uc002jph.2_Missense_Mutation_p.M1391T|ITGB4_uc002jpi.3_Missense_Mutation_p.M1391T|ITGB4_uc002jpj.2_Missense_Mutation_p.M1391T|GALK1_uc010wsi.1_Intron	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor	1461	Cytoplasmic (Potential).				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
TRIM65	201292	broad.mit.edu	37	17	73888350	73888350	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73888350G>A	uc002jpx.2	-	3	778	c.742C>T	c.(742-744)CAG>TAG	p.Q248*		NM_173547	NP_775818	Q6PJ69	TRI65_HUMAN	tripartite motif-containing 65	248						intracellular	zinc ion binding				0			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
EXOC7	23265	broad.mit.edu	37	17	74097459	74097459	+	Splice_Site	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74097459T>C	uc002jqs.2	-	4	407	c.312_splice	c.e4-1	p.G104_splice	EXOC7_uc010dgv.1_Splice_Site_p.G51_splice|EXOC7_uc002jqq.2_Splice_Site_p.G104_splice|EXOC7_uc010wsw.1_Splice_Site_p.G104_splice|EXOC7_uc010wsx.1_Splice_Site_p.G104_splice|EXOC7_uc002jqr.2_Splice_Site_p.G104_splice|EXOC7_uc010wsv.1_Splice_Site_p.G63_splice|EXOC7_uc002jqu.2_Splice_Site_p.G104_splice|EXOC7_uc002jqv.2_Intron	NM_001145297	NP_001138769			exocyst complex component 7 isoform 4						exocytosis|protein transport	centriolar satellite|cytosol|exocyst|plasma membrane	protein binding				0			LUSC - Lung squamous cell carcinoma(166;0.187)															---	---	---	---
PGS1	9489	broad.mit.edu	37	17	76395508	76395508	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76395508G>A	uc002jvm.2	+	5	603	c.591G>A	c.(589-591)ACG>ACA	p.T197T	PGS1_uc010wtt.1_RNA|PGS1_uc010dho.2_RNA|PGS1_uc002jvn.2_5'UTR|PGS1_uc002jvo.2_RNA|PGS1_uc002jvp.1_5'Flank	NM_024419	NP_077733	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1	197					phospholipid biosynthetic process	endoplasmic reticulum|mitochondrion	ATP binding|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity				0			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)															---	---	---	---
TBC1D16	125058	broad.mit.edu	37	17	77922698	77922698	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77922698T>C	uc002jxj.2	-	8	1630	c.1514A>G	c.(1513-1515)GAA>GGA	p.E505G	TBC1D16_uc002jxh.2_Missense_Mutation_p.E143G|TBC1D16_uc002jxi.2_Missense_Mutation_p.E130G|TBC1D16_uc002jxk.1_Missense_Mutation_p.E143G	NM_019020	NP_061893	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	505	Rab-GAP TBC.					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)															---	---	---	---
RNF213	57674	broad.mit.edu	37	17	78321528	78321528	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78321528C>T	uc002jyh.1	+	4	3835	c.3612C>T	c.(3610-3612)CTC>CTT	p.L1204L		NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)															---	---	---	---
BAHCC1	57597	broad.mit.edu	37	17	79419741	79419741	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79419741G>A	uc002kaf.2	+						BAHCC1_uc002kae.2_Intron|hsa-mir-3186|MI0014229_5'Flank	NM_001080519	NP_001073988			BAH domain and coiled-coil containing 1								DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)															---	---	---	---
FASN	2194	broad.mit.edu	37	17	80039902	80039902	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80039902C>A	uc002kdu.2	-	36	6263	c.6146G>T	c.(6145-6147)CGG>CTG	p.R2049L	FASN_uc002kdv.1_RNA	NM_004104	NP_004095	P49327	FAS_HUMAN	fatty acid synthase	2049	Beta-ketoacyl reductase (By similarity).				energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	cytosol|Golgi apparatus|melanosome|plasma membrane	3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339)													---	---	---	---
C17orf101	79701	broad.mit.edu	37	17	80369341	80369341	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80369341G>A	uc002keu.1	-	3	471	c.370C>T	c.(370-372)CGG>TGG	p.R124W	C17orf101_uc002ket.1_Missense_Mutation_p.R124W|C17orf101_uc010dip.1_RNA	NM_024648	NP_078924	Q6PK18	CQ101_HUMAN	hypothetical protein LOC79701 isoform 1	124	Lumenal (Potential).					integral to membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(1)	1																		---	---	---	---
HEXDC	284004	broad.mit.edu	37	17	80398968	80398968	+	Intron	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80398968C>A	uc002kew.2	+						HEXDC_uc002kev.3_Missense_Mutation_p.P360T|HEXDC_uc010diq.2_Intron|HEXDC_uc010wvm.1_Intron					SubName: Full=Hexosaminidase (Glycosyl hydrolase family 20, catalytic domain) containing, isoform CRA_c; SubName: Full=Hexosaminidase D;						carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)|skin(1)	2	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)															---	---	---	---
THOC1	9984	broad.mit.edu	37	18	216495	216495	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:216495C>A	uc002kkj.3	-	19	1633	c.1593G>T	c.(1591-1593)AAG>AAT	p.K531N	THOC1_uc002kkk.3_RNA|THOC1_uc002kkh.3_Missense_Mutation_p.K155N	NM_005131	NP_005122	Q96FV9	THOC1_HUMAN	THO complex 1	531					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)																---	---	---	---
LPIN2	9663	broad.mit.edu	37	18	2925364	2925364	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2925364G>A	uc002klo.2	-	14	2035	c.1796C>T	c.(1795-1797)CCG>CTG	p.P599L		NM_014646	NP_055461	Q92539	LPIN2_HUMAN	lipin 2	599					fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity			ovary(1)|skin(1)	2				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)														---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8076526	8076526	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8076526A>C	uc002knn.3	+	9	2018	c.1515A>C	c.(1513-1515)GAA>GAC	p.E505D	PTPRM_uc010dkv.2_Missense_Mutation_p.E505D|PTPRM_uc010wzl.1_Missense_Mutation_p.E292D	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	505	Fibronectin type-III 3.|Extracellular (Potential).				homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
RAB12	201475	broad.mit.edu	37	18	8633208	8633208	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8633208A>G	uc002knp.2	+	3	592	c.309A>G	c.(307-309)AGA>AGG	p.R103R		NM_001025300	NP_001020471	Q6IQ22	RAB12_HUMAN	RAB12, member RAS oncogene family	103					protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding				0																		---	---	---	---
SEH1L	81929	broad.mit.edu	37	18	12955468	12955468	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12955468A>G	uc002krr.2	+	3	307	c.169A>G	c.(169-171)AGT>GGT	p.S57G	SEH1L_uc002krq.2_Missense_Mutation_p.S57G	NM_031216	NP_112493	Q96EE3	SEH1_HUMAN	sec13-like protein isoform 2	57	WD 2.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|carbohydrate metabolic process|cell division|glucose transport|mitotic metaphase plate congression|mitotic prometaphase|mRNA transport|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex					0																		---	---	---	---
C18orf1	753	broad.mit.edu	37	18	13621221	13621221	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13621221T>C	uc002ksa.2	+	5	955	c.287T>C	c.(286-288)TTC>TCC	p.F96S	C18orf1_uc002ksb.2_Missense_Mutation_p.F96S|C18orf1_uc002kse.2_Missense_Mutation_p.F59S|C18orf1_uc002ksf.2_Missense_Mutation_p.F59S|C18orf1_uc002ksg.1_Missense_Mutation_p.F19S|C18orf1_uc002ksh.1_Missense_Mutation_p.F38S|C18orf1_uc002ksi.1_Missense_Mutation_p.F38S	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1	96	Cytoplasmic (Potential).					integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)														---	---	---	---
RBBP8	5932	broad.mit.edu	37	18	20570945	20570945	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20570945T>G	uc002ktw.2	+	10	1184	c.853T>G	c.(853-855)TGT>GGT	p.C285G	RBBP8_uc002kty.2_Missense_Mutation_p.C285G|RBBP8_uc002ktz.2_Missense_Mutation_p.C285G|RBBP8_uc002kua.2_Missense_Mutation_p.C285G|RBBP8_uc002ktx.1_Missense_Mutation_p.C285G	NM_002894	NP_002885	Q99708	COM1_HUMAN	retinoblastoma binding protein 8 isoform a	285					cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter	nucleus	damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)|lung(1)|skin(1)	3	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
CABLES1	91768	broad.mit.edu	37	18	20832918	20832918	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20832918T>C	uc002kuc.2	+						C18orf45_uc010xaq.1_Intron|CABLES1_uc002kub.2_Intron|CABLES1_uc002kud.2_Intron	NM_001100619	NP_001094089			Cdk5 and Abl enzyme substrate 1 isoform 2						blood coagulation|cell cycle|cell division|regulation of cell cycle|regulation of cell division	cytosol|nucleus	cyclin-dependent protein kinase regulator activity|protein binding			breast(1)	1	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
CHST9	83539	broad.mit.edu	37	18	24496988	24496988	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24496988G>A	uc002kwd.2	-	5	765	c.567C>T	c.(565-567)TAC>TAT	p.Y189Y	C18orf16_uc002kwb.2_Intron|C18orf16_uc010xbm.1_Intron|CHST9_uc002kwc.2_Silent_p.Y104Y|CHST9_uc002kwe.2_Silent_p.Y189Y	NM_031422	NP_113610	Q7L1S5	CHST9_HUMAN	GalNAc-4-sulfotransferase 2	189	Lumenal (Potential).				carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)																	---	---	---	---
DSC2	1824	broad.mit.edu	37	18	28654723	28654723	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28654723C>T	uc002kwl.3	-	12	2268	c.1814G>A	c.(1813-1815)GGC>GAC	p.G605D	DSC2_uc002kwk.3_Missense_Mutation_p.G605D	NM_024422	NP_077740	Q02487	DSC2_HUMAN	desmocollin 2 isoform Dsc2a preproprotein	605	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(10;0.0241)															---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29410772	29410772	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29410772A>G	uc002kxc.3	-	29	4618	c.4254T>C	c.(4252-4254)TTT>TTC	p.F1418F	KIAA1012_uc002kxb.3_Silent_p.F1364F|KIAA1012_uc002kxd.3_RNA	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878	1418					ER to Golgi vesicle-mediated transport	cis-Golgi network					0																		---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31319536	31319536	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31319536C>A	uc010dmg.1	+	11	2223	c.2168C>A	c.(2167-2169)CCT>CAT	p.P723H	ASXL3_uc002kxq.2_Missense_Mutation_p.P430H	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	723	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31325381	31325381	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31325381G>A	uc010dmg.1	+	12	5624	c.5569G>A	c.(5569-5571)GTG>ATG	p.V1857M	ASXL3_uc002kxq.2_Missense_Mutation_p.V1564M	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1857					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
MOCOS	55034	broad.mit.edu	37	18	33800060	33800060	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33800060C>T	uc002kzq.3	+	9	1863	c.1840C>T	c.(1840-1842)CGG>TGG	p.R614W		NM_017947	NP_060417	Q96EN8	MOCOS_HUMAN	molybdenum cofactor sulfurase	614					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)													---	---	---	---
PSTPIP2	9050	broad.mit.edu	37	18	43585486	43585486	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43585486T>C	uc002lbp.3	-	6	462	c.366A>G	c.(364-366)ATA>ATG	p.I122M	PSTPIP2_uc002lbq.3_Missense_Mutation_p.I122M	NM_024430	NP_077748	Q9H939	PPIP2_HUMAN	proline-serine-threonine phosphatase interacting	122	Potential.					membrane				ovary(1)	1																		---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46385794	46385794	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46385794T>G	uc002ldc.2	+	12	1946	c.1661T>G	c.(1660-1662)ATG>AGG	p.M554R	KIAA0427_uc002ldd.2_Missense_Mutation_p.M556R|KIAA0427_uc002lde.3_Missense_Mutation_p.M183R	NM_014772	NP_055587	O43310	CTIF_HUMAN	hypothetical protein LOC9811 isoform 1	554	MIF4G.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48190611	48190611	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48190611C>T	uc002lev.2	+	2	1283	c.283C>T	c.(283-285)CTG>TTG	p.L95L	MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Silent_p.L95L	NM_002747	NP_002738	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	95	Protein kinase.				cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)														---	---	---	---
ALPK2	115701	broad.mit.edu	37	18	56247010	56247010	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56247010G>A	uc002lhj.3	-	4	1212	c.998C>T	c.(997-999)TCT>TTT	p.S333F		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	333							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14																OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CCBE1	147372	broad.mit.edu	37	18	57103367	57103367	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57103367G>A	uc002lib.2	-	11	1064	c.994C>T	c.(994-996)CCT>TCT	p.P332S	CCBE1_uc010dpq.2_Missense_Mutation_p.P61S|CCBE1_uc002lia.2_Missense_Mutation_p.P185S	NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	332	Collagen-like 2.				lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)																---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59157845	59157845	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59157845T>C	uc010dps.1	+	1	71	c.59T>C	c.(58-60)TTG>TCG	p.L20S	CDH20_uc002lif.2_Missense_Mutation_p.L14S	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	20					homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)																---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59221588	59221588	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59221588C>T	uc010dps.1	+	11	2078	c.2066C>T	c.(2065-2067)GCG>GTG	p.A689V	CDH20_uc002lif.2_Missense_Mutation_p.A683V	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	689	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)																---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59221697	59221697	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59221697C>T	uc010dps.1	+	11	2187	c.2175C>T	c.(2173-2175)TAC>TAT	p.Y725Y	CDH20_uc002lif.2_Silent_p.Y719Y	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	725	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)																---	---	---	---
ZADH2	284273	broad.mit.edu	37	18	72913987	72913987	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72913987C>A	uc002llx.2	-	2	786	c.518G>T	c.(517-519)GGG>GTG	p.G173V	ZADH2_uc010dqv.2_Missense_Mutation_p.G50V	NM_175907	NP_787103	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain	173						peroxisome	oxidoreductase activity|zinc ion binding				0		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)														---	---	---	---
TSHZ1	10194	broad.mit.edu	37	18	73000192	73000192	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73000192C>A	uc002lly.2	+	2	3258	c.2695C>A	c.(2695-2697)CTG>ATG	p.L899M		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	944	Homeobox; atypical.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)														---	---	---	---
CTDP1	9150	broad.mit.edu	37	18	77477859	77477859	+	Missense_Mutation	SNP	G	A	A	rs142285723	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77477859G>A	uc002lnh.1	+	10	2407	c.2260G>A	c.(2260-2262)GCC>ACC	p.A754T	CTDP1_uc002lni.1_Missense_Mutation_p.A754T|CTDP1_uc010drd.1_Missense_Mutation_p.A754T	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	754					positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)														---	---	---	---
SBNO2	22904	broad.mit.edu	37	19	1119609	1119609	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1119609G>A	uc002lrk.3	-	13	1517	c.1279C>T	c.(1279-1281)CCT>TCT	p.P427S	SBNO2_uc002lrj.3_Missense_Mutation_p.P370S|SBNO2_uc010dse.2_Missense_Mutation_p.P420S|SBNO2_uc010xgj.1_Missense_Mutation_p.P370S|SBNO2_uc010dsf.2_Missense_Mutation_p.P370S	NM_014963	NP_055778	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 isoform 1	427					macrophage activation involved in immune response|negative regulation of transcription, DNA-dependent|regulation of inflammatory response|transcription, DNA-dependent						0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
JSRP1	126306	broad.mit.edu	37	19	2255302	2255302	+	Silent	SNP	T	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2255302T>A	uc002lvi.1	-	1	47	c.12A>T	c.(10-12)ACA>ACT	p.T4T	JSRP1_uc002lvj.1_Silent_p.T4T	NM_144616	NP_653217	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	4	Mediates interaction with CACNA1S (By similarity).					sarcoplasmic reticulum membrane				pancreas(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
FZR1	51343	broad.mit.edu	37	19	3527034	3527034	+	Nonsense_Mutation	SNP	C	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3527034C>G	uc010dtk.2	+	5	478	c.444C>G	c.(442-444)TAC>TAG	p.Y148*	FZR1_uc002lxt.2_Nonsense_Mutation_p.Y148*|FZR1_uc002lxv.2_Intron	NM_001136198	NP_001129670	Q9UM11	FZR_HUMAN	Fzr1 protein isoform 1	148					activation of anaphase-promoting complex activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|DNA repair|G2/M transition DNA damage checkpoint|mitosis|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of protein catabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle	cytosol|nucleoplasm	protein binding			lung(1)|kidney(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5286136	5286136	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5286136C>A	uc002mbv.2	-	2	250	c.16G>T	c.(16-18)GGC>TGC	p.G6C	PTPRS_uc002mbu.1_Missense_Mutation_p.G6C|PTPRS_uc010xin.1_Missense_Mutation_p.G6C|PTPRS_uc002mbw.2_Missense_Mutation_p.G6C|PTPRS_uc002mbx.2_Missense_Mutation_p.G6C|PTPRS_uc002mby.2_Missense_Mutation_p.G6C|PTPRS_uc002mbz.1_Missense_Mutation_p.G6C	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	6					cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)														---	---	---	---
GTF2F1	2962	broad.mit.edu	37	19	6381412	6381412	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6381412C>T	uc002meq.2	-	9	1261	c.976G>A	c.(976-978)GAG>AAG	p.E326K	GTF2F1_uc010xjb.1_Missense_Mutation_p.E147K|GTF2F1_uc010xjc.1_Missense_Mutation_p.E241K	NM_002096	NP_002087	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1,	326	Glu-rich.				mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|response to virus|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cell junction|transcription factor TFIIF complex	catalytic activity|DNA binding|phosphatase activator activity|transcription coactivator activity|transcription factor binding				0																		---	---	---	---
TUBB4	10382	broad.mit.edu	37	19	6495193	6495193	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6495193C>A	uc002mfg.1	-	4	1424	c.1317G>T	c.(1315-1317)GCG>GCT	p.A439A	TUBB4_uc002mff.1_Silent_p.A367A|MIR220B_hsa-mir-220b|MI0005529_5'Flank	NM_006087	NP_006078	P04350	TBB4_HUMAN	tubulin, beta 4	439					'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(2)	2		Hepatocellular(1079;0.00213)|Renal(1328;0.0183)		Lung(535;3.23e-05)|STAD - Stomach adenocarcinoma(1328;8.24e-05)|GBM - Glioblastoma multiforme(1328;0.00839)|READ - Rectum adenocarcinoma(264;0.155)														---	---	---	---
ARHGEF18	23370	broad.mit.edu	37	19	7518449	7518449	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7518449G>A	uc002mgi.2	+	7	1641	c.1388G>A	c.(1387-1389)GGC>GAC	p.G463D	ARHGEF18_uc010xjm.1_Missense_Mutation_p.G305D|ARHGEF18_uc002mgh.2_Missense_Mutation_p.G305D|ARHGEF18_uc002mgj.1_Missense_Mutation_p.G106D	NM_001130955	NP_001124427	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor 18	463					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)																---	---	---	---
MCOLN1	57192	broad.mit.edu	37	19	7598461	7598461	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7598461A>G	uc002mgo.2	+	13	1753	c.1628A>G	c.(1627-1629)CAG>CGG	p.Q543R	PNPLA6_uc002mgq.1_5'Flank|PNPLA6_uc010xjp.1_5'Flank|PNPLA6_uc002mgr.1_5'Flank|PNPLA6_uc010xjq.1_5'Flank|PNPLA6_uc002mgs.2_5'Flank|MCOLN1_uc002mgp.2_Missense_Mutation_p.Q508R	NM_020533	NP_065394	Q9GZU1	MCLN1_HUMAN	mucolipin 1	543					calcium ion transport|cellular iron ion homeostasis|transferrin transport	integral to plasma membrane|late endosome membrane|lysosomal membrane	cation channel activity|iron ion transmembrane transporter activity			breast(1)	1																		---	---	---	---
CLEC4M	10332	broad.mit.edu	37	19	7830544	7830544	+	Missense_Mutation	SNP	C	A	A	rs147993793	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7830544C>A	uc002mih.2	+	4	353	c.235C>A	c.(235-237)CTA>ATA	p.L79I	CLEC4M_uc010xjv.1_Missense_Mutation_p.L51I|CLEC4M_uc002mhy.2_Missense_Mutation_p.L23I|CLEC4M_uc010xjw.1_Missense_Mutation_p.L58I|CLEC4M_uc010dvt.2_Missense_Mutation_p.L79I|CLEC4M_uc010dvs.2_Missense_Mutation_p.L78I|CLEC4M_uc010xjx.1_Missense_Mutation_p.L51I|CLEC4M_uc002mhz.2_Missense_Mutation_p.L79I|CLEC4M_uc002mic.2_Missense_Mutation_p.L51I|CLEC4M_uc002mia.2_Missense_Mutation_p.L58I	NM_001144910	NP_001138382	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M isoform	79	Extracellular (Probable).				cell-cell recognition|endocytosis|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to plasma membrane	ICAM-3 receptor activity|mannose binding|metal ion binding|peptide antigen binding|virion binding			pancreas(1)	1																		---	---	---	---
TIMM44	10469	broad.mit.edu	37	19	7998751	7998751	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7998751G>A	uc002miz.2	-	6	683	c.681C>T	c.(679-681)AAC>AAT	p.N227N	TIMM44_uc002mja.2_Translation_Start_Site|TIMM44_uc010dvx.1_RNA	NM_006351	NP_006342	O43615	TIM44_HUMAN	translocase of inner mitochondrial membrane 44	227					protein targeting to mitochondrion	mitochondrial inner membrane presequence translocase complex|mitochondrial matrix	ATP binding|P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1																		---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8176624	8176624	+	Missense_Mutation	SNP	C	T	T	rs143347714		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8176624C>T	uc002mjf.2	-	31	4013	c.3992G>A	c.(3991-3993)CGG>CAG	p.R1331Q		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1331	EGF-like 20; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11																		---	---	---	---
ZNF699	374879	broad.mit.edu	37	19	9406969	9406969	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9406969C>T	uc002mlc.1	-	5	1111	c.1111G>A	c.(1111-1113)GCC>ACC	p.A371T		NM_198535	NP_940937	Q32M78	ZN699_HUMAN	zinc finger protein 699	371	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
TYK2	7297	broad.mit.edu	37	19	10463629	10463629	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10463629C>T	uc002moc.3	-	22	3551	c.3173G>A	c.(3172-3174)CGC>CAC	p.R1058H	TYK2_uc010dxe.2_Missense_Mutation_p.R873H	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2	1058	Protein kinase 2.				intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)															---	---	---	---
KANK2	25959	broad.mit.edu	37	19	11304155	11304155	+	Missense_Mutation	SNP	G	T	T	rs148328896	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11304155G>T	uc010dxv.2	-	6	1159	c.601C>A	c.(601-603)CAG>AAG	p.Q201K	KANK2_uc002mqm.2_Missense_Mutation_p.Q201K|KANK2_uc002mqo.3_Missense_Mutation_p.Q201K|KANK2_uc002mqp.1_Missense_Mutation_p.Q10K|KANK2_uc002mqq.2_Missense_Mutation_p.Q201K	NM_015493	NP_056308	Q63ZY3	KANK2_HUMAN	ankyrin repeat domain 25 isoform 1	201	Potential.										0																		---	---	---	---
RGL3	57139	broad.mit.edu	37	19	11508219	11508219	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11508219T>G	uc002mrp.2	-	17	1865	c.1801A>C	c.(1801-1803)AGC>CGC	p.S601R	RGL3_uc002mrn.2_Missense_Mutation_p.S365R|RGL3_uc002mrm.2_Missense_Mutation_p.S365R|RGL3_uc002mro.2_Missense_Mutation_p.S607R	NM_001035223	NP_001030300	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation	601	Pro-rich.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1																		---	---	---	---
ZNF653	115950	broad.mit.edu	37	19	11597863	11597863	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11597863C>A	uc002mrz.1	-	5	1335	c.1282G>T	c.(1282-1284)GAG>TAG	p.E428*		NM_138783	NP_620138	Q96CK0	ZN653_HUMAN	zinc finger protein 653	428					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF442	79973	broad.mit.edu	37	19	12460790	12460790	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12460790T>A	uc002mtr.1	-	6	2220	c.1609A>T	c.(1609-1611)ATT>TTT	p.I537F	ZNF442_uc010xmk.1_Missense_Mutation_p.I468F	NM_030824	NP_110451	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	537	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(2)|breast(1)|kidney(1)	4																		---	---	---	---
C19orf57	79173	broad.mit.edu	37	19	14000035	14000035	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14000035A>G	uc002mxl.1	-	6	1693	c.1634T>C	c.(1633-1635)CTG>CCG	p.L545P	C19orf57_uc002mxk.1_Missense_Mutation_p.L427P|C19orf57_uc002mxm.1_Intron	NM_024323	NP_077299	Q0VDD7	CS057_HUMAN	hypothetical protein LOC79173	545					multicellular organismal development		protein binding			ovary(2)|upper_aerodigestive_tract(1)	3			OV - Ovarian serous cystadenocarcinoma(19;2e-21)															---	---	---	---
OR7C1	26664	broad.mit.edu	37	19	14910600	14910600	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14910600C>T	uc010xnz.1	-	1	349	c.349G>A	c.(349-351)GTG>ATG	p.V117M		NM_198944	NP_945182	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C,	117	Helical; Name=3; (Potential).				sensory perception of smell|spermatogenesis	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2																		---	---	---	---
ANO8	57719	broad.mit.edu	37	19	17438659	17438659	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17438659C>T	uc002ngf.2	-	14	2416	c.2257G>A	c.(2257-2259)GTG>ATG	p.V753M	ANO8_uc010eap.2_RNA	NM_020959	NP_066010	Q9HCE9	ANO8_HUMAN	anoctamin 8	753	Helical; (Potential).					chloride channel complex	chloride channel activity			ovary(3)	3																		---	---	---	---
UNC13A	23025	broad.mit.edu	37	19	17759368	17759368	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17759368G>A	uc002nhd.2	-	16	1952	c.1952C>T	c.(1951-1953)ACG>ATG	p.T651M		NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A	563	Phorbol-ester/DAG-type.				exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3																		---	---	---	---
WDR88	126248	broad.mit.edu	37	19	33647411	33647411	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33647411T>C	uc002nui.2	+	7	1038	c.960T>C	c.(958-960)CAT>CAC	p.H320H		NM_173479	NP_775750	Q6ZMY6	WDR88_HUMAN	PQQ repeat and WD repeat domain containing	320	WD 6.									ovary(1)|breast(1)|central_nervous_system(1)	3	Esophageal squamous(110;0.137)																	---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36218589	36218589	+	Intron	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36218589C>T	uc010eei.2	+							NM_014727	NP_055542			myeloid/lymphoid or mixed-lineage leukemia 4						chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36594075	36594075	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36594075G>T	uc002odc.2	+	29	3556	c.3465G>T	c.(3463-3465)AAG>AAT	p.K1155N	WDR62_uc002odd.2_Missense_Mutation_p.K1160N	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2	1155	WD 14.				cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
ZNF461	92283	broad.mit.edu	37	19	37130098	37130098	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37130098T>A	uc002oem.2	-	6	1377	c.1149A>T	c.(1147-1149)AAA>AAT	p.K383N	ZNF461_uc002oen.2_Missense_Mutation_p.K352N|ZNF461_uc010xtj.1_Missense_Mutation_p.K360N	NM_153257	NP_694989	Q8TAF7	ZN461_HUMAN	gonadotropin inducible transcription repressor	383					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)															---	---	---	---
ZNF568	374900	broad.mit.edu	37	19	37440970	37440970	+	Silent	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37440970T>G	uc002ofc.2	+	7	1430	c.915T>G	c.(913-915)CCT>CCG	p.P305P	ZNF568_uc010efg.2_Intron|ZNF568_uc010xtn.1_Intron|ZNF568_uc002ofd.2_Silent_p.P229P|ZNF568_uc010efe.2_Silent_p.P229P|ZNF568_uc010eff.1_Intron	NM_198539	NP_940941	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	305					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39038982	39038982	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39038982G>T	uc002oit.2	+	89	12334	c.12204G>T	c.(12202-12204)AAG>AAT	p.K4068N	RYR1_uc002oiu.2_Missense_Mutation_p.K4063N|RYR1_uc002oiv.1_Missense_Mutation_p.K977N	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4068					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
HNRNPL	3191	broad.mit.edu	37	19	39322070	39322070	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39322070G>T	uc002ojj.1	-	6	846	c.766C>A	c.(766-768)CTC>ATC	p.L256I	ECH1_uc002oji.2_Missense_Mutation_p.L47I|ECH1_uc010xuk.1_Missense_Mutation_p.L47I|HNRNPL_uc010ege.1_Intron	NM_001005335	NP_001005335	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	Error:Variant_position_missing_in_P14866_after_alignment					nuclear mRNA splicing, via spliceosome	cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|transcription regulatory region DNA binding				0	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)															---	---	---	---
C19orf47	126526	broad.mit.edu	37	19	40828262	40828262	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40828262G>T	uc002oni.3	-	9	797	c.796C>A	c.(796-798)CTG>ATG	p.L266M	C19orf47_uc002ong.2_Missense_Mutation_p.L125M|C19orf47_uc002onh.2_Missense_Mutation_p.L199M	NM_178830	NP_849152	Q8N9M1	CS047_HUMAN	hypothetical protein LOC126526	266										ovary(1)|skin(1)	2			Lung(22;0.000636)															---	---	---	---
ZNF234	10780	broad.mit.edu	37	19	44661951	44661951	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44661951A>C	uc002oym.2	+	6	2089	c.1782A>C	c.(1780-1782)AAA>AAC	p.K594N	ZNF234_uc002oyl.3_Missense_Mutation_p.K594N	NM_006630	NP_006621	Q14588	ZN234_HUMAN	zinc finger protein 234	594					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)																---	---	---	---
SYMPK	8189	broad.mit.edu	37	19	46351244	46351244	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46351244G>A	uc002pdn.2	-	7	687	c.442C>T	c.(442-444)CGG>TGG	p.R148W	SYMPK_uc002pdo.1_Missense_Mutation_p.R148W|SYMPK_uc002pdp.1_Missense_Mutation_p.R148W|SYMPK_uc002pdq.1_Missense_Mutation_p.R148W	NM_004819	NP_004810	Q92797	SYMPK_HUMAN	symplekin	148					cell adhesion|mRNA processing	cytoplasm|cytoskeleton|nucleoplasm|tight junction	protein binding			ovary(1)	1		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)														---	---	---	---
PGLYRP1	8993	broad.mit.edu	37	19	46522617	46522617	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46522617G>A	uc002pdx.1	-	3	514	c.470C>T	c.(469-471)GCT>GTT	p.A157V		NM_005091	NP_005082	O75594	PGRP1_HUMAN	peptidoglycan recognition protein 1 precursor	157					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region	bacterial cell surface binding|N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(2)	2		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.0036)|GBM - Glioblastoma multiforme(486;0.022)|Epithelial(262;0.208)														---	---	---	---
PNMAL2	57469	broad.mit.edu	37	19	46998154	46998154	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46998154G>A	uc002pes.2	-	1	1016	c.569C>T	c.(568-570)GCG>GTG	p.A190V	uc002peu.1_Missense_Mutation_p.A89T	NM_020709	NP_065760	Q9ULN7	PNML2_HUMAN	PNMA-like 2	190										central_nervous_system(1)	1		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)														---	---	---	---
CCDC114	93233	broad.mit.edu	37	19	48807230	48807230	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48807230A>G	uc002pir.2	-	7	1405	c.722T>C	c.(721-723)CTG>CCG	p.L241P	CCDC114_uc002piq.2_Missense_Mutation_p.L50P|CCDC114_uc002pio.2_Missense_Mutation_p.L278P|CCDC114_uc002pis.1_5'Flank|CCDC114_uc002pit.1_Missense_Mutation_p.L278P|CCDC114_uc002piu.1_Missense_Mutation_p.L278P	NM_144577	NP_653178	Q96M63	CC114_HUMAN	coiled-coil domain containing 114 isoform 2	241										ovary(1)	1		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)														---	---	---	---
TRPM4	54795	broad.mit.edu	37	19	49674945	49674945	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49674945T>C	uc002pmw.2	+	8	1041	c.969T>C	c.(967-969)AGT>AGC	p.S323S	TRPM4_uc010emu.2_Silent_p.S323S|TRPM4_uc010yak.1_5'UTR|TRPM4_uc002pmx.2_Silent_p.S149S|TRPM4_uc010emv.2_Silent_p.S208S|TRPM4_uc010yal.1_Silent_p.S40S	NM_017636	NP_060106	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel,	323	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)														---	---	---	---
PTOV1	53635	broad.mit.edu	37	19	50363375	50363375	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50363375C>T	uc002pqf.1	+	11	1344	c.1174C>T	c.(1174-1176)CGT>TGT	p.R392C	PTOV1_uc002ppz.3_RNA|PTOV1_uc002pqb.3_Silent_p.G336G|PTOV1_uc002pqa.2_RNA|PTOV1_uc002pqc.1_RNA|PTOV1_uc002pqd.2_RNA|PTOV1_uc002pqe.1_RNA	NM_017432	NP_059128	Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	392	Interaction with FLOT1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|plasma membrane					0		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)														---	---	---	---
NUP62	23636	broad.mit.edu	37	19	50412513	50412513	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50412513T>C	uc002pqx.2	-	2	656	c.552A>G	c.(550-552)GCA>GCG	p.A184A	IL4I1_uc002pqv.1_Intron|IL4I1_uc010eno.1_Intron|IL4I1_uc002pqw.1_Intron|IL4I1_uc002pqu.1_Intron|NUP62_uc002pqy.2_Silent_p.A184A|NUP62_uc002pqz.2_Silent_p.A184A|NUP62_uc002pra.2_Silent_p.A184A|NUP62_uc002prb.2_Silent_p.A184A|NUP62_uc002prc.2_Silent_p.A184A	NM_153719	NP_714941	P37198	NUP62_HUMAN	nucleoporin 62kDa	184	15 X 9 AA approximate repeats.|Ala-rich.|Thr-rich.				carbohydrate metabolic process|cell death|cell surface receptor linked signaling pathway|glucose transport|hormone-mediated signaling pathway|mRNA transport|negative regulation of apoptosis|negative regulation of cell proliferation|nucleocytoplasmic transport|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription, DNA-dependent|protein transport|regulation of glucose transport|transcription, DNA-dependent|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleocytoplasmic shuttling complex|ribonucleoprotein complex|spindle pole	chromatin binding|protein serine/threonine kinase activity|receptor signaling complex scaffold activity|SH2 domain binding|structural constituent of nuclear pore|thyroid hormone receptor binding|ubiquitin binding				0		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)														---	---	---	---
VRK3	51231	broad.mit.edu	37	19	50491647	50491647	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50491647A>G	uc002prg.2	-	12	1297	c.1199T>C	c.(1198-1200)ATC>ACC	p.I400T	VRK3_uc002prh.1_Missense_Mutation_p.I400T|VRK3_uc002pri.1_Missense_Mutation_p.I350T|VRK3_uc010ens.2_Missense_Mutation_p.I400T|VRK3_uc010ybl.1_Missense_Mutation_p.I350T|VRK3_uc010ybm.1_Missense_Mutation_p.I169T|VRK3_uc002prj.1_Missense_Mutation_p.I350T|VRK3_uc002prk.1_Missense_Mutation_p.I400T|VRK3_uc010ent.1_Missense_Mutation_p.I156T|VRK3_uc002prl.2_Missense_Mutation_p.I400T	NM_016440	NP_057524	Q8IV63	VRK3_HUMAN	vaccinia related kinase 3 isoform 1	400	Protein kinase.					nucleus	ATP binding|protein kinase activity			stomach(1)|skin(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)														---	---	---	---
NR1H2	7376	broad.mit.edu	37	19	50882025	50882025	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50882025G>A	uc010enw.2	+	7	998	c.722G>A	c.(721-723)CGC>CAC	p.R241H	NR1H2_uc002prv.3_RNA|NR1H2_uc002prz.3_Missense_Mutation_p.R240H|NR1H2_uc002psa.3_Missense_Mutation_p.R143H	NM_007121	NP_009052	P55055	NR1H2_HUMAN	nuclear receptor subfamily 1, group H, member 2	240	Ligand-binding (Potential).				negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of pinocytosis|negative regulation of transcription, DNA-dependent|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)														---	---	---	---
FAM71E1	112703	broad.mit.edu	37	19	50970986	50970986	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50970986G>A	uc002psh.2	-	4	998	c.640C>T	c.(640-642)CGG>TGG	p.R214W	FAM71E1_uc002psg.2_Missense_Mutation_p.R198W|FAM71E1_uc002psi.2_RNA	NM_138411	NP_612420	Q6IPT2	F71E1_HUMAN	hypothetical protein LOC112703	214										breast(1)	1		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.0077)|GBM - Glioblastoma multiforme(134;0.026)														---	---	---	---
SHANK1	50944	broad.mit.edu	37	19	51165362	51165362	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51165362G>A	uc002psx.1	-	23	6365	c.6346C>T	c.(6346-6348)CGA>TGA	p.R2116*	SHANK1_uc002psw.1_Nonsense_Mutation_p.R1500*	NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	2116	SAM.				cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)														---	---	---	---
SHANK1	50944	broad.mit.edu	37	19	51190039	51190039	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51190039C>T	uc002psx.1	-	19	2439	c.2420G>A	c.(2419-2421)AGC>AAC	p.S807N	SHANK1_uc002psw.1_Missense_Mutation_p.S191N	NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	807					cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)														---	---	---	---
SHANK1	50944	broad.mit.edu	37	19	51191203	51191203	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51191203A>G	uc002psx.1	-	17	2304	c.2285T>C	c.(2284-2286)ATG>ACG	p.M762T	SHANK1_uc002psw.1_Missense_Mutation_p.M146T	NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	762					cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)														---	---	---	---
SIGLEC6	946	broad.mit.edu	37	19	52034212	52034212	+	Silent	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52034212G>T	uc002pwy.2	-	3	591	c.429C>A	c.(427-429)GCC>GCA	p.A143A	SIGLEC6_uc002pwz.2_Silent_p.A143A|SIGLEC6_uc002pxa.2_Silent_p.A143A|SIGLEC6_uc010ydb.1_Silent_p.A96A|SIGLEC6_uc010ydc.1_Silent_p.A132A|SIGLEC6_uc010eoz.1_Intron|SIGLEC6_uc010epb.1_Silent_p.A96A|SIGLEC6_uc010epa.1_Silent_p.A132A	NM_001245	NP_001236	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6 isoform 1	143	Extracellular (Potential).				cell adhesion|cell-cell signaling	cytoplasm|extracellular region|integral to plasma membrane|membrane fraction|nucleus				ovary(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)														---	---	---	---
ZNF766	90321	broad.mit.edu	37	19	52794408	52794408	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52794408T>C	uc002pyr.1	+	4	1407	c.1364T>C	c.(1363-1365)GTA>GCA	p.V455A	ZNF766_uc002pys.1_3'UTR|ZNF766_uc002pyt.1_Intron	NM_001010851	NP_001010851	Q5HY98	ZN766_HUMAN	zinc finger protein 766	455	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00236)|OV - Ovarian serous cystadenocarcinoma(262;0.00871)														---	---	---	---
ZNF808	388558	broad.mit.edu	37	19	53057126	53057126	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53057126G>A	uc010epq.1	+	5	1134	c.957G>A	c.(955-957)GAG>GAA	p.E319E	ZNF808_uc002pzq.2_RNA|ZNF808_uc010epr.1_5'Flank	NM_001039886	NP_001034975	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	319	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)														---	---	---	---
NLRP12	91662	broad.mit.edu	37	19	54314476	54314476	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54314476C>T	uc002qch.3	-	3	657	c.437G>A	c.(436-438)CGC>CAC	p.R146H	NLRP12_uc010eqw.2_5'Flank|NLRP12_uc002qci.3_Missense_Mutation_p.R146H|NLRP12_uc002qcj.3_Missense_Mutation_p.R146H|NLRP12_uc002qck.3_RNA|NLRP12_uc010eqx.2_Missense_Mutation_p.R146H	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	146					negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)														---	---	---	---
GP6	51206	broad.mit.edu	37	19	55530055	55530055	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55530055A>G	uc002qik.2	-	6	717	c.689T>C	c.(688-690)CTG>CCG	p.L230P	GP6_uc002qil.2_Missense_Mutation_p.L230P|GP6_uc010esq.2_Missense_Mutation_p.L212P	NM_016363	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet) isoform 2	230	Extracellular (Potential).				enzyme linked receptor protein signaling pathway|leukocyte migration|platelet activation	integral to plasma membrane	collagen binding|transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)														---	---	---	---
BRSK1	84446	broad.mit.edu	37	19	55812988	55812988	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55812988A>G	uc002qkg.2	+	8	1064	c.787A>G	c.(787-789)AGG>GGG	p.R263G	BRSK1_uc002qkf.2_Missense_Mutation_p.R279G|BRSK1_uc002qkh.2_5'Flank	NM_032430	NP_115806	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	263	Protein kinase.				establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV	cell junction|cytoplasm|nucleus	magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1)	6		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)														---	---	---	---
ZNF543	125919	broad.mit.edu	37	19	57839832	57839832	+	Silent	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57839832G>T	uc002qoi.1	+	4	1347	c.1002G>T	c.(1000-1002)ACG>ACT	p.T334T		NM_213598	NP_998763	Q08ER8	ZN543_HUMAN	zinc finger protein 543	334					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)|pancreas(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)														---	---	---	---
SIGLEC1	6614	broad.mit.edu	37	20	3686656	3686656	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3686656C>T	uc002wja.2	-	3	441	c.441G>A	c.(439-441)CCG>CCA	p.P147P	SIGLEC1_uc002wiz.3_Silent_p.P147P|SIGLEC1_uc002wjc.2_Silent_p.P58P	NM_023068	NP_075556	Q9BZZ2	SN_HUMAN	sialoadhesin precursor	147	Ig-like C2-type 1.|Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|endocytosis|inflammatory response	extracellular region|integral to membrane|plasma membrane	sugar binding			pancreas(4)|ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	10																		---	---	---	---
ADRA1D	146	broad.mit.edu	37	20	4202221	4202221	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4202221G>A	uc002wkr.2	-	2	1723	c.1668C>T	c.(1666-1668)TGC>TGT	p.C556C		NM_000678	NP_000669	P25100	ADA1D_HUMAN	alpha-1D-adrenergic receptor	556	Cytoplasmic (By similarity).			KPPSAFREWRLLGPFRRPTTQLRAKVSSLSHKIRAGGAQRA EAACAQRSEVEAVSLGVPHEVAEGATCQAYELADYSNLRET DI -> SHPAPSASGGCWGRSGDPRPSCAPKSPACRTRSPP GARSAQRQRAPSAQRWRLCP (in Ref. 1).	cell proliferation|cell-cell signaling|DNA metabolic process|G-protein signaling, coupled to cAMP nucleotide second messenger|multicellular organismal development|positive regulation of cell proliferation	integral to plasma membrane	alpha1-adrenergic receptor activity				0					Alfuzosin(DB00346)|Bethanidine(DB00217)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Doxazosin(DB00590)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Methotrimeprazine(DB01403)|Norepinephrine(DB00368)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)													---	---	---	---
CHGB	1114	broad.mit.edu	37	20	5904215	5904215	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5904215T>C	uc002wmg.2	+	4	1731	c.1425T>C	c.(1423-1425)GGT>GGC	p.G475G	CHGB_uc010zqz.1_Silent_p.G158G	NM_001819	NP_001810	P05060	SCG1_HUMAN	chromogranin B precursor	475						extracellular region	hormone activity			breast(3)|skin(2)|ovary(1)	6																		---	---	---	---
BTBD3	22903	broad.mit.edu	37	20	11898985	11898985	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11898985C>T	uc002wnz.2	+	1	421	c.62C>T	c.(61-63)ACG>ATG	p.T21M	BTBD3_uc002wny.2_Translation_Start_Site|BTBD3_uc002woa.2_Translation_Start_Site|BTBD3_uc010zrf.1_Translation_Start_Site|BTBD3_uc010zrg.1_5'Flank|BTBD3_uc010zrh.1_5'Flank	NM_014962	NP_055777	Q9Y2F9	BTBD3_HUMAN	BTB/POZ domain containing protein 3 isoform a	21										ovary(2)|central_nervous_system(1)	3																		---	---	---	---
SEC23B	10483	broad.mit.edu	37	20	18535045	18535045	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18535045T>C	uc002wqz.1	+						SEC23B_uc002wra.1_Intron|SEC23B_uc002wrb.1_Intron|SEC23B_uc010zsb.1_Intron|SEC23B_uc002wrc.1_Intron	NM_006363	NP_006354			Sec23 homolog B						ER to Golgi vesicle-mediated transport|intracellular protein transport	COPII vesicle coat|endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
DTD1	92675	broad.mit.edu	37	20	18608856	18608856	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18608856T>C	uc002wrf.3	+	4	617	c.456T>C	c.(454-456)ACT>ACC	p.T152T		NM_080820	NP_543010	Q8TEA8	DTD1_HUMAN	D-tyrosyl-tRNA deacylase 1	152					D-amino acid catabolic process	cytoplasm	hydrolase activity, acting on ester bonds			ovary(2)	2																		---	---	---	---
CRNKL1	51340	broad.mit.edu	37	20	20024194	20024194	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20024194C>A	uc002wrs.2	-	8	1429	c.1397G>T	c.(1396-1398)CGG>CTG	p.R466L		NM_016652	NP_057736	Q9BZJ0	CRNL1_HUMAN	crooked neck-like 1 protein	466					spliceosome assembly	catalytic step 2 spliceosome|cytoplasm|nuclear speck	RNA binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
GZF1	64412	broad.mit.edu	37	20	23345800	23345800	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23345800T>C	uc010gdb.2	+	3	954	c.780T>C	c.(778-780)TGT>TGC	p.C260C	GZF1_uc002wsy.2_Silent_p.C260C|GZF1_uc010zsq.1_Intron|GZF1_uc010zsr.1_Intron|GZF1_uc002wsz.2_Silent_p.C260C	NM_022482	NP_071927	Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	260					transcription, DNA-dependent	nucleolus|nucleoplasm	sequence-specific DNA binding|zinc ion binding			kidney(1)	1	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)																	---	---	---	---
ACSS1	84532	broad.mit.edu	37	20	24993453	24993453	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24993453C>T	uc002wub.2	-	11	2580	c.1702G>A	c.(1702-1704)GCC>ACC	p.A568T	ACSS1_uc002wuc.2_Missense_Mutation_p.A566T|ACSS1_uc010gdc.2_Missense_Mutation_p.A363T|ACSS1_uc002wud.1_RNA|ACSS1_uc002wua.2_Missense_Mutation_p.A485T	NM_032501	NP_115890	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	568					acetyl-CoA biosynthetic process|ethanol oxidation|xenobiotic metabolic process	mitochondrial matrix	acetate-CoA ligase activity|AMP binding|ATP binding|protein binding			ovary(1)|skin(1)	2					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
TPX2	22974	broad.mit.edu	37	20	30345300	30345300	+	Silent	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30345300T>G	uc002wwp.1	+	3	719	c.21T>G	c.(19-21)TCT>TCG	p.S7S	TPX2_uc010gdv.1_Silent_p.S7S	NM_012112	NP_036244	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated protein homolog	7					activation of protein kinase activity|apoptosis|cell division|cell proliferation|mitosis|regulation of mitotic spindle organization	cytoplasm|microtubule|nucleus|spindle pole	ATP binding|GTP binding|protein kinase binding			large_intestine(1)|ovary(1)	2			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)															---	---	---	---
MYLK2	85366	broad.mit.edu	37	20	30411335	30411335	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30411335C>T	uc002wwq.2	+	5	930	c.828C>T	c.(826-828)ACC>ACT	p.T276T		NM_033118	NP_149109	Q9H1R3	MYLK2_HUMAN	skeletal myosin light chain kinase	276					cardiac muscle tissue morphogenesis|regulation of muscle filament sliding		ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			lung(2)|skin(2)|ovary(1)|central_nervous_system(1)	6			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)													OREG0025856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
AHCY	191	broad.mit.edu	37	20	32881918	32881918	+	Silent	SNP	C	A	A	rs146302783	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32881918C>A	uc002xai.2	-	3	403	c.264G>T	c.(262-264)GCG>GCT	p.A88A	AHCY_uc002xaj.2_Silent_p.A60A|AHCY_uc010get.2_Missense_Mutation_p.R146L	NM_000687	NP_000678	P23526	SAHH_HUMAN	adenosylhomocysteinase isoform 1	88					methylation|xenobiotic metabolic process	cytosol|melanosome	adenosylhomocysteinase activity|protein binding				0																		---	---	---	---
SAMHD1	25939	broad.mit.edu	37	20	35521337	35521337	+	Nonstop_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35521337A>C	uc002xgh.1	-	16	2009	c.1879T>G	c.(1879-1881)TGA>GGA	p.*627G	C20orf118_uc002xgg.1_3'UTR|SAMHD1_uc010gft.1_RNA	NM_015474	NP_056289	Q9Y3Z3	SAMH1_HUMAN	SAM domain- and HD domain-containing protein 1	627					defense response to virus|innate immune response|regulation of innate immune response	nucleus	metal ion binding|phosphoric diester hydrolase activity				0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
TGM2	7052	broad.mit.edu	37	20	36760864	36760864	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36760864G>A	uc002xhr.2	-	11	1754	c.1654C>T	c.(1654-1656)CGT>TGT	p.R552C	TGM2_uc002xhq.2_Missense_Mutation_p.R153C|TGM2_uc010zvx.1_Missense_Mutation_p.R471C|TGM2_uc010zvy.1_Missense_Mutation_p.R492C|TGM2_uc002xhs.1_Missense_Mutation_p.R528C	NM_004613	NP_004604	P21980	TGM2_HUMAN	transglutaminase 2 isoform a	552					apoptotic cell clearance|peptide cross-linking|positive regulation of cell adhesion		acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(1)|lung(1)|ovary(1)	3		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)													---	---	---	---
HNF4A	3172	broad.mit.edu	37	20	43034707	43034707	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43034707C>A	uc002xma.2	+	2	214	c.125C>A	c.(124-126)CCA>CAA	p.P42Q	HNF4A_uc010zwo.1_Missense_Mutation_p.H33N|HNF4A_uc002xlt.2_Missense_Mutation_p.P20Q|HNF4A_uc002xlu.2_Missense_Mutation_p.P20Q|HNF4A_uc002xlv.2_Missense_Mutation_p.P20Q|HNF4A_uc002xly.2_Missense_Mutation_p.P42Q|HNF4A_uc002xlz.2_Missense_Mutation_p.P42Q|HNF4A_uc010ggq.2_Missense_Mutation_p.P35Q	NM_000457	NP_000448	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4 alpha isoform b	42					blood coagulation|endocrine pancreas development|glucose homeostasis|negative regulation of cell growth|negative regulation of cell proliferation|ornithine metabolic process|phospholipid homeostasis|positive regulation of cholesterol homeostasis|regulation of growth hormone receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to glucose stimulus|triglyceride homeostasis|xenobiotic metabolic process	cytoplasm	activating transcription factor binding|protein homodimerization activity|receptor binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
SERINC3	10955	broad.mit.edu	37	20	43142670	43142670	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43142670G>A	uc002xme.2	-	2	185	c.51C>T	c.(49-51)CTC>CTT	p.L17L	SERINC3_uc002xmf.1_Silent_p.L17L|SERINC3_uc010ggs.1_Silent_p.L10L|SERINC3_uc010zwp.1_5'UTR	NM_198941	NP_945179	Q13530	SERC3_HUMAN	tumor differentially expressed protein 1	17	Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			skin(3)	3		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.000291)|COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
SYS1	90196	broad.mit.edu	37	20	43995615	43995615	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43995615T>G	uc002xnv.2	+	4	589	c.331T>G	c.(331-333)TCC>GCC	p.S111A	SYS1_uc010gha.2_RNA|SYS1_uc002xnw.1_Intron|SYS1-DBNDD2_uc002xnx.2_Intron	NM_033542	NP_291020	Q8N2H4	SYS1_HUMAN	SYS1 Golgi-localized integral membrane protein	111	Helical; (Potential).				protein transport	Golgi membrane|integral to membrane				skin(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
WFDC13	164237	broad.mit.edu	37	20	44333226	44333226	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44333226C>T	uc002xpd.2	+	2	340	c.232C>T	c.(232-234)CGC>TGC	p.R78C	WFDC10B_uc002xpb.2_Intron|WFDC10B_uc002xpc.2_Intron	NM_172005	NP_742002	Q8IUB5	WFD13_HUMAN	WAP four-disulfide core domain 13 precursor	78						extracellular region	peptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZSWIM3	140831	broad.mit.edu	37	20	44486535	44486535	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44486535A>C	uc002xqd.2	+	1	274	c.71A>C	c.(70-72)AAC>ACC	p.N24T	ACOT8_uc002xqa.1_5'Flank|ACOT8_uc010zxe.1_5'Flank|ACOT8_uc002xqc.1_5'Flank|ACOT8_uc010zxf.1_5'Flank|ZSWIM3_uc010zxg.1_5'UTR	NM_080752	NP_542790	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM domain containing 3	24							zinc ion binding			ovary(2)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45702826	45702826	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45702826G>T	uc002xsm.2	+	7	887	c.513G>T	c.(511-513)CAG>CAT	p.Q171H	EYA2_uc010ghp.2_Missense_Mutation_p.Q171H|EYA2_uc002xsn.2_Missense_Mutation_p.Q176H|EYA2_uc002xso.2_Missense_Mutation_p.Q171H|EYA2_uc002xsp.2_Missense_Mutation_p.Q171H|EYA2_uc002xsq.2_Missense_Mutation_p.Q171H	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a	171					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)																---	---	---	---
ARFGEF2	10564	broad.mit.edu	37	20	47589799	47589799	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47589799A>C	uc002xtx.3	+	12	1795	c.1643A>C	c.(1642-1644)GAG>GCG	p.E548A		NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine	548					exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)															---	---	---	---
ARFGEF2	10564	broad.mit.edu	37	20	47649737	47649737	+	3'UTR	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47649737C>T	uc002xtx.3	+	39					ARFGEF2_uc010zyf.1_3'UTR	NM_006420	NP_006411			ADP-ribosylation factor guanine						exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)															---	---	---	---
ZNFX1	57169	broad.mit.edu	37	20	47887312	47887312	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47887312T>C	uc002xui.2	-	3	1284	c.1037A>G	c.(1036-1038)CAC>CGC	p.H346R		NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	346							metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
PTGIS	5740	broad.mit.edu	37	20	48166644	48166644	+	Missense_Mutation	SNP	A	G	G	rs148875055		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48166644A>G	uc002xut.2	-	2	211	c.157T>C	c.(157-159)TTC>CTC	p.F53L	PTGIS_uc010zyi.1_5'UTR	NM_000961	NP_000952	Q16647	PTGIS_HUMAN	prostaglandin I2 synthase	53					hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|prostaglandin-I synthase activity			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Phenylbutazone(DB00812)													---	---	---	---
FAM65C	140876	broad.mit.edu	37	20	49225479	49225479	+	Silent	SNP	G	A	A	rs149203288		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49225479G>A	uc002xvm.2	-	9	960	c.642C>T	c.(640-642)TAC>TAT	p.Y214Y	FAM65C_uc010zyt.1_Silent_p.Y218Y|FAM65C_uc010zyu.1_RNA|FAM65C_uc002xvn.1_Silent_p.Y214Y	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876	214										ovary(2)	2																		---	---	---	---
PFDN4	5203	broad.mit.edu	37	20	52830939	52830939	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52830939A>C	uc002xwx.2	+	2	212	c.74A>C	c.(73-75)AAA>ACA	p.K25T		NM_002623	NP_002614	Q9NQP4	PFD4_HUMAN	prefoldin subunit 4	25					'de novo' posttranslational protein folding	prefoldin complex	chaperone binding|unfolded protein binding				0	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		Colorectal(105;0.124)|STAD - Stomach adenocarcinoma(23;0.206)															---	---	---	---
CASS4	57091	broad.mit.edu	37	20	55027197	55027197	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55027197C>A	uc002xxp.2	+	6	1190	c.965C>A	c.(964-966)CCT>CAT	p.P322H	CASS4_uc002xxq.3_Missense_Mutation_p.P322H|CASS4_uc002xxr.2_Missense_Mutation_p.P322H|CASS4_uc010zze.1_Missense_Mutation_p.P268H|CASS4_uc010gio.2_Intron	NM_001164116	NP_001157588	Q9NQ75	CASS4_HUMAN	HEF-like protein isoform a	322					cell adhesion	cytoplasm|cytoskeleton|focal adhesion	two-component sensor activity			ovary(2)|skin(1)	3																		---	---	---	---
STX16	8675	broad.mit.edu	37	20	57243094	57243094	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57243094C>A	uc002xzi.2	+	4	1039	c.304C>A	c.(304-306)CTT>ATT	p.L102I	STX16_uc010zzq.1_5'UTR|STX16_uc002xzk.2_Missense_Mutation_p.L85I|STX16_uc002xzm.2_Missense_Mutation_p.L98I|STX16_uc002xzj.2_Missense_Mutation_p.L81I|STX16_uc002xzl.2_5'UTR	NM_001001433	NP_001001433	O14662	STX16_HUMAN	syntaxin 16 isoform a	102	Cytoplasmic (Potential).				intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane|microsome|SNARE complex	SNAP receptor activity			ovary(1)	1	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)															---	---	---	---
LAMA5	3911	broad.mit.edu	37	20	60899186	60899186	+	Silent	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60899186G>T	uc002ycq.2	-	43	5785	c.5718C>A	c.(5716-5718)CCC>CCA	p.P1906P		NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor	1906	Laminin EGF-like 17.				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
C20orf166	128826	broad.mit.edu	37	20	61151587	61151587	+	Intron	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61151587C>T	uc011aaj.1	+						C20orf200_uc002ycy.2_5'Flank|C20orf200_uc002ycz.1_5'Flank	NM_178463	NP_848558			hypothetical protein LOC128826												0	Breast(26;1.04e-08)		BRCA - Breast invasive adenocarcinoma(19;7.17e-06)															---	---	---	---
EEF1A2	1917	broad.mit.edu	37	20	62128966	62128966	+	Intron	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62128966A>G	uc002yfd.1	-						EEF1A2_uc002yfe.1_Intron|EEF1A2_uc010gkg.1_Intron	NM_001958	NP_001949			eukaryotic translation elongation factor 1 alpha							nucleus	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)															---	---	---	---
ZBTB46	140685	broad.mit.edu	37	20	62407094	62407094	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62407094C>T	uc002ygv.1	-	3	1360	c.1159G>A	c.(1159-1161)GTG>ATG	p.V387M	ZBTB46_uc002ygu.2_RNA	NM_025224	NP_079500	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	387					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)															OREG0026130	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RGS19	10287	broad.mit.edu	37	20	62705590	62705590	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62705590G>A	uc002yhy.2	-	5	636	c.369C>T	c.(367-369)TGC>TGT	p.C123C	RGS19_uc002yhz.2_Silent_p.C101C|RGS19_uc002yia.2_Silent_p.C123C|RGS19_uc002yib.2_Silent_p.C123C	NM_005873	NP_005864	P49795	RGS19_HUMAN	G protein signalling regulator 19	123	RGS.				autophagy|G-protein coupled receptor protein signaling pathway|negative regulation of signal transduction|small GTPase mediated signal transduction	Golgi apparatus|membrane fraction|plasma membrane	GTPase activator activity|protein binding|signal transducer activity			skin(1)	1	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)																	---	---	---	---
OPRL1	4987	broad.mit.edu	37	20	62730104	62730104	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62730104C>T	uc002yic.2	+	5	1467	c.1065C>T	c.(1063-1065)GAC>GAT	p.D355D	OPRL1_uc002yid.2_Silent_p.D355D|OPRL1_uc002yif.3_Silent_p.D350D	NM_182647	NP_872588	P41146	OPRX_HUMAN	opiate receptor-like 1	355	Cytoplasmic (Potential).				elevation of cytosolic calcium ion concentration|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception	integral to plasma membrane	protein binding|X-opioid receptor activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)																	---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10951287	10951287	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10951287A>C	uc002yip.1	-	10	793	c.425T>G	c.(424-426)CTT>CGT	p.L142R	TPTE_uc002yis.1_RNA|TPTE_uc002yiq.1_Missense_Mutation_p.L124R|TPTE_uc002yir.1_Missense_Mutation_p.L104R|TPTE_uc010gkv.1_Missense_Mutation_p.L4R	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	142	Helical; (Potential).				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)														---	---	---	---
BTG3	10950	broad.mit.edu	37	21	18966578	18966578	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18966578C>A	uc002ykk.2	-	5	852	c.592G>T	c.(592-594)GGG>TGG	p.G198W	BTG3_uc002ykl.2_Missense_Mutation_p.G242W	NM_006806	NP_006797	Q14201	BTG3_HUMAN	B-cell translocation gene 3 isoform b	198					negative regulation of cell proliferation|negative regulation of mitotic cell cycle	cytoplasm					0				Epithelial(23;0.000283)|all cancers(11;0.0012)|Lung(58;0.0191)|OV - Ovarian serous cystadenocarcinoma(11;0.0206)|COAD - Colon adenocarcinoma(22;0.0315)|LUSC - Lung squamous cell carcinoma(23;0.0703)|Colorectal(24;0.0971)														---	---	---	---
ADAMTS5	11096	broad.mit.edu	37	21	28338331	28338331	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28338331C>T	uc002ymg.2	-	1	1109	c.380G>A	c.(379-381)CGG>CAG	p.R127Q		NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1	127					proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30316746	30316746	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30316746C>T	uc002ymr.2	-	22	4092	c.4079G>A	c.(4078-4080)GGC>GAC	p.G1360D		NM_015565	NP_056380	O94822	LTN1_HUMAN	zinc finger protein 294	1314							ligase activity|zinc ion binding				0																		---	---	---	---
KRTAP19-5	337972	broad.mit.edu	37	21	31874258	31874258	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31874258C>T	uc011ada.1	-	1	151	c.151G>A	c.(151-153)GGA>AGA	p.G51R		NM_181611	NP_853642	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	51						intermediate filament	protein binding				0																		---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37605234	37605234	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37605234C>T	uc002yvg.2	+	15	2562	c.2483C>T	c.(2482-2484)GCG>GTG	p.A828V	DOPEY2_uc011aeb.1_Missense_Mutation_p.A828V	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like	828					endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
MORC3	23515	broad.mit.edu	37	21	37710204	37710204	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37710204G>A	uc002yvi.2	+	4	496	c.420G>A	c.(418-420)GCG>GCA	p.A140A		NM_015358	NP_056173	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	140					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																		---	---	---	---
CBS	875	broad.mit.edu	37	21	44474020	44474020	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44474020G>A	uc002zcu.2	-	17	1871	c.1626C>T	c.(1624-1626)TTC>TTT	p.F542F	CBS_uc002zcs.1_Silent_p.F437F|CBS_uc002zct.2_Silent_p.F542F|CBS_uc002zcw.3_Silent_p.F542F|CBS_uc002zcv.2_Silent_p.F542F	NM_000071	NP_000062	P35520	CBS_HUMAN	cystathionine-beta-synthase	542					cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process	cytosol|nucleolus	cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding				0					L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118)													---	---	---	---
ADARB1	104	broad.mit.edu	37	21	46595860	46595860	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46595860G>A	uc002zgy.2	+	4	679	c.244G>A	c.(244-246)GCC>ACC	p.A82T	ADARB1_uc002zgr.2_Missense_Mutation_p.A82T|ADARB1_uc002zgs.2_RNA|ADARB1_uc002zgw.2_Missense_Mutation_p.A82T|ADARB1_uc002zgv.2_RNA|ADARB1_uc002zgt.2_Missense_Mutation_p.A82T|ADARB1_uc010gpx.2_Intron|ADARB1_uc002zgq.2_RNA|ADARB1_uc002zgu.2_RNA|ADARB1_uc011afo.1_Missense_Mutation_p.A131T	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2	82	DRBM 1.				adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)														---	---	---	---
CDC45	8318	broad.mit.edu	37	22	19495010	19495010	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19495010A>G	uc002zpr.2	+	11	1002	c.926A>G	c.(925-927)AAG>AGG	p.K309R	CDC45_uc011agz.1_Missense_Mutation_p.K304R|CDC45_uc011aha.1_Missense_Mutation_p.K341R|CDC45_uc002zps.2_Missense_Mutation_p.K309R|CDC45_uc002zpt.2_Missense_Mutation_p.K263R	NM_003504	NP_003495	O75419	CDC45_HUMAN	CDC45-like	309					DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	centrosome|nucleoplasm	protein binding			lung(1)	1																		---	---	---	---
COMT	1312	broad.mit.edu	37	22	19951793	19951793	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19951793C>T	uc002zqu.2	+	5	835	c.586C>T	c.(586-588)CGG>TGG	p.R196W	COMT_uc002zqt.2_Missense_Mutation_p.R196W|COMT_uc002zqv.2_Missense_Mutation_p.R196W|COMT_uc002zqw.2_Missense_Mutation_p.R196W|COMT_uc011ahd.1_Missense_Mutation_p.R196W|COMT_uc002zqx.2_Missense_Mutation_p.R196W	NM_000754	NP_000745	P21964	COMT_HUMAN	catechol-O-methyltransferase isoform MB-COMT	196					neurotransmitter biosynthetic process|neurotransmitter catabolic process|xenobiotic metabolic process	cytosol|integral to membrane|intracellular membrane-bounded organelle|microsome|plasma membrane|soluble fraction	catechol O-methyltransferase activity|magnesium ion binding|protein binding			ovary(1)	1	Colorectal(54;0.0993)				Carbidopa(DB00190)|Conjugated Estrogens(DB00286)|Diethylstilbestrol(DB00255)|Dobutamine(DB00841)|Dopamine(DB00988)|Entacapone(DB00494)|Folic Acid(DB00158)|L-Valine(DB00161)|Levodopa(DB01235)|Methyldopa(DB00968)|Modafinil(DB00745)|Morphine(DB00295)|S-Adenosylmethionine(DB00118)|Tolcapone(DB00323)													---	---	---	---
TRMT2A	27037	broad.mit.edu	37	22	20103762	20103762	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20103762A>G	uc002zrk.1	-	3	613	c.398T>C	c.(397-399)CTC>CCC	p.L133P	TRMT2A_uc002zrl.1_Missense_Mutation_p.L133P|TRMT2A_uc002zrm.1_5'UTR|TRMT2A_uc002zrn.1_Missense_Mutation_p.L133P|TRMT2A_uc011ahk.1_Missense_Mutation_p.L133P|RANBP1_uc011ahl.1_5'Flank|RANBP1_uc002zro.1_5'Flank|RANBP1_uc002zrp.2_5'Flank	NM_182984	NP_892029	Q8IZ69	TRM2A_HUMAN	HpaII tiny fragments locus 9C	133	RRM.				RNA processing		nucleotide binding|RNA binding|RNA methyltransferase activity			breast(1)	1																		---	---	---	---
HIC2	23119	broad.mit.edu	37	22	21800714	21800714	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21800714C>T	uc002zur.3	+	3	1760	c.1530C>T	c.(1528-1530)TGC>TGT	p.C510C	HIC2_uc002zus.3_Silent_p.C510C	NM_015094	NP_055909	Q96JB3	HIC2_HUMAN	hypermethylated in cancer 2	510	C2H2-type 2.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	focal adhesion|nucleus	DNA binding|protein C-terminus binding|zinc ion binding			skin(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00438)|Colorectal(54;0.0968)	Lung SC(17;0.0262)|all_lung(157;0.205)																---	---	---	---
HSCB	150274	broad.mit.edu	37	22	29141880	29141880	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29141880A>G	uc003aea.2	+	4	493	c.452A>G	c.(451-453)GAA>GGA	p.E151G		NM_172002	NP_741999	Q8IWL3	HSC20_HUMAN	J-type co-chaperone HSC20 precursor	151					iron-sulfur cluster assembly|protein folding	mitochondrion	chaperone binding|heat shock protein binding|metal ion binding			kidney(1)	1																		---	---	---	---
NEFH	4744	broad.mit.edu	37	22	29885456	29885456	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29885456G>T	uc003afo.2	+	4	1898	c.1827G>T	c.(1825-1827)AAG>AAT	p.K609N	NEFH_uc003afp.2_Intron	NM_021076	NP_066554	P12036	NFH_HUMAN	neurofilament, heavy polypeptide 200kDa	609	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				cell death|nervous system development	neurofilament					0																		---	---	---	---
CABP7	164633	broad.mit.edu	37	22	30125551	30125551	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30125551T>C	uc003agl.2	+	5	711	c.641T>C	c.(640-642)ATG>ACG	p.M214T		NM_182527	NP_872333	Q86V35	CABP7_HUMAN	calcium binding protein 7	214	Extracellular (Potential).					Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding				0			OV - Ovarian serous cystadenocarcinoma(5;0.00442)|Epithelial(10;0.215)|all cancers(5;0.233)															---	---	---	---
TBC1D10A	83874	broad.mit.edu	37	22	30695501	30695501	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30695501G>A	uc011akt.1	-	3	373	c.349C>T	c.(349-351)CGG>TGG	p.R117W	GATSL3_uc003ahg.2_RNA|GATSL3_uc003ahh.2_RNA|GATSL3_uc010gvq.2_RNA|GATSL3_uc003ahi.2_5'UTR|TBC1D10A_uc003ahj.3_Missense_Mutation_p.R29W|TBC1D10A_uc010gvu.2_Missense_Mutation_p.R124W|TBC1D10A_uc003ahk.3_Missense_Mutation_p.R117W	NM_031937	NP_114143	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	117	Rab-GAP TBC.					intracellular|microvillus	guanyl-nucleotide exchange factor activity|PDZ domain binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
FBXO7	25793	broad.mit.edu	37	22	32880008	32880008	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32880008A>C	uc003amq.2	+	3	825	c.542A>C	c.(541-543)CAT>CCT	p.H181P	FBXO7_uc003amp.1_Missense_Mutation_p.H67P|FBXO7_uc003amr.2_Missense_Mutation_p.H67P|FBXO7_uc003ams.2_Missense_Mutation_p.H25P|FBXO7_uc003amt.2_Missense_Mutation_p.H102P|FBXO7_uc003amu.2_Missense_Mutation_p.H67P	NM_012179	NP_036311	Q9Y3I1	FBX7_HUMAN	F-box only protein 7 isoform 1	181					cell death|regulation of protein stability|ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
MCM5	4174	broad.mit.edu	37	22	35812348	35812348	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35812348G>A	uc003anu.3	+	11	1458	c.1364G>A	c.(1363-1365)CGT>CAT	p.R455H	MCM5_uc010gwr.2_Missense_Mutation_p.R264H|MCM5_uc003anv.3_Missense_Mutation_p.R412H|MCM5_uc010gws.1_RNA|MCM5_uc003anw.1_Missense_Mutation_p.R239H	NM_006739	NP_006730	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	455	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|DNA binding|helicase activity|protein binding			ovary(1)	1																		---	---	---	---
TRIOBP	11078	broad.mit.edu	37	22	38109376	38109376	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38109376T>C	uc003atr.2	+	5	685	c.414T>C	c.(412-414)CCT>CCC	p.P138P	TRIOBP_uc003atu.2_Intron|TRIOBP_uc003atq.1_Silent_p.P138P|TRIOBP_uc003ats.1_Intron	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	138					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)																	---	---	---	---
GRAP2	9402	broad.mit.edu	37	22	40366977	40366977	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40366977C>T	uc003ayh.1	+	8	1145	c.882C>T	c.(880-882)AGC>AGT	p.S294S	GRAP2_uc003ayi.2_RNA|GRAP2_uc011aom.1_Silent_p.S268S|GRAP2_uc011aon.1_Silent_p.S228S|GRAP2_uc010gya.1_Silent_p.S294S|GRAP2_uc011aoo.1_Silent_p.S222S|GRAP2_uc011aop.1_Silent_p.S254S|GRAP2_uc011aoq.1_Silent_p.S181S|GRAP2_uc003ayj.1_Silent_p.S294S	NM_004810	NP_004801	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	294	SH3 2.				cell-cell signaling|Ras protein signal transduction|T cell costimulation|T cell receptor signaling pathway	cytosol	SH3/SH2 adaptor activity			upper_aerodigestive_tract(1)|central_nervous_system(1)	2																		---	---	---	---
TOB2	10766	broad.mit.edu	37	22	41832689	41832689	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41832689G>A	uc003azz.1	-	2	1368	c.661C>T	c.(661-663)CGC>TGC	p.R221C		NM_016272	NP_057356	Q14106	TOB2_HUMAN	transducer of ERBB2, 2	221					female gamete generation|negative regulation of cell proliferation	cytoplasm|nucleus				ovary(1)	1																		---	---	---	---
PMM1	5372	broad.mit.edu	37	22	41973879	41973879	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41973879T>C	uc003bal.2	-	7	661	c.599A>G	c.(598-600)TAC>TGC	p.Y200C		NM_002676	NP_002667	Q92871	PMM1_HUMAN	phosphomannomutase 1	200					dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	cytosol	metal ion binding|phosphomannomutase activity			ovary(1)	1																		---	---	---	---
PNPLA5	150379	broad.mit.edu	37	22	44277498	44277498	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44277498A>G	uc003beg.2	-	8	1236	c.1139T>C	c.(1138-1140)CTG>CCG	p.L380P	PNPLA5_uc011aqc.1_Missense_Mutation_p.L240P|PNPLA5_uc003beh.2_Missense_Mutation_p.L266P	NM_138814	NP_620169	Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	380					lipid catabolic process		hydrolase activity				0		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)																---	---	---	---
PRR5-ARHGAP8	553158	broad.mit.edu	37	22	45182488	45182488	+	Splice_Site	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45182488T>C	uc003bfd.2	+	8	1113	c.841_splice	c.e8+2	p.G281_splice	PRR5-ARHGAP8_uc003bfc.2_Splice_Site_p.G158_splice|PRR5-ARHGAP8_uc011aqi.1_Splice_Site_p.G149_splice|PRR5-ARHGAP8_uc011aqj.1_Splice_Site_p.G63_splice|ARHGAP8_uc003bfi.2_Splice_Site_p.G27_splice|ARHGAP8_uc010gzv.2_Splice_Site_p.G27_splice|ARHGAP8_uc003bfj.2_Splice_Site_p.G27_splice|ARHGAP8_uc003bfk.2_Splice_Site_p.G27_splice|ARHGAP8_uc003bfl.2_Splice_Site|PRR5-ARHGAP8_uc003bfg.1_Splice_Site_p.G63_splice	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2											skin(2)	2																		---	---	---	---
ARSE	415	broad.mit.edu	37	X	2878425	2878425	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2878425T>C	uc004crc.3	-	2	267	c.17A>G	c.(16-18)CAT>CGT	p.H6R	ARSE_uc011mhi.1_Missense_Mutation_p.H6R|ARSE_uc011mhh.1_5'UTR	NM_000047	NP_000038	P51690	ARSE_HUMAN	arylsulfatase E precursor	6					skeletal system development	Golgi stack	arylsulfatase activity|metal ion binding			ovary(1)|central_nervous_system(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)																---	---	---	---
PNPLA4	8228	broad.mit.edu	37	X	7880058	7880058	+	Intron	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7880058A>G	uc011mhq.1	-						PNPLA4_uc011mhr.1_Intron|PNPLA4_uc011mhs.1_Intron	NM_004650	NP_004641			patatin-like phospholipase domain containing 4						lipid catabolic process		triglyceride lipase activity				0		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)																---	---	---	---
KAL1	3730	broad.mit.edu	37	X	8555928	8555928	+	Silent	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8555928A>C	uc004csf.2	-	5	783	c.633T>G	c.(631-633)TCT>TCG	p.S211S		NM_000216	NP_000207	P23352	KALM_HUMAN	Kallmann syndrome 1 protein precursor	211	Fibronectin type-III 1.				axon guidance|cell adhesion|cellular component movement	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|serine-type endopeptidase inhibitor activity			ovary(3)|pancreas(1)	4																		---	---	---	---
KAL1	3730	broad.mit.edu	37	X	8555953	8555953	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8555953T>G	uc004csf.2	-	5	758	c.608A>C	c.(607-609)AAG>ACG	p.K203T		NM_000216	NP_000207	P23352	KALM_HUMAN	Kallmann syndrome 1 protein precursor	203	Fibronectin type-III 1.				axon guidance|cell adhesion|cellular component movement	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|serine-type endopeptidase inhibitor activity			ovary(3)|pancreas(1)	4																		---	---	---	---
WWC3	55841	broad.mit.edu	37	X	10094344	10094344	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10094344C>T	uc004csx.3	+	15	2302	c.2104C>T	c.(2104-2106)CTG>TTG	p.L702L	WWC3_uc010nds.2_Silent_p.L366L|WWC3_uc010ndt.2_RNA	NM_015691	NP_056506	Q9ULE0	WWC3_HUMAN	WWC family member 3	702	C2.									ovary(4)	4																		---	---	---	---
WWC3	55841	broad.mit.edu	37	X	10106971	10106971	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10106971C>T	uc004csx.3	+	21	3277	c.3079C>T	c.(3079-3081)CGG>TGG	p.R1027W	WWC3_uc010nds.2_Missense_Mutation_p.R691W|WWC3_uc010ndt.2_RNA	NM_015691	NP_056506	Q9ULE0	WWC3_HUMAN	WWC family member 3	1027	Potential.									ovary(4)	4																		---	---	---	---
CLCN4	1183	broad.mit.edu	37	X	10176103	10176103	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10176103C>A	uc004csy.3	+	9	1292	c.862C>A	c.(862-864)CTG>ATG	p.L288M	CLCN4_uc011mid.1_Missense_Mutation_p.L194M	NM_001830	NP_001821	P51793	CLCN4_HUMAN	chloride channel 4	288						early endosome membrane|integral to membrane|late endosome membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5																		---	---	---	---
ASB11	140456	broad.mit.edu	37	X	15307687	15307687	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15307687A>G	uc004cwp.1	-	5	594	c.594T>C	c.(592-594)ACT>ACC	p.T198T	ASB11_uc004cwo.1_Silent_p.T177T|ASB11_uc010nes.1_RNA|ASB11_uc010net.1_Silent_p.T181T	NM_080873	NP_543149	Q8WXH4	ASB11_HUMAN	ankyrin repeat and SOCS box-containing protein	198	ANK 5.				intracellular signal transduction					breast(2)|skin(1)	3	Hepatocellular(33;0.183)																	---	---	---	---
SH3KBP1	30011	broad.mit.edu	37	X	19626152	19626152	+	Silent	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19626152G>A	uc004czm.2	-	9	1225	c.909C>T	c.(907-909)GAC>GAT	p.D303D	SH3KBP1_uc011mje.1_Silent_p.D42D|SH3KBP1_uc011mjf.1_Silent_p.D65D|SH3KBP1_uc004czl.2_Silent_p.D266D	NM_031892	NP_114098	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1 isoform a	303	SH3 3.				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																		---	---	---	---
YY2	404281	broad.mit.edu	37	X	21875159	21875159	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21875159C>T	uc011mjp.1	+	1	557	c.557C>T	c.(556-558)ACT>ATT	p.T186I	MBTPS2_uc004dae.2_Intron|MBTPS2_uc010nfr.2_Intron|YY2_uc010nfq.2_Missense_Mutation_p.T404I|MBTPS2_uc004dab.2_Intron	NM_206923	NP_996806	O15391	TYY2_HUMAN	YY2 transcription factor	186					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	DNA binding|zinc ion binding			breast(1)|skin(1)	2																		---	---	---	---
FAM48B1	100130302	broad.mit.edu	37	X	24381312	24381312	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24381312A>C	uc011mjx.1	+	1	435	c.435A>C	c.(433-435)GAA>GAC	p.E145D		NM_001136234	NP_001129706			hypothetical protein LOC100130302											kidney(1)	1																		---	---	---	---
FAM48B1	100130302	broad.mit.edu	37	X	24381937	24381937	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24381937A>G	uc011mjx.1	+	1	1060	c.1060A>G	c.(1060-1062)ATC>GTC	p.I354V		NM_001136234	NP_001129706			hypothetical protein LOC100130302											kidney(1)	1																		---	---	---	---
POLA1	5422	broad.mit.edu	37	X	24742543	24742543	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24742543A>G	uc004dbl.2	+	12	1297	c.1274A>G	c.(1273-1275)TAT>TGT	p.Y425C	POLA1_uc004dbm.2_Missense_Mutation_p.Y431C|POLA1_uc004dbn.2_Missense_Mutation_p.Y289C	NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1	425					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)													---	---	---	---
CXorf22	170063	broad.mit.edu	37	X	35938122	35938122	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35938122G>A	uc004ddj.2	+	1	265	c.206G>A	c.(205-207)CGC>CAC	p.R69H	CXorf22_uc010ngv.2_RNA	NM_152632	NP_689845	Q6ZTR5	CX022_HUMAN	hypothetical protein LOC170063	69										large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
XK	7504	broad.mit.edu	37	X	37553709	37553709	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37553709C>T	uc004ddq.2	+	2	498	c.416C>T	c.(415-417)GCG>GTG	p.A139V		NM_021083	NP_066569	P51811	XK_HUMAN	membrane transport protein XK	139	Extracellular (Potential).				amino acid transport	integral to membrane	protein binding|transporter activity				0		all_lung(315;0.175)																---	---	---	---
BCOR	54880	broad.mit.edu	37	X	39932620	39932620	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39932620T>G	uc004den.3	-	4	2271	c.1979A>C	c.(1978-1980)TAC>TCC	p.Y660S	BCOR_uc004dep.3_Missense_Mutation_p.Y660S|BCOR_uc004deo.3_Missense_Mutation_p.Y660S|BCOR_uc004dem.3_Missense_Mutation_p.Y660S|BCOR_uc004deq.3_Missense_Mutation_p.Y660S	NM_001123385	NP_001116857	Q6W2J9	BCOR_HUMAN	BCL-6 interacting corepressor isoform c	660	Pro-rich.				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																		---	---	---	---
DUSP21	63904	broad.mit.edu	37	X	44703932	44703932	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44703932G>A	uc004dgd.2	+	1	684	c.554G>A	c.(553-555)CGT>CAT	p.R185H		NM_022076	NP_071359	Q9H596	DUS21_HUMAN	dual specificity phosphatase 21	185						cytoplasm|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			large_intestine(1)|lung(1)	2																		---	---	---	---
SLC9A7	84679	broad.mit.edu	37	X	46508175	46508175	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46508175A>C	uc004dgu.1	-	11	1413	c.1405T>G	c.(1405-1407)TTG>GTG	p.L469V		NM_032591	NP_115980	Q96T83	SL9A7_HUMAN	solute carrier family 9, member 7	469					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																		---	---	---	---
ZNF41	7592	broad.mit.edu	37	X	47308161	47308161	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47308161A>G	uc004dhs.3	-	4	1201	c.1134T>C	c.(1132-1134)TTT>TTC	p.F378F	ZNF41_uc004dhu.3_Silent_p.F370F|ZNF41_uc004dht.3_Silent_p.F250F|ZNF41_uc004dhv.3_Silent_p.F346F|ZNF41_uc004dhw.3_Silent_p.F338F|ZNF41_uc004dhy.3_Silent_p.F336F|ZNF41_uc004dhx.3_Silent_p.F336F|ZNF41_uc011mlm.1_Silent_p.F250F	NM_153380	NP_700359	P51814	ZNF41_HUMAN	zinc finger protein 41	378	C2H2-type 3.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3		all_lung(315;0.000129)																---	---	---	---
WDR13	64743	broad.mit.edu	37	X	48458724	48458724	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48458724G>A	uc004dkh.1	+	6	688	c.541G>A	c.(541-543)GCC>ACC	p.A181T	WDR13_uc010nif.1_Missense_Mutation_p.A59T|WDR13_uc004dki.1_Missense_Mutation_p.A89T|WDR13_uc004dkj.1_Missense_Mutation_p.A181T|WDR13_uc004dkk.1_Missense_Mutation_p.A89T|WDR13_uc004dkl.3_Missense_Mutation_p.A89T|WDR13_uc011mme.1_Missense_Mutation_p.A59T	NM_017883	NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13 protein	181	WD 1.					cytoplasm|nucleus				ovary(2)	2																		---	---	---	---
AKAP4	8852	broad.mit.edu	37	X	49957256	49957256	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49957256G>A	uc004dow.1	-	5	2232	c.2108C>T	c.(2107-2109)TCT>TTT	p.S703F	AKAP4_uc004dov.1_Missense_Mutation_p.S320F|AKAP4_uc010njp.1_Missense_Mutation_p.S525F|AKAP4_uc004dou.1_Missense_Mutation_p.S694F	NM_003886	NP_003877	Q5JQC9	AKAP4_HUMAN	A-kinase anchor protein 4 isoform 1	703					cell projection organization|single fertilization|sperm motility	cAMP-dependent protein kinase complex|cilium|cytoskeleton|microtubule-based flagellum	protein kinase A binding			kidney(3)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	8	Ovarian(276;0.236)																	---	---	---	---
AKAP4	8852	broad.mit.edu	37	X	49958092	49958092	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49958092C>A	uc004dow.1	-	5	1396	c.1272G>T	c.(1270-1272)GAG>GAT	p.E424D	AKAP4_uc004dov.1_Intron|AKAP4_uc010njp.1_Missense_Mutation_p.E246D|AKAP4_uc004dou.1_Missense_Mutation_p.E415D	NM_003886	NP_003877	Q5JQC9	AKAP4_HUMAN	A-kinase anchor protein 4 isoform 1	424					cell projection organization|single fertilization|sperm motility	cAMP-dependent protein kinase complex|cilium|cytoskeleton|microtubule-based flagellum	protein kinase A binding			kidney(3)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	8	Ovarian(276;0.236)																	---	---	---	---
AKAP4	8852	broad.mit.edu	37	X	49962191	49962191	+	Intron	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49962191G>A	uc004dow.1	-						AKAP4_uc004dov.1_Intron|AKAP4_uc010njp.1_Intron|AKAP4_uc004dou.1_Intron	NM_003886	NP_003877			A-kinase anchor protein 4 isoform 1						cell projection organization|single fertilization|sperm motility	cAMP-dependent protein kinase complex|cilium|cytoskeleton|microtubule-based flagellum	protein kinase A binding			kidney(3)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	8	Ovarian(276;0.236)																	---	---	---	---
XAGE3	170626	broad.mit.edu	37	X	52893814	52893814	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:52893814C>T	uc004dre.2	-	4	363	c.303G>A	c.(301-303)ATG>ATA	p.M101I	XAGE3_uc004drf.2_Missense_Mutation_p.M101I	NM_130776	NP_570132	Q8WTP9	GAGD4_HUMAN	XAGE-3 protein	101											0																		---	---	---	---
GNL3L	54552	broad.mit.edu	37	X	54559016	54559016	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54559016A>G	uc004dth.1	+	2	156	c.17A>G	c.(16-18)CAC>CGC	p.H6R	GNL3L_uc004dti.2_RNA	NM_019067	NP_061940	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3	6					ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1																		---	---	---	---
FAAH2	158584	broad.mit.edu	37	X	57367803	57367803	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57367803T>G	uc004dvc.2	+	5	871	c.722T>G	c.(721-723)TTT>TGT	p.F241C		NM_174912	NP_777572	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	241						integral to membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|hydrolase activity			ovary(3)	3															HNSCC(52;0.14)			---	---	---	---
FAM123B	139285	broad.mit.edu	37	X	63411827	63411827	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:63411827C>A	uc004dvo.2	-	2	1613	c.1340G>T	c.(1339-1341)GGC>GTC	p.G447V		NM_152424	NP_689637	Q5JTC6	F123B_HUMAN	family with sequence similarity 123B	447					Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane		p.0?(40)		kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1)	112																		---	---	---	---
FOXO4	4303	broad.mit.edu	37	X	70320655	70320655	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70320655G>A	uc004dys.1	+	2	928	c.575G>A	c.(574-576)CGC>CAC	p.R192H	FOXO4_uc010nkz.2_Missense_Mutation_p.R192H|FOXO4_uc004dyt.1_Missense_Mutation_p.R137H	NM_005938	NP_005929	P98177	FOXO4_HUMAN	forkhead box O4	192					cell cycle arrest|cell differentiation|embryo development|G1 phase of mitotic cell cycle|insulin receptor signaling pathway|mitotic cell cycle G2/M transition DNA damage checkpoint|muscle organ development|negative regulation of angiogenesis|negative regulation of cell proliferation|negative regulation of smooth muscle cell differentiation|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific 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			central_nervous_system(2)|prostate(1)	3	Renal(35;0.156)															OREG0019856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ACRC	93953	broad.mit.edu	37	X	70824105	70824105	+	Missense_Mutation	SNP	T	A	A	rs151063209		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70824105T>A	uc004eae.2	+	8	1479	c.978T>A	c.(976-978)GAT>GAA	p.D326E	BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	326	Asp/Ser-rich.					nucleus				ovary(3)	3	Renal(35;0.156)																	---	---	---	---
ACRC	93953	broad.mit.edu	37	X	70824111	70824111	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70824111T>G	uc004eae.2	+	8	1485	c.984T>G	c.(982-984)AAT>AAG	p.N328K	BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	328	Asp/Ser-rich.					nucleus				ovary(3)	3	Renal(35;0.156)																	---	---	---	---
XIST	7503	broad.mit.edu	37	X	73062930	73062930	+	RNA	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73062930C>T	uc004ebm.1	-	1		c.9659G>A				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0																		---	---	---	---
XIST	7503	broad.mit.edu	37	X	73071272	73071272	+	RNA	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73071272G>T	uc004ebm.1	-	1		c.1317C>A				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0																		---	---	---	---
KIAA2022	340533	broad.mit.edu	37	X	73959959	73959959	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73959959C>A	uc004eby.2	-	3	5050	c.4433G>T	c.(4432-4434)GGG>GTG	p.G1478V		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	1478					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																		---	---	---	---
P2RY10	27334	broad.mit.edu	37	X	78216820	78216820	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78216820T>C	uc004ede.2	+	4	1172	c.803T>C	c.(802-804)ATG>ACG	p.M268T	P2RY10_uc004edf.2_Missense_Mutation_p.M268T	NM_014499	NP_055314	O00398	P2Y10_HUMAN	G-protein coupled purinergic receptor P2Y10	268	Extracellular (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(2)|lung(2)|breast(1)	5																		---	---	---	---
POU3F4	5456	broad.mit.edu	37	X	82764202	82764202	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82764202G>T	uc004eeg.2	+	1	934	c.870G>T	c.(868-870)AAG>AAT	p.K290N		NM_000307	NP_000298	P49335	PO3F4_HUMAN	POU domain, class 3, transcription factor 4	290	Homeobox.				sensory perception of sound	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
DACH2	117154	broad.mit.edu	37	X	85950100	85950100	+	Silent	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85950100T>G	uc004eew.2	+	5	1019	c.849T>G	c.(847-849)GCT>GCG	p.A283A	DACH2_uc004eex.2_Silent_p.A270A|DACH2_uc010nmq.2_Silent_p.A149A|DACH2_uc011mra.1_Silent_p.A116A|DACH2_uc010nmr.2_Silent_p.A64A	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a	283					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5																		---	---	---	---
TGIF2LX	90316	broad.mit.edu	37	X	89177518	89177518	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89177518A>C	uc004efe.2	+	2	483	c.434A>C	c.(433-435)AAG>ACG	p.K145T		NM_138960	NP_620410	Q8IUE1	TF2LX_HUMAN	TGFB-induced factor homeobox 2-like, X-linked	145						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2																		---	---	---	---
PCDH11X	27328	broad.mit.edu	37	X	91873813	91873813	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91873813C>A	uc004efk.1	+	7	4763	c.3918C>A	c.(3916-3918)ACC>ACA	p.T1306T	PCDH11X_uc004efl.1_Silent_p.T1296T|PCDH11X_uc004efo.1_Silent_p.T1269T|PCDH11X_uc010nmv.1_3'UTR|PCDH11X_uc004efm.1_Silent_p.T1298T|PCDH11X_uc004efn.1_Silent_p.T1288T	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	1306	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2																		---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96502819	96502819	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96502819A>C	uc004efu.3	+	23	3221	c.2825A>C	c.(2824-2826)AAG>ACG	p.K942T	DIAPH2_uc004eft.3_Missense_Mutation_p.K942T	NM_006729	NP_006720	O60879	DIAP2_HUMAN	diaphanous 2 isoform 156	942	Potential.|FH2.				cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4																		---	---	---	---
PCDH19	57526	broad.mit.edu	37	X	99662916	99662916	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99662916T>G	uc010nmz.2	-	1	2356	c.680A>C	c.(679-681)AAG>ACG	p.K227T	PCDH19_uc004efw.3_Missense_Mutation_p.K227T|PCDH19_uc004efx.3_Missense_Mutation_p.K227T	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b	227	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7																		---	---	---	---
DRP2	1821	broad.mit.edu	37	X	100511132	100511132	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100511132C>G	uc004egz.2	+	21	2641	c.2272C>G	c.(2272-2274)CAC>GAC	p.H758D	DRP2_uc011mrh.1_Missense_Mutation_p.H680D	NM_001939	NP_001930	Q13474	DRP2_HUMAN	dystrophin related protein 2	758					central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2																		---	---	---	---
BHLHB9	80823	broad.mit.edu	37	X	102004719	102004719	+	Missense_Mutation	SNP	C	T	T	rs149330911		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102004719C>T	uc010nog.2	+	4	1367	c.796C>T	c.(796-798)CGC>TGC	p.R266C	BHLHB9_uc011mrq.1_Missense_Mutation_p.R266C|BHLHB9_uc011mrr.1_Missense_Mutation_p.R266C|BHLHB9_uc011mrs.1_Missense_Mutation_p.R266C|BHLHB9_uc011mrt.1_Missense_Mutation_p.R266C|BHLHB9_uc004ejo.2_Missense_Mutation_p.R266C|BHLHB9_uc011mru.1_Missense_Mutation_p.R266C|BHLHB9_uc011mrv.1_Missense_Mutation_p.R266C	NM_001142526	NP_001135998	Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class	266						cytoplasm|nucleus	binding			ovary(2)	2																		---	---	---	---
TCEAL5	340543	broad.mit.edu	37	X	102529417	102529417	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102529417C>A	uc004ejz.1	-	3	370	c.75G>T	c.(73-75)GAG>GAT	p.E25D		NM_001012979	NP_001012997	Q5H9L2	TCAL5_HUMAN	transcription elongation factor A (SII)-like 5	25	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(1)|breast(1)	2																		---	---	---	---
GUCY2F	2986	broad.mit.edu	37	X	108718959	108718959	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108718959C>A	uc004eod.3	-	2	483	c.207G>T	c.(205-207)AAG>AAT	p.K69N	GUCY2F_uc011msq.1_RNA	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	69	Extracellular (Potential).				intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8																OREG0019905	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TRPC5	7224	broad.mit.edu	37	X	111155719	111155719	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111155719C>G	uc004epl.1	-	3	1619	c.700G>C	c.(700-702)GAG>CAG	p.E234Q	TRPC5_uc004epm.1_Missense_Mutation_p.E234Q	NM_012471	NP_036603	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel,	234	Cytoplasmic (Potential).				axon guidance	calcium channel complex|integral to plasma membrane	protein binding|store-operated calcium channel activity			urinary_tract(1)	1																		---	---	---	---
KLHL13	90293	broad.mit.edu	37	X	117054219	117054219	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117054219A>G	uc004eql.2	-	3	417	c.355T>C	c.(355-357)TTC>CTC	p.F119L	KLHL13_uc004eqk.2_Missense_Mutation_p.F68L|KLHL13_uc011mtn.1_5'UTR|KLHL13_uc011mto.1_Missense_Mutation_p.F113L|KLHL13_uc011mtp.1_Missense_Mutation_p.F121L|KLHL13_uc004eqm.2_Missense_Mutation_p.F68L|KLHL13_uc011mtq.1_Missense_Mutation_p.F103L	NM_033495	NP_277030	Q9P2N7	KLH13_HUMAN	kelch-like 13	119	BTB.				cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex				kidney(1)|skin(1)	2																		---	---	---	---
SLC25A5	292	broad.mit.edu	37	X	118604463	118604463	+	Silent	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118604463A>G	uc004erh.3	+	3	842	c.726A>G	c.(724-726)TCA>TCG	p.S242S	LOC100303728_uc004ere.1_5'Flank|LOC100303728_uc004erg.1_5'Flank	NM_001152	NP_001143	P05141	ADT2_HUMAN	adenine nucleotide translocator 2	242	Solcar 3.				chromosome segregation|energy reserve metabolic process|interspecies interaction between organisms|regulation of insulin secretion|viral reproduction	integral to plasma membrane|mitochondrial inner membrane|mitochondrial nucleoid|MMXD complex	adenine transmembrane transporter activity|protein binding			ovary(1)	1					Clodronate(DB00720)													---	---	---	---
CUL4B	8450	broad.mit.edu	37	X	119669715	119669715	+	Silent	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119669715T>C	uc004esw.2	-	18	2621	c.2184A>G	c.(2182-2184)GGA>GGG	p.G728G	CUL4B_uc010nqq.2_Silent_p.G429G|CUL4B_uc004esv.2_Silent_p.G710G	NM_003588	NP_003579	Q13620	CUL4B_HUMAN	cullin 4B isoform 1	728					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	123517645	123517645	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123517645T>C	uc004euj.2	-	29	7179	c.7115A>G	c.(7114-7116)CAC>CGC	p.H2372R	ODZ1_uc011muj.1_Missense_Mutation_p.H2378R|ODZ1_uc010nqy.2_Missense_Mutation_p.H2379R	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	2372	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																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123526074	123526074	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123526074C>A	uc004euj.2	-	27	5559	c.5495G>T	c.(5494-5496)TGG>TTG	p.W1832L	ODZ1_uc011muj.1_Missense_Mutation_p.W1838L|ODZ1_uc010nqy.2_Missense_Mutation_p.W1839L	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	1832	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																		---	---	---	---
UTP14A	10813	broad.mit.edu	37	X	129055391	129055391	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129055391C>G	uc004euz.2	+	11	1204	c.1176C>G	c.(1174-1176)GAC>GAG	p.D392E	UTP14A_uc011mup.1_Missense_Mutation_p.D340E|UTP14A_uc011muq.1_Missense_Mutation_p.D338E|UTP14A_uc004eva.1_Missense_Mutation_p.D98E	NM_006649	NP_006640	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein,	392					rRNA processing	nucleolus|small-subunit processome	protein binding			ovary(2)	2																		---	---	---	---
ARHGAP36	158763	broad.mit.edu	37	X	130215768	130215768	+	Silent	SNP	C	A	A	rs150725005	byFrequency	TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130215768C>A	uc004evz.2	+	2	474	c.129C>A	c.(127-129)CCC>CCA	p.P43P	ARHGAP36_uc004ewa.2_Silent_p.P31P|ARHGAP36_uc004ewb.2_Silent_p.P12P|ARHGAP36_uc004ewc.2_5'Flank	NM_144967	NP_659404	Q6ZRI8	RHG36_HUMAN	hypothetical protein LOC158763 precursor	43					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3																		---	---	---	---
IGSF1	3547	broad.mit.edu	37	X	130410940	130410940	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130410940T>C	uc004ewd.2	-	14	2819	c.2581A>G	c.(2581-2583)AGC>GGC	p.S861G	IGSF1_uc004ewe.3_Missense_Mutation_p.S855G|IGSF1_uc004ewf.2_Missense_Mutation_p.S841G	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	861	Extracellular (Potential).|Ig-like C2-type 8.				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
FRMD7	90167	broad.mit.edu	37	X	131216453	131216453	+	Silent	SNP	C	T	T	rs145014972		TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131216453C>T	uc004ewn.2	-	9	1021	c.843G>A	c.(841-843)TCG>TCA	p.S281S	FRMD7_uc011muy.1_Silent_p.S266S	NM_194277	NP_919253	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	281	FERM.				regulation of neuron projection development	cytoskeleton|growth cone|neuronal cell body	binding			skin(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
GPR112	139378	broad.mit.edu	37	X	135405357	135405357	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135405357T>C	uc004ezu.1	+	5	782	c.491T>C	c.(490-492)CTC>CCC	p.L164P	GPR112_uc010nsb.1_Intron	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	164	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1)	12	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MAGEC1	9947	broad.mit.edu	37	X	140995628	140995628	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140995628C>A	uc004fbt.2	+	4	2724	c.2438C>A	c.(2437-2439)CCT>CAT	p.P813H	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	813							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)														HNSCC(15;0.026)			---	---	---	---
AFF2	2334	broad.mit.edu	37	X	147891389	147891389	+	Intron	SNP	T	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147891389T>C	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)																	---	---	---	---
AFF2	2334	broad.mit.edu	37	X	148037692	148037692	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148037692A>G	uc004fcp.2	+	11	2596	c.2117A>G	c.(2116-2118)AAG>AGG	p.K706R	AFF2_uc004fcq.2_Missense_Mutation_p.K696R|AFF2_uc004fcr.2_Missense_Mutation_p.K667R|AFF2_uc011mxb.1_Missense_Mutation_p.K671R|AFF2_uc004fcs.2_Missense_Mutation_p.K673R|AFF2_uc011mxc.1_Missense_Mutation_p.K347R	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2	706					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)																	---	---	---	---
MTMR1	8776	broad.mit.edu	37	X	149905924	149905924	+	Intron	SNP	A	C	C			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149905924A>C	uc004fei.2	+						MTMR1_uc011mya.1_Intron|MTMR1_uc004feh.1_Intron|MTMR1_uc004fej.2_Intron|MTMR1_uc010ntf.2_Intron	NM_003828	NP_003819			myotubularin-related protein 1							plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PRRG3	79057	broad.mit.edu	37	X	150869254	150869254	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150869254C>T	uc004few.1	+	4	835	c.445C>T	c.(445-447)CGA>TGA	p.R149*		NM_024082	NP_076987	Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3	149	Cytoplasmic (Potential).					extracellular region|integral to membrane	calcium ion binding			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
CNGA2	1260	broad.mit.edu	37	X	150912578	150912578	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150912578C>T	uc004fey.1	+	7	1827	c.1603C>T	c.(1603-1605)CGA>TGA	p.R535*		NM_005140	NP_005131	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	535	cAMP (By similarity).|Cytoplasmic (Potential).				response to stimulus|sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
ATP2B3	492	broad.mit.edu	37	X	152814984	152814984	+	Silent	SNP	C	T	T			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152814984C>T	uc004fht.1	+	9	1494	c.1368C>T	c.(1366-1368)CGC>CGT	p.R456R	ATP2B3_uc004fhs.1_Silent_p.R456R	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	456	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
DUSP9	1852	broad.mit.edu	37	X	152915040	152915040	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152915040T>G	uc004fhx.3	+	3	931	c.727T>G	c.(727-729)TTC>GTC	p.F243V	DUSP9_uc004fhy.3_Missense_Mutation_p.F243V	NM_001395	NP_001386	Q99956	DUS9_HUMAN	dual specificity phosphatase 9	243	Tyrosine-protein phosphatase.				inactivation of MAPK activity|JNK cascade	cytosol|endoplasmic reticulum|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)	2	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
HCFC1	3054	broad.mit.edu	37	X	153219666	153219666	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153219666G>A	uc004fjp.2	-	17	4712	c.4184C>T	c.(4183-4185)GCG>GTG	p.A1395V		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	1395					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)																	---	---	---	---
OPN1LW	5956	broad.mit.edu	37	X	153422003	153422003	+	Silent	SNP	C	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153422003C>A	uc004fjz.3	+	5	1012	c.979C>A	c.(979-981)CGG>AGG	p.R327R		NM_020061	NP_064445	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	327	Cytoplasmic.				phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity				0	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
EMD	2010	broad.mit.edu	37	X	153609454	153609454	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4280-01A-01D-1126-08	TCGA-BR-4280-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153609454G>A	uc004fkl.2	+	6	910	c.662G>A	c.(661-663)CGC>CAC	p.R221H		NM_000117	NP_000108	P50402	EMD_HUMAN	emerin	221	Interaction with F-actin (Probable).				cellular response to growth factor stimulus|muscle contraction|muscle organ development|negative regulation of catenin import into nucleus|negative regulation of fibroblast proliferation|positive regulation of protein export from nucleus|regulation of canonical Wnt receptor signaling pathway	endoplasmic reticulum|integral to membrane|microtubule|nuclear inner membrane|nuclear outer membrane	actin binding|beta-tubulin binding				0	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
