Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	validation_status	validation_method	validation_tumor_sample	validation_alt_allele
Unknown	0	broad.mit.edu	37	1	757808	757842	+	IGR	DEL	CCTGGCCAGCAGATCCACCCTGTCTATACTACCTG	-	-	rs12736354	by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:757808_757842delCCTGGCCAGCAGATCCACCCTGTCTATACTACCTG								LOC100133331 (78072 upstream) : NCRNA00115 (3745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	826182	826183	+	IGR	DEL	AG	-	-	rs75585849		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:826182_826183delAG								FAM41C (14000 upstream) : FLJ39609 (26770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	1531384	1531385	+	IGR	INS	-	AG	AG			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1531384_1531385insAG								SSU72 (21122 upstream) : MIB2 (19499 downstream)																																			---	---	---	---
GNB1	2782	broad.mit.edu	37	1	1814718	1814719	+	Intron	DEL	AA	-	-	rs71578348		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1814718_1814719delAA	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	2812239	2812240	+	IGR	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2812239_2812240insG								MMEL1 (247758 upstream) : ACTRT2 (125806 downstream)																																			---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3098005	3098014	+	Intron	DEL	GTCTTACACG	-	-	rs143051454	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3098005_3098014delGTCTTACACG	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397			PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)				T	EVI1	MDS|AML								---	---	---	---
AJAP1	55966	broad.mit.edu	37	1	4813139	4813141	+	Intron	DEL	CTC	-	-	rs141619940		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4813139_4813141delCTC	uc001alm.1	+						AJAP1_uc001aln.2_Intron	NM_001042478	NP_001035943			adherens junction associated protein 1						cell adhesion	adherens junction|apical plasma membrane|basolateral plasma membrane|integral to membrane				lung(1)	1	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	5163906	5163907	+	IGR	INS	-	AC	AC	rs151011907	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5163906_5163907insAC								AJAP1 (320056 upstream) : NPHP4 (758963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5488960	5488961	+	IGR	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5488960_5488961delAG								AJAP1 (645110 upstream) : NPHP4 (433909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5694102	5694103	+	Intron	INS	-	TG	TG	rs141852834	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5694102_5694103insTG	uc001alp.1	-											Homo sapiens cDNA FLJ43088 fis, clone BRTHA3025826.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	5901220	5901220	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5901220delA								None (None upstream) : NPHP4 (21650 downstream)																																			---	---	---	---
TAS1R1	80835	broad.mit.edu	37	1	6621046	6621047	+	Intron	INS	-	AA	AA	rs35928406		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6621046_6621047insAA	uc001ant.2	+						TAS1R1_uc001anu.2_Intron|TAS1R1_uc001anv.2_Intron|TAS1R1_uc001anw.2_Intron	NM_138697	NP_619642			sweet taste receptor T1r isoform b						sensory perception of umami taste	plasma membrane	protein heterodimerization activity|taste receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7196587	7196587	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7196587delA	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)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8652309	8652309	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8652309delA	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc001aph.1_Intron	NM_012102	NP_036234			atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8751354	8751355	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8751354_8751355insT	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)														---	---	---	---
SLC2A5	6518	broad.mit.edu	37	1	9130896	9130897	+	5'Flank	DEL	TG	-	-	rs111643348		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9130896_9130897delTG	uc001apo.2	-						SLC2A5_uc010nzz.1_5'Flank|SLC2A5_uc010oaa.1_5'Flank|SLC2A5_uc010oab.1_Intron|SLC2A5_uc010oac.1_5'Flank|SLC2A5_uc001app.3_5'Flank	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)														---	---	---	---
GPR157	80045	broad.mit.edu	37	1	9168052	9168074	+	Intron	DEL	GAGGTGGAAGTTGCAGTGAGCCA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9168052_9168074delGAGGTGGAAGTTGCAGTGAGCCA	uc001apq.1	-						GPR157_uc010oad.1_Intron	NM_024980	NP_079256			G protein-coupled receptor 157							integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_lung(157;0.185)	all_epithelial(116;5.02e-20)|all_lung(118;3.6e-06)|Lung NSC(185;7.93e-06)|Renal(390;0.000147)|Breast(348;0.000688)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.16e-07)|COAD - Colon adenocarcinoma(227;7.73e-05)|Kidney(185;0.000252)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.00178)|BRCA - Breast invasive adenocarcinoma(304;0.00186)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
SPSB1	80176	broad.mit.edu	37	1	9422238	9422239	+	Intron	INS	-	CCCT	CCCT	rs144540586	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9422238_9422239insCCCT	uc010oae.1	+						SPSB1_uc001apv.2_Intron	NM_025106	NP_079382			splA/ryanodine receptor domain and SOCS box						intracellular signal transduction	cytoplasm					0	all_lung(157;0.194)	all_epithelial(116;4.38e-15)|all_lung(118;0.000156)|Lung NSC(185;0.000446)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.72e-07)|COAD - Colon adenocarcinoma(227;9.12e-05)|Kidney(185;0.000296)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00193)|BRCA - Breast invasive adenocarcinoma(304;0.00202)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
PEX14	5195	broad.mit.edu	37	1	10626551	10626551	+	Intron	DEL	T	-	-	rs71583881		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10626551delT	uc001arn.2	+						PEX14_uc001arm.1_Intron|PEX14_uc009vmu.1_Intron|PEX14_uc009vmv.2_Intron|PEX14_uc010oam.1_Intron|PEX14_uc010oan.1_Intron|PEX14_uc009vmw.2_Intron	NM_004565	NP_004556			peroxisomal biogenesis factor 14						negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|protein homooligomerization|protein import into peroxisome matrix|transmembrane transport	integral to membrane|nucleus|peroxisomal membrane|protein complex	protein N-terminus binding|transcription corepressor activity			breast(1)	1	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	10958077	10958078	+	IGR	DEL	GT	-	-	rs35259916		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10958077_10958078delGT								CASZ1 (101370 upstream) : C1orf127 (48455 downstream)																																			---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11303745	11303745	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11303745delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	11469516	11469516	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11469516delT								UBIAD1 (121026 upstream) : PTCHD2 (69779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	11616734	11616735	+	IGR	DEL	GT	-	-	rs112989824		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11616734_11616735delGT								PTCHD2 (19095 upstream) : FBXO2 (91715 downstream)																																			---	---	---	---
AGTRAP	57085	broad.mit.edu	37	1	11793674	11793675	+	5'Flank	INS	-	T	T	rs71585867		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11793674_11793675insT	uc001asv.2	+						AGTRAP_uc001ast.2_5'Flank|AGTRAP_uc001asu.2_5'Flank|AGTRAP_uc001asw.2_5'Flank|AGTRAP_uc001asx.2_5'Flank	NM_020350	NP_065083			angiotensin II receptor-associated protein							cytoplasmic vesicle membrane|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein binding		AGTRAP/BRAF(2)	stomach(2)	2	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.46e-06)|COAD - Colon adenocarcinoma(227;0.000256)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
AGTRAP	57085	broad.mit.edu	37	1	11802499	11802506	+	Intron	DEL	TTCCTTCC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11802499_11802506delTTCCTTCC	uc001asv.2	+						AGTRAP_uc001ast.2_Intron|AGTRAP_uc001asu.2_Intron|AGTRAP_uc001asw.2_Intron|AGTRAP_uc001asx.2_Intron	NM_020350	NP_065083			angiotensin II receptor-associated protein							cytoplasmic vesicle membrane|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein binding		AGTRAP/BRAF(2)	stomach(2)	2	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.46e-06)|COAD - Colon adenocarcinoma(227;0.000256)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	11989909	11989909	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11989909delA								KIAA2013 (3429 upstream) : PLOD1 (4837 downstream)																																			---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12288133	12288134	+	5'Flank	INS	-	TT	TT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12288133_12288134insTT	uc001atv.2	+						VPS13D_uc001atw.2_5'Flank	NM_015378	NP_056193			vacuolar protein sorting 13D isoform 1						protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	12747800	12747800	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12747800delA								AADACL4 (20704 upstream) : AADACL3 (28318 downstream)																																			---	---	---	---
LOC440563	440563	broad.mit.edu	37	1	13184079	13184080	+	5'Flank	INS	-	T	T	rs146762683	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13184079_13184080insT	uc010obg.1	-							NM_001136561	NP_001130033			heterogeneous nuclear ribonucleoprotein C-like							ribonucleoprotein complex	nucleic acid binding|nucleotide binding				0																		---	---	---	---
PDPN	10630	broad.mit.edu	37	1	13910742	13910744	+	Intron	DEL	GGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13910742_13910744delGGA	uc001avd.2	+						PDPN_uc001avc.2_Intron|PDPN_uc009vob.2_5'Flank|PDPN_uc009voc.2_5'Flank|PDPN_uc001ave.2_5'Flank|PDPN_uc001avf.2_5'Flank	NM_006474	NP_006465			lung type-I cell membrane-associated						cell morphogenesis|lymphangiogenesis|regulation of cell shape	filopodium membrane|integral to plasma membrane|lamellipodium membrane|microvillus membrane|ruffle membrane				ovary(2)	2	Ovarian(185;0.249)	all_lung(284;2.29e-05)|Lung NSC(185;4.37e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00969)|Colorectal(212;4.48e-06)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000347)|Kidney(185;0.00087)|KIRC - Kidney renal clear cell carcinoma(229;0.0027)|STAD - Stomach adenocarcinoma(313;0.00802)|READ - Rectum adenocarcinoma(331;0.0678)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	14226652	14226653	+	IGR	INS	-	TT	TT	rs144203715	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14226652_14226653insTT								PRDM2 (75080 upstream) : KAZ (698560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14390450	14390451	+	IGR	INS	-	TT	TT	rs149930474	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14390450_14390451insTT								PRDM2 (238878 upstream) : KAZ (534762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14506625	14506625	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14506625delT								PRDM2 (355053 upstream) : KAZ (418588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14665110	14665111	+	IGR	INS	-	G	G	rs145925640	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14665110_14665111insG								PRDM2 (513538 upstream) : KAZ (260102 downstream)																																			---	---	---	---
KAZ	23254	broad.mit.edu	37	1	15375597	15375598	+	Intron	INS	-	G	G	rs145123266	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15375597_15375598insG	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron|KAZ_uc001avo.2_Intron|KAZ_uc001avp.2_Intron|KAZ_uc001avq.2_Intron|KAZ_uc001avr.2_Intron	NM_201628	NP_963922			kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0																		---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16190241	16190242	+	Intron	INS	-	A	A	rs138522564	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16190241_16190242insA	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	16517923	16517926	+	IGR	DEL	GGAG	-	-	rs111976774		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16517923_16517926delGGAG								EPHA2 (35359 upstream) : ARHGEF19 (6673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	16834393	16834393	+	IGR	DEL	G	-	-	rs6603868		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16834393delG								CROCCL2 (15197 upstream) : NBPF1 (56019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	16840176	16840177	+	IGR	INS	-	AG	AG	rs59871634		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16840176_16840177insAG								CROCCL2 (20980 upstream) : NBPF1 (50235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	16856184	16856184	+	IGR	DEL	T	-	-	rs76459018		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16856184delT								CROCCL2 (36988 upstream) : NBPF1 (34228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	16982682	16982683	+	IGR	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16982682_16982683delCT								MST1P2 (5768 upstream) : ESPNP (35030 downstream)																																			---	---	---	---
ESPNP	284729	broad.mit.edu	37	1	17048585	17048586	+	5'Flank	DEL	TA	-	-	rs3982087		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17048585_17048586delTA	uc001azn.1	-							NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	17730431	17730431	+	IGR	DEL	A	-	-	rs35524229		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17730431delA								PADI6 (2236 upstream) : RCC2 (2821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	19387850	19387858	+	IGR	DEL	CATCATCAC	-	-	rs11267789		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19387850_19387858delCATCATCAC								IFFO2 (105024 upstream) : UBR4 (10746 downstream)																																			---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19474009	19474009	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19474009delT	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)														---	---	---	---
CAPZB	832	broad.mit.edu	37	1	19686833	19686833	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19686833delA	uc010ocz.1	-						CAPZB_uc001bce.2_Intron|CAPZB_uc009vpk.2_Intron|CAPZB_uc001bcd.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)														---	---	---	---
TMCO4	255104	broad.mit.edu	37	1	20083937	20083937	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20083937delC	uc001bcn.2	-						TMCO4_uc001bcm.2_Intron|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron|TMCO4_uc009vpn.1_Intron|TMCO4_uc001bcq.1_Intron	NM_181719	NP_859070			transmembrane and coiled-coil domains 4							integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	20614034	20614034	+	IGR	DEL	T	-	-	rs35255386		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20614034delT								UBXN10 (94093 upstream) : VWA5B1 (3378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	20709118	20709119	+	Intron	DEL	GG	-	-	rs143708145		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20709118_20709119delGG	uc009vpu.1	-						uc001bdf.1_Intron					Homo sapiens cDNA clone IMAGE:5269505.																														---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21162552	21162552	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21162552delA	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron	NM_003760	NP_003751			eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	22514281	22514282	+	IGR	INS	-	T	T	rs35946822		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22514281_22514282insT								WNT4 (43896 upstream) : ZBTB40 (264062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22976426	22976427	+	IGR	DEL	AT	-	-	rs140433226		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22976426_22976427delAT								C1QC (1824 upstream) : C1QB (3255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	24957088	24957089	+	IGR	INS	-	A	A	rs11422133		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24957088_24957089insA								C1orf130 (21272 upstream) : SRRM1 (12505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25512662	25512663	+	IGR	INS	-	T	T	rs139375924		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25512662_25512663insT								RUNX3 (221050 upstream) : SYF2 (36104 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25587291	25587291	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25587291delT								C1orf63 (13306 upstream) : RHD (11690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	26471159	26471159	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26471159delA								PDIK1L (19135 upstream) : GRRP1 (14352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	27148757	27148757	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27148757delT								PIGV (23871 upstream) : ZDHHC18 (4444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	28192018	28192018	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28192018delA								PPP1R8 (13835 upstream) : C1orf38 (7037 downstream)																																			---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28776362	28776362	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28776362delA	uc001bpw.2	+						PHACTR4_uc001bpu.2_Intron|PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron	NM_001048183	NP_001041648			phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29277874	29277879	+	Intron	DEL	ACACAC	-	-	rs112426364		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29277874_29277879delACACAC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	29719418	29719421	+	IGR	DEL	TGGG	-	-	rs2764520		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29719418_29719421delTGGG								PTPRU (66103 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30291482	30291483	+	IGR	INS	-	TG	TG	rs151259923	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30291482_30291483insTG								PTPRU (638167 upstream) : MATN1 (892643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30988406	30988429	+	IGR	DEL	AGAAGGGTGGACAGGACTTAGCAG	-	-	rs146166054		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30988406_30988429delAGAAGGGTGGACAGGACTTAGCAG								None (None upstream) : MATN1 (195697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30992656	30992657	+	IGR	INS	-	G	G	rs145067832	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30992656_30992657insG								None (None upstream) : MATN1 (191469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	31128526	31128528	+	IGR	DEL	CGG	-	-	rs71028713		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31128526_31128528delCGG								None (None upstream) : MATN1 (55598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	31853901	31853908	+	IGR	DEL	AAACAAAC	-	-	rs72039797		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31853901_31853908delAAACAAAC								FABP3 (7978 upstream) : SERINC2 (29140 downstream)																																			---	---	---	---
RNF19B	127544	broad.mit.edu	37	1	33416445	33416446	+	Intron	DEL	TT	-	-	rs111860334		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33416445_33416446delTT	uc010oho.1	-						RNF19B_uc001bwm.3_Intron|RNF19B_uc010ohp.1_Intron	NM_153341	NP_699172			ring finger protein 19B isoform a							integral to membrane	ligase activity|protein binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
PHC2	1912	broad.mit.edu	37	1	33857768	33857769	+	Intron	INS	-	CA	CA	rs145325204	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33857768_33857769insCA	uc009vuh.1	-						PHC2_uc001bxi.1_Intron	NM_198040	NP_932157			polyhomeotic-like 2 isoform a						multicellular organismal development	PcG protein complex	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34368950	34368950	+	Intron	DEL	A	-	-	rs10914811	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34368950delA	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	34767343	34767343	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34767343delT								C1orf94 (82614 upstream) : MIR552 (367857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	34907193	34907194	+	IGR	INS	-	C	C	rs143825347	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34907193_34907194insC								C1orf94 (222464 upstream) : MIR552 (228006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	35509102	35509103	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35509102_35509103insA								ZMYM6 (11533 upstream) : ZMYM1 (35869 downstream)																																			---	---	---	---
PSMB2	5690	broad.mit.edu	37	1	36088411	36088412	+	Intron	INS	-	A	A	rs113355309		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36088411_36088412insA	uc001bzf.1	-						PSMB2_uc001bzd.1_Intron|PSMB2_uc010ohz.1_Intron|PSMB2_uc001bzg.1_Intron	NM_002794	NP_002785			proteasome beta 2 subunit						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)													---	---	---	---
EIF2C3	192669	broad.mit.edu	37	1	36482198	36482198	+	Intron	DEL	T	-	-	rs75395552		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36482198delT	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)																---	---	---	---
THRAP3	9967	broad.mit.edu	37	1	36715286	36715287	+	Intron	INS	-	GT	GT	rs112896222		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36715286_36715287insGT	uc001cae.3	+						THRAP3_uc001caf.3_Intron|THRAP3_uc001cag.1_Intron	NM_005119	NP_005110			thyroid hormone receptor associated protein 3						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(5)|lung(3)|breast(1)	9		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)						T	USP6	aneurysmal bone cysts								---	---	---	---
Unknown	0	broad.mit.edu	37	1	37581908	37581908	+	IGR	DEL	T	-	-	rs67813249		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37581908delT								GRIK3 (82064 upstream) : ZC3H12A (358211 downstream)																																			---	---	---	---
C1orf109	54955	broad.mit.edu	37	1	38150669	38150670	+	Intron	INS	-	A	A	rs146561239	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38150669_38150670insA	uc001cbp.2	-						C1orf109_uc001cbn.2_5'Flank|C1orf109_uc010oig.1_Intron|C1orf109_uc001cbo.2_Intron	NM_017850	NP_060320			hypothetical protein LOC54955												0		Myeloproliferative disorder(586;0.0393)																---	---	---	---
CDCA8	55143	broad.mit.edu	37	1	38173233	38173236	+	Intron	DEL	CTTA	-	-	rs138000023		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38173233_38173236delCTTA	uc001cbr.2	+						CDCA8_uc001cbs.2_Intron	NM_018101	NP_060571			cell division cycle associated 8						cell division|chromosome organization|mitotic metaphase|mitotic prometaphase	chromosome passenger complex|chromosome, centromeric region|cytosol|nucleolus|spindle	protein binding			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
INPP5B	3633	broad.mit.edu	37	1	38399053	38399061	+	Intron	DEL	CACAAAAAA	-	-	rs28597889	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38399053_38399061delCACAAAAAA	uc001ccg.1	-						INPP5B_uc009vvk.1_Intron|INPP5B_uc001cch.2_Intron|INPP5B_uc001ccf.1_5'Flank	NM_005540	NP_005531			inositol polyphosphate-5-phosphatase, 75kDa						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to membrane|microtubule cytoskeleton	GTPase activator activity|inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			urinary_tract(1)	1	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	38733849	38733850	+	IGR	INS	-	AT	AT	rs150311367	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38733849_38733850insAT								POU3F1 (221399 upstream) : RRAGC (571165 downstream)																																			---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39668307	39668307	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39668307delA	uc010ois.1	+						MACF1_uc001cda.1_Intron|MACF1_uc010oit.1_5'Flank	NM_012090	NP_036222			microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	40495526	40495527	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40495526_40495527delAC								MFSD2A (59899 upstream) : CAP1 (10728 downstream)																																			---	---	---	---
CAP1	10487	broad.mit.edu	37	1	40528445	40528446	+	Intron	INS	-	TGTG	TGTG	rs149848747	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40528445_40528446insTGTG	uc001cfa.3	+						CAP1_uc001cey.3_Intron|CAP1_uc001cez.3_Intron|CAP1_uc009vvz.2_Intron|CAP1_uc010oje.1_Intron	NM_006367	NP_006358			adenylyl cyclase-associated protein						activation of adenylate cyclase activity|axon guidance|establishment or maintenance of cell polarity|platelet activation|platelet degranulation|signal transduction	plasma membrane	actin binding			ovary(1)	1	Lung NSC(20;5.03e-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;4.63e-18)|Epithelial(16;1.27e-16)|all cancers(16;2.3e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
KCNQ4	9132	broad.mit.edu	37	1	41281720	41281720	+	Intron	DEL	T	-	-	rs35550137		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41281720delT	uc001cgh.1	+						KCNQ4_uc001cgi.1_Intron	NM_004700	NP_004691			potassium voltage-gated channel KQT-like protein						sensory perception of sound	basal plasma membrane|voltage-gated potassium channel complex				central_nervous_system(1)	1	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	41851503	41851506	+	IGR	DEL	TGTC	-	-	rs5773726		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41851503_41851506delTGTC								SCMH1 (143715 upstream) : EDN2 (92943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	41887181	41887181	+	IGR	DEL	T	-	-	rs144726054		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41887181delT								SCMH1 (179393 upstream) : EDN2 (57268 downstream)																																			---	---	---	---
FOXJ3	22887	broad.mit.edu	37	1	42753985	42753986	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42753985_42753986delAC	uc001che.2	-						FOXJ3_uc001chf.2_Intron|FOXJ3_uc001chg.2_Intron|FOXJ3_uc001chh.1_Intron	NM_014947	NP_055762			forkhead box J3						embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
CCDC30	728621	broad.mit.edu	37	1	42986649	42986650	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42986649_42986650insT	uc001chn.2	+						CCDC30_uc001chm.2_Intron|CCDC30_uc010oju.1_Intron	NM_001080850	NP_001074319			coiled-coil domain containing 30												0																		---	---	---	---
YBX1	4904	broad.mit.edu	37	1	43162183	43162183	+	Intron	DEL	C	-	-	rs113762321		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43162183delC	uc001chs.2	+							NM_004559	NP_004550			nuclease sensitive element binding protein 1						CRD-mediated mRNA stabilization|negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|positive regulation of cell division|transcription from RNA polymerase II promoter	CRD-mediated mRNA stability complex|extracellular region|histone pre-mRNA 3'end processing complex|nucleoplasm|stress granule|U12-type spliceosomal complex	double-stranded DNA binding|protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(4)|upper_aerodigestive_tract(1)	5	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44283237	44283242	+	Intron	DEL	CTTCTT	-	-	rs71701036	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44283237_44283242delCTTCTT	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)																---	---	---	---
RNF220	55182	broad.mit.edu	37	1	44935103	44935109	+	Intron	DEL	AAAGCAC	-	-	rs67698705		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44935103_44935109delAAAGCAC	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620			ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
RNF220	55182	broad.mit.edu	37	1	45114687	45114688	+	Intron	INS	-	G	G	rs140860973	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45114687_45114688insG	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010oky.1_Intron|RNF220_uc010okz.1_Intron|RNF220_uc001clx.1_Intron|RNF220_uc001cly.1_Intron|RNF220_uc001clz.1_Intron|RNF220_uc001cma.1_Intron|TMEM53_uc001cmb.1_Intron	NM_018150	NP_060620			ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
PTCH2	8643	broad.mit.edu	37	1	45295911	45295912	+	Intron	INS	-	TA	TA	rs72513279		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45295911_45295912insTA	uc010olf.1	-						PTCH2_uc010olg.1_Intron	NM_003738	NP_003729			patched 2						protein complex assembly|spermatogenesis	integral to plasma membrane	hedgehog receptor activity			lung(6)|breast(6)|central_nervous_system(3)|skin(2)|ovary(1)	18	Acute lymphoblastic leukemia(166;0.155)													Basal_Cell_Nevus_syndrome				---	---	---	---
MAST2	23139	broad.mit.edu	37	1	46434549	46434550	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46434549_46434550insT	uc001cov.2	+						MAST2_uc001cow.2_Intron|MAST2_uc001cox.1_Intron|MAST2_uc001coy.1_Intron|MAST2_uc001coz.1_Intron|MAST2_uc009vya.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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	46791630	46791630	+	IGR	DEL	T	-	-	rs1810584		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46791630delT								UQCRH (9185 upstream) : NSUN4 (14760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	46909044	46909044	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46909044delT								FAAH (29524 upstream) : DMBX1 (63624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	47672367	47672368	+	IGR	DEL	AC	-	-	rs66999330		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47672367_47672368delAC								PDZK1IP1 (16596 upstream) : TAL1 (9595 downstream)																																			---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49337026	49337027	+	Intron	DEL	TG	-	-	rs66506623		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49337026_49337027delTG	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	50395336	50395336	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50395336delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
FAF1	11124	broad.mit.edu	37	1	51391135	51391135	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51391135delA	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron	NM_007051	NP_008982			FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)														---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52617192	52617193	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52617192_52617193insT	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																		---	---	---	---
ZYG11A	440590	broad.mit.edu	37	1	53345602	53345602	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53345602delT	uc001cuk.2	+						ZYG11A_uc001cul.2_Intron	NM_001004339	NP_001004339			zyg-11 homolog A								binding				0																		---	---	---	---
SCP2	6342	broad.mit.edu	37	1	53403741	53403741	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53403741delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	53876670	53876671	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53876670_53876671delGT								LRP8 (82849 upstream) : FLJ40434 (27373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	55730845	55730845	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55730845delT								USP24 (50083 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	55731772	55731773	+	IGR	DEL	TC	-	-	rs141835748		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55731772_55731773delTC								USP24 (51010 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	55821616	55821617	+	IGR	INS	-	T	T	rs67835870		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55821616_55821617insT								USP24 (140854 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	56482884	56482885	+	IGR	INS	-	TCT	TCT	rs139288501	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56482884_56482885insTCT								USP24 (802122 upstream) : PPAP2B (477548 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	56813450	56813451	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56813450_56813451insA								None (None upstream) : PPAP2B (146982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	57073648	57073648	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57073648delA								PPAP2B (28391 upstream) : PRKAA2 (37342 downstream)																																			---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57755566	57755567	+	Intron	INS	-	G	G	rs138474260	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57755566_57755567insG	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	57830299	57830299	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57830299delA	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57896830	57896830	+	Intron	DEL	G	-	-	rs61690673		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57896830delG	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
FGGY	55277	broad.mit.edu	37	1	59957365	59957366	+	Intron	INS	-	T	T	rs11353839		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59957365_59957366insT	uc001czi.3	+						FGGY_uc001czg.2_Intron|FGGY_uc001czh.2_Intron|FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron	NM_018291	NP_060761			FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	60423354	60423355	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60423354_60423355delAC								CYP2J2 (30931 upstream) : C1orf87 (31469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	60584282	60584282	+	IGR	DEL	T	-	-	rs68039873		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60584282delT								C1orf87 (44856 upstream) : NFIA (958664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	60881945	60881946	+	IGR	INS	-	AC	AC	rs142636906	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60881945_60881946insAC								C1orf87 (342519 upstream) : NFIA (661000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	61039285	61039285	+	IGR	DEL	T	-	-	rs72448794		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61039285delT								C1orf87 (499859 upstream) : NFIA (503661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	62644638	62644639	+	IGR	DEL	CG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62644638_62644639delCG								INADL (292 upstream) : L1TD1 (15857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	63487482	63487483	+	IGR	INS	-	T	T	rs145728390	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63487482_63487483insT								ATG4C (157433 upstream) : FOXD3 (301247 downstream)																																			---	---	---	---
ROR1	4919	broad.mit.edu	37	1	64393631	64393631	+	Intron	DEL	T	-	-	rs55728360		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64393631delT	uc001dbj.2	+						ROR1_uc001dbi.3_Intron	NM_005012	NP_005003			receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	64753686	64753688	+	IGR	DEL	AAG	-	-	rs71584442		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64753686_64753688delAAG								UBE2U (43659 upstream) : CACHD1 (182788 downstream)																																			---	---	---	---
RAVER2	55225	broad.mit.edu	37	1	65229600	65229601	+	Intron	INS	-	AC	AC	rs139979731	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65229600_65229601insAC	uc001dbs.1	+							NM_018211	NP_060681			ribonucleoprotein, PTB-binding 2							cytoplasm|nucleus	nucleotide binding|RNA binding			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	65574936	65574937	+	IGR	INS	-	TT	TT	rs3051679		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65574936_65574937insTT								MIR101-1 (50745 upstream) : AK3L1 (38295 downstream)																																			---	---	---	---
IL12RB2	3595	broad.mit.edu	37	1	67771998	67771999	+	5'Flank	INS	-	T	T	rs139110091	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67771998_67771999insT	uc001ddu.2	+						IL12RB2_uc010oqi.1_5'Flank|IL12RB2_uc010oqj.1_5'Flank	NM_001559	NP_001550			interleukin 12 receptor, beta 2 precursor						positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	68101316	68101317	+	IGR	DEL	AC	-	-	rs111572255		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68101316_68101317delAC								SERBP1 (205193 upstream) : GADD45A (49566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	68383738	68383738	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68383738delA	uc001deb.1	+						uc001dec.1_Intron					Homo sapiens cDNA FLJ38762 fis, clone KIDNE2013801.																														---	---	---	---
WLS	79971	broad.mit.edu	37	1	68593251	68593254	+	Intron	DEL	CTGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68593251_68593254delCTGA	uc001def.1	-						uc001deb.1_Intron|uc001dec.1_Intron|WLS_uc001dee.2_Intron|WLS_uc001deg.1_Intron|WLS_uc009wbf.1_Intron	NM_024911	NP_079187			G protein-coupled receptor 177 isoform 1						multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Wnt receptor signaling pathway	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	signal transducer activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	69171553	69171554	+	IGR	INS	-	GTGA	GTGA	rs151309984	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69171553_69171554insGTGA								DEPDC1 (208754 upstream) : LRRC7 (861314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69266982	69266982	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69266982delA								DEPDC1 (304183 upstream) : LRRC7 (765886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69710262	69710263	+	IGR	INS	-	TTGT	TTGT	rs141408905	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69710262_69710263insTTGT								DEPDC1 (747463 upstream) : LRRC7 (322605 downstream)																																			---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70501308	70501309	+	Intron	INS	-	AA	AA	rs71716575		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70501308_70501309insAA	uc001dep.2	+						LRRC7_uc009wbg.2_Intron|LRRC7_uc001deq.2_5'Flank	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																		---	---	---	---
PTGER3	5733	broad.mit.edu	37	1	71383087	71383090	+	Intron	DEL	TGTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71383087_71383090delTGTG	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	NM_198714	NP_942007			prostaglandin E receptor 3, subtype EP3 isoform						cell death|positive regulation of fever generation|transcription, DNA-dependent	integral to plasma membrane|nuclear envelope	ligand-dependent nuclear receptor activity|prostaglandin E receptor activity			pancreas(1)|lung(1)|skin(1)	3					Bimatoprost(DB00905)													---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72434482	72434483	+	Intron	INS	-	T	T	rs148348370	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72434482_72434483insT	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	73182236	73182236	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73182236delT								NEGR1 (433831 upstream) : None (None downstream)																																			---	---	---	---
LRRIQ3	127255	broad.mit.edu	37	1	74646954	74646954	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74646954delT	uc001dfy.3	-						LRRIQ3_uc001dfz.3_Intron	NM_001105659	NP_001099129			leucine-rich repeats and IQ motif containing 3											ovary(2)	2																		---	---	---	---
TNNI3K	51086	broad.mit.edu	37	1	74859351	74859351	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74859351delT	uc001dgf.1	+						TNNI3K_uc001dgd.2_Intron|TNNI3K_uc001dge.1_Intron	NM_015978	NP_057062			TNNI3 interacting kinase isoform b							cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10																		---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75857835	75857835	+	Intron	DEL	A	-	-	rs78101191		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75857835delA	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910			solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75957417	75957418	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75957417_75957418delCA	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910			solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	78690291	78690291	+	IGR	DEL	A	-	-	rs10713126		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78690291delA								GIPC2 (87180 upstream) : MGC27382 (4992 downstream)																																			---	---	---	---
MGC27382	149047	broad.mit.edu	37	1	78705193	78705194	+	Intron	INS	-	A	A	rs11587036		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78705193_78705194insA	uc001dil.1	+						MGC27382_uc009wcc.2_Intron					Homo sapiens cDNA FLJ34438 fis, clone HLUNG2001144.												0																		---	---	---	---
MGC27382	149047	broad.mit.edu	37	1	78713434	78713435	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78713434_78713435delTG	uc001dil.1	+						MGC27382_uc009wcc.2_Intron					Homo sapiens cDNA FLJ34438 fis, clone HLUNG2001144.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	80048007	80048010	+	IGR	DEL	TCTT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80048007_80048010delTCTT								ELTD1 (575512 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	80082529	80082530	+	IGR	INS	-	T	T	rs138416023	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80082529_80082530insT								ELTD1 (610034 upstream) : None (None downstream)																																			---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	82107934	82107934	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82107934delA	uc001dis.2	+											SubName: Full=cDNA FLJ41428 fis, clone BRHIP2005236, highly similar to Latrophilin-2;						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	82533065	82533065	+	IGR	DEL	A	-	-	rs76219319		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-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	83243401	83243402	+	IGR	INS	-	C	C	rs148497460	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83243401_83243402insC								LPHN2 (785295 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	84215975	84215976	+	RNA	INS	-	T	T	rs143591671	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84215975_84215976insT	uc001diz.3	-	2		c.185_186insA								Homo sapiens cDNA clone IMAGE:4815396.																														---	---	---	---
PRKACB	5567	broad.mit.edu	37	1	84689059	84689061	+	Intron	DEL	TTG	-	-	rs12127903		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84689059_84689061delTTG	uc001djj.2	+						PRKACB_uc001djl.2_Intron|PRKACB_uc010ort.1_Intron|PRKACB_uc001djn.2_Intron|PRKACB_uc010oru.1_Intron|PRKACB_uc001djp.2_Intron|PRKACB_uc001djq.2_Intron|PRKACB_uc010orv.1_Intron	NM_002731	NP_002722			cAMP-dependent protein kinase catalytic subunit						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein signaling, coupled to cAMP nucleotide second messenger|gluconeogenesis|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|regulation of insulin secretion|synaptic transmission|transmembrane transport|triglyceride catabolic process|water transport	cAMP-dependent protein kinase complex|centrosome|cytosol|nucleoplasm|plasma membrane	ATP binding|cAMP-dependent protein kinase activity|magnesium ion binding|protein binding			lung(2)|ovary(1)	3				all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141)														---	---	---	---
SSX2IP	117178	broad.mit.edu	37	1	85148834	85148834	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85148834delT	uc001dkh.2	-						SSX2IP_uc001dkg.2_Intron|SSX2IP_uc010orz.1_Intron|SSX2IP_uc001dki.2_Intron|SSX2IP_uc010osa.1_Intron|SSX2IP_uc001dkj.2_Intron|SSX2IP_uc009wci.2_Intron|SSX2IP_uc001dkk.1_Intron	NM_014021	NP_054740			synovial sarcoma, X breakpoint 2 interacting						cell adhesion	nucleus|protein complex				ovary(2)	2				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	85247580	85247581	+	IGR	INS	-	AGAAA	AGAAA	rs150123403	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85247580_85247581insAGAAA								SSX2IP (91140 upstream) : LPAR3 (31505 downstream)																																			---	---	---	---
LPAR3	23566	broad.mit.edu	37	1	85356843	85356844	+	Intron	INS	-	AAAAA	AAAAA	rs5775803		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85356843_85356844insAAAAA	uc009wcj.1	-							NM_012152	NP_036284			lysophosphatidic acid receptor 3						G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane|intracellular membrane-bounded organelle				lung(3)|ovary(2)	5																		---	---	---	---
MCOLN3	55283	broad.mit.edu	37	1	85515519	85515524	+	5'Flank	DEL	GAGAGG	-	-	rs66591089		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85515519_85515524delGAGAGG	uc001dkp.2	-						MCOLN3_uc001dkq.2_5'Flank|MCOLN3_uc001dkr.2_5'Flank|MCOLN3_uc001dks.3_5'Flank	NM_018298	NP_060768			mucolipin 3							integral to membrane	ion channel activity			skin(1)	1				all cancers(265;0.00957)|Epithelial(280;0.0254)														---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	85980700	85980701	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85980700_85980701delAC	uc001dlc.2	-							NM_001134445	NP_001127917			dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)													---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86481729	86481729	+	Intron	DEL	T	-	-	rs112210090		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86481729delT	uc001dlj.2	-						COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850			collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)														---	---	---	---
ODF2L	57489	broad.mit.edu	37	1	86825241	86825243	+	Intron	DEL	TGT	-	-	rs71078655		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86825241_86825243delTGT	uc001dll.1	-						ODF2L_uc001dlm.1_Intron|ODF2L_uc001dln.2_Intron|ODF2L_uc001dlo.2_Intron|ODF2L_uc001dlp.2_Intron|ODF2L_uc010osg.1_Intron|ODF2L_uc001dlq.1_Intron	NM_020729	NP_065780			outer dense fiber of sperm tails 2-like isoform							centrosome				ovary(1)	1				all cancers(265;0.0313)|Epithelial(280;0.0611)														---	---	---	---
LOC339524	339524	broad.mit.edu	37	1	87612397	87612398	+	Intron	INS	-	C	C	rs137996065	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87612397_87612398insC	uc001dme.1	+						LOC339524_uc001dmf.2_Intron	NM_001134492	NP_001127964			heparan sulfate 2-O-sulfotransferase 1 isoform												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	88124723	88124724	+	IGR	DEL	TA	-	-	rs113166473		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88124723_88124724delTA								LMO4 (310120 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	89536938	89536938	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89536938delA								GBP1 (5895 upstream) : GBP2 (34905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91312539	91312541	+	Intron	DEL	AAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91312539_91312541delAAC	uc001dnu.1	-											Homo sapiens cDNA FLJ12836 fis, clone NT2RP2003206.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	91494017	91494017	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91494017delC								ZNF644 (6346 upstream) : HFM1 (232307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91538545	91538546	+	IGR	INS	-	AAG	AAG	rs142016580	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91538545_91538546insAAG								ZNF644 (50874 upstream) : HFM1 (187778 downstream)																																			---	---	---	---
RPAP2	79871	broad.mit.edu	37	1	92785556	92785556	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92785556delA	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	92921046	92921069	+	IGR	DEL	AGAGAGAGAGAGAGAGAGAGAGAG	-	-	rs67639237	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92921046_92921069delAGAGAGAGAGAGAGAGAGAGAGAG								RPAP2 (67314 upstream) : GFI1 (19250 downstream)																																			---	---	---	---
FAM69A	388650	broad.mit.edu	37	1	93394519	93394529	+	Intron	DEL	AAAGAAAAAAA	-	-	rs72071488		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93394519_93394529delAAAGAAAAAAA	uc001dpg.2	-						FAM69A_uc001dpc.2_Intron	NM_001006605	NP_001006606			family with sequence similarity 69, member A							endoplasmic reticulum membrane|integral to membrane					0		all_lung(203;0.00265)|Lung NSC(277;0.00562)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000563)|all cancers(265;0.000751)|Epithelial(280;0.127)														---	---	---	---
BCAR3	8412	broad.mit.edu	37	1	94076990	94076990	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94076990delC	uc001dpz.2	-						BCAR3_uc001dqa.2_Intron|BCAR3_uc001dqb.2_Intron|BCAR3_uc001dpy.2_Intron	NM_003567	NP_003558			breast cancer antiestrogen resistance 3						response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)														---	---	---	---
BCAR3	8412	broad.mit.edu	37	1	94246127	94246127	+	Intron	DEL	A	-	-	rs68137511		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94246127delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	94871896	94871896	+	IGR	DEL	G	-	-	rs12091363		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94871896delG								ARHGAP29 (131272 upstream) : ABCD3 (12037 downstream)																																			---	---	---	---
ALG14	199857	broad.mit.edu	37	1	95494764	95494765	+	Intron	INS	-	T	T	rs143575762	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95494764_95494765insT	uc001dra.2	-							NM_144988	NP_659425			asparagine-linked glycosylation 14 homolog						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity				0		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	95546332	95546333	+	IGR	DEL	TG	-	-	rs150939912		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95546332_95546333delTG								ALG14 (7825 upstream) : TMEM56 (36561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	95970267	95970267	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95970267delT								RWDD3 (257494 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96082229	96082229	+	IGR	DEL	A	-	-	rs147884407		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96082229delA								RWDD3 (369456 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96507060	96507061	+	IGR	INS	-	G	G	rs148867751	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96507060_96507061insG								RWDD3 (794287 upstream) : PTBP2 (680114 downstream)																																			---	---	---	---
PTBP2	58155	broad.mit.edu	37	1	97274367	97274370	+	Intron	DEL	ACAC	-	-	rs72295337		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97274367_97274370delACAC	uc001drq.2	+						PTBP2_uc001drn.2_Intron|PTBP2_uc001dro.2_Intron|PTBP2_uc010otz.1_Intron|PTBP2_uc001drp.2_Intron|PTBP2_uc009wdw.2_Intron|PTBP2_uc001drr.2_Intron|PTBP2_uc010oua.1_Intron|PTBP2_uc001dru.2_Intron|PTBP2_uc001drs.1_Intron|PTBP2_uc001drt.2_Intron	NM_021190	NP_067013			polypyrimidine tract binding protein 2								nucleotide binding				0		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	98514591	98514592	+	Intron	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98514591_98514592delCT	uc001drx.1	-						uc009wdx.2_5'Flank|MIR137_hsa-mir-137|MI0000454_5'Flank					Homo sapiens cDNA FLJ37288 fis, clone BRAMY2014205.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	98838600	98838600	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98838600delA								MIR137 (326873 upstream) : SNX7 (288636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	99032443	99032444	+	IGR	INS	-	TC	TC	rs5776423		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99032443_99032444insTC								MIR137 (520716 upstream) : SNX7 (94792 downstream)																																			---	---	---	---
VCAM1	7412	broad.mit.edu	37	1	101201841	101201841	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101201841delA	uc001dti.2	+						VCAM1_uc001dtj.2_Intron|VCAM1_uc010ouj.1_Intron	NM_001078	NP_001069			vascular cell adhesion molecule 1 isoform a						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	101763791	101763791	+	IGR	DEL	T	-	-	rs148843129		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101763791delT								S1PR1 (56715 upstream) : OLFM3 (504336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	102189524	102189525	+	IGR	INS	-	T	T	rs150343300	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102189524_102189525insT								S1PR1 (482448 upstream) : OLFM3 (78602 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	102705480	102705480	+	IGR	DEL	A	-	-	rs34432618		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102705480delA								OLFM3 (242690 upstream) : COL11A1 (636544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	103020378	103020379	+	IGR	INS	-	T	T	rs141504756	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103020378_103020379insT								OLFM3 (557588 upstream) : COL11A1 (321645 downstream)																																			---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103401795	103401796	+	Intron	DEL	AA	-	-	rs72103913		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103401795_103401796delAA	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	103585771	103585771	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103585771delT								COL11A1 (11719 upstream) : RNPC3 (482807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	103682642	103682642	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103682642delT								COL11A1 (108590 upstream) : RNPC3 (385936 downstream)																																			---	---	---	---
AMY1A	276	broad.mit.edu	37	1	104204863	104204863	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104204863delA	uc001duu.2	+						AMY1A_uc001duv.2_Intron	NM_001008221	NP_001008222			salivary amylase alpha 1A precursor						carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding|protein binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	104863645	104863646	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104863645_104863646delTT								AMY1A (656473 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	104966966	104966966	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104966966delA								AMY1A (759794 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105310940	105310940	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105310940delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	106176003	106176003	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106176003delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	110510158	110510158	+	IGR	DEL	A	-	-	rs75743741		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110510158delA								CSF1 (37804 upstream) : AHCYL1 (17150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	110782654	110782657	+	IGR	DEL	AGAA	-	-	rs5777006		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110782654_110782657delAGAA								KCNC4 (5989 upstream) : RBM15 (99288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	110818017	110818017	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110818017delT								KCNC4 (41352 upstream) : RBM15 (63928 downstream)																																			---	---	---	---
RAP1A	5906	broad.mit.edu	37	1	112182188	112182189	+	Intron	INS	-	T	T	rs11435910		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112182188_112182189insT	uc001ebi.2	+						RAP1A_uc001ebk.2_Intron|RAP1A_uc001ebl.2_Intron|RAP1A_uc001ebm.2_Intron	NM_002884	NP_002875			RAP1A, member of RAS oncogene family precursor						activation of MAPKK activity|blood coagulation|energy reserve metabolic process|nerve growth factor receptor signaling pathway|regulation of insulin secretion	cytosol|plasma membrane	GTP binding|GTPase activity				0		all_cancers(81;6.79e-06)|all_epithelial(167;2.42e-05)|all_lung(203;0.000105)|Lung NSC(277;0.00021)		Lung(183;0.0183)|Colorectal(144;0.0418)|LUSC - Lung squamous cell carcinoma(189;0.0966)|all cancers(265;0.098)|Epithelial(280;0.0981)|COAD - Colon adenocarcinoma(174;0.141)														---	---	---	---
KCND3	3752	broad.mit.edu	37	1	112384058	112384059	+	Intron	INS	-	G	G	rs148912100	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112384058_112384059insG	uc001ebu.1	-						KCND3_uc001ebv.1_Intron	NM_004980	NP_004971			potassium voltage-gated channel, Shal-related							sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	113536483	113536483	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113536483delA	uc001edc.1	+											Homo sapiens cDNA clone IMAGE:4620359, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	113545970	113545973	+	IGR	DEL	TTTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113545970_113545973delTTTG								SLC16A1 (46995 upstream) : LRIG2 (69858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	114524981	114524981	+	IGR	DEL	G	-	-	rs66544538		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114524981delG								OLFML3 (105 upstream) : SYT6 (106934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	115059996	115059996	+	IGR	DEL	A	-	-	rs74929199		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115059996delA								TRIM33 (6215 upstream) : DENND2C (4022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	116073217	116073217	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116073217delA								NGF (192360 upstream) : VANGL1 (111357 downstream)																																			---	---	---	---
VANGL1	81839	broad.mit.edu	37	1	116184159	116184160	+	5'Flank	DEL	TG	-	-	rs113290245		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116184159_116184160delTG	uc001efv.1	+						VANGL1_uc009wgy.1_5'Flank	NM_138959	NP_620409			vang-like 1						multicellular organismal development	integral to membrane	protein binding			central_nervous_system(1)	1	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)														---	---	---	---
CD2	914	broad.mit.edu	37	1	117299450	117299450	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117299450delT	uc001egu.3	+						CD2_uc010owz.1_Intron|CD2_uc010oxa.1_Intron	NM_001767	NP_001758			CD2 molecule precursor						blood coagulation|cell surface receptor linked signaling pathway|cell-cell adhesion|induction of apoptosis|leukocyte migration|membrane raft polarization|natural killer cell activation|positive regulation of myeloid dendritic cell activation|regulation of T cell differentiation|T cell activation	integral to plasma membrane	receptor activity			breast(1)	1	Lung SC(450;0.225)	all_cancers(81;3.15e-06)|Acute lymphoblastic leukemia(138;1.7e-08)|all_epithelial(167;8.38e-07)|all_lung(203;3.37e-06)|Lung NSC(69;2.31e-05)		Epithelial(280;6.71e-26)|OV - Ovarian serous cystadenocarcinoma(397;4.74e-24)|all cancers(265;1.93e-22)|Lung(183;0.0543)|Kidney(133;0.0813)|Colorectal(144;0.174)|KIRC - Kidney renal clear cell carcinoma(1967;0.176)|LUSC - Lung squamous cell carcinoma(189;0.189)|BRCA - Breast invasive adenocarcinoma(282;0.201)	Alefacept(DB00092)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	117312857	117312857	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117312857delA								CD2 (1007 upstream) : PTGFRN (139832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	117434970	117434977	+	IGR	DEL	ACACACAC	-	-	rs67241397		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117434970_117434977delACACACAC								CD2 (123120 upstream) : PTGFRN (17712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	117678111	117678112	+	IGR	INS	-	TTG	TTG	rs75461726		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117678111_117678112insTTG								TRIM45 (13697 upstream) : VTCN1 (8098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	117831489	117831491	+	IGR	DEL	TGT	-	-	rs72048380		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117831489_117831491delTGT								VTCN1 (77940 upstream) : MAN1A2 (78594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118314699	118314700	+	IGR	INS	-	T	T	rs141086820		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118314699_118314700insT								FAM46C (143689 upstream) : GDAP2 (91408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	119080169	119080174	+	IGR	DEL	AGCCTG	-	-	rs66464718	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119080169_119080174delAGCCTG								SPAG17 (352321 upstream) : TBX15 (345492 downstream)																																			---	---	---	---
WARS2	10352	broad.mit.edu	37	1	119650295	119650308	+	Intron	DEL	AGAGAGAGAGAGAG	-	-	rs10563228		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119650295_119650308delAGAGAGAGAGAGAG	uc001ehn.2	-						WARS2_uc010oxf.1_Intron|WARS2_uc001ehm.2_Intron|WARS2_uc010oxg.1_Intron|WARS2_uc010oxh.1_Intron|WARS2_uc010oxi.1_Intron	NM_015836	NP_056651			mitochondrial tryptophanyl tRNA synthetase 2						tryptophanyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|tryptophan-tRNA ligase activity				0	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	119814319	119814319	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119814319delA	uc001ehp.1	+											Homo sapiens cDNA FLJ43771 fis, clone TESTI2049553.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	120004436	120004436	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120004436delT								HSD3B2 (15316 upstream) : HSD3B1 (45390 downstream)																																			---	---	---	---
HMGCS2	3158	broad.mit.edu	37	1	120302991	120302991	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120302991delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	142542919	142542923	+	IGR	DEL	TGAGG	-	-	rs7555663		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142542919_142542923delTGAGG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142559278	142559279	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142559278_142559279insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142609661	142609661	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142609661delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142663441	142663442	+	Intron	INS	-	A	A	rs147458002		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142663441_142663442insA	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143120268	143120268	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143120268delA	uc001eiw.1	+						uc001ejf.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143151918	143151918	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143151918delA	uc001eiw.1	+						uc001ejf.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143275770	143275771	+	IGR	INS	-	A	A	rs138591393	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143275770_143275771insA								None (None upstream) : LOC100286793 (371868 downstream)																																			---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144536014	144536015	+	Intron	INS	-	A	A	rs143907098		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144536014_144536015insA	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145073411	145073412	+	Intron	INS	-	AA	AA	rs3978517		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145073411_145073412insAA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145741280	145741280	+	Intron	DEL	T	-	-	rs35999622		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145741280delT	uc001emp.3	+						PDZK1_uc001eon.1_Intron|PDZK1_uc001eoo.1_Intron|PDZK1_uc010oza.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
FMO5	2330	broad.mit.edu	37	1	146670820	146670820	+	Intron	DEL	T	-	-	rs76315499		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146670820delT	uc001epi.2	-						FMO5_uc001eph.3_Intron|FMO5_uc001epj.2_Intron	NM_001461	NP_001452			flavin containing monooxygenase 5 isoform 1							integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			ovary(3)	3	all_hematologic(923;0.0487)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	146776214	146776214	+	Intron	DEL	C	-	-	rs58505817		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146776214delC	uc001epp.2	-											Homo sapiens cDNA clone IMAGE:5266739.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	147005028	147005031	+	IGR	DEL	TCTC	-	-	rs148910970		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147005028_147005031delTCTC								CHD1L (237587 upstream) : BCL9 (8151 downstream)																																			---	---	---	---
LOC200030	200030	broad.mit.edu	37	1	148220905	148220905	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148220905delA	uc001eqf.2	-						LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc010pae.1_Intron|NBPF14_uc010paf.1_Intron|NBPF14_uc009wkf.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0																		---	---	---	---
LOC200030	200030	broad.mit.edu	37	1	148248156	148248157	+	Intron	INS	-	T	T	rs141456338	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148248156_148248157insT	uc001eqf.2	-						LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc010pae.1_Intron|NBPF14_uc010paf.1_Intron|NBPF14_uc009wkf.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0																		---	---	---	---
NBPF15	284565	broad.mit.edu	37	1	148559549	148559549	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148559549delT	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	148661709	148661709	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148661709delG								PPIAL4E (16916 upstream) : NBPF16 (77733 downstream)																																			---	---	---	---
NBPF16	728936	broad.mit.edu	37	1	148756337	148756337	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148756337delT	uc010pba.1	+						NBPF16_uc009wkt.1_Intron	NM_001102663	NP_001096133			hypothetical protein LOC728936												0	all_hematologic(923;0.032)																	---	---	---	---
LOC645166	645166	broad.mit.edu	37	1	148948880	148948881	+	Intron	INS	-	A	A	rs144249846		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148948880_148948881insA	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	149204701	149204702	+	IGR	INS	-	AACT	AACT	rs148978560	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149204701_149204702insAACT								LOC645166 (251647 upstream) : LOC388692 (74774 downstream)																																	OREG0013773	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	1	149239465	149239465	+	IGR	DEL	C	-	-	rs11284561		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149239465delC								LOC645166 (286411 upstream) : LOC388692 (40011 downstream)																																			---	---	---	---
LOC728855	728855	broad.mit.edu	37	1	149598878	149598878	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149598878delG	uc001esk.3	+						LOC728855_uc001esl.3_Intron|LOC728855_uc009wlc.2_Intron|LOC728855_uc009wld.2_Intron	NR_024510				Homo sapiens mRNA, chromosome 1 specific transcript KIAA0493.												0																		---	---	---	---
OTUD7B	56957	broad.mit.edu	37	1	149930234	149930235	+	Intron	INS	-	T	T	rs72286770		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149930234_149930235insT	uc001etn.2	-							NM_020205	NP_064590			zinc finger protein Cezanne						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)															---	---	---	---
PRPF3	9129	broad.mit.edu	37	1	150323437	150323437	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150323437delA	uc001eum.3	+						PRPF3_uc010pca.1_Intron|PRPF3_uc010pcb.1_Intron	NM_004698	NP_004689			PRP3 pre-mRNA processing factor 3 homolog						nuclear mRNA splicing, via spliceosome	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding			ovary(1)	1	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	150543904	150543904	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150543904delA								ADAMTSL4 (10494 upstream) : MCL1 (3133 downstream)																																			---	---	---	---
PI4KB	5298	broad.mit.edu	37	1	151291404	151291405	+	Intron	INS	-	CAT	CAT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151291404_151291405insCAT	uc001ext.2	-						PI4KB_uc001exr.2_Intron|PI4KB_uc001exs.2_Intron|PI4KB_uc001exu.2_Intron|PI4KB_uc010pcw.1_Intron|PI4KB_uc009wmq.1_Intron	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)															---	---	---	---
SNX27	81609	broad.mit.edu	37	1	151606441	151606442	+	Intron	DEL	TA	-	-	rs1196347	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151606441_151606442delTA	uc001eyn.1	+							NM_030918	NP_112180			sorting nexin family member 27						cell communication|protein transport|signal transduction	cytosol|early endosome	phosphatidylinositol binding|protein binding			ovary(2)|central_nervous_system(1)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	152253796	152253796	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152253796delC								HRNR (57127 upstream) : FLG (20855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	152429198	152429198	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152429198delT								CRNN (42448 upstream) : LCE5A (54122 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	152654065	152654068	+	IGR	DEL	ACAC	-	-	rs112460096		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152654065_152654068delACAC								LCE2C (5018 upstream) : LCE2B (4531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	153228203	153228204	+	IGR	INS	-	CACACA	CACACA	rs146751011	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153228203_153228204insCACACA								LELP1 (50609 upstream) : LOR (3975 downstream)																																			---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	153969941	153969943	+	Intron	DEL	CTG	-	-	rs115274846		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153969941_153969943delCTG	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)															---	---	---	---
RAG1AP1	55974	broad.mit.edu	37	1	155136017	155136018	+	Intron	DEL	AC	-	-	rs112335888		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155136017_155136018delAC	uc010pey.1	+							NM_018845				recombination activating gene 1 activating						positive regulation of gene expression, epigenetic	Golgi membrane|integral to membrane|plasma membrane	glucoside transmembrane transporter activity				0	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155516548	155516548	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155516548delA	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)															---	---	---	---
RIT1	6016	broad.mit.edu	37	1	155881465	155881465	+	5'Flank	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155881465delA	uc001fmh.1	-						RIT1_uc010pgr.1_5'Flank	NM_006912	NP_008843			Ras-like without CAAX 1						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			breast(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)															---	---	---	---
RXFP4	339403	broad.mit.edu	37	1	155908617	155908617	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155908617delT	uc010pgs.1	+							NM_181885	NP_871001			relaxin 3 receptor 2							integral to membrane|plasma membrane	angiotensin type II receptor activity				0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	156858051	156858052	+	IGR	INS	-	ACACACACAC	ACACACACAC	rs72312257		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156858051_156858052insACACACACAC								NTRK1 (6409 upstream) : PEAR1 (5471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157045429	157045429	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157045429delT								ARHGEF11 (30267 upstream) : ETV3L (16407 downstream)																																			---	---	---	---
CD1B	910	broad.mit.edu	37	1	158302956	158302956	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158302956delT	uc001frx.2	-						CD1B_uc001frw.2_5'Flank|CD1B_uc010pic.1_5'Flank	NM_001764	NP_001755			CD1B antigen precursor						antigen processing and presentation|immune response	endosome membrane|integral to membrane|lysosomal membrane|plasma membrane	protein binding			ovary(2)	2	all_hematologic(112;0.0378)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	158401411	158401411	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158401411delT								OR10K2 (10755 upstream) : OR10K1 (33941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158457587	158457587	+	Intron	DEL	T	-	-	rs5778079		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158457587delT	uc001fso.1	-											Homo sapiens cDNA FLJ32992 fis, clone THYMU1000098.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	158770955	158770956	+	IGR	DEL	GT	-	-	rs72182541		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158770955_158770956delGT								OR6N2 (23530 upstream) : MNDA (30212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159133401	159133401	+	IGR	DEL	A	-	-	rs67613638		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159133401delA								AIM2 (86754 upstream) : CADM3 (7976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159229314	159229315	+	IGR	INS	-	T	T	rs141902051	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159229314_159229315insT								DARC (53026 upstream) : FCER1A (30191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159289768	159289768	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159289768delT								OR10J3 (5319 upstream) : OR10J1 (119781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159490369	159490370	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159490369_159490370delGT								OR10J1 (79859 upstream) : OR10J5 (14500 downstream)																																			---	---	---	---
OR10J5	127385	broad.mit.edu	37	1	159506484	159506485	+	5'Flank	DEL	TT	-	-	rs34356128		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159506484_159506485delTT	uc010piw.1	-							NM_001004469	NP_001004469			olfactory receptor, family 10, subfamily J,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	all_hematologic(112;0.0429)																	---	---	---	---
COPA	1314	broad.mit.edu	37	1	160279322	160279322	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160279322delA	uc009wti.2	-						COPA_uc001fvv.3_Intron|COPA_uc009wtj.1_Intron	NM_004371	NP_004362			coatomer protein complex, subunit alpha isoform						COPI coating of Golgi vesicle|intracellular protein transport|pancreatic juice secretion|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|extracellular space|microsome|soluble fraction	hormone activity|structural molecule activity			ovary(1)|skin(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
CD48	962	broad.mit.edu	37	1	160650793	160650793	+	Intron	DEL	C	-	-	rs67044560		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160650793delC	uc001fwn.2	-						CD48_uc001fwo.1_3'UTR	NM_001778	NP_001769			CD48 molecule precursor						blood coagulation|defense response|leukocyte migration	integral to plasma membrane|membrane raft	protein binding				0	all_cancers(52;2.18e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160745332	160745333	+	IGR	INS	-	TC	TC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160745332_160745333insTC								SLAMF7 (20732 upstream) : LY9 (20595 downstream)																																			---	---	---	---
NR1I3	9970	broad.mit.edu	37	1	161206997	161206997	+	Intron	DEL	T	-	-	rs66782410		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161206997delT	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)															---	---	---	---
RPL31P11	641311	broad.mit.edu	37	1	161656867	161656868	+	5'Flank	INS	-	TGTG	TGTG	rs139325130	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161656867_161656868insTGTG	uc001gbc.2	-							NR_002595				Homo sapiens cDNA clone IMAGE:6574909, containing frame-shift errors.												0																		---	---	---	---
OLFML2B	25903	broad.mit.edu	37	1	161962755	161962756	+	Intron	INS	-	A	A	rs150854852	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161962755_161962756insA	uc001gbu.2	-						OLFML2B_uc010pkq.1_Intron	NM_015441	NP_056256			olfactomedin-like 2B precursor											skin(1)	1	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	163745930	163745933	+	IGR	DEL	TTTG	-	-	rs111594782		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163745930_163745933delTTTG								NUF2 (420377 upstream) : PBX1 (782869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164289893	164289893	+	IGR	DEL	A	-	-	rs57869713		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164289893delA								NUF2 (964340 upstream) : PBX1 (238909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164514959	164514959	+	IGR	DEL	T	-	-	rs34561181		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164514959delT								None (None upstream) : PBX1 (13843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164913497	164913497	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164913497delT								PBX1 (59197 upstream) : LMX1A (257608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	166411150	166411151	+	IGR	INS	-	A	A	rs143218730	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166411150_166411151insA								FAM78B (274944 upstream) : FMO9P (162002 downstream)																																			---	---	---	---
ADCY10	55811	broad.mit.edu	37	1	167819900	167819901	+	Intron	INS	-	GT	GT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167819900_167819901insGT	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																		---	---	---	---
ADCY10	55811	broad.mit.edu	37	1	167867833	167867833	+	Intron	DEL	T	-	-	rs72341152		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167867833delT	uc001ger.2	-						ADCY10_uc009wvk.2_Intron|ADCY10_uc010plj.1_Intron|ADCY10_uc009wvl.2_Intron|ADCY10_uc009wvm.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	168370700	168370701	+	IGR	INS	-	TTT	TTT	rs78285429		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168370700_168370701insTTT								MIR557 (25841 upstream) : XCL2 (139304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	168429411	168429412	+	IGR	INS	-	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168429411_168429412insC								MIR557 (84552 upstream) : XCL2 (80593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	170290290	170290290	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170290290delT								LOC284688 (36941 upstream) : GORAB (210973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	172944275	172944276	+	IGR	INS	-	TA	TA	rs148135907	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172944275_172944276insTA								FASLG (308265 upstream) : TNFSF18 (66084 downstream)																																			---	---	---	---
TNFSF18	8995	broad.mit.edu	37	1	173020270	173020270	+	5'Flank	DEL	A	-	-	rs72718913	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173020270delA	uc001giu.2	-							NM_005092	NP_005083			tumor necrosis factor (ligand) superfamily,						anti-apoptosis|cell-cell signaling|immune response|signal transduction	extracellular space|integral to membrane	cytokine activity|tumor necrosis factor receptor binding			central_nervous_system(1)	1																		---	---	---	---
SERPINC1	462	broad.mit.edu	37	1	173874604	173874604	+	Intron	DEL	T	-	-	rs2227616		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173874604delT	uc001gjt.2	-							NM_000488	NP_000479			serpin peptidase inhibitor, clade C, member 1						blood coagulation|regulation of proteolysis	extracellular space|plasma membrane	heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(1)	1					Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)													---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174177403	174177403	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174177403delT	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174855949	174855950	+	Intron	INS	-	T	T	rs147880009	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174855949_174855950insT	uc001gjx.2	+						RABGAP1L_uc001gkb.3_Intron|RABGAP1L_uc001gkc.3_Intron|RABGAP1L_uc001gkd.3_Intron|RABGAP1L_uc001gke.3_Intron|RABGAP1L_uc001gkf.2_Intron|RABGAP1L_uc001gkg.2_Intron|RABGAP1L_uc001gkh.3_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
TNR	7143	broad.mit.edu	37	1	175621577	175621577	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175621577delA	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276			tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)																	---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	175977259	175977259	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175977259delC	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																		---	---	---	---
ASTN1	460	broad.mit.edu	37	1	176989996	176989997	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176989996_176989997delTG	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron|ASTN1_uc009wwx.1_Intron|ASTN1_uc001gle.3_Intron	NM_004319	NP_004310			astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15																		---	---	---	---
SEC16B	89866	broad.mit.edu	37	1	177904798	177904798	+	Intron	DEL	A	-	-	rs76410383		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177904798delA	uc001gli.1	-						SEC16B_uc001glk.1_Intron|SEC16B_uc009wwy.1_Intron|SEC16B_uc001glh.1_Intron|SEC16B_uc009wwz.1_Intron|SEC16B_uc001glj.1_Intron	NM_033127	NP_149118			leucine zipper transcription regulator 2						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
FAM20B	9917	broad.mit.edu	37	1	179016880	179016881	+	Intron	INS	-	C	C	rs143992121	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179016880_179016881insC	uc001gmc.2	+							NM_014864	NP_055679			hypothetical protein LOC9917 precursor							Golgi membrane|integral to membrane	ATP binding|kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(3)	3																		---	---	---	---
SOAT1	6646	broad.mit.edu	37	1	179274243	179274244	+	Intron	INS	-	TT	TT	rs72501155	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179274243_179274244insTT	uc001gml.2	+						SOAT1_uc010pni.1_Intron|SOAT1_uc001gmm.2_Intron|SOAT1_uc010pnj.1_Intron	NM_003101	NP_003092			sterol O-acyltransferase 1						cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|cholesterol storage|macrophage derived foam cell differentiation|positive regulation of amyloid precursor protein biosynthetic process|very-low-density lipoprotein particle assembly	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			central_nervous_system(1)|skin(1)	2					Ezetimibe(DB00973)|Hesperetin(DB01094)													---	---	---	---
CEP350	9857	broad.mit.edu	37	1	180076965	180076966	+	Intron	INS	-	AAAAC	AAAAC	rs143060440	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180076965_180076966insAAAAC	uc001gnt.2	+						CEP350_uc009wxl.2_Intron|CEP350_uc001gnv.2_Intron|CEP350_uc001gnw.1_Intron|CEP350_uc001gnx.1_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
ACBD6	84320	broad.mit.edu	37	1	180451645	180451645	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180451645delA	uc001gog.2	-							NM_032360	NP_115736			acyl-coenzyme A binding domain containing 6							cytoplasm|nucleus	fatty-acyl-CoA binding			ovary(1)	1																		---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180618922	180618925	+	Intron	DEL	TTAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180618922_180618925delTTAA	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727			xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	181361080	181361083	+	IGR	DEL	TCTG	-	-	rs35372127		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181361080_181361083delTCTG								IER5 (301103 upstream) : CACNA1E (91633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182204650	182204652	+	IGR	DEL	CCT	-	-	rs34804515		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182204650_182204652delCCT								ZNF648 (173803 upstream) : GLUL (147017 downstream)																																			---	---	---	---
GLUL	2752	broad.mit.edu	37	1	182358154	182358160	+	Intron	DEL	GGCCCTT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182358154_182358160delGGCCCTT	uc001gpa.1	-						GLUL_uc001gpb.1_Intron|GLUL_uc001gpc.1_Intron|GLUL_uc001gpd.1_Intron	NM_001033056	NP_001028228			glutamine synthetase						cell proliferation|glutamine biosynthetic process|neurotransmitter uptake	cytosol|Golgi apparatus|mitochondrion	ATP binding|glutamate decarboxylase activity|glutamate-ammonia ligase activity|identical protein binding				0					Asparaginase(DB00023)|L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)|L-Methionine(DB00134)													---	---	---	---
SMG7	9887	broad.mit.edu	37	1	183446686	183446687	+	Intron	INS	-	AT	AT	rs149184153	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183446686_183446687insAT	uc001gqg.2	+						SMG7_uc010pob.1_Intron|SMG7_uc001gqf.2_Intron|SMG7_uc001gqh.2_Intron|SMG7_uc001gqi.2_Intron|SMG7_uc010poc.1_Intron	NM_173156	NP_775179			SMG-7 homolog isoform 1						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
SMG7	9887	broad.mit.edu	37	1	183508286	183508287	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183508286_183508287insA	uc001gqg.2	+						SMG7_uc010pob.1_Intron|SMG7_uc001gqf.2_Intron|SMG7_uc001gqh.2_Intron|SMG7_uc001gqi.2_Intron|SMG7_uc010poc.1_Intron	NM_173156	NP_775179			SMG-7 homolog isoform 1						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
GLT25D2	23127	broad.mit.edu	37	1	183972513	183972514	+	Intron	INS	-	C	C	rs148438872	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-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																		---	---	---	---
C1orf21	81563	broad.mit.edu	37	1	184541034	184541036	+	Intron	DEL	TTC	-	-	rs66495354		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184541034_184541036delTTC	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)														---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185828152	185828153	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185828152_185828153delTG	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	186008543	186008544	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186008543_186008544delCA	uc001grq.1	+							NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	186210298	186210299	+	IGR	INS	-	GAA	GAA	rs144973430	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186210298_186210299insGAA								HMCN1 (50213 upstream) : PRG4 (55106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187485309	187485309	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187485309delT								PLA2G4A (527204 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188124917	188124917	+	IGR	DEL	C	-	-	rs11341827		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188124917delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188909488	188909488	+	IGR	DEL	T	-	-	rs144169696		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188909488delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189041866	189041867	+	IGR	INS	-	ATTGC	ATTGC	rs142717735	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189041866_189041867insATTGC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189509012	189509015	+	IGR	DEL	AAAC	-	-	rs34229204		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189509012_189509015delAAAC								None (None upstream) : FAM5C (557782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189879613	189879613	+	IGR	DEL	T	-	-	rs113862416		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189879613delT								None (None upstream) : FAM5C (187184 downstream)																																			---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190430007	190430007	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190430007delT	uc001gse.1	-						FAM5C_uc010pot.1_Intron	NM_199051	NP_950252			family with sequence similarity 5, member C							extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	190796161	190796163	+	IGR	DEL	AAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190796161_190796163delAAG								FAM5C (349402 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191570065	191570070	+	IGR	DEL	AGAGAG	-	-	rs71701645		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191570065_191570070delAGAGAG								None (None upstream) : RGS18 (557522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191630463	191630464	+	IGR	DEL	CT	-	-	rs146693030		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191630463_191630464delCT								None (None upstream) : RGS18 (497128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192460260	192460261	+	IGR	INS	-	TG	TG	rs146275788	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192460260_192460261insTG								RGS21 (123848 upstream) : RGS1 (84596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193617442	193617442	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193617442delA								CDC73 (393502 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193671212	193671212	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193671212delT								CDC73 (447272 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193929968	193929968	+	IGR	DEL	T	-	-	rs34992634		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193929968delT								CDC73 (706028 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195865682	195865683	+	IGR	INS	-	TCTGAGAG	TCTGAGAG	rs150935208	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195865682_195865683insTCTGAGAG								None (None upstream) : KCNT2 (329230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	196043197	196043200	+	IGR	DEL	GTGT	-	-	rs144741411		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196043197_196043200delGTGT								None (None upstream) : KCNT2 (151713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	196116645	196116646	+	IGR	INS	-	AAC	AAC	rs144170975	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196116645_196116646insAAC								None (None upstream) : KCNT2 (78267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	196724985	196724985	+	IGR	DEL	C	-	-	rs138396963		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196724985delC								CFH (8354 upstream) : CFHR3 (18945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	197978324	197978326	+	IGR	DEL	AAT	-	-	rs34897064		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197978324_197978326delAAT								LHX9 (76609 upstream) : NEK7 (147782 downstream)																																			---	---	---	---
NEK7	140609	broad.mit.edu	37	1	198148929	198148930	+	Intron	DEL	GT	-	-	rs35749704		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198148929_198148930delGT	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																		---	---	---	---
PTPRC	5788	broad.mit.edu	37	1	198647881	198647882	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198647881_198647882insT	uc001gur.1	+						PTPRC_uc001gus.1_Intron|PTPRC_uc001gut.1_Intron|PTPRC_uc001guq.2_Intron|PTPRC_uc009wze.1_Intron|PTPRC_uc009wzf.1_Intron|PTPRC_uc010ppg.1_Intron|PTPRC_uc001guu.1_Intron|PTPRC_uc001guv.1_Intron|PTPRC_uc001guw.1_Intron	NM_002838	NP_002829			protein tyrosine phosphatase, receptor type, C						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	199973789	199973790	+	IGR	DEL	GA	-	-	rs71850066		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199973789_199973790delGA								None (None upstream) : NR5A2 (22980 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	200474537	200474540	+	IGR	DEL	AAGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200474537_200474540delAAGA								ZNF281 (95371 upstream) : KIF14 (46085 downstream)																																			---	---	---	---
KIF14	9928	broad.mit.edu	37	1	200560177	200560177	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200560177delA	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																		---	---	---	---
CACNA1S	779	broad.mit.edu	37	1	201049859	201049860	+	Intron	INS	-	G	G	rs140823263	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201049859_201049860insG	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)													---	---	---	---
LAD1	3898	broad.mit.edu	37	1	201362979	201362980	+	Intron	INS	-	TT	TT	rs35169716		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201362979_201362980insTT	uc001gwm.2	-						LAD1_uc009wzu.1_Intron	NM_005558	NP_005549			ladinin 1							basement membrane	structural molecule activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	201590461	201590462	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201590461_201590462delTT								RPS10P7 (90859 upstream) : NAV1 (26988 downstream)																																			---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201614818	201614819	+	5'Flank	INS	-	CACAGTGAAAATATA	CACAGTGAAAATATA	rs141727738	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201614818_201614819insCACAGTGAAAATATA	uc001gwu.2	+							NM_020443	NP_065176			neuron navigator 1						cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
IPO9	55705	broad.mit.edu	37	1	201825798	201825800	+	Intron	DEL	TTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201825798_201825800delTTG	uc001gwz.2	+							NM_018085	NP_060555			importin 9						protein import into nucleus	cytoplasm|nucleus	histone binding|protein transporter activity			ovary(2)	2																		---	---	---	---
KLHL12	59349	broad.mit.edu	37	1	202882117	202882117	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202882117delT	uc001gyo.1	-						KLHL12_uc001gyn.1_Intron|KLHL12_uc010pqc.1_Intron|KLHL12_uc009xah.1_Intron	NM_021633	NP_067646			kelch-like 12						Wnt receptor signaling pathway		protein binding				0			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
ADORA1	134	broad.mit.edu	37	1	203135610	203135610	+	3'UTR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203135610delC	uc001gze.1	+	4					FMOD_uc010pqi.1_Intron|ADORA1_uc001gzf.1_3'UTR|ADORA1_uc009xak.1_3'UTR|ADORA1_uc010pqh.1_3'UTR	NM_000674	NP_000665			adenosine A1 receptor						induction of apoptosis by extracellular signals|inflammatory response|nervous system development|phagocytosis	integral to plasma membrane				large_intestine(1)	1					Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Gabapentin(DB00996)|Imipramine(DB00458)|Pegademase bovine(DB00061)|Theophylline(DB00277)													---	---	---	---
SOX13	9580	broad.mit.edu	37	1	204055097	204055097	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204055097delA	uc001ham.2	+						SOX13_uc001hal.2_Intron	NM_005686	NP_005677			SRY-box 13						anatomical structure morphogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
PLEKHA6	22874	broad.mit.edu	37	1	204305692	204305693	+	Intron	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204305692_204305693delGT	uc001hau.2	-							NM_014935	NP_055750			phosphoinositol 3-phosphate-binding protein-3											ovary(3)|pancreas(1)	4	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)															---	---	---	---
MDM4	4194	broad.mit.edu	37	1	204544246	204544247	+	Intron	INS	-	AG	AG	rs145879229	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204544246_204544247insAG	uc001hbd.1	+						MDM4_uc001hbc.2_Intron	NM_002393				mouse double minute 4 homolog						apoptosis|cell proliferation|cellular response to hypoxia|G0 to G1 transition|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of protein catabolic process|negative regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization	nucleus	enzyme binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)					A		GBM|bladder|retinoblastoma								---	---	---	---
Unknown	0	broad.mit.edu	37	1	205750971	205750972	+	IGR	INS	-	T	T	rs34596053		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205750971_205750972insT								RAB7L1 (6361 upstream) : SLC41A1 (7249 downstream)																																			---	---	---	---
MAPKAPK2	9261	broad.mit.edu	37	1	206873303	206873304	+	Intron	INS	-	TCTC	TCTC	rs142636837	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206873303_206873304insTCTC	uc001hem.1	+						MAPKAPK2_uc001hel.1_Intron	NM_032960	NP_116584			mitogen-activated protein kinase-activated						activation of MAPK activity|hormone biosynthetic process|innate immune response|leukotriene biosynthetic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|prostanoid metabolic process|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)															---	---	---	---
IL10	3586	broad.mit.edu	37	1	206944845	206944846	+	Intron	INS	-	T	T	rs78550221		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206944845_206944846insT	uc001hen.1	-							NM_000572	NP_000563			interleukin 10 precursor						anti-apoptosis|B cell differentiation|B cell proliferation|cytoplasmic sequestering of NF-kappaB|inflammatory response|leukocyte chemotaxis|negative regulation of B cell proliferation|negative regulation of cytokine secretion involved in immune response|negative regulation of interferon-alpha biosynthetic process|negative regulation of interleukin-6 production|negative regulation of membrane protein ectodomain proteolysis|negative regulation of MHC class II biosynthetic process|negative regulation of T cell proliferation|positive regulation of B cell apoptosis|positive regulation of cytokine secretion|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|receptor biosynthetic process|regulation of isotype switching|response to glucocorticoid stimulus|type 2 immune response	extracellular space	cytokine activity|growth factor activity|interleukin-10 receptor binding				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)															---	---	---	---
IL20	50604	broad.mit.edu	37	1	207041516	207041517	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207041516_207041517delCA	uc001her.2	+						IL20_uc010pry.1_Intron|IL20_uc009xby.2_Intron	NM_018724	NP_061194			interleukin 20 precursor						positive regulation of keratinocyte differentiation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of inflammatory response	extracellular space	cytokine activity|interleukin-20 receptor binding				0	Breast(84;0.201)			OV - Ovarian serous cystadenocarcinoma(81;0.00459)														---	---	---	---
PFKFB2	5208	broad.mit.edu	37	1	207223646	207223647	+	Intron	INS	-	A	A	rs79573332		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207223646_207223647insA	uc010psc.1	+						YOD1_uc001hff.1_Intron|YOD1_uc001hfe.1_Intron					SubName: Full=cDNA FLJ53941, highly similar to 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2;						fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity			ovary(1)	1	Prostate(682;0.19)															OREG0014189	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	207341264	207341265	+	IGR	INS	-	TC	TC	rs149349758		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207341264_207341265insTC								C4BPA (22956 upstream) : CD55 (153552 downstream)																																			---	---	---	---
CD55	1604	broad.mit.edu	37	1	207494222	207494223	+	5'Flank	DEL	GC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207494222_207494223delGC	uc001hfq.3	+						CD55_uc001hfp.3_5'Flank|CD55_uc001hfr.3_5'Flank|CD55_uc010psf.1_5'Flank|CD55_uc009xcf.2_5'Flank|CD55_uc009xce.2_5'Flank	NM_000574	NP_000565			decay accelerating factor for complement isoform						complement activation, classical pathway|elevation of cytosolic calcium ion concentration|innate immune response|respiratory burst	anchored to membrane|extracellular region|integral to plasma membrane|membrane raft|soluble fraction	receptor activity			ovary(1)	1					Chloramphenicol(DB00446)													---	---	---	---
CR2	1380	broad.mit.edu	37	1	207634537	207634537	+	Intron	DEL	A	-	-	rs113002324		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207634537delA	uc001hfw.2	+						CR2_uc001hfv.2_Intron|CR2_uc009xch.2_Intron	NM_001877	NP_001868			complement component (3d/Epstein Barr virus)						complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(3)|skin(3)|urinary_tract(1)|ovary(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	208650985	208650985	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208650985delT								PLXNA2 (233320 upstream) : LOC642587 (951183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	208756303	208756304	+	IGR	INS	-	A	A	rs146698819	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208756303_208756304insA								PLXNA2 (338638 upstream) : LOC642587 (845864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	208803371	208803372	+	IGR	INS	-	A	A	rs3061648		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208803371_208803372insA								PLXNA2 (385706 upstream) : LOC642587 (798796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	208895815	208895815	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208895815delA								PLXNA2 (478150 upstream) : LOC642587 (706353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	208921011	208921011	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208921011delA								PLXNA2 (503346 upstream) : LOC642587 (681157 downstream)																																			---	---	---	---
SYT14	255928	broad.mit.edu	37	1	210128054	210128054	+	Intron	DEL	T	-	-	rs78147086		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210128054delT	uc009xcv.2	+						SYT14_uc001hhs.3_Intron|SYT14_uc001hht.3_Intron|SYT14_uc001hhu.3_Intron|SYT14_uc010psn.1_Intron|SYT14_uc010pso.1_Intron	NM_153262	NP_694994			synaptotagmin XIV isoform 4							integral to membrane				ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.085)														---	---	---	---
HHAT	55733	broad.mit.edu	37	1	210568783	210568783	+	Intron	DEL	A	-	-	rs3834004		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210568783delA	uc009xcx.2	+						HHAT_uc010psq.1_Intron|HHAT_uc001hhz.3_Intron|HHAT_uc010psr.1_Intron|HHAT_uc010pss.1_Intron|HHAT_uc009xcy.2_Intron|HHAT_uc010pst.1_Intron|HHAT_uc010psu.1_Intron	NM_001122834	NP_001116306			hedgehog acyltransferase						multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)														---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	211257376	211257376	+	Intron	DEL	C	-	-	rs5780624		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211257376delC	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872			potassium voltage-gated channel, subfamily H,						myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	212023989	212023991	+	IGR	DEL	TTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212023989_212023991delTTC								LPGAT1 (19875 upstream) : INTS7 (90707 downstream)																																			---	---	---	---
NENF	29937	broad.mit.edu	37	1	212617908	212617911	+	Intron	DEL	TGTA	-	-	rs10590281		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212617908_212617911delTGTA	uc001hjd.2	+						NENF_uc010ptf.1_Intron	NM_013349	NP_037481			neuron derived neurotrophic factor precursor							extracellular space	heme binding				0				all cancers(67;0.00967)|OV - Ovarian serous cystadenocarcinoma(81;0.0108)|GBM - Glioblastoma multiforme(131;0.0325)|Epithelial(68;0.132)														---	---	---	---
ATF3	467	broad.mit.edu	37	1	212765518	212765518	+	Intron	DEL	T	-	-	rs113551451		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212765518delT	uc001hjf.2	+							NM_001030287	NP_001025458			activating transcription factor 3 isoform 1							nucleolus	identical protein binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)														---	---	---	---
VASH2	79805	broad.mit.edu	37	1	213142537	213142537	+	Intron	DEL	T	-	-	rs112251005		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213142537delT	uc001hjy.2	+						VASH2_uc001hju.2_3'UTR|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)														---	---	---	---
RPS6KC1	26750	broad.mit.edu	37	1	213270010	213270011	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213270010_213270011insA	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc001hke.2_Intron	NM_012424	NP_036556			ribosomal protein S6 kinase, 52kDa, polypeptide						cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	213580556	213580557	+	IGR	DEL	CG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213580556_213580557delCG								RPS6KC1 (133749 upstream) : PROX1 (580729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	213604999	213605000	+	IGR	DEL	TG	-	-	rs72016628		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213604999_213605000delTG								RPS6KC1 (158192 upstream) : PROX1 (556286 downstream)																																			---	---	---	---
PTPN14	5784	broad.mit.edu	37	1	214687927	214687927	+	Intron	DEL	C	-	-	rs11290113		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214687927delC	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	214729052	214729053	+	IGR	INS	-	TG	TG	rs142250873	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214729052_214729053insTG								PTPN14 (4410 upstream) : CENPF (47479 downstream)																																			---	---	---	---
CENPF	1063	broad.mit.edu	37	1	214794663	214794664	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214794663_214794664delTG	uc001hkm.2	+							NM_016343	NP_057427			centromere protein F						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)														---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	216813831	216813834	+	Intron	DEL	GAGA	-	-	rs141545957		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216813831_216813834delGAGA	uc001hkw.1	-						ESRRG_uc001hky.1_Intron|ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron|ESRRG_uc001hkx.1_Intron|ESRRG_uc009xdo.1_Intron|ESRRG_uc001hle.1_Intron	NM_001438	NP_001429			estrogen-related receptor gamma isoform 1						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	217138502	217138503	+	Intron	INS	-	T	T	rs112198123		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217138502_217138503insT	uc010puc.1	-						ESRRG_uc001hkz.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318			estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	217167807	217167810	+	Intron	DEL	ACAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217167807_217167810delACAC	uc010puc.1	-						ESRRG_uc001hkz.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318			estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	218149890	218149890	+	IGR	DEL	A	-	-	rs78554513		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218149890delA								SPATA17 (109388 upstream) : RRP15 (308739 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	218309378	218309379	+	IGR	INS	-	T	T	rs147630490	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218309378_218309379insT								SPATA17 (268876 upstream) : RRP15 (149250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219324499	219324501	+	Intron	DEL	TTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219324499_219324501delTTG	uc001hlp.2	-											Homo sapiens cDNA clone IMAGE:6189076.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	219735615	219735616	+	IGR	INS	-	C	C	rs71560582		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219735615_219735616insC								LYPLAL1 (349409 upstream) : SLC30A10 (123153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	220997525	220997526	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220997525_220997526delTG								MOSC1 (9785 upstream) : HLX (55217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221110268	221110269	+	IGR	INS	-	AC	AC	rs143711696	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221110268_221110269insAC								HLX (51870 upstream) : LOC400804 (393001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221413814	221413817	+	IGR	DEL	ACAC	-	-	rs148075970		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221413814_221413817delACAC								HLX (355416 upstream) : LOC400804 (89453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221484396	221484397	+	IGR	INS	-	TT	TT	rs145183704	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221484396_221484397insTT								HLX (425998 upstream) : LOC400804 (18873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222411258	222411258	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222411258delA								DUSP10 (495797 upstream) : HHIPL2 (284344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222624299	222624299	+	IGR	DEL	A	-	-	rs66883968		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222624299delA								DUSP10 (708838 upstream) : HHIPL2 (71303 downstream)																																			---	---	---	---
DISP1	84976	broad.mit.edu	37	1	223133145	223133145	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223133145delA	uc001hnu.1	+							NM_032890	NP_116279			dispatched A						diaphragm development|protein homotrimerization|regulation of protein secretion|smoothened signaling pathway	basolateral plasma membrane|integral to membrane	hedgehog receptor activity|peptide transporter activity				0				GBM - Glioblastoma multiforme(131;0.102)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	224262210	224262211	+	IGR	INS	-	TTCCTTCC	TTCCTTCC	rs143257946	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224262210_224262211insTTCCTTCC								TP53BP2 (228536 upstream) : FBXO28 (39580 downstream)																																			---	---	---	---
NVL	4931	broad.mit.edu	37	1	224445050	224445050	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224445050delA	uc001hok.2	-						NVL_uc001hol.2_Intron|NVL_uc010pvd.1_Intron|NVL_uc010pve.1_Intron|NVL_uc010pvf.1_Intron|MIR320B-2_hsa-mir-320b-2|MI0003839_5'Flank	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	225092171	225092171	+	IGR	DEL	T	-	-	rs112498546		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225092171delT								CNIH3 (163922 upstream) : DNAH14 (25185 downstream)																																			---	---	---	---
ENAH	55740	broad.mit.edu	37	1	225833870	225833870	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225833870delA	uc001hpc.1	-						ENAH_uc001hpd.1_Intron	NM_001008493	NP_001008493			enabled homolog isoform a						axon guidance|intracellular transport|T cell receptor signaling pathway	cytosol|filopodium|focal adhesion|lamellipodium|synapse	actin binding|SH3 domain binding|WW domain binding			ovary(1)|skin(1)	2	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)														---	---	---	---
EPHX1	2052	broad.mit.edu	37	1	226030913	226030914	+	Intron	INS	-	TC	TC	rs147908947	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226030913_226030914insTC	uc001hpk.2	+						EPHX1_uc001hpl.2_Intron	NM_001136018	NP_001129490			epoxide hydrolase 1						aromatic compound catabolic process|response to toxin	endoplasmic reticulum membrane|integral to membrane|microsome	cis-stilbene-oxide hydrolase activity|epoxide hydrolase activity			ovary(3)|lung(1)	4	Breast(184;0.197)																	---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227203389	227203390	+	Intron	INS	-	AA	AA	rs148877902	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227203389_227203390insAA	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	227552056	227552057	+	IGR	INS	-	A	A	rs10458380	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227552056_227552057insA								CDC42BPA (46230 upstream) : ZNF678 (199187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	227702432	227702432	+	IGR	DEL	A	-	-	rs35543592		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227702432delA								CDC42BPA (196606 upstream) : ZNF678 (48812 downstream)																																			---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228426425	228426428	+	Intron	DEL	ACTC	-	-	rs35732204		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228426425_228426428delACTC	uc009xez.1	+						OBSCN_uc001hsn.2_Intron	NM_001098623	NP_001092093			obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	228947838	228947838	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228947838delG								RHOU (65429 upstream) : RAB4A (459041 downstream)																																			---	---	---	---
RAB4A	5867	broad.mit.edu	37	1	229417005	229417008	+	Intron	DEL	TGTC	-	-	rs60310291		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229417005_229417008delTGTC	uc001hth.2	+						RAB4A_uc001hti.2_Intron|RAB4A_uc001htj.2_Intron	NM_004578	NP_004569			RAB4A, member RAS oncogene family								GDP binding|GTP binding|GTPase activity			ovary(1)	1	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	229560856	229560878	+	IGR	DEL	AGGTGGGTGGATCGCTTGAGGCC	-	-	rs71561737		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229560856_229560878delAGGTGGGTGGATCGCTTGAGGCC								C1orf96 (82168 upstream) : ACTA1 (6117 downstream)																																			---	---	---	---
TAF5L	27097	broad.mit.edu	37	1	229745556	229745557	+	Intron	INS	-	A	A	rs150995669	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229745556_229745557insA	uc001htq.2	-						TAF5L_uc001htr.2_Intron	NM_014409	NP_055224			PCAF associated factor 65 beta isoform a						histone H3 acetylation|transcription from RNA polymerase II promoter	STAGA complex|transcription factor TFTC complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)																---	---	---	---
TAF5L	27097	broad.mit.edu	37	1	229748735	229748736	+	Intron	INS	-	T	T	rs143762768	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229748735_229748736insT	uc001htq.2	-						TAF5L_uc001htr.2_Intron	NM_014409	NP_055224			PCAF associated factor 65 beta isoform a						histone H3 acetylation|transcription from RNA polymerase II promoter	STAGA complex|transcription factor TFTC complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	230524921	230524921	+	IGR	DEL	T	-	-	rs35135641		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230524921delT								PGBD5 (11554 upstream) : COG2 (253281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230550382	230550382	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230550382delG								PGBD5 (37015 upstream) : COG2 (227820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230588349	230588349	+	IGR	DEL	C	-	-	rs35283293		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230588349delC								PGBD5 (74982 upstream) : COG2 (189853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230612113	230612114	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230612113_230612114insT								PGBD5 (98746 upstream) : COG2 (166088 downstream)																																			---	---	---	---
TSNAX-DISC1	100303453	broad.mit.edu	37	1	231714405	231714416	+	Intron	DEL	CTCTCTCTCTCT	-	-	rs71179787		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231714405_231714416delCTCTCTCTCTCT	uc010pwg.1	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron	NM_001012959	NP_001012977			disrupted in schizophrenia 1 isoform S												0																		---	---	---	---
TSNAX-DISC1	100303453	broad.mit.edu	37	1	231740569	231740570	+	Intron	INS	-	ATAC	ATAC	rs142014062	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231740569_231740570insATAC	uc010pwg.1	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron	NM_001012959	NP_001012977			disrupted in schizophrenia 1 isoform S												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	232231447	232231448	+	IGR	INS	-	T	T	rs151229017	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232231447_232231448insT								DISC1 (54431 upstream) : SIPA1L2 (302266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	232430277	232430278	+	IGR	INS	-	T	T	rs145465559	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232430277_232430278insT								DISC1 (253261 upstream) : SIPA1L2 (103436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	232711363	232711364	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232711363_232711364insA								SIPA1L2 (60120 upstream) : KIAA1383 (229274 downstream)																																			---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233431748	233431749	+	5'Flank	INS	-	T	T	rs1294350		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233431748_233431749insT	uc001hvl.2	-							NM_014801	NP_055616			pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234053185	234053186	+	Intron	INS	-	T	T	rs145001578	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234053185_234053186insT	uc001hvy.1	+							NM_173508	NP_775779			solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234429402	234429405	+	Intron	DEL	AGAG	-	-	rs35613998		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234429402_234429405delAGAG	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	234667973	234667974	+	5'Flank	DEL	AC	-	-	rs71759534		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234667973_234667974delAC	uc001hwe.2	-											Homo sapiens cDNA clone IMAGE:4816129.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	236083459	236083460	+	IGR	INS	-	TC	TC	rs144213587	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236083459_236083460insTC								LYST (36519 upstream) : NID1 (55681 downstream)																																			---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237580059	237580060	+	Intron	INS	-	AG	AG	rs148312293	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237580059_237580060insAG	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	237952760	237952763	+	Intron	DEL	TAAC	-	-	rs146054663		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237952760_237952763delTAAC	uc001hyl.1	+						RYR2_uc010pyb.1_5'Flank	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	238264844	238264853	+	IGR	DEL	AAACAAAACA	-	-	rs66514172		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238264844_238264853delAAACAAAACA								LOC100130331 (173227 upstream) : LOC339535 (378833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	238273832	238273834	+	IGR	DEL	GTG	-	-	rs57305643		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238273832_238273834delGTG								LOC100130331 (182215 upstream) : LOC339535 (369852 downstream)																																			---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	239922469	239922470	+	Intron	INS	-	T	T	rs35624317		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239922469_239922470insT	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)													---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242570864	242570864	+	Intron	DEL	T	-	-	rs58679212		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242570864delT	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	242787112	242787115	+	IGR	DEL	CTTA	-	-	rs10541881		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242787112_242787115delCTTA								PLD5 (99114 upstream) : CEP170 (500616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	244031144	244031145	+	IGR	DEL	GT	-	-	rs146770053	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244031144_244031145delGT								AKT3 (24591 upstream) : ZNF238 (183416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	244079065	244079066	+	5'Flank	DEL	AA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244079065_244079066delAA	uc001iac.2	+											Homo sapiens cDNA clone IMAGE:5244187.																														---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245581957	245581957	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245581957delT	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245817620	245817621	+	Intron	INS	-	G	G	rs148057078	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245817620_245817621insG	uc001ibf.1	+						KIF26B_uc001ibg.1_Intron|KIF26B_uc001ibh.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	245888450	245888450	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245888450delA								KIF26B (22022 upstream) : SMYD3 (24195 downstream)																																			---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246206058	246206058	+	Intron	DEL	G	-	-	rs11355012		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246206058delG	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	246519436	246519437	+	Intron	INS	-	C	C	rs141022744	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246519436_246519437insC	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	246592127	246592127	+	Intron	DEL	G	-	-	rs11351590		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246592127delG	uc001ibl.2	-							NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
CNST	163882	broad.mit.edu	37	1	246737163	246737164	+	Intron	INS	-	A	A	rs143323730	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246737163_246737164insA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	248690015	248690015	+	IGR	DEL	C	-	-	rs34098303		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248690015delC								OR2G6 (4117 upstream) : OR2T29 (31830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	249099176	249099176	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249099176delA								LOC646627 (196025 upstream) : SH3BP5L (5475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	249162856	249162857	+	IGR	INS	-	A	A	rs35621709		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249162856_249162857insA								ZNF692 (9572 upstream) : PGBD2 (37585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	37433	37435	+	IGR	DEL	AAC	-	-	rs112658597		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37433_37435delAAC								None (None upstream) : FAM110C (4174 downstream)																																			---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	958494	958494	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:958494delA	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	1261726	1261726	+	Intron	DEL	T	-	-	rs13029737	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1261726delT	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	1606228	1606229	+	IGR	DEL	AA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1606228_1606229delAA								TPO (59730 upstream) : PXDN (29431 downstream)																																			---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	2154687	2154688	+	Intron	INS	-	GGAG	GGAG	rs144888184	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2154687_2154688insGGAG	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc002qxf.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	2266465	2266465	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2266465delA	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	2551860	2551860	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2551860delA								MYT1L (216815 upstream) : TSSC1 (640881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	3943662	3943663	+	IGR	INS	-	TT	TT	rs3067158		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3943662_3943663insTT								ALLC (193404 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5417356	5417356	+	IGR	DEL	A	-	-	rs11307158		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5417356delA								None (None upstream) : SOX11 (415443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	7470313	7470313	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7470313delA								RNF144A (286006 upstream) : LOC339788 (592245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	7751483	7751484	+	IGR	INS	-	CT	CT	rs140564193	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7751483_7751484insCT								RNF144A (567176 upstream) : LOC339788 (311074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	7755000	7755001	+	IGR	INS	-	TTT	TTT	rs145338266	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7755000_7755001insTTT								RNF144A (570693 upstream) : LOC339788 (307557 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	7829372	7829373	+	IGR	DEL	TA	-	-	rs67352770		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7829372_7829373delTA								RNF144A (645065 upstream) : LOC339788 (233185 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8209412	8209412	+	Intron	DEL	A	-	-	rs5829146		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8209412delA	uc010eww.1	-											Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	8702296	8702297	+	IGR	INS	-	A	A	rs113267741		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8702296_8702297insA								LOC339788 (585319 upstream) : ID2 (117043 downstream)																																			---	---	---	---
ASAP2	8853	broad.mit.edu	37	2	9457166	9457169	+	Intron	DEL	CAAT	-	-	rs149312154		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9457166_9457169delCAAT	uc002qzh.2	+						ASAP2_uc002qzi.2_Intron	NM_003887	NP_003878			ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0																		---	---	---	---
ASAP2	8853	broad.mit.edu	37	2	9527342	9527343	+	Intron	INS	-	A	A	rs74944996		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9527342_9527343insA	uc002qzh.2	+						ASAP2_uc002qzi.2_Intron	NM_003887	NP_003878			ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0																		---	---	---	---
CPSF3	51692	broad.mit.edu	37	2	9606001	9606002	+	Intron	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9606001_9606002delGT	uc002qzo.1	+						CPSF3_uc002qzp.1_Intron|CPSF3_uc002qzq.1_Intron	NM_016207	NP_057291			cleavage and polyadenylation specific factor 3,						histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding			breast(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	10353338	10353342	+	IGR	DEL	GAAAA	-	-	rs72788368	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10353338_10353342delGAAAA								C2orf48 (1482 upstream) : HPCAL1 (89698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	10403711	10403711	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10403711delA								C2orf48 (51855 upstream) : HPCAL1 (39329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	12208946	12208947	+	Intron	INS	-	A	A	rs141481415	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12208946_12208947insA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12600034	12600035	+	Intron	INS	-	T	T	rs147293261	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12600034_12600035insT	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12800695	12800696	+	IGR	INS	-	T	T	rs141362121	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12800695_12800696insT								LPIN1 (833164 upstream) : TRIB2 (56302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	12832555	12832560	+	IGR	DEL	GTGTGT	-	-	rs62124722		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12832555_12832560delGTGTGT								LPIN1 (865024 upstream) : TRIB2 (24438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	13205843	13205844	+	IGR	INS	-	TA	TA	rs139215177	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13205843_13205844insTA								TRIB2 (322987 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	13690338	13690338	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13690338delA								TRIB2 (807482 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	14961986	14961986	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14961986delA								FAM84A (171053 upstream) : NBAS (345046 downstream)																																			---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15614673	15614674	+	Intron	INS	-	TTC	TTC	rs145872560	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15614673_15614674insTTC	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	15847021	15847022	+	Intron	INS	-	A	A	rs77552974	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15847021_15847022insA	uc002rcf.1	+											Homo sapiens cDNA FLJ36206 fis, clone TESTI2028662.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	16331808	16331808	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16331808delT								MYCN (244680 upstream) : FAM49A (402093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16714938	16714938	+	IGR	DEL	A	-	-	rs111551716		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16714938delA								MYCN (627810 upstream) : FAM49A (18963 downstream)																																			---	---	---	---
FAM49A	81553	broad.mit.edu	37	2	16787651	16787654	+	Intron	DEL	TCTC	-	-	rs71983601		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16787651_16787654delTCTC	uc010exm.1	-						FAM49A_uc002rck.1_Intron	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)															---	---	---	---
FAM49A	81553	broad.mit.edu	37	2	16814675	16814678	+	Intron	DEL	TTTA	-	-	rs10558897		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16814675_16814678delTTTA	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)															---	---	---	---
VSNL1	7447	broad.mit.edu	37	2	17791783	17791783	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17791783delT	uc002rcm.2	+							NM_003385	NP_003376			visinin-like 1								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	18232933	18232934	+	IGR	INS	-	AGG	AGG	rs150217266	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18232933_18232934insAGG								KCNS3 (118709 upstream) : NT5C1B (503057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	18249284	18249284	+	IGR	DEL	A	-	-	rs149498034		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18249284delA								KCNS3 (135060 upstream) : NT5C1B (486707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	18537052	18537052	+	IGR	DEL	T	-	-	rs71969931		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18537052delT								KCNS3 (422828 upstream) : NT5C1B (198939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19722403	19722403	+	IGR	DEL	T	-	-	rs5829702		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19722403delT								OSR1 (164031 upstream) : TTC32 (374115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19909521	19909522	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19909521_19909522insA								OSR1 (351149 upstream) : TTC32 (186996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	21589471	21589472	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21589471_21589472insT								APOB (322526 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	21611765	21611765	+	IGR	DEL	A	-	-	rs67974345		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21611765delA								APOB (344820 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	22068980	22068980	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22068980delT								APOB (802035 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	22695719	22695720	+	IGR	INS	-	A	A	rs111365194		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22695719_22695720insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23373337	23373344	+	IGR	DEL	ACACACAC	-	-	rs36157053		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23373337_23373344delACACACAC								None (None upstream) : KLHL29 (382111 downstream)																																			---	---	---	---
KLHL29	114818	broad.mit.edu	37	2	23757404	23757405	+	Intron	DEL	TT	-	-	rs146487324		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23757404_23757405delTT	uc002ref.2	+											SubName: Full=KLHL29 protein; Flags: Fragment;											ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	24613039	24613040	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24613039_24613040insT								ITSN2 (29642 upstream) : NCOA1 (174139 downstream)																																			---	---	---	---
C2orf39	92749	broad.mit.edu	37	2	26671093	26671093	+	Intron	DEL	A	-	-	rs34461558		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26671093delA	uc002rhg.2	+							NM_145038	NP_659475			hypothetical protein LOC92749												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
CIB4	130106	broad.mit.edu	37	2	26833696	26833696	+	Intron	DEL	G	-	-	rs11304295		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26833696delG	uc002rhm.2	-							NM_001029881	NP_001025052			calcium and integrin binding family member 4								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
CIB4	130106	broad.mit.edu	37	2	26835815	26835815	+	Intron	DEL	T	-	-	rs5830018		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26835815delT	uc002rhm.2	-							NM_001029881	NP_001025052			calcium and integrin binding family member 4								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
BRE	9577	broad.mit.edu	37	2	28400132	28400132	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28400132delA	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)																	---	---	---	---
BRE	9577	broad.mit.edu	37	2	28409676	28409676	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28409676delT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664			brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	28932580	28932580	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28932580delT								PLB1 (65967 upstream) : PPP1CB (42032 downstream)																																			---	---	---	---
FAM179A	165186	broad.mit.edu	37	2	29228002	29228018	+	Intron	DEL	TGTGTGTGAGTGCATGT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29228002_29228018delTGTGTGTGAGTGCATGT	uc010ezl.2	+						FAM179A_uc010ymm.1_Intron	NM_199280	NP_954974			hypothetical protein LOC165186								binding			ovary(3)|skin(1)	4																		---	---	---	---
ALK	238	broad.mit.edu	37	2	29439602	29439604	+	Intron	DEL	GTG	-	-	rs34383389		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29439602_29439604delGTG	uc002rmy.2	-						ALK_uc010ymo.1_Intron	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	30418315	30418318	+	IGR	DEL	AGAG	-	-	rs146229197		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30418315_30418318delAGAG								YPEL5 (34917 upstream) : LBH (36079 downstream)																																			---	---	---	---
XDH	7498	broad.mit.edu	37	2	31606985	31606986	+	Intron	INS	-	GTGTGTGT	GTGTGTGT	rs143765010	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31606985_31606986insGTGTGTGT	uc002rnv.1	-							NM_000379	NP_000370			xanthine dehydrogenase						purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	33834749	33834750	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33834749_33834750delAC								FAM98A (10387 upstream) : MYADML (116382 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34001860	34001861	+	IGR	INS	-	TT	TT	rs147307101	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34001860_34001861insTT								MYADML (48576 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34526774	34526774	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34526774delT								MYADML (573490 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35006975	35006975	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35006975delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35063674	35063675	+	IGR	INS	-	TCA	TCA	rs149911513	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35063674_35063675insTCA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35833159	35833159	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35833159delA								None (None upstream) : CRIM1 (750238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36027545	36027545	+	IGR	DEL	A	-	-	rs149342664		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36027545delA								None (None upstream) : CRIM1 (555852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	37984142	37984142	+	IGR	DEL	T	-	-	rs112508808		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37984142delT								CDC42EP3 (84816 upstream) : FAM82A1 (168320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	40034398	40034399	+	IGR	INS	-	AA	AA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40034398_40034399insAA								THUMPD2 (27982 upstream) : SLC8A1 (304888 downstream)																																			---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40362305	40362305	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40362305delG	uc002rrx.2	-						uc002rrw.2_Intron|SLC8A1_uc002rry.2_Intron|SLC8A1_uc002rrz.2_Intron|SLC8A1_uc002rsa.2_Intron|SLC8A1_uc002rsd.3_Intron	NM_021097	NP_066920			solute carrier family 8 (sodium/calcium						cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	40771542	40771542	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40771542delT								SLC8A1 (31967 upstream) : None (None downstream)																																			---	---	---	---
KCNG3	170850	broad.mit.edu	37	2	42686339	42686340	+	Intron	INS	-	A	A	rs77695398		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42686339_42686340insA	uc002rsn.2	-						KCNG3_uc002rsm.2_Intron	NM_133329	NP_579875			potassium voltage-gated channel, subfamily G,							endoplasmic reticulum|voltage-gated potassium channel complex	protein binding			central_nervous_system(1)	1																		---	---	---	---
MTA3	57504	broad.mit.edu	37	2	42856925	42856926	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42856925_42856926insT	uc002rso.1	+						MTA3_uc002rsp.1_Intron|MTA3_uc002rsq.2_Intron|MTA3_uc002rsr.2_Intron	NM_020744	NP_065795			metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	43232562	43232562	+	IGR	DEL	T	-	-	rs112033394		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43232562delT								HAAO (212811 upstream) : ZFP36L2 (216980 downstream)																																			---	---	---	---
C2orf34	79823	broad.mit.edu	37	2	44657849	44657849	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44657849delT	uc002rum.2	+						C2orf34_uc002rul.2_Intron	NM_024766	NP_079042			hypothetical protein LOC79823							cytoplasm	calmodulin-lysine N-methyltransferase activity				0		all_hematologic(82;0.0892)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	45145730	45145730	+	IGR	DEL	C	-	-	rs34438374		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45145730delC								C2orf34 (146001 upstream) : SIX3 (23307 downstream)																																			---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45697928	45697932	+	Intron	DEL	TATGT	-	-	rs57351770		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45697928_45697932delTATGT	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	46488996	46489005	+	IGR	DEL	TGTGTGTGTG	-	-	rs71846543		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46488996_46489005delTGTGTGTGTG								PRKCE (73868 upstream) : EPAS1 (35558 downstream)																																			---	---	---	---
SOCS5	9655	broad.mit.edu	37	2	46945335	46945335	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46945335delT	uc002rvf.2	+						SOCS5_uc010yoe.1_Intron|SOCS5_uc002rvg.2_Intron	NM_014011	NP_054730			suppressor of cytokine signaling 5						cell growth|cytokine-mediated signaling pathway|intracellular signal transduction|negative regulation of signal transduction|negative regulation of T-helper 2 cell differentiation|positive regulation of T-helper 1 cell differentiation|regulation of growth					ovary(1)|lung(1)|central_nervous_system(1)	3		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
LOC100134259	100134259	broad.mit.edu	37	2	47079885	47079886	+	Intron	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47079885_47079886delTT	uc002rvi.3	+						LOC100134259_uc002rvj.1_Intron	NR_024452				Homo sapiens cDNA FLJ35178 fis, clone PLACE6014043.												0																		---	---	---	---
TTC7A	57217	broad.mit.edu	37	2	47214944	47214947	+	Intron	DEL	CGCG	-	-	rs6727457		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47214944_47214947delCGCG	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	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)													OREG0014606	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FBXO11	80204	broad.mit.edu	37	2	48063836	48063836	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48063836delT	uc010fbl.2	-						FBXO11_uc002rwe.2_Intron|FBXO11_uc002rwf.2_Intron|FBXO11_uc002rwg.1_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)															---	---	---	---
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48797478	48797478	+	Intron	DEL	A	-	-	rs74666215		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48797478delA	uc002rwp.1	+						STON1_uc002rwo.3_Intron|STON1_uc010fbm.2_Intron	NM_172311	NP_758515			STON1-GTF2A1L protein						endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49380564	49380568	+	Intron	DEL	AAAAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49380564_49380568delAAAAC	uc002rww.2	-						FSHR_uc002rwx.2_Intron|FSHR_uc010fbn.2_Intron|FSHR_uc010fbo.1_Intron	NM_000145	NP_000136			follicle stimulating hormone receptor isoform 1						female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50609257	50609258	+	Intron	INS	-	C	C	rs68050123		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50609257_50609258insC	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	51258018	51258018	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51258018delT	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	51575813	51575814	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51575813_51575814delAC								NRXN1 (316139 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53187024	53187024	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53187024delA								None (None upstream) : ASB3 (710094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53702764	53702768	+	IGR	DEL	AAGTT	-	-	rs72453501		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53702764_53702768delAAGTT								None (None upstream) : ASB3 (194350 downstream)																																			---	---	---	---
ASB3	51130	broad.mit.edu	37	2	54047419	54047419	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54047419delT	uc002rxi.3	-							NM_001164165	NP_001157637			hypothetical protein LOC100302652						intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
CCDC88A	55704	broad.mit.edu	37	2	55634855	55634856	+	Intron	INS	-	T	T	rs74527982		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55634855_55634856insT	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron|CCDC88A_uc010fbz.2_Intron	NM_001135597	NP_001129069			coiled-coil domain containing 88A isoform 1						activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	56324520	56324520	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56324520delC	uc002rzk.2	+											Homo sapiens, clone IMAGE:3873411, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	57571396	57571399	+	IGR	DEL	GTGT	-	-	rs67444670		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57571396_57571399delGTGT								CCDC85A (958088 upstream) : VRK2 (563387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	58628955	58628970	+	IGR	DEL	TTGCATCACTGTGACA	-	-	rs58283809		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58628955_58628970delTTGCATCACTGTGACA								FANCL (160440 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60273952	60273952	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60273952delT								None (None upstream) : BCL11A (404351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60573815	60573815	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60573815delT								None (None upstream) : BCL11A (104488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60611229	60611230	+	IGR	DEL	AG	-	-	rs67958750		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60611229_60611230delAG								None (None upstream) : BCL11A (67073 downstream)																																			---	---	---	---
BCL11A	53335	broad.mit.edu	37	2	60765873	60765878	+	Intron	DEL	TCTGTG	-	-	rs147754388		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60765873_60765878delTCTGTG	uc002sae.1	-						BCL11A_uc002sab.2_Intron|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Intron|BCL11A_uc002sad.1_5'Flank|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								---	---	---	---
AHSA2	130872	broad.mit.edu	37	2	61413038	61413041	+	Intron	DEL	ATTA	-	-	rs3214802		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61413038_61413041delATTA	uc002sbc.1	+						AHSA2_uc002sbb.1_Intron	NM_152392	NP_689605			AHA1, activator of heat shock 90kDa protein						response to stress	cytoplasm	ATPase activator activity|chaperone binding			breast(1)	1			Epithelial(17;0.0994)															---	---	---	---
COMMD1	150684	broad.mit.edu	37	2	62263190	62263193	+	Intron	DEL	CACA	-	-	rs71714041	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62263190_62263193delCACA	uc002sbp.2	+							NM_152516	NP_689729			MURR1						copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)															---	---	---	---
C2orf86	51057	broad.mit.edu	37	2	63704030	63704031	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63704030_63704031insT	uc002sch.2	-						C2orf86_uc002sci.1_Intron|C2orf86_uc010fcr.1_Intron	NM_015910	NP_056994			hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	64263421	64263421	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64263421delC								VPS54 (17207 upstream) : PELI1 (56367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	65016714	65016715	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65016714_65016715insA								SERTAD2 (135668 upstream) : SLC1A4 (198864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	65947974	65947975	+	Intron	INS	-	TGTC	TGTC	rs28483523		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65947974_65947975insTGTC	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	68166150	68166151	+	IGR	INS	-	TTAC	TTAC	rs139969420	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68166150_68166151insTTAC								ETAA1 (528617 upstream) : C1D (103182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	68671794	68671795	+	IGR	INS	-	A	A	rs113788468		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68671794_68671795insA								PLEK (47210 upstream) : FBXO48 (17712 downstream)																																			---	---	---	---
AAK1	22848	broad.mit.edu	37	2	69716145	69716145	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69716145delT	uc002sfp.2	-						AAK1_uc010fdk.2_Intron|AAK1_uc010yqm.1_Intron	NM_014911	NP_055726			AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0																		---	---	---	---
TIA1	7072	broad.mit.edu	37	2	70477077	70477078	+	5'Flank	DEL	TA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70477077_70477078delTA	uc002sgj.3	-						TIA1_uc002sgk.3_5'Flank|TIA1_uc002sgl.3_5'Flank|TIA1_uc002sgm.3_5'Flank|TIA1_uc010yqt.1_5'Flank	NM_022173	NP_071505			TIA1 cytotoxic granule-associated RNA binding						apoptosis|induction of apoptosis|regulation of nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|poly(A) RNA binding|protein binding				0																		---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71799336	71799336	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71799336delA	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron	NM_003494	NP_003485			dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	72170078	72170085	+	IGR	DEL	GTGTGTGT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72170078_72170085delGTGTGTGT								DYSF (256186 upstream) : CYP26B1 (186282 downstream)																																			---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72739457	72739496	+	Intron	DEL	GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAA	-	-	rs143739965		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72739457_72739496delGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAA	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	74943888	74943891	+	IGR	DEL	TAAC	-	-	rs67934853		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74943888_74943891delTAAC								SEMA4F (34703 upstream) : HK2 (115891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	75051445	75051446	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75051445_75051446insA								SEMA4F (142260 upstream) : HK2 (8336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	75439510	75439511	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75439510_75439511delTG								TACR1 (12865 upstream) : FAM176A (279933 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	75832091	75832092	+	IGR	DEL	CT	-	-	rs71992148		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75832091_75832092delCT								FAM176A (35243 upstream) : MRPL19 (41817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	75860958	75860961	+	IGR	DEL	TCAT	-	-	rs10609102		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75860958_75860961delTCAT								FAM176A (64110 upstream) : MRPL19 (12948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76755020	76755020	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76755020delT								C2orf3 (816909 upstream) : LRRTM4 (219838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76809837	76809837	+	IGR	DEL	T	-	-	rs71374372		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76809837delT								C2orf3 (871726 upstream) : LRRTM4 (165021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76822888	76822888	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76822888delA								C2orf3 (884777 upstream) : LRRTM4 (151970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	79182606	79182606	+	IGR	DEL	T	-	-	rs138167310		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79182606delT								None (None upstream) : REG3G (70220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	79320763	79320764	+	IGR	INS	-	T	T	rs150576833	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79320763_79320764insT								REG1B (5613 upstream) : REG1A (26820 downstream)																																			---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80013294	80013295	+	Intron	DEL	AG	-	-	rs80170109		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80013294_80013295delAG	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	80034142	80034142	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80034142delT	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	80698946	80698946	+	Intron	DEL	A	-	-	rs76304275		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80698946delA	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysi.1_Intron	NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	80876676	80876677	+	IGR	INS	-	TAAC	TAAC	rs146171104	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80876676_80876677insTAAC								CTNNA2 (772 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82141243	82141244	+	IGR	INS	-	TC	TC	rs138938448	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82141243_82141244insTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83040901	83040901	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83040901delC								None (None upstream) : None (None downstream)																																			---	---	---	---
TCF7L1	83439	broad.mit.edu	37	2	85367603	85367604	+	Intron	INS	-	C	C	rs143080778	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85367603_85367604insC	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																		---	---	---	---
VAMP5	10791	broad.mit.edu	37	2	85819923	85819924	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85819923_85819924insA	uc002spu.1	+						RNF181_uc002spv.1_5'Flank	NM_006634	NP_006625			vesicle-associated membrane protein 5						cell differentiation|vesicle-mediated transport	endomembrane system					0																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86924595	86924595	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86924595delA	uc010ytl.1	-							NM_001005753	NP_001005753			vacuolar protein sorting 24 isoform 2						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87377432	87377433	+	Intron	INS	-	T	T	rs68166409		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87377432_87377433insT	uc002srs.3	+											SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	88308534	88308535	+	IGR	INS	-	T	T	rs146989919	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88308534_88308535insT								RMND5A (269768 upstream) : KRCC1 (18189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	89876129	89876133	+	IGR	DEL	GAGAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89876129_89876133delGAGAA								FLJ40330 (770004 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	90007219	90007219	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90007219delT	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	91690216	91690217	+	IGR	INS	-	G	G	rs113837807		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91690216_91690217insG								None (None upstream) : LOC654342 (114975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91738235	91738237	+	IGR	DEL	TCA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91738235_91738237delTCA								None (None upstream) : LOC654342 (66955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91773058	91773059	+	IGR	INS	-	CTGT	CTGT	rs147631432		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91773058_91773059insCTGT								None (None upstream) : LOC654342 (32133 downstream)																																			---	---	---	---
LOC654342	654342	broad.mit.edu	37	2	91810712	91810713	+	Intron	INS	-	T	T	rs139062859	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91810712_91810713insT	uc002sts.3	-						LOC654342_uc002stt.2_Intron					Homo sapiens cDNA clone IMAGE:4801360.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	91896230	91896231	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91896230_91896231insT								LOC654342 (48255 upstream) : GGT8P (67137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91976432	91976432	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91976432delA								GGT8P (6279 upstream) : FKSG73 (152727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	95406568	95406569	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95406568_95406569delAC								None (None upstream) : ANKRD20B (20106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	95549798	95549798	+	Intron	DEL	T	-	-	rs34804061		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95549798delT	uc002stv.1	-											Homo sapiens cDNA FLJ44118 fis, clone TESTI4047069.																														---	---	---	---
KCNIP3	30818	broad.mit.edu	37	2	96048860	96048875	+	Intron	DEL	CCCACCCGCCCATCCA	-	-	rs58372613	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96048860_96048875delCCCACCCGCCCATCCA	uc002sup.2	+						KCNIP3_uc002suq.2_Intron	NM_013434	NP_038462			Kv channel interacting protein 3 isoform 1						apoptosis|signal transduction|transcription, DNA-dependent	endoplasmic reticulum|Golgi apparatus|nucleus|plasma membrane	calcium ion binding|DNA binding|potassium channel activity|transcription corepressor activity|voltage-gated ion channel activity			breast(2)|ovary(1)	3				READ - Rectum adenocarcinoma(193;0.13)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	97189271	97189272	+	IGR	INS	-	AA	AA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97189271_97189272insAA								NEURL3 (15425 upstream) : ARID5A (13192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	97197103	97197103	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97197103delT	uc002swd.2	-											full-length cDNA clone CS0DH007YI06 of T cells (Jurkat cell line) of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	98269781	98269782	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98269781_98269782insA								COX5B (5125 upstream) : ACTR1B (2620 downstream)																																			---	---	---	---
MGAT4A	11320	broad.mit.edu	37	2	99331397	99331397	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99331397delA	uc002sze.2	-						MGAT4A_uc010fil.2_Intron	NM_012214	NP_036346			alpha-1,3-mannosyl-glycoprotein						N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	101339353	101339354	+	IGR	INS	-	C	C	rs149961369	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101339353_101339354insC								PDCL3 (146152 upstream) : NPAS2 (97259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	101778731	101778732	+	IGR	DEL	AC	-	-	rs3841079		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101778731_101778732delAC								TBC1D8 (10885 upstream) : C2orf29 (90613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	102136585	102136586	+	IGR	INS	-	T	T	rs143841092	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102136585_102136586insT								RFX8 (45420 upstream) : MAP4K4 (177902 downstream)																																			---	---	---	---
MAP4K4	9448	broad.mit.edu	37	2	102507895	102507895	+	3'UTR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102507895delT	uc002tbg.2	+	30					MAP4K4_uc002tbc.2_3'UTR|MAP4K4_uc002tbd.2_3'UTR|MAP4K4_uc002tbe.2_3'UTR|MAP4K4_uc002tbf.2_3'UTR|MAP4K4_uc010yvy.1_3'UTR|MAP4K4_uc002tbh.2_3'UTR|MAP4K4_uc002tbi.2_3'UTR|MAP4K4_uc010yvz.1_3'UTR|MAP4K4_uc002tbk.2_3'UTR|MAP4K4_uc002tbl.2_3'UTR	NM_145687	NP_663720			mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	102521661	102521661	+	IGR	DEL	T	-	-	rs71996398		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102521661delT								MAP4K4 (10510 upstream) : IL1R2 (86645 downstream)																																			---	---	---	---
IL1RL2	8808	broad.mit.edu	37	2	102801214	102801215	+	5'Flank	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102801214_102801215insA	uc002tbs.2	+						IL1RL2_uc002tbt.2_5'Flank	NM_003854	NP_003845			interleukin 1 receptor-like 2 precursor						cellular defense response|innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	103871553	103871554	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103871553_103871554insT								TMEM182 (437417 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	104789041	104789042	+	IGR	INS	-	A	A	rs145007635		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104789041_104789042insA								None (None upstream) : LOC150568 (261763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	104985485	104985485	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104985485delA								None (None upstream) : LOC150568 (65320 downstream)																																			---	---	---	---
LOC150568	150568	broad.mit.edu	37	2	105105324	105105324	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105105324delT	uc002tch.2	+							NR_015399				Homo sapiens cDNA FLJ30528 fis, clone BRAWH2001037.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	105866009	105866009	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105866009delA								GPR45 (6085 upstream) : TGFBRAP1 (17533 downstream)																																			---	---	---	---
NCK2	8440	broad.mit.edu	37	2	106423294	106423294	+	Intron	DEL	A	-	-	rs66728470		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106423294delA	uc002tdg.2	+						NCK2_uc002tdh.2_Intron	NM_003581	NP_003572			NCK adaptor protein 2 isoform A						axon guidance|epidermal growth factor receptor signaling pathway|negative regulation of cell proliferation|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of epidermal growth factor receptor activity|regulation of translation|signal complex assembly|T cell activation	cytosol|endoplasmic reticulum	cytoskeletal adaptor activity|receptor signaling complex scaffold activity			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	106589047	106589048	+	IGR	DEL	AT	-	-	rs55713417		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106589047_106589048delAT								NCK2 (78321 upstream) : C2orf40 (93065 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	106662201	106662201	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106662201delA								NCK2 (151475 upstream) : C2orf40 (19912 downstream)																																			---	---	---	---
ST6GAL2	84620	broad.mit.edu	37	2	107476338	107476338	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107476338delA	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	108321431	108321431	+	IGR	DEL	T	-	-	rs72134405		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108321431delT								ST6GAL2 (817868 upstream) : LOC729121 (118089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	109331687	109331687	+	IGR	DEL	A	-	-	rs112603163		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109331687delA								LIMS1 (30800 upstream) : RANBP2 (4250 downstream)																																			---	---	---	---
SH3RF3	344558	broad.mit.edu	37	2	109865344	109865358	+	Intron	DEL	TCCTGTCCTGTCCTG	-	-	rs151034319		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109865344_109865358delTCCTGTCCTGTCCTG	uc010ywt.1	+							NM_001099289	NP_001092759			SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1																		---	---	---	---
ACOXL	55289	broad.mit.edu	37	2	111513483	111513484	+	Intron	INS	-	A	A	rs151151259	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111513483_111513484insA	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	113758035	113758036	+	IGR	INS	-	CCA	CCA	rs148998329	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113758035_113758036insCCA								IL1F9 (14808 upstream) : IL1F6 (5413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	113836841	113836841	+	IGR	DEL	A	-	-	rs35997925		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113836841delA								IL1F10 (3416 upstream) : IL1RN (20096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	114525161	114525161	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114525161delC								SLC35F5 (10761 upstream) : ACTR3 (122376 downstream)																																			---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115808953	115808953	+	Intron	DEL	A	-	-	rs138639059		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115808953delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	118357058	118357060	+	IGR	DEL	AGA	-	-	rs36081408		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118357058_118357060delAGA								None (None upstream) : DDX18 (215195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118619112	118619112	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118619112delT								DDX18 (29159 upstream) : CCDC93 (54037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118626454	118626457	+	IGR	DEL	TGAC	-	-	rs139072969		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118626454_118626457delTGAC								DDX18 (36501 upstream) : CCDC93 (46692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119646620	119646620	+	IGR	DEL	C	-	-	rs67893903		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119646620delC								EN1 (40861 upstream) : MARCO (53125 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119929899	119929899	+	IGR	DEL	A	-	-	rs35213148		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119929899delA								C1QL2 (13428 upstream) : STEAP3 (51485 downstream)																																			---	---	---	---
C2orf76	130355	broad.mit.edu	37	2	120115173	120115174	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120115173_120115174insA	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																		---	---	---	---
TMEM177	80775	broad.mit.edu	37	2	120451642	120451645	+	Intron	DEL	ACAC	-	-	rs147833710	byFrequency;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120451642_120451645delACAC	uc002tme.2	+											Homo sapiens cDNA FLJ32751 fis, clone TESTI2001621.							integral to membrane				ovary(1)	1	Colorectal(110;0.196)																	---	---	---	---
TMEM177	80775	broad.mit.edu	37	2	120466432	120466433	+	Intron	INS	-	TT	TT	rs142161781	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120466432_120466433insTT	uc002tme.2	+											Homo sapiens cDNA FLJ32751 fis, clone TESTI2001621.							integral to membrane				ovary(1)	1	Colorectal(110;0.196)																	---	---	---	---
RALB	5899	broad.mit.edu	37	2	121046819	121046820	+	Intron	DEL	TG	-	-	rs72389638		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121046819_121046820delTG	uc002tmk.2	+						RALB_uc010yys.1_Intron|RALB_uc002tml.2_Intron|RALB_uc002tmm.2_Intron|RALB_uc010yyt.1_Intron	NM_002881	NP_002872			v-ral simian leukemia viral oncogene homolog B						apoptosis|cell cycle|cytokinesis|nerve growth factor receptor signaling pathway|Ras protein signal transduction|regulation of exocyst assembly|regulation of exocyst localization	cytosol|midbody|plasma membrane	GTP binding|GTPase activity|protein binding			lung(3)	3		Prostate(154;0.122)																---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121651234	121651234	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121651234delA	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	121898198	121898199	+	IGR	DEL	CA	-	-	rs149808766		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121898198_121898199delCA								GLI2 (147970 upstream) : TFCP2L1 (75967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	122585526	122585527	+	IGR	INS	-	A	A	rs11423815		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122585526_122585527insA								TSN (60100 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123072718	123072719	+	IGR	DEL	AT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123072718_123072719delAT								TSN (547292 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123317447	123317448	+	IGR	INS	-	T	T	rs138570342	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123317447_123317448insT								TSN (792021 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124509652	124509653	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124509652_124509653insA								None (None upstream) : CNTNAP5 (273211 downstream)																																			---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125249333	125249333	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125249333delT	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	126406396	126406397	+	IGR	INS	-	TTG	TTG			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126406396_126406397insTTG								CNTNAP5 (733535 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126431912	126431912	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126431912delT								CNTNAP5 (759051 upstream) : GYPC (981772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127507848	127507848	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127507848delT								GYPC (53603 upstream) : BIN1 (297759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127554688	127554691	+	IGR	DEL	ACAG	-	-	rs10606959		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127554688_127554691delACAG								GYPC (100443 upstream) : BIN1 (250916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129386143	129386154	+	IGR	DEL	CCTCCCTCCCTT	-	-	rs113171159	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129386143_129386154delCCTCCCTCCCTT								HS6ST1 (309972 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129713353	129713354	+	IGR	INS	-	G	G	rs76193934		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129713353_129713354insG								HS6ST1 (637182 upstream) : LOC389033 (967081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129778624	129778624	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129778624delA								HS6ST1 (702453 upstream) : LOC389033 (901811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130401525	130401526	+	IGR	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130401525_130401526insG								None (None upstream) : LOC389033 (278909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130540847	130540848	+	IGR	DEL	AC	-	-	rs149828650		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130540847_130540848delAC								None (None upstream) : LOC389033 (139587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130735001	130735002	+	Intron	DEL	TT	-	-	rs56175110		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130735001_130735002delTT	uc002tpw.1	-						RAB6C_uc002tpx.1_5'Flank					Homo sapiens cDNA FLJ41458 fis, clone BRSTN2014490.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	132764649	132764649	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132764649delA								C2orf27B (205415 upstream) : NCRNA00164 (140515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	132788553	132788554	+	IGR	DEL	AA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132788553_132788554delAA								C2orf27B (229319 upstream) : NCRNA00164 (116610 downstream)																																			---	---	---	---
NCRNA00164	554226	broad.mit.edu	37	2	133011694	133011695	+	Intron	INS	-	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133011694_133011695insC	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	133043027	133043027	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133043027delG								NCRNA00164 (27485 upstream) : GPR39 (131120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133047450	133047453	+	IGR	DEL	GTAA	-	-	rs148933193		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133047450_133047453delGTAA								NCRNA00164 (31908 upstream) : GPR39 (126694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133066592	133066592	+	Intron	DEL	G	-	-	rs78544491		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133066592delG	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	133102238	133102241	+	IGR	DEL	TTGA	-	-	rs112951297		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133102238_133102241delTTGA								NCRNA00164 (86696 upstream) : GPR39 (71906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133127487	133127487	+	IGR	DEL	T	-	-	rs67346890		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133127487delT								NCRNA00164 (111945 upstream) : GPR39 (46660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133161775	133161775	+	IGR	DEL	G	-	-	rs67496354		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133161775delG								NCRNA00164 (146233 upstream) : GPR39 (12372 downstream)																																			---	---	---	---
GPR39	2863	broad.mit.edu	37	2	133198957	133198958	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133198957_133198958insT	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	133297825	133297825	+	Intron	DEL	T	-	-	rs111468814		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133297825delT	uc002ttl.2	+							NM_001508	NP_001499			G protein-coupled receptor 39							integral to plasma membrane	G-protein coupled receptor activity|metal ion binding				0																		---	---	---	---
ACMSD	130013	broad.mit.edu	37	2	135629251	135629252	+	Intron	DEL	AG	-	-	rs113876209		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135629251_135629252delAG	uc002ttz.2	+						ACMSD_uc002tua.2_Intron|uc010zbe.1_Intron	NM_138326	NP_612199			aminocarboxymuconate semialdehyde decarboxylase						quinolinate metabolic process|tryptophan catabolic process	cytosol	aminocarboxymuconate-semialdehyde decarboxylase activity|metal ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.115)														---	---	---	---
YSK4	80122	broad.mit.edu	37	2	135769237	135769240	+	Intron	DEL	TTGT	-	-	rs72220680	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135769237_135769240delTTGT	uc002tue.1	-						YSK4_uc010fne.1_Intron|YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Intron|YSK4_uc010zbg.1_Intron|YSK4_uc002tui.3_Intron	NM_025052	NP_079328			Yeast Sps1/Ste20-related kinase 4 isoform 1								ATP binding|protein serine/threonine kinase activity			stomach(2)|urinary_tract(1)|ovary(1)|breast(1)	5				BRCA - Breast invasive adenocarcinoma(221;0.112)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	136913770	136913771	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136913770_136913771delGT								CXCR4 (38045 upstream) : THSD7B (609344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	137222880	137222880	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137222880delA								CXCR4 (347155 upstream) : THSD7B (300235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	137490438	137490439	+	IGR	DEL	CG	-	-	rs7340231	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137490438_137490439delCG								CXCR4 (614713 upstream) : THSD7B (32676 downstream)																																			---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137656216	137656217	+	Intron	INS	-	T	T	rs34410826		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137656216_137656217insT	uc010zbj.1	+											Homo sapiens mRNA for KIAA1679 protein, partial cds.											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
SPOPL	339745	broad.mit.edu	37	2	139312702	139312703	+	Intron	DEL	GT	-	-	rs61000380		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139312702_139312703delGT	uc002tvh.2	+							NM_001001664	NP_001001664			speckle-type POZ protein-like							nucleus				skin(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0296)														---	---	---	---
NXPH2	11249	broad.mit.edu	37	2	139472199	139472200	+	Intron	INS	-	A	A	rs151136285	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139472199_139472200insA	uc002tvi.2	-							NM_007226	NP_009157			neurexophilin 2 precursor						neuropeptide signaling pathway	extracellular region				ovary(3)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(221;0.101)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	139704105	139704105	+	IGR	DEL	A	-	-	rs67700105		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139704105delA								NXPH2 (166294 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140926928	140926931	+	IGR	DEL	AAGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140926928_140926931delAAGA								None (None upstream) : LRP1B (62065 downstream)																																			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141851280	141851281	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141851280_141851281insA	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	142192033	142192033	+	Intron	DEL	T	-	-	rs112320313		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142192033delT	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	142603579	142603580	+	Intron	INS	-	AG	AG	rs143708372	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142603579_142603580insAG	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)			---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	143969708	143969709	+	Intron	INS	-	A	A	rs148312216	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143969708_143969709insA	uc002tvm.3	+						ARHGAP15_uc010zbl.1_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144046775	144046775	+	Intron	DEL	G	-	-	rs35822113		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144046775delG	uc002tvm.3	+						ARHGAP15_uc010zbl.1_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144269137	144269138	+	Intron	INS	-	TTTG	TTTG	rs143846725	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144269137_144269138insTTTG	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144323666	144323666	+	Intron	DEL	T	-	-	rs71892836		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144323666delT	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
ZEB2	9839	broad.mit.edu	37	2	145172515	145172516	+	Intron	INS	-	TGTG	TGTG	rs137905559	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145172515_145172516insTGTG	uc002tvu.2	-						ZEB2_uc002tvv.2_Intron|ZEB2_uc010zbm.1_Intron|ZEB2_uc010fnp.2_Intron|ZEB2_uc010fnq.1_Intron	NM_014795	NP_055610			zinc finger homeobox 1b							cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	145862910	145862910	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145862910delT	uc002twd.2	+						uc002twe.2_Intron					Homo sapiens, clone IMAGE:5538654, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	148365688	148365689	+	IGR	INS	-	GATGGATGGATGGATG	GATGGATGGATGGATG	rs150347493	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148365688_148365689insGATGGATGGATGGATG								None (None upstream) : ACVR2A (236397 downstream)																																			---	---	---	---
MBD5	55777	broad.mit.edu	37	2	148860270	148860277	+	Intron	DEL	CACACACA	-	-	rs72105542		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148860270_148860277delCACACACA	uc002twm.3	+							NM_018328	NP_060798			methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)														---	---	---	---
MBD5	55777	broad.mit.edu	37	2	148891803	148891804	+	Intron	INS	-	GATC	GATC	rs147393201	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148891803_148891804insGATC	uc002twm.3	+							NM_018328	NP_060798			methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	150626445	150626446	+	IGR	INS	-	A	A	rs145703595	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150626445_150626446insA								MMADHC (182115 upstream) : RND3 (698266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	150967345	150967346	+	IGR	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150967345_150967346delCT								MMADHC (523015 upstream) : RND3 (357366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151268977	151268980	+	IGR	DEL	AAAC	-	-	rs142569316		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151268977_151268980delAAAC								MMADHC (824647 upstream) : RND3 (55732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151280322	151280322	+	IGR	DEL	A	-	-	rs75705128		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151280322delA								MMADHC (835992 upstream) : RND3 (44390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151579204	151579205	+	IGR	INS	-	C	C	rs143458454	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151579204_151579205insC								RND3 (235024 upstream) : RBM43 (525524 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151677741	151677742	+	IGR	INS	-	AAA	AAA	rs146412021	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151677741_151677742insAAA								RND3 (333561 upstream) : RBM43 (426987 downstream)																																			---	---	---	---
STAM2	10254	broad.mit.edu	37	2	152987207	152987207	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152987207delA	uc002tyc.3	-						STAM2_uc010foa.1_Intron	NM_005843	NP_005834			signal transducing adaptor molecule 2						cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.22)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	153754970	153754971	+	IGR	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153754970_153754971delTC								ARL6IP6 (137203 upstream) : RPRM (578881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	153797842	153797845	+	IGR	DEL	CTTT	-	-	rs150476417		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153797842_153797845delCTTT								ARL6IP6 (180075 upstream) : RPRM (536007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	154003671	154003671	+	IGR	DEL	A	-	-	rs5835467		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154003671delA								ARL6IP6 (385904 upstream) : RPRM (330181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	154543620	154543621	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154543620_154543621delTG								RPRM (208298 upstream) : GALNT13 (184805 downstream)																																			---	---	---	---
GALNT13	114805	broad.mit.edu	37	2	155000008	155000008	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155000008delA	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	156366007	156366007	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156366007delT								KCNJ3 (652993 upstream) : NR4A2 (814939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156902335	156902336	+	Intron	DEL	TG	-	-	rs75308958		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156902335_156902336delTG	uc002tyw.2	-											Homo sapiens cDNA clone IMAGE:5209417.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	156959007	156959007	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156959007delC	uc002tyw.2	-											Homo sapiens cDNA clone IMAGE:5209417.																														---	---	---	---
NR4A2	4929	broad.mit.edu	37	2	157181837	157181838	+	3'UTR	DEL	TG	-	-	rs3832066		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157181837_157181838delTG	uc002tyz.3	-	8					NR4A2_uc002tyx.3_3'UTR|NR4A2_uc010zcf.1_3'UTR	NM_006186	NP_006177			nuclear receptor subfamily 4, group A, member 2						cellular response to extracellular stimulus|dopaminergic neuron differentiation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus	nucleoplasm	sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	157591088	157591088	+	IGR	DEL	A	-	-	rs77689070		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157591088delA								GPD2 (120841 upstream) : GALNT5 (523252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	157821213	157821216	+	IGR	DEL	ATAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157821213_157821216delATAA								GPD2 (350966 upstream) : GALNT5 (293124 downstream)																																			---	---	---	---
ACVR1	90	broad.mit.edu	37	2	158604326	158604327	+	Intron	INS	-	A	A	rs142430381	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158604326_158604327insA	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)													---	---	---	---
TANC1	85461	broad.mit.edu	37	2	159992561	159992562	+	Intron	DEL	GC	-	-	rs35231270		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159992561_159992562delGC	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron|TANC1_uc002uah.1_5'Flank	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
WDSUB1	151525	broad.mit.edu	37	2	160145682	160145683	+	5'Flank	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160145682_160145683delCT	uc002uaj.3	-						WDSUB1_uc002uak.3_5'Flank|WDSUB1_uc002ual.3_5'Flank|WDSUB1_uc002uam.3_5'Flank|WDSUB1_uc010foo.2_5'Flank	NM_152528	NP_689741			WD repeat, sterile alpha motif and U-box domain							ubiquitin ligase complex	ubiquitin-protein ligase activity				0																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160394320	160394320	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160394320delT	uc002uao.2	-						BAZ2B_uc002uap.2_Intron|BAZ2B_uc002uas.1_Intron|BAZ2B_uc002uau.1_Intron|BAZ2B_uc002uat.3_Intron	NM_013450	NP_038478			bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
LY75	4065	broad.mit.edu	37	2	160646492	160646494	+	Intron	DEL	GTT	-	-	rs34754260		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160646492_160646494delGTT	uc002ubb.3	-						LY75_uc010fos.2_Intron|CD302_uc002uba.2_Intron|CD302_uc010zco.1_Intron	NM_002349	NP_002340			lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)														---	---	---	---
RBMS1	5937	broad.mit.edu	37	2	161285032	161285032	+	Intron	DEL	G	-	-	rs145730219		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161285032delG	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	161741998	161741998	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161741998delA								RBMS1 (391680 upstream) : TANK (251468 downstream)																																			---	---	---	---
KCNH7	90134	broad.mit.edu	37	2	163545242	163545243	+	Intron	INS	-	T	T	rs71410027		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163545242_163545243insT	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	163796175	163796176	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163796175_163796176insA								KCNH7 (100935 upstream) : FIGN (667942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	164033825	164033825	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164033825delT								KCNH7 (338585 upstream) : FIGN (430293 downstream)																																			---	---	---	---
FIGN	55137	broad.mit.edu	37	2	164469097	164469098	+	Intron	INS	-	A	A	rs139810766	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164469097_164469098insA	uc002uck.1	-							NM_018086	NP_060556			fidgetin							nuclear matrix	ATP binding|nucleoside-triphosphatase activity			large_intestine(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	164973004	164973005	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164973004_164973005insA								FIGN (380491 upstream) : GRB14 (376328 downstream)																																			---	---	---	---
GRB14	2888	broad.mit.edu	37	2	165367172	165367172	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165367172delA	uc002ucl.2	-						GRB14_uc010zcv.1_Intron|GRB14_uc002ucm.2_Intron	NM_004490	NP_004481			growth factor receptor-bound protein 14						blood coagulation|leukocyte migration	cytosol|endosome membrane|Golgi membrane|microsome|plasma membrane	SH3/SH2 adaptor activity			ovary(5)|upper_aerodigestive_tract(1)|lung(1)	7																		---	---	---	---
GRB14	2888	broad.mit.edu	37	2	165480175	165480176	+	5'Flank	INS	-	AGAG	AGAG	rs147025708	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165480175_165480176insAGAG	uc002ucl.2	-						GRB14_uc002ucm.2_5'Flank	NM_004490	NP_004481			growth factor receptor-bound protein 14						blood coagulation|leukocyte migration	cytosol|endosome membrane|Golgi membrane|microsome|plasma membrane	SH3/SH2 adaptor activity			ovary(5)|upper_aerodigestive_tract(1)|lung(1)	7																		---	---	---	---
SLC38A11	151258	broad.mit.edu	37	2	165798943	165798943	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165798943delA	uc002ucv.1	-						SLC38A11_uc002ucu.1_Intron|SLC38A11_uc002ucw.1_Intron	NM_173512	NP_775783			solute carrier family 38, member 11						amino acid transport|sodium ion transport	integral to membrane				ovary(1)	1																		---	---	---	---
SCN7A	6332	broad.mit.edu	37	2	167318173	167318174	+	Intron	INS	-	TTTA	TTTA	rs143584381	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167318173_167318174insTTTA	uc002udu.1	-						SCN7A_uc010fpm.1_Intron	NM_002976	NP_002967			sodium channel, voltage-gated, type VII, alpha						muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	167553671	167553672	+	IGR	INS	-	G	G	rs140501930	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167553671_167553672insG								SCN7A (202954 upstream) : XIRP2 (191325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	168349387	168349388	+	IGR	INS	-	TGTG	TGTG	rs142936467	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168349387_168349388insTGTG								XIRP2 (233128 upstream) : B3GALT1 (325794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	168511312	168511312	+	IGR	DEL	T	-	-	rs150797058		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168511312delT								XIRP2 (395053 upstream) : B3GALT1 (163870 downstream)																																			---	---	---	---
STK39	27347	broad.mit.edu	37	2	168990366	168990367	+	Intron	INS	-	A	A	rs140053662	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168990366_168990367insA	uc002uea.2	-							NM_013233	NP_037365			serine threonine kinase 39 (STE20/SPS1 homolog,						response to stress	cytoplasm|nucleus	ATP binding|protein binding|receptor signaling protein serine/threonine kinase activity			central_nervous_system(1)|skin(1)	2																		---	---	---	---
LASS6	253782	broad.mit.edu	37	2	169361172	169361172	+	Intron	DEL	C	-	-	rs35631999		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169361172delC	uc002ueb.1	+						LASS6_uc002uec.1_Intron	NM_203463	NP_982288			longevity assurance homolog 6							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1																		---	---	---	---
KLHL23	151230	broad.mit.edu	37	2	170601072	170601073	+	Intron	INS	-	T	T	rs139426346		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170601072_170601073insT	uc002ufh.1	+						KLHL23_uc002ufi.1_Intron	NM_144711	NP_653312			kelch-like 23												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	170995014	170995015	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170995014_170995015insA								UBR3 (54377 upstream) : MYO3B (39640 downstream)																																			---	---	---	---
MYO3B	140469	broad.mit.edu	37	2	171332583	171332584	+	Intron	INS	-	C	C	rs141545520	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171332583_171332584insC	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482			myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	172138037	172138038	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172138037_172138038insT								TLK1 (50213 upstream) : METTL8 (35877 downstream)																																			---	---	---	---
METTL8	79828	broad.mit.edu	37	2	172275532	172275532	+	Intron	DEL	A	-	-	rs75761108		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172275532delA	uc010zdo.1	-						METTL8_uc002ugu.3_Intron|METTL8_uc002ugv.3_Intron|METTL8_uc002ugt.3_Intron|METTL8_uc002ugs.3_Intron|METTL8_uc010zdp.1_Intron	NM_024770	NP_079046			methyltransferase like 8								methyltransferase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	172522685	172522686	+	IGR	INS	-	AC	AC	rs111355202		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172522685_172522686insAC								CYBRD1 (108042 upstream) : DYNC1I2 (21296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	172755684	172755689	+	IGR	DEL	CCTCTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172755684_172755689delCCTCTG								SLC25A12 (4871 upstream) : HAT1 (23246 downstream)																																			---	---	---	---
SP3	6670	broad.mit.edu	37	2	174814094	174814095	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174814094_174814095insA	uc002uig.2	-						SP3_uc002uie.2_Intron|SP3_uc002uif.2_Intron|SP3_uc010zel.1_Intron	NM_003111	NP_003102			Sp3 transcription factor isoform 1						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	protein binding|zinc ion binding		EWSR1/SP3(3)	soft_tissue(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.185)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	176710489	176710492	+	IGR	DEL	CACA	-	-	rs10530228	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176710489_176710492delCACA								ATP5G3 (663999 upstream) : KIAA1715 (79918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	177048460	177048460	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177048460delA								HOXD3 (10634 upstream) : HOXD1 (4847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	177708584	177708584	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177708584delT								MIR1246 (242804 upstream) : HNRNPA3 (368838 downstream)																																			---	---	---	---
AGPS	8540	broad.mit.edu	37	2	178366979	178366979	+	Intron	DEL	T	-	-	rs11300745		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178366979delT	uc002ull.2	+						AGPS_uc010zfb.1_Intron	NM_003659	NP_003650			alkyldihydroxyacetone phosphate synthase						ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity			ovary(2)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	179006351	179006351	+	IGR	DEL	A	-	-	rs67424658		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179006351delA								RBM45 (11971 upstream) : OSBPL6 (53023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	180262227	180262228	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180262227_180262228delAC								SESTD1 (132877 upstream) : ZNF385B (44492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	181539766	181539767	+	IGR	DEL	AT	-	-	rs57226321		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181539766_181539767delAT								CWC22 (667926 upstream) : UBE2E3 (305345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	181737422	181737423	+	IGR	INS	-	T	T	rs146639187	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181737422_181737423insT								CWC22 (865582 upstream) : UBE2E3 (107689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	182064417	182064418	+	Intron	INS	-	G	G	rs150409398	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182064417_182064418insG	uc002uns.1	+											Homo sapiens cDNA FLJ43011 fis, clone BRTHA2015853.																														---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183013641	183013642	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183013641_183013642insT	uc002uoq.1	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc010zfq.1_Intron	NM_005019	NP_005010			phosphodiesterase 1A isoform 1						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)															---	---	---	---
NUP35	129401	broad.mit.edu	37	2	184016839	184016856	+	Intron	DEL	ACACACACACACACACAC	-	-	rs141396036		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184016839_184016856delACACACACACACACACAC	uc002upf.2	+						NUP35_uc010zfs.1_Intron|NUP35_uc010zft.1_Intron|NUP35_uc002upg.2_Intron	NM_138285	NP_612142			nucleoporin 35kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	intermediate filament cytoskeleton|nuclear membrane|nuclear pore|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	184923164	184923164	+	IGR	DEL	T	-	-	rs113529184		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184923164delT								NUP35 (896757 upstream) : ZNF804A (539929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	185149959	185149961	+	IGR	DEL	CTT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185149959_185149961delCTT								None (None upstream) : ZNF804A (313132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	186188557	186188557	+	IGR	DEL	T	-	-	rs67966515		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186188557delT								ZNF804A (384345 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	186331365	186331366	+	IGR	DEL	AA	-	-	rs3054708		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186331365_186331366delAA								ZNF804A (527153 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	188975168	188975168	+	IGR	DEL	C	-	-	rs11688380	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188975168delC								TFPI (555949 upstream) : GULP1 (181436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	189051682	189051685	+	IGR	DEL	AAAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189051682_189051685delAAAA								TFPI (632463 upstream) : GULP1 (104919 downstream)																																			---	---	---	---
SLC40A1	30061	broad.mit.edu	37	2	190430751	190430752	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190430751_190430752delTG	uc002uqp.3	-							NM_014585	NP_055400			solute carrier family 40 (iron-regulated						anatomical structure morphogenesis|cellular iron ion homeostasis	cytoplasm|integral to plasma membrane	iron ion transmembrane transporter activity|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)															---	---	---	---
HIBCH	26275	broad.mit.edu	37	2	191127838	191127838	+	Intron	DEL	A	-	-	rs34646136		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191127838delA	uc002uru.2	-						HIBCH_uc002urv.2_Intron	NM_014362	NP_055177			3-hydroxyisobutyryl-Coenzyme A hydrolase isoform						branched chain family amino acid catabolic process	mitochondrial matrix	3-hydroxyisobutyryl-CoA hydrolase activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	191412419	191412436	+	IGR	DEL	TTTTTTTTCTTTTTGTAT	-	-	rs66824323		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191412419_191412436delTTTTTTTTCTTTTTGTAT								TMEM194B (12951 upstream) : NAB1 (101412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	191622415	191622420	+	IGR	DEL	CACACA	-	-	rs112383923		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191622415_191622420delCACACA								NAB1 (64924 upstream) : GLS (123127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194621100	194621101	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194621100_194621101delAC								PCGEM1 (979479 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195414941	195414942	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195414941_195414942insA								None (None upstream) : None (None downstream)																																			---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196715010	196715010	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196715010delA	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	196966419	196966420	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196966419_196966420insT								DNAH7 (32883 upstream) : STK17B (31888 downstream)																																			---	---	---	---
PLCL1	5334	broad.mit.edu	37	2	198911890	198911891	+	Intron	DEL	TG	-	-	rs149620681		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198911890_198911891delTG	uc010fsp.2	+						PLCL1_uc002uuv.3_Intron	NM_001114661	NP_001108133			RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	199291114	199291114	+	IGR	DEL	T	-	-	rs139823893		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199291114delT								PLCL1 (276508 upstream) : SATB2 (843110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	199424199	199424201	+	IGR	DEL	AAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199424199_199424201delAAA								PLCL1 (409593 upstream) : SATB2 (710023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	199864502	199864502	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199864502delA								PLCL1 (849896 upstream) : SATB2 (269722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	200653500	200653501	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200653500_200653501insA	uc002uvg.2	-											Homo sapiens hypothetical protein LOC348751, mRNA (cDNA clone IMAGE:5311172).																														---	---	---	---
CDK15	65061	broad.mit.edu	37	2	202690227	202690227	+	Intron	DEL	A	-	-	rs11344911		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202690227delA	uc002uyt.2	+						CDK15_uc010ftm.2_Intron|CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc010fto.1_Intron	NM_139158	NP_631897			PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)													---	---	---	---
CDK15	65061	broad.mit.edu	37	2	202702186	202702187	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202702186_202702187insA	uc002uyt.2	+						CDK15_uc010ftm.2_Intron|CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc010fto.1_Intron	NM_139158	NP_631897			PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	202876856	202876867	+	IGR	DEL	GAAAGAAAGAAT	-	-	rs72289966		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202876856_202876867delGAAAGAAAGAAT								CDK15 (118593 upstream) : FZD7 (22443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	203202215	203202215	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203202215delA								NOP58 (33833 upstream) : BMPR2 (38835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	203862040	203862040	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203862040delA								ALS2CR8 (10980 upstream) : NBEAL1 (17562 downstream)																																			---	---	---	---
CD28	940	broad.mit.edu	37	2	204578576	204578579	+	Intron	DEL	GAGA	-	-	rs72302211		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204578576_204578579delGAGA	uc002vah.3	+						CD28_uc002vag.1_Intron|CD28_uc010zio.1_Intron|CD28_uc010ftx.2_Intron|CD28_uc002vaj.3_Intron	NM_006139	NP_006130			CD28 antigen precursor						cell surface receptor linked signaling pathway|cytokine biosynthetic process|humoral immune response|positive regulation of anti-apoptosis|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation of translation|positive regulation of viral genome replication|regulation of defense response to virus by virus|regulatory T cell differentiation|T cell costimulation|viral reproduction	cytosol|external side of plasma membrane|integral to plasma membrane	coreceptor activity|protease binding|SH3/SH2 adaptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	204668542	204668542	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204668542delA								CD28 (65986 upstream) : CTLA4 (63967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	204707764	204707764	+	IGR	DEL	T	-	-	rs5837881		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204707764delT								CD28 (105208 upstream) : CTLA4 (24745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	204774189	204774192	+	IGR	DEL	ACAC	-	-	rs34827694		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204774189_204774192delACAC								CTLA4 (35506 upstream) : ICOS (27279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	205038283	205038284	+	IGR	DEL	TG	-	-	rs72214749		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205038283_205038284delTG								ICOS (211987 upstream) : PARD3B (372232 downstream)																																			---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	206200367	206200367	+	Intron	DEL	A	-	-	rs35633269		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206200367delA	uc002var.1	+						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)														---	---	---	---
INO80D	54891	broad.mit.edu	37	2	206928481	206928483	+	Intron	DEL	TGG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206928481_206928483delTGG	uc002vaz.3	-							NM_017759	NP_060229			INO80 complex subunit D						DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	208341371	208341372	+	IGR	DEL	AA	-	-	rs35235933		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208341371_208341372delAA								MIR1302-4 (207223 upstream) : CREB1 (53244 downstream)																																			---	---	---	---
CREB1	1385	broad.mit.edu	37	2	208397811	208397811	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208397811delT	uc002vcc.2	+						CREB1_uc010ziz.1_Intron|CREB1_uc002vcd.2_Intron	NM_134442	NP_604391			cAMP responsive element binding protein 1						activation of phospholipase C activity|axon guidance|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway		protein dimerization activity|transcription cofactor activity		EWSR1/CREB1(42)	soft_tissue(42)|breast(1)|central_nervous_system(1)	44				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Bromocriptine(DB01200)|Naloxone(DB01183)			T	EWSR1	clear cell sarcoma|angiomatoid fibrous histiocytoma								---	---	---	---
Unknown	0	broad.mit.edu	37	2	208651768	208651768	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208651768delA								FZD5 (17625 upstream) : PLEKHM3 (34244 downstream)																																			---	---	---	---
PLEKHM3	389072	broad.mit.edu	37	2	208849121	208849121	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208849121delT	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																		---	---	---	---
PTH2R	5746	broad.mit.edu	37	2	209244366	209244366	+	Intron	DEL	C	-	-	rs36056829		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209244366delC	uc010zjb.1	+							NM_005048	NP_005039			parathyroid hormone 2 receptor precursor							integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)														---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210557061	210557062	+	Intron	INS	-	A	A	rs35518879		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210557061_210557062insA	uc002vde.1	+						MAP2_uc002vdc.1_Intron|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Intron	NM_002374	NP_002365			microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	211142508	211142509	+	IGR	INS	-	T	T	rs138806816	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211142508_211142509insT								ACADL (52293 upstream) : MYL1 (12360 downstream)																																			---	---	---	---
CPS1	1373	broad.mit.edu	37	2	211436735	211436735	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211436735delT	uc002vee.3	+						CPS1_uc010fur.2_Intron	NM_001875	NP_001866			carbamoyl-phosphate synthetase 1 isoform b						carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	211962140	211962140	+	IGR	DEL	T	-	-	rs35777829		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211962140delT								CPS1 (418311 upstream) : ERBB4 (278302 downstream)																																			---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	213248715	213248716	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213248715_213248716insT	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	213733412	213733414	+	IGR	DEL	AGG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213733412_213733414delAGG								ERBB4 (330060 upstream) : IKZF2 (130999 downstream)																																			---	---	---	---
IKZF2	22807	broad.mit.edu	37	2	213974217	213974218	+	Intron	INS	-	T	T	rs145099681	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213974217_213974218insT	uc002vem.2	-						IKZF2_uc010fuu.2_Intron|IKZF2_uc002vej.2_Intron|IKZF2_uc002vek.2_Intron|IKZF2_uc010fuv.2_Intron|IKZF2_uc002vel.2_Intron|IKZF2_uc010fuw.2_Intron|IKZF2_uc010fux.2_Intron|IKZF2_uc010fuy.2_Intron|IKZF2_uc002ven.2_Intron	NM_016260	NP_057344			helios isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)														---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214473572	214473573	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214473572_214473573insA	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808			sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)														---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	215041532	215041533	+	Intron	INS	-	TG	TG	rs150156744	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215041532_215041533insTG	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808			sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)														---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	215045078	215045078	+	Intron	DEL	C	-	-	rs34464590		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215045078delC	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808			sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)														---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215822674	215822674	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215822674delG	uc002vew.2	-						ABCA12_uc002vev.2_Intron|ABCA12_uc010zjn.1_Intron	NM_173076	NP_775099			ATP-binding cassette, sub-family A, member 12						cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)														---	---	---	---
PECR	55825	broad.mit.edu	37	2	216900211	216900212	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216900211_216900212insT	uc010zjq.1	-											Synthetic construct DNA, clone: pF1KB6394, Homo sapiens PECR gene for peroxisomal trans-2-enoyl-CoA reductase, without stop codon, in Flexi system.						fatty acid biosynthetic process|regulation of apoptosis	peroxisome	binding|trans-2-enoyl-CoA reductase (NADPH) activity				0		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)													---	---	---	---
PECR	55825	broad.mit.edu	37	2	216939217	216939228	+	Intron	DEL	AAGGAAGGAAGG	-	-	rs72274918		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216939217_216939228delAAGGAAGGAAGG	uc002vft.2	-						PECR_uc010zjq.1_Intron|PECR_uc002vfu.1_Intron	NM_018441	NP_060911			peroxisomal trans-2-enoyl-CoA reductase						fatty acid biosynthetic process|regulation of apoptosis	peroxisome	binding|trans-2-enoyl-CoA reductase (NADPH) activity				0		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)													---	---	---	---
IGFBP5	3488	broad.mit.edu	37	2	217541832	217541832	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217541832delT	uc002vgj.3	-							NM_000599	NP_000590			insulin-like growth factor binding protein 5						negative regulation of insulin-like growth factor receptor signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|negative regulation of translation|signal transduction		insulin-like growth factor I binding				0		Renal(323;0.0822)		Epithelial(149;2.1e-06)|all cancers(144;0.000165)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	218108297	218108315	+	IGR	DEL	ACACACAACACACAAACAC	-	-	rs72264305	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218108297_218108315delACACACAACACACAAACAC								TNP1 (383515 upstream) : DIRC3 (40433 downstream)																																			---	---	---	---
VIL1	7429	broad.mit.edu	37	2	219283646	219283646	+	5'Flank	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219283646delA	uc002via.2	+						VIL1_uc010zke.1_5'Flank	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)														---	---	---	---
WNT10A	80326	broad.mit.edu	37	2	219746263	219746264	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219746263_219746264delTG	uc002vjd.1	+							NM_025216	NP_079492			wingless-type MMTV integration site family,						anterior/posterior pattern formation|axis specification|canonical Wnt receptor signaling pathway|cellular response to transforming growth factor beta stimulus|female gonad development|hair follicle morphogenesis|odontogenesis|regulation of odontogenesis of dentine-containing tooth|sebaceous gland development|skin development|tongue development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	G-protein-coupled receptor binding|signal transducer activity			lung(1)|skin(1)	2		Renal(207;0.0474)		Epithelial(149;4.26e-07)|all cancers(144;8.8e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	219813369	219813369	+	IGR	DEL	A	-	-	rs112559036		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219813369delA								WNT10A (54718 upstream) : CDK5R2 (11029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	220960433	220960433	+	IGR	DEL	C	-	-	rs34764654		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220960433delC								SLC4A3 (453732 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221684103	221684104	+	IGR	INS	-	TGTG	TGTG	rs144057826	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221684103_221684104insTGTG								None (None upstream) : EPHA4 (598645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222143987	222143988	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222143987_222143988insT								None (None upstream) : EPHA4 (138761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222237427	222237428	+	IGR	DEL	AC	-	-	rs10578961		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222237427_222237428delAC								None (None upstream) : EPHA4 (45321 downstream)																																	OREG0015236	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	222467920	222467920	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222467920delC								EPHA4 (28998 upstream) : PAX3 (596687 downstream)																																			---	---	---	---
ACSL3	2181	broad.mit.edu	37	2	223727432	223727433	+	Intron	INS	-	G	G	rs140292377	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223727432_223727433insG	uc002vni.2	+						ACSL3_uc002vnj.2_Intron	NM_004457	NP_004448			acyl-CoA synthetase long-chain family member 3						long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|fatty-acyl-CoA synthase activity|long-chain fatty acid-CoA ligase activity|protein binding			ovary(2)	2		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)			T	ETV1	prostate								---	---	---	---
Unknown	0	broad.mit.edu	37	2	224567814	224567815	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224567814_224567815insA								SCG2 (100693 upstream) : AP1S3 (52233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	224611516	224611516	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224611516delA								SCG2 (144395 upstream) : AP1S3 (8532 downstream)																																			---	---	---	---
AP1S3	130340	broad.mit.edu	37	2	224652466	224652467	+	Intron	INS	-	AC	AC	rs145208667	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224652466_224652467insAC	uc010fwx.1	-						AP1S3_uc002vnn.2_Intron|AP1S3_uc010fww.2_Intron|AP1S3_uc002vno.2_Intron	NM_001039569	NP_001034658			adaptor-related protein complex 1, sigma 3						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane coat	protein transporter activity				0		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)														---	---	---	---
AP1S3	130340	broad.mit.edu	37	2	224664830	224664830	+	Intron	DEL	G	-	-	rs58636006		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224664830delG	uc010fwx.1	-						AP1S3_uc002vnn.2_Intron|AP1S3_uc010fww.2_Intron|AP1S3_uc002vno.2_Intron	NM_001039569	NP_001034658			adaptor-related protein complex 1, sigma 3						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane coat	protein transporter activity				0		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	225008631	225008632	+	IGR	DEL	TT	-	-	rs71991964		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225008631_225008632delTT								SERPINE2 (104595 upstream) : FAM124B (234784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	225472287	225472288	+	IGR	INS	-	A	A	rs148098506	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225472287_225472288insA								CUL3 (22177 upstream) : DOCK10 (157519 downstream)																																			---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225721131	225721131	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225721131delT	uc010fwz.1	-						DOCK10_uc002vob.2_Intron	NM_014689	NP_055504			dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)														---	---	---	---
KIAA1486	57624	broad.mit.edu	37	2	226431632	226431633	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226431632_226431633delTG	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)														---	---	---	---
RHBDD1	84236	broad.mit.edu	37	2	227757144	227757144	+	Intron	DEL	T	-	-	rs66891531		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227757144delT	uc002voi.2	+						RHBDD1_uc010fxc.2_Intron	NM_032276	NP_115652			rhomboid domain containing 1							integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)														---	---	---	---
WDR69	164781	broad.mit.edu	37	2	228776746	228776748	+	Intron	DEL	ACA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228776746_228776748delACA	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)														---	---	---	---
WDR69	164781	broad.mit.edu	37	2	228781829	228781840	+	Intron	DEL	TATCTATCTATC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228781829_228781840delTATCTATCTATC	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	229135126	229135127	+	IGR	INS	-	A	A	rs150164299	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229135126_229135127insA								SPHKAP (88765 upstream) : PID1 (753563 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229353385	229353386	+	IGR	INS	-	TCTA	TCTA	rs138411693	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229353385_229353386insTCTA								SPHKAP (307024 upstream) : PID1 (535304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229530378	229530379	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229530378_229530379insT								SPHKAP (484017 upstream) : PID1 (358311 downstream)																																			---	---	---	---
SLC16A14	151473	broad.mit.edu	37	2	230928813	230928813	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230928813delA	uc002vqd.1	-						FBXO36_uc010fxi.1_Intron|SLC16A14_uc002vqe.2_Intron|SLC16A14_uc002vqf.2_Intron	NM_152527	NP_689740			solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			ovary(4)|skin(2)	6		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	230951038	230951039	+	IGR	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230951038_230951039delTC								FBXO36 (3022 upstream) : SP110 (82606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	230999327	230999327	+	IGR	DEL	A	-	-	rs71842645		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230999327delA								FBXO36 (51311 upstream) : SP110 (34318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	232370203	232370203	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232370203delA								NCL (40998 upstream) : C2orf52 (2934 downstream)																																			---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233578665	233578665	+	Intron	DEL	T	-	-	rs34183844		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233578665delT	uc002vti.3	+						GIGYF2_uc002vte.2_Intron|GIGYF2_uc002vtf.2_Intron|GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc002vtl.2_Intron	NM_015575	NP_056390			GRB10 interacting GYF protein 2 isoform b						cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)														---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	234084961	234084961	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234084961delC	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915			SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)														---	---	---	---
UGT1A8	54576	broad.mit.edu	37	2	234599423	234599424	+	Intron	DEL	AC	-	-	rs34459843		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234599423_234599424delAC	uc002vup.2	+						UGT1A8_uc010zmv.1_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_5'Flank|UGT1A6_uc010zmy.1_5'Flank|UGT1A6_uc002vuv.3_5'Flank	NM_019076	NP_061949			UDP glycosyltransferase 1 family, polypeptide A8						drug metabolic process|fatty acid metabolic process|flavone metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme inhibitor activity|fatty acid binding|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|steroid binding			ovary(2)	2		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;2.56e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000482)|Lung(119;0.00404)|LUSC - Lung squamous cell carcinoma(224;0.008)														---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236477571	236477574	+	Intron	DEL	GGAT	-	-	rs35965697		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236477571_236477574delGGAT	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	236564741	236564741	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236564741delC	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	236711555	236711556	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236711555_236711556insA	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	237601529	237601529	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237601529delA								CXCR7 (110537 upstream) : COPS8 (392555 downstream)																																			---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238309205	238309205	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238309205delA	uc002vwl.2	-						COL6A3_uc002vwo.2_Intron|COL6A3_uc010znj.1_Intron|COL6A3_uc002vwq.2_Intron|COL6A3_uc002vwr.2_Intron|COL6A3_uc010znk.1_Intron	NM_004369	NP_004360			alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
LRRFIP1	9208	broad.mit.edu	37	2	238606495	238606496	+	Intron	INS	-	TCA	TCA	rs143576743	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238606495_238606496insTCA	uc002vxe.2	+						LRRFIP1_uc002vxc.2_Intron|LRRFIP1_uc010znm.1_Intron|LRRFIP1_uc002vxd.2_Intron|LRRFIP1_uc002vxf.2_Intron	NM_001137552	NP_001131024			leucine rich repeat (in FLII) interacting						negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|cytoskeleton|nucleus	DNA binding|double-stranded RNA binding|protein binding			breast(3)	3		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)														---	---	---	---
ILKAP	80895	broad.mit.edu	37	2	239083763	239083764	+	Intron	INS	-	T	T	rs148488168		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239083763_239083764insT	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)														---	---	---	---
ILKAP	80895	broad.mit.edu	37	2	239101656	239101657	+	Intron	INS	-	A	A	rs142440092	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239101656_239101657insA	uc002vxv.2	-						ILKAP_uc010zns.1_Intron|ILKAP_uc002vxw.2_Intron|ILKAP_uc010znt.1_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	239308382	239308382	+	3'UTR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239308382delT	uc002vye.2	+	17					TRAF3IP1_uc002vyf.2_3'UTR	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	239384645	239384645	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239384645delA								ASB1 (23755 upstream) : TWIST2 (372028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	239392892	239392892	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239392892delT								ASB1 (32002 upstream) : TWIST2 (363781 downstream)																																			---	---	---	---
TWIST2	117581	broad.mit.edu	37	2	239790695	239790696	+	Intron	INS	-	TC	TC	rs143351834	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239790695_239790696insTC	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	240411985	240411986	+	IGR	INS	-	ATCCATCCATCC	ATCCATCCATCC	rs78354358		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240411985_240411986insATCCATCCATCC								HDAC4 (88639 upstream) : NDUFA10 (488172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	900728	900728	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:900728delG								CHL1 (449633 upstream) : CNTN6 (233892 downstream)																																			---	---	---	---
CNTN6	27255	broad.mit.edu	37	3	1335006	1335006	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1335006delT	uc003boz.2	+						CNTN6_uc010hbo.2_Intron|CNTN6_uc011asj.1_Intron|CNTN6_uc003bpa.2_Intron	NM_014461	NP_055276			contactin 6 precursor						axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	3006588	3006588	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3006588delA	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron|CNTN4_uc003bpd.1_Intron|CNTN4_uc003bpe.2_Intron|CNTN4_uc003bpf.2_Intron	NM_175607	NP_783200			contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)														---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	4167070	4167072	+	Intron	DEL	TTA	-	-	rs34450541		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4167070_4167072delTTA	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)														---	---	---	---
ARL8B	55207	broad.mit.edu	37	3	5179875	5179876	+	Intron	INS	-	TT	TT	rs35653002		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5179875_5179876insTT	uc003bqg.2	+						ARL8B_uc011asx.1_Intron|ARL8B_uc011asy.1_Intron	NM_018184	NP_060654			ADP-ribosylation factor-like 10C						cell cycle|cell division|chromosome segregation|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GDP binding|GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)														---	---	---	---
ARL8B	55207	broad.mit.edu	37	3	5211252	5211252	+	Intron	DEL	C	-	-	rs341983		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5211252delC	uc003bqg.2	+						ARL8B_uc011asx.1_Intron|ARL8B_uc011asy.1_Intron	NM_018184	NP_060654			ADP-ribosylation factor-like 10C						cell cycle|cell division|chromosome segregation|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GDP binding|GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	6002762	6002762	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6002762delT								EDEM1 (741113 upstream) : GRM7 (900040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6681662	6681663	+	Intron	DEL	CA	-	-	rs34167042		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6681662_6681663delCA	uc003bqj.1	+											Homo sapiens clone P1 NTera2D1 teratocarcinoma mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	8334488	8334488	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8334488delG	uc003bqp.2	-											Homo sapiens cDNA FLJ42094 fis, clone TESOP2002489.																														---	---	---	---
SRGAP3	9901	broad.mit.edu	37	3	9048197	9048197	+	Intron	DEL	A	-	-	rs112155557		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9048197delA	uc003brf.1	-						SRGAP3_uc003brg.1_Intron	NM_014850	NP_055665			SLIT-ROBO Rho GTPase activating protein 3						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)				T	RAF1	pilocytic astrocytoma								---	---	---	---
SRGAP3	9901	broad.mit.edu	37	3	9165472	9165473	+	Intron	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9165472_9165473delAG	uc003brf.1	-						SRGAP3_uc003brg.1_Intron|SRGAP3_uc003bri.1_Intron|SRGAP3_uc003brk.2_Intron	NM_014850	NP_055665			SLIT-ROBO Rho GTPase activating protein 3						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)				T	RAF1	pilocytic astrocytoma								---	---	---	---
SETD5	55209	broad.mit.edu	37	3	9462516	9462517	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9462516_9462517insT	uc003brt.2	+						SETD5_uc003brs.1_Intron	NM_001080517	NP_001073986			SET domain containing 5											ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)														---	---	---	---
LHFPL4	375323	broad.mit.edu	37	3	9568434	9568435	+	Intron	INS	-	C	C	rs148542418	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9568434_9568435insC	uc003bry.2	-							NM_198560	NP_940962			lipoma HMGIC fusion partner-like 4							integral to membrane				ovary(2)|skin(1)	3	Medulloblastoma(99;0.227)																	---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10088598	10088599	+	Intron	INS	-	C	C	rs142887274	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10088598_10088599insC	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_5'Flank	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				---	---	---	---
IRAK2	3656	broad.mit.edu	37	3	10257435	10257436	+	Intron	INS	-	AC	AC	rs145978380	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10257435_10257436insAC	uc003bve.1	+							NM_001570	NP_001561			interleukin-1 receptor-associated kinase 2						activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|endosome membrane|plasma membrane	ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity			lung(5)|breast(3)	8																		---	---	---	---
ATG7	10533	broad.mit.edu	37	3	11549426	11549427	+	Intron	INS	-	A	A	rs150284314	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11549426_11549427insA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	12282357	12282358	+	IGR	DEL	GT	-	-	rs112812655		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12282357_12282358delGT								SYN2 (48827 upstream) : PPARG (46991 downstream)																																			---	---	---	---
CAND2	23066	broad.mit.edu	37	3	12865648	12865648	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12865648delT	uc003bxk.2	+						CAND2_uc003bxj.2_Intron	NM_001162499	NP_001155971			TBP-interacting protein isoform 1						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			skin(3)|pancreas(1)	4																		---	---	---	---
LOC285375	285375	broad.mit.edu	37	3	13691123	13691123	+	5'Flank	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13691123delC	uc003byd.1	+							NR_027103				Homo sapiens, clone IMAGE:5742174, mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	14376193	14376194	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14376193_14376194delAC								LSM3 (136357 upstream) : SLC6A6 (67912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	15386243	15386243	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15386243delT								SH3BP5 (3342 upstream) : METTL6 (36541 downstream)																																			---	---	---	---
GALNTL2	117248	broad.mit.edu	37	3	16245094	16245097	+	Intron	DEL	ACAG	-	-	rs10578044		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16245094_16245097delACAG	uc003car.3	+						GALNTL2_uc003caq.3_Intron	NM_054110	NP_473451			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1																		---	---	---	---
PLCL2	23228	broad.mit.edu	37	3	16923523	16923524	+	5'Flank	INS	-	CACTT	CACTT	rs145460310	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16923523_16923524insCACTT	uc011awc.1	+						PLCL2_uc010het.1_Intron	NM_001144382	NP_001137854			phospholipase C-like 2 isoform 1						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
PLCL2	23228	broad.mit.edu	37	3	17076403	17076404	+	Intron	INS	-	CTT	CTT	rs141179799	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17076403_17076404insCTT	uc011awc.1	+						PLCL2_uc011awd.1_Intron	NM_001144382	NP_001137854			phospholipase C-like 2 isoform 1						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	17965868	17965868	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17965868delT								TBC1D5 (181628 upstream) : SATB1 (423398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	18365093	18365095	+	IGR	DEL	ACA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18365093_18365095delACA								TBC1D5 (580853 upstream) : SATB1 (24171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	18618695	18618695	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18618695delA								SATB1 (138443 upstream) : KCNH8 (571322 downstream)																																			---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19453269	19453270	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19453269_19453270delAC	uc003cbk.1	+						KCNH8_uc011awe.1_Intron|KCNH8_uc010hex.1_Intron|KCNH8_uc011awf.1_Intron	NM_144633	NP_653234			potassium voltage-gated channel, subfamily H,							integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5																		---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19465128	19465129	+	Intron	INS	-	TG	TG	rs149629798	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19465128_19465129insTG	uc003cbk.1	+						KCNH8_uc011awe.1_Intron|KCNH8_uc010hex.1_Intron|KCNH8_uc011awf.1_Intron	NM_144633	NP_653234			potassium voltage-gated channel, subfamily H,							integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	20992870	20992870	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20992870delA								SGOL1 (765187 upstream) : VENTXP7 (454348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	21229344	21229347	+	IGR	DEL	TATC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21229344_21229347delTATC								None (None upstream) : VENTXP7 (217871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	22427884	22427888	+	IGR	DEL	CCTCT	-	-	rs57337434		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22427884_22427888delCCTCT								ZNF385D (13761 upstream) : UBE2E2 (816765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	22461305	22461309	+	IGR	DEL	GTGGT	-	-	rs138359856	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22461305_22461309delGTGGT								ZNF385D (47182 upstream) : UBE2E2 (783344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	23039009	23039009	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23039009delC								ZNF385D (624886 upstream) : UBE2E2 (205644 downstream)																																			---	---	---	---
THRB	7068	broad.mit.edu	37	3	24477485	24477485	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24477485delC	uc003ccx.3	-						THRB_uc010hfe.2_Intron|THRB_uc003ccy.3_Intron|THRB_uc003ccz.3_Intron|THRB_uc003cdc.2_Intron|THRB_uc003cdd.2_Intron|THRB_uc003cde.1_Intron	NM_001128176	NP_001121648			thyroid hormone receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(2)|pancreas(1)	3					Levothyroxine(DB00451)|Liothyronine(DB00279)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	24967303	24967303	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24967303delA								THRB (430850 upstream) : RARB (248520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	25836487	25836487	+	IGR	DEL	C	-	-	rs144968064		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25836487delC								OXSM (463 upstream) : LRRC3B (827813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	26373014	26373015	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26373014_26373015delGT								OXSM (536990 upstream) : LRRC3B (291285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27621042	27621042	+	IGR	DEL	C	-	-	rs66660621		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27621042delC								SLC4A7 (95204 upstream) : EOMES (136846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27623291	27623298	+	IGR	DEL	CACGCATG	-	-	rs4992745	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27623291_27623298delCACGCATG								SLC4A7 (97453 upstream) : EOMES (134590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27623297	27623298	+	IGR	DEL	TG	-	-	rs112847907		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27623297_27623298delTG								SLC4A7 (97459 upstream) : EOMES (134590 downstream)																																			---	---	---	---
AZI2	64343	broad.mit.edu	37	3	28376794	28376795	+	Intron	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28376794_28376795delAG	uc003ceb.2	-						AZI2_uc003cec.2_Intron|AZI2_uc003ced.2_Intron|AZI2_uc003cee.3_Intron|AZI2_uc003ceg.2_Intron|AZI2_uc011axd.1_Intron|AZI2_uc003cef.2_Intron	NM_022461	NP_071906			5-azacytidine induced 2 isoform a							mitochondrion|plasma membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	28648293	28648293	+	IGR	DEL	A	-	-	rs35795984		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28648293delA								ZCWPW2 (81663 upstream) : RBMS3 (674650 downstream)																																			---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29778049	29778050	+	Intron	INS	-	G	G	rs144074676	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29778049_29778050insG	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	30199372	30199372	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30199372delA								RBMS3 (152753 upstream) : TGFBR2 (448622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	30269772	30269772	+	IGR	DEL	A	-	-	rs72075198		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30269772delA								RBMS3 (223153 upstream) : TGFBR2 (378222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	30416648	30416649	+	IGR	INS	-	T	T	rs138402944	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30416648_30416649insT								RBMS3 (370029 upstream) : TGFBR2 (231345 downstream)																																			---	---	---	---
GADL1	339896	broad.mit.edu	37	3	30826403	30826403	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30826403delT	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	32720501	32720501	+	IGR	DEL	A	-	-	rs36017977		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32720501delA								DYNC1LI1 (108151 upstream) : CNOT10 (6197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	33268786	33268790	+	IGR	DEL	TGTAT	-	-	rs66924297		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33268786_33268790delTGTAT								SUSD5 (8079 upstream) : FBXL2 (50144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	35395674	35395674	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35395674delT								None (None upstream) : ARPP21 (285407 downstream)																																			---	---	---	---
ARPP21	10777	broad.mit.edu	37	3	35720969	35720969	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35720969delT	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc011axy.1_5'Flank|ARPP21_uc003cfz.2_Intron|ARPP21_uc003cgc.2_5'Flank|ARPP21_uc003cgd.2_5'Flank|ARPP21_uc011axx.1_5'Flank|ARPP21_uc003cge.2_5'Flank	NM_016300	NP_057384			cyclic AMP-regulated phosphoprotein, 21 kD							cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3																		---	---	---	---
LRRFIP2	9209	broad.mit.edu	37	3	37123661	37123661	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37123661delA	uc003cgp.2	-						LRRFIP2_uc011ayf.1_Intron|LRRFIP2_uc003cgr.2_Intron|LRRFIP2_uc003cgs.3_Intron|LRRFIP2_uc003cgt.3_Intron	NM_006309	NP_006300			leucine rich repeat (in FLII) interacting						Wnt receptor signaling pathway		LRR domain binding			ovary(1)	1																		---	---	---	---
LRRFIP2	9209	broad.mit.edu	37	3	37172926	37172927	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37172926_37172927insA	uc003cgp.2	-						LRRFIP2_uc011ayf.1_Intron|LRRFIP2_uc003cgr.2_Intron|LRRFIP2_uc003cgs.3_Intron|LRRFIP2_uc003cgt.3_Intron	NM_006309	NP_006300			leucine rich repeat (in FLII) interacting						Wnt receptor signaling pathway		LRR domain binding			ovary(1)	1																		---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37695682	37695683	+	Intron	DEL	CA	-	-	rs72095644		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37695682_37695683delCA	uc003chd.2	+							NM_002207	NP_002198			integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	39023029	39023030	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39023029_39023030delTG								SCN11A (30977 upstream) : WDR48 (70477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39215478	39215478	+	IGR	DEL	T	-	-	rs34157623		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39215478delT								CSRNP1 (19425 upstream) : XIRP1 (9229 downstream)																																			---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	39863960	39863960	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39863960delT	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	40149666	40149669	+	Intron	DEL	GAGA	-	-	rs72410286		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40149666_40149669delGAGA	uc003cka.2	+						MYRIP_uc010hhu.2_Intron|MYRIP_uc010hhv.2_Intron|MYRIP_uc010hhw.2_Intron|MYRIP_uc010hhx.1_Intron|MYRIP_uc011ayz.1_Intron	NM_015460	NP_056275			myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	40601623	40601623	+	IGR	DEL	T	-	-	rs34139159		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40601623delT								ZNF621 (20580 upstream) : CTNNB1 (634778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	40848397	40848397	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40848397delG								ZNF621 (267354 upstream) : CTNNB1 (388004 downstream)																																			---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42185760	42185760	+	Intron	DEL	A	-	-	rs34065536		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42185760delA	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron	NM_001042646	NP_001036111			OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	43156583	43156584	+	IGR	DEL	TC	-	-	rs150035244		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43156583_43156584delTC								C3orf39 (9018 upstream) : SNRK (171420 downstream)																																			---	---	---	---
ANO10	55129	broad.mit.edu	37	3	43557991	43557992	+	Intron	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43557991_43557992insG	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																		---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45489029	45489030	+	Intron	INS	-	TG	TG	rs149232554	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45489029_45489030insTG	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155			leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)													---	---	---	---
SMARCC1	6599	broad.mit.edu	37	3	47791160	47791161	+	Intron	INS	-	ACAC	ACAC	rs138400474	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47791160_47791161insACAC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	48891225	48891225	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48891225delA								PRKAR2A (5955 upstream) : SLC25A20 (3132 downstream)																																			---	---	---	---
RHOA	387	broad.mit.edu	37	3	49401298	49401298	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49401298delA	uc003cwu.2	-						RHOA_uc010hku.2_Intron	NM_001664	NP_001655			ras homolog gene family, member A precursor						axon guidance|interspecies interaction between organisms|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of axonogenesis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of neuron differentiation|positive regulation of NF-kappaB import into nucleus|positive regulation of stress fiber assembly|regulation of cell migration|regulation of small GTPase mediated signal transduction|Rho protein signal transduction|spindle assembly involved in mitosis	cytoskeleton|cytosol|plasma membrane	GTP binding|GTPase activity|myosin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	Atorvastatin(DB01076)|Simvastatin(DB00641)													---	---	---	---
TRAIP	10293	broad.mit.edu	37	3	49892336	49892336	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49892336delA	uc003cxs.1	-						TRAIP_uc010hla.1_Intron|TRAIP_uc011bcx.1_Intron	NM_005879	NP_005870			TRAF interacting protein						cell proliferation|induction of apoptosis	perinuclear region of cytoplasm	protein binding|zinc ion binding			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
RBM6	10180	broad.mit.edu	37	3	50037203	50037203	+	Intron	DEL	A	-	-	rs34706045		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50037203delA	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)														---	---	---	---
CACNA2D2	9254	broad.mit.edu	37	3	50537682	50537683	+	Intron	INS	-	C	C	rs143578015	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50537682_50537683insC	uc003daq.2	-						CACNA2D2_uc003dap.2_Intron	NM_006030	NP_006021			calcium channel, voltage-dependent, alpha						energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Gabapentin(DB00996)													---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51296826	51296826	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51296826delT	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)														---	---	---	---
SFMBT1	51460	broad.mit.edu	37	3	53006857	53006858	+	Intron	INS	-	AC	AC	rs144706305	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53006857_53006858insAC	uc003dgf.2	-						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)														---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53716584	53716584	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53716584delA	uc003dgv.3	+						CACNA1D_uc003dgu.3_Intron|CACNA1D_uc003dgy.3_Intron|CACNA1D_uc003dgw.3_Intron	NM_001128840	NP_001122312			calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	55395613	55395613	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55395613delA								CACNA2D3 (287031 upstream) : WNT5A (104131 downstream)																																			---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56003421	56003424	+	Intron	DEL	ACAC	-	-	rs150783692		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56003421_56003424delACAC	uc003dhr.1	-						ERC2_uc003dht.1_Intron	NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56165595	56165595	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56165595delT	uc003dhr.1	-							NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	56510408	56510409	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56510408_56510409insA								ERC2 (8017 upstream) : CCDC66 (80775 downstream)																																			---	---	---	---
ARHGEF3	50650	broad.mit.edu	37	3	56848693	56848694	+	Intron	INS	-	T	T	rs141247428	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56848693_56848694insT	uc003dih.2	-						ARHGEF3_uc011bew.1_Intron	NM_001128615	NP_001122087			Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)														---	---	---	---
ARHGEF3	50650	broad.mit.edu	37	3	57051033	57051034	+	Intron	INS	-	TC	TC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57051033_57051034insTC	uc003dih.2	-							NM_001128615	NP_001122087			Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)														---	---	---	---
PXK	54899	broad.mit.edu	37	3	58402325	58402327	+	Intron	DEL	AGG	-	-	rs151217600		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58402325_58402327delAGG	uc003djz.1	+						PXK_uc003djx.1_Intron|PXK_uc003djy.1_Intron|PXK_uc003dka.1_Intron|PXK_uc003dkb.1_Intron|PXK_uc003dkc.1_Intron|PXK_uc011bfe.1_Intron|PXK_uc010hnj.1_Intron|PXK_uc003dkd.1_Intron|PXK_uc010hnk.1_Intron	NM_017771	NP_060241			PX domain containing serine/threonine kinase						cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|regulation of synaptic transmission	centrosome|cytoplasm|nucleus|plasma membrane	actin binding|ATP binding|phosphatidylinositol binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	59061439	59061439	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59061439delT								C3orf67 (25681 upstream) : FHIT (673599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59367703	59367704	+	IGR	INS	-	AAAT	AAAT	rs146012739	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59367703_59367704insAAAT								C3orf67 (331945 upstream) : FHIT (367334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59399389	59399389	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59399389delC								C3orf67 (363631 upstream) : FHIT (335649 downstream)																																			---	---	---	---
FHIT	2272	broad.mit.edu	37	3	60243793	60243794	+	Intron	INS	-	ACAC	ACAC	rs149081614	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60243793_60243794insACAC	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				---	---	---	---
CADPS	8618	broad.mit.edu	37	3	62713398	62713399	+	Intron	INS	-	ACC	ACC	rs147587228	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62713398_62713399insACC	uc003dll.2	-						CADPS_uc003dlm.2_Intron|CADPS_uc003dln.2_Intron	NM_003716	NP_003707			Ca2+-dependent secretion activator isoform 1						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)														---	---	---	---
SYNPR	132204	broad.mit.edu	37	3	63499510	63499511	+	Intron	DEL	GA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63499510_63499511delGA	uc003dlq.2	+						SYNPR_uc003dlp.2_Intron|SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_Intron|SYNPR_uc010hnt.2_Intron|SYNPR_uc011bfm.1_Intron	NM_144642	NP_653243			synaptoporin isoform 2							cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65720245	65720246	+	Intron	INS	-	GA	GA	rs143441869	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65720245_65720246insGA	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	65911365	65911365	+	Intron	DEL	T	-	-	rs11318858		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65911365delT	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229			membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65915021	65915022	+	Intron	INS	-	T	T	rs11369311		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65915021_65915022insT	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229			membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)														---	---	---	---
LRIG1	26018	broad.mit.edu	37	3	66453836	66453837	+	Intron	DEL	AG	-	-	rs67502081		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66453836_66453837delAG	uc003dmx.2	-						LRIG1_uc011bfu.1_Intron|LRIG1_uc003dmw.2_Intron|LRIG1_uc010hnz.2_Intron|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	66831316	66831316	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66831316delT								LRIG1 (280471 upstream) : KBTBD8 (217411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	66855654	66855654	+	IGR	DEL	T	-	-	rs35940449		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66855654delT								LRIG1 (304809 upstream) : KBTBD8 (193073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	66923645	66923646	+	IGR	INS	-	A	A	rs140817254	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66923645_66923646insA								LRIG1 (372800 upstream) : KBTBD8 (125081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	67341315	67341315	+	IGR	DEL	T	-	-	rs34557668		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67341315delT								KBTBD8 (279685 upstream) : SUCLG2 (83830 downstream)																																			---	---	---	---
FAM19A1	407738	broad.mit.edu	37	3	68331571	68331571	+	Intron	DEL	A	-	-	rs75417448		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68331571delA	uc003dnd.2	+						FAM19A1_uc003dne.2_Intron|FAM19A1_uc003dng.2_Intron	NM_213609	NP_998774			family with sequence similarity 19 (chemokine							endoplasmic reticulum|extracellular region				ovary(1)	1		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)														---	---	---	---
FAM19A4	151647	broad.mit.edu	37	3	68837769	68837769	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68837769delT	uc003dnh.1	-						FAM19A4_uc003dni.1_Intron	NM_182522	NP_872328			family with sequence similarity 19 (chemokine							extracellular region				skin(2)	2		Lung NSC(201;0.0198)		BRCA - Breast invasive adenocarcinoma(55;1.38e-05)|Epithelial(33;0.000124)|LUSC - Lung squamous cell carcinoma(21;0.0248)|KIRC - Kidney renal clear cell carcinoma(39;0.0729)|Kidney(39;0.0904)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69481736	69481739	+	Intron	DEL	TCTA	-	-	rs74816196		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69481736_69481739delTCTA	uc003dnw.2	-											Homo sapiens mRNA for KIAA1013 protein, partial cds.							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
MITF	4286	broad.mit.edu	37	3	69985676	69985676	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69985676delT	uc003dnz.2	+						MITF_uc011bgb.1_Intron|MITF_uc003doa.2_Intron|MITF_uc003dob.2_Intron|MITF_uc003dod.2_Intron|MITF_uc003doe.2_5'Flank|MITF_uc003dof.2_5'Flank	NM_198159	NP_937802			microphthalmia-associated transcription factor						melanocyte differentiation|multicellular organismal development|protein complex assembly	nucleus|protein complex	DNA binding|protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription			ovary(2)	2		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)				A		melanoma 		Waardenburg syndrome type 2|Tietz syndrome						---	---	---	---
MITF	4286	broad.mit.edu	37	3	70004983	70004983	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70004983delA	uc003dnz.2	+						MITF_uc011bgb.1_Intron|MITF_uc003doa.2_Intron|MITF_uc003dob.2_Intron|MITF_uc003dod.2_Intron|MITF_uc003doe.2_Intron|MITF_uc003dof.2_Intron	NM_198159	NP_937802			microphthalmia-associated transcription factor						melanocyte differentiation|multicellular organismal development|protein complex assembly	nucleus|protein complex	DNA binding|protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription			ovary(2)	2		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)				A		melanoma 		Waardenburg syndrome type 2|Tietz syndrome						---	---	---	---
Unknown	0	broad.mit.edu	37	3	70050604	70050605	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70050604_70050605insT	uc003dog.2	+											Homo sapiens cDNA clone IMAGE:4643842, partial cds.																														---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71460430	71460439	+	Intron	DEL	GTGTGTGTGT	-	-	rs72140858		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71460430_71460439delGTGTGTGTGT	uc003dop.2	-						FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dos.2_Intron	NM_032682	NP_116071			forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)				T	PAX5	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	3	72386674	72386675	+	IGR	DEL	TA	-	-	rs13072296		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72386674_72386675delTA								PROK2 (552317 upstream) : RYBP (37076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	73927010	73927010	+	IGR	DEL	T	-	-	rs63034760		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73927010delT								PDZRN3 (252938 upstream) : CNTN3 (384712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75181044	75181045	+	IGR	DEL	AC	-	-	rs138377545		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75181044_75181045delAC								CNTN3 (610701 upstream) : FAM86D (289660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75273367	75273368	+	IGR	INS	-	T	T	rs138338678	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75273367_75273368insT								CNTN3 (703024 upstream) : FAM86D (197337 downstream)																																			---	---	---	---
ZNF717	100131827	broad.mit.edu	37	3	75830177	75830177	+	Intron	DEL	G	-	-	rs113347200		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75830177delG	uc011bgi.1	-						ZNF717_uc003dpw.3_Intron	NM_001128223	NP_001121695			zinc finger protein 717						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	75892201	75892202	+	IGR	DEL	AC	-	-	rs147776391	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75892201_75892202delAC								ZNF717 (57531 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75988002	75988005	+	IGR	DEL	CATT	-	-	rs113095420		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75988002_75988005delCATT								ZNF717 (153332 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75988309	75988310	+	IGR	INS	-	A	A	rs115678830	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75988309_75988310insA								ZNF717 (153639 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75991116	75991121	+	IGR	DEL	CTCTCT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75991116_75991121delCTCTCT								ZNF717 (156446 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75995840	75995840	+	IGR	DEL	A	-	-	rs113854229		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75995840delA								ZNF717 (161170 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76430185	76430186	+	IGR	INS	-	A	A	rs63479060		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76430185_76430186insA								ZNF717 (595515 upstream) : ROBO2 (659108 downstream)																																			---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79644874	79644875	+	Intron	INS	-	T	T	rs76736774		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79644874_79644875insT	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)														---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79736422	79736427	+	Intron	DEL	AAACCT	-	-	rs140600515		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79736422_79736427delAAACCT	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	79868593	79868614	+	IGR	DEL	TTTCCTCAGCAAAGCTCTTCAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79868593_79868614delTTTCCTCAGCAAAGCTCTTCAA								ROBO1 (51534 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	79966491	79966498	+	IGR	DEL	AAAGAAGG	-	-	rs111827390		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79966491_79966498delAAAGAAGG								ROBO1 (149432 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80008841	80008841	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80008841delA								ROBO1 (191782 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80551899	80551899	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80551899delA								ROBO1 (734840 upstream) : GBE1 (986951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83379325	83379326	+	IGR	DEL	CA	-	-	rs80266392		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83379325_83379326delCA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84423939	84423940	+	IGR	INS	-	T	T	rs139391801	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84423939_84423940insT								None (None upstream) : CADM2 (584193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84670728	84670729	+	IGR	INS	-	GT	GT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84670728_84670729insGT								None (None upstream) : CADM2 (337404 downstream)																																			---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85882429	85882431	+	Intron	DEL	TTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85882429_85882431delTTG	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	87537877	87537878	+	IGR	INS	-	AA	AA	rs72398898		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87537877_87537878insAA								POU1F1 (212140 upstream) : HTR1F (493848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	88752126	88752141	+	IGR	DEL	TTCCTTCCTTCCTTCC	-	-	rs66786643	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88752126_88752141delTTCCTTCCTTCCTTCC								C3orf38 (545013 upstream) : EPHA3 (404533 downstream)																																			---	---	---	---
NSUN3	63899	broad.mit.edu	37	3	93815341	93815344	+	Intron	DEL	TGTT	-	-	rs71621585		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93815341_93815344delTGTT	uc003drl.1	+							NM_022072	NP_071355			NOL1/NOP2/Sun domain family, member 3								methyltransferase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	94644118	94644118	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94644118delT								NSUN3 (798488 upstream) : LOC255025 (12989 downstream)																																			---	---	---	---
LOC255025	255025	broad.mit.edu	37	3	94792998	94792998	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94792998delG	uc003drn.2	+											Homo sapiens hypothetical protein LOC255025, mRNA (cDNA clone IMAGE:5267157).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	95875029	95875029	+	IGR	DEL	G	-	-	rs35598547		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95875029delG								LOC255025 (979950 upstream) : EPHA6 (658396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96062340	96062341	+	IGR	INS	-	CA	CA	rs139999591	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96062340_96062341insCA								None (None upstream) : EPHA6 (471084 downstream)																																			---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	97037762	97037763	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97037762_97037763insA	uc010how.1	+							NM_001080448	NP_001073917			EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	97882081	97882082	+	IGR	INS	-	T	T	rs139443728	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97882081_97882082insT								OR5H14 (12919 upstream) : OR5H15 (5462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	97998340	97998340	+	IGR	DEL	G	-	-	rs145829176		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97998340delG								OR5H6 (14234 upstream) : OR5H2 (3392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	98201894	98201894	+	IGR	DEL	T	-	-	rs140496200		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98201894delT								OR5K1 (12523 upstream) : OR5K2 (14631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	99216125	99216126	+	IGR	INS	-	ACAC	ACAC	rs146954569	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99216125_99216126insACAC								DCBLD2 (595592 upstream) : COL8A1 (141328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	100047059	100047060	+	IGR	DEL	AG	-	-	rs138714597		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100047059_100047060delAG								TBC1D23 (2981 upstream) : NIT2 (6502 downstream)																																			---	---	---	---
GPR128	84873	broad.mit.edu	37	3	100395057	100395058	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100395057_100395058insT	uc003duc.2	+						GPR128_uc011bhc.1_Intron|GPR128_uc003dud.2_Intron	NM_032787	NP_116176			G protein-coupled receptor 128 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	100904183	100904206	+	IGR	DEL	GAAGGAAGGAAGGAAGGAAGGAAA	-	-	rs74986375	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100904183_100904206delGAAGGAAGGAAGGAAGGAAGGAAA								ABI3BP (191849 upstream) : IMPG2 (41082 downstream)																																			---	---	---	---
ZPLD1	131368	broad.mit.edu	37	3	101901054	101901056	+	Intron	DEL	AGG	-	-	rs143396314		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101901054_101901056delAGG	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	104059797	104059798	+	IGR	INS	-	T	T	rs111235006		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104059797_104059798insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104371297	104371297	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104371297delT								None (None upstream) : ALCAM (714416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	105302359	105302359	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105302359delT								ALCAM (6616 upstream) : CBLB (74751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	105696246	105696247	+	IGR	INS	-	T	T	rs146249825	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105696246_105696247insT								CBLB (107980 upstream) : LOC100302640 (859413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	106021907	106021907	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106021907delC								CBLB (433641 upstream) : LOC100302640 (533753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	106121620	106121620	+	IGR	DEL	C	-	-	rs76867683		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106121620delC								CBLB (533354 upstream) : LOC100302640 (434040 downstream)																																			---	---	---	---
BBX	56987	broad.mit.edu	37	3	107417499	107417499	+	Intron	DEL	A	-	-	rs72167747		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107417499delA	uc010hpr.2	+						BBX_uc003dwk.3_Intron|BBX_uc003dwl.3_Intron|BBX_uc010hps.1_Intron|BBX_uc003dwm.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)															---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108703391	108703392	+	Intron	INS	-	GG	GG	rs145625526	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108703391_108703392insGG	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244			MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	109068274	109068275	+	IGR	INS	-	TT	TT	rs10644452		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109068274_109068275insTT								DPPA4 (11855 upstream) : FLJ25363 (60562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109998733	109998733	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109998733delT								FLJ25363 (784719 upstream) : PVRL3 (792132 downstream)																																			---	---	---	---
PVRL3	25945	broad.mit.edu	37	3	110859205	110859205	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110859205delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	110994603	110994604	+	IGR	INS	-	T	T	rs150187000	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110994603_110994604insT								PVRL3 (82230 upstream) : CD96 (266322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	111149404	111149404	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111149404delT								PVRL3 (237031 upstream) : CD96 (111522 downstream)																																			---	---	---	---
SLC9A10	285335	broad.mit.edu	37	3	112015601	112015601	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112015601delT	uc003dyu.2	-						SLC9A10_uc010hqc.2_5'Flank	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	112028936	112028936	+	Intron	DEL	A	-	-	rs62845960		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112028936delA	uc003dyv.2	+											Homo sapiens, clone IMAGE:5418716, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	112627155	112627156	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112627155_112627156insT								CD200R1L (62358 upstream) : CD200R1 (14376 downstream)																																			---	---	---	---
CD200R1	131450	broad.mit.edu	37	3	112654903	112654903	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112654903delT	uc003dzk.1	-						CD200R1_uc003dzj.1_Intron|CD200R1_uc011bhx.1_Intron|CD200R1_uc003dzl.1_Intron|CD200R1_uc003dzm.1_Intron	NM_170780	NP_740750			CD200 receptor 1 isoform d						interspecies interaction between organisms|regulation of immune response	extracellular region|integral to membrane|plasma membrane	receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
DRD3	1814	broad.mit.edu	37	3	113878321	113878321	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113878321delA	uc003ebd.2	-						DRD3_uc010hqn.1_Intron|DRD3_uc003ebb.1_Intron|DRD3_uc003ebc.1_Intron	NM_000796	NP_000787			dopamine receptor D3 isoform a						activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	116798914	116798916	+	IGR	DEL	AAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116798914_116798916delAAT								LOC285194 (363029 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	118519650	118519651	+	Intron	INS	-	CT	CT	rs138370214	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118519650_118519651insCT	uc011biu.1	-											Homo sapiens clone HA_003061 mRNA sequence.																														---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118774138	118774148	+	Intron	DEL	CAGCTTCTCAC	-	-	rs146453595		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118774138_118774148delCAGCTTCTCAC	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																		---	---	---	---
GSK3B	2932	broad.mit.edu	37	3	119711881	119711881	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119711881delA	uc003edo.2	-						GSK3B_uc003edn.2_Intron	NM_001146156	NP_001139628			glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)													---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	121002741	121002742	+	Intron	DEL	CT	-	-	rs4462890		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121002741_121002742delCT	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)														---	---	---	---
EAF2	55840	broad.mit.edu	37	3	121563552	121563553	+	Intron	INS	-	T	T	rs138950114	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121563552_121563553insT	uc003een.2	+						EAF2_uc003eeo.2_Intron	NM_018456	NP_060926			ELL associated factor 2						apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	protein binding				0				GBM - Glioblastoma multiforme(114;0.0972)														---	---	---	---
CASR	846	broad.mit.edu	37	3	121967456	121967456	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121967456delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	122014187	122014188	+	IGR	DEL	CT	-	-	rs72057880		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122014187_122014188delCT								CASR (8844 upstream) : CSTA (29823 downstream)																																			---	---	---	---
ADCY5	111	broad.mit.edu	37	3	123064615	123064616	+	Intron	DEL	AG	-	-	rs111848088		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123064615_123064616delAG	uc003egh.1	-						ADCY5_uc003egg.1_Intron|ADCY5_uc003egi.1_Intron	NM_183357	NP_899200			adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	123173998	123173998	+	IGR	DEL	A	-	-	rs148528266		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123173998delA								ADCY5 (6606 upstream) : PTPLB (39365 downstream)																																			---	---	---	---
OSBPL11	114885	broad.mit.edu	37	3	125310845	125310846	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125310845_125310846insA	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	125421128	125421128	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125421128delT								OSBPL11 (106747 upstream) : MIR548I1 (88119 downstream)																																			---	---	---	---
SLC41A3	54946	broad.mit.edu	37	3	125748213	125748213	+	Intron	DEL	T	-	-	rs66513227		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125748213delT	uc003eij.2	-						SLC41A3_uc003eii.2_Intron|SLC41A3_uc003eil.2_Intron|SLC41A3_uc003eik.2_Intron|SLC41A3_uc011bkh.1_Intron|SLC41A3_uc010hsd.1_Intron	NM_001008485	NP_001008485			solute carrier family 41, member 3 isoform 1							integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(114;0.167)														---	---	---	---
MGLL	11343	broad.mit.edu	37	3	127440706	127440709	+	Intron	DEL	TGTC	-	-	rs138910019		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127440706_127440709delTGTC	uc003ejx.2	-						MGLL_uc003ejw.2_Intron|MGLL_uc011bko.1_Intron|MGLL_uc010hsp.1_Intron|MGLL_uc003ejv.2_Intron	NM_001003794	NP_001003794			monoglyceride lipase isoform 2						arachidonic acid metabolic process|fatty acid biosynthetic process|inflammatory response|platelet activation|regulation of endocannabinoid signaling pathway|regulation of inflammatory response|regulation of sensory perception of pain|triglyceride catabolic process	plasma membrane	acylglycerol lipase activity|carboxylesterase activity|lysophospholipase activity|protein homodimerization activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	130563540	130563540	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130563540delA								PIK3R4 (97844 upstream) : ATP2C1 (5905 downstream)																																			---	---	---	---
NCRNA00119	348808	broad.mit.edu	37	3	132554139	132554140	+	Intron	INS	-	T	T	rs147686414	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132554139_132554140insT	uc003epg.1	+							NR_002811				Homo sapiens cDNA clone IMAGE:4826885.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	132600984	132600985	+	IGR	DEL	TG	-	-	rs71931303		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132600984_132600985delTG								NCRNA00119 (7934 upstream) : TMEM108 (156186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	132614549	132614551	+	IGR	DEL	GAG	-	-	rs143164037		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132614549_132614551delGAG								NCRNA00119 (21499 upstream) : TMEM108 (142620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	132752054	132752055	+	IGR	INS	-	C	C	rs146418584	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132752054_132752055insC								NCRNA00119 (159004 upstream) : TMEM108 (5116 downstream)																																			---	---	---	---
TMEM108	66000	broad.mit.edu	37	3	133048498	133048498	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133048498delT	uc003eph.2	+						TMEM108_uc003epi.2_Intron|TMEM108_uc003epj.1_Intron|TMEM108_uc003epk.2_Intron	NM_023943	NP_076432			transmembrane protein 108 precursor							integral to membrane				ovary(2)|skin(2)	4																		---	---	---	---
BFSP2	8419	broad.mit.edu	37	3	133134521	133134532	+	Intron	DEL	CCCCTCTACTCA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133134521_133134532delCCCCTCTACTCA	uc003epn.1	+							NM_003571	NP_003562			phakinin						response to stimulus|visual perception	cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens				0																		---	---	---	---
BFSP2	8419	broad.mit.edu	37	3	133188863	133188863	+	Intron	DEL	T	-	-	rs146343554		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133188863delT	uc003epn.1	+							NM_003571	NP_003562			phakinin						response to stimulus|visual perception	cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens				0																		---	---	---	---
TF	7018	broad.mit.edu	37	3	133452712	133452712	+	Intron	DEL	A	-	-	rs144480920		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133452712delA	uc003epu.1	+							NM_001063	NP_001054			transferrin precursor						cellular iron ion homeostasis|platelet activation|platelet degranulation|transferrin transport|transmembrane transport	apical plasma membrane|basal plasma membrane|coated pit|early endosome|endocytic vesicle|endosome membrane|extracellular region|late endosome|perinuclear region of cytoplasm|recycling endosome|stored secretory granule	ferric iron binding			ovary(1)|skin(1)	2					Aluminium(DB01370)|Bismuth(DB01402)|Iron Dextran(DB00893)													---	---	---	---
SRPRB	58477	broad.mit.edu	37	3	133537629	133537630	+	Intron	INS	-	GT	GT	rs146467727	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133537629_133537630insGT	uc003epx.1	+							NM_021203	NP_067026			signal recognition particle receptor, beta							endoplasmic reticulum membrane|integral to membrane	GTP binding|protein binding|receptor activity			ovary(1)	1																		---	---	---	---
SLCO2A1	6578	broad.mit.edu	37	3	133691269	133691270	+	Intron	INS	-	AAA	AAA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133691269_133691270insAAA	uc003eqa.3	-						SLCO2A1_uc003eqb.3_Intron|SLCO2A1_uc011blv.1_Intron|SLCO2A1_uc010htw.1_Intron	NM_005630	NP_005621			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to plasma membrane|membrane fraction	prostaglandin transmembrane transporter activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	133948223	133948223	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133948223delG								RYK (-21363 upstream) : RYK (-72245 downstream)																																			---	---	---	---
CEP63	80254	broad.mit.edu	37	3	134234657	134234657	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134234657delA	uc003eqo.1	+						CEP63_uc003eql.1_Intron|CEP63_uc003eqm.2_Intron|CEP63_uc003eqn.1_Intron	NM_025180	NP_079456			centrosomal protein 63 isoform a						cell division|DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitosis|signal transduction in response to DNA damage|spindle assembly	centrosome|cytosol|spindle pole	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	134383510	134383511	+	IGR	DEL	TT	-	-	rs10563578		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134383510_134383511delTT								KY (13032 upstream) : EPHB1 (130749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	135165617	135165618	+	IGR	INS	-	C	C	rs74979823		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135165617_135165618insC								EPHB1 (186312 upstream) : PPP2R3A (518949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	135484352	135484353	+	IGR	INS	-	T	T	rs148793111	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135484352_135484353insT								EPHB1 (505047 upstream) : PPP2R3A (200214 downstream)																																			---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136293186	136293189	+	Intron	DEL	ACAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136293186_136293189delACAC	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_Intron|STAG1_uc003erd.2_Intron|STAG1_uc003ere.2_Intron	NM_005862	NP_005853			stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136330346	136330347	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136330346_136330347insT	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	137048732	137048732	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137048732delA								IL20RB (318812 upstream) : SOX14 (434847 downstream)																																	OREG0002750	type=REGULATORY REGION|Gene=MGC34923-SOX14|Dataset=Vista Enhancers|EvidenceSubtype=In-vivo LacZ Expression Assay	---	---	---	---
Unknown	0	broad.mit.edu	37	3	137475988	137475989	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137475988_137475989insA								IL20RB (746068 upstream) : SOX14 (7590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137538180	137538181	+	IGR	INS	-	A	A	rs143109126	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137538180_137538181insA								SOX14 (53784 upstream) : CLDN18 (179477 downstream)																																			---	---	---	---
DZIP1L	199221	broad.mit.edu	37	3	137822004	137822007	+	Intron	DEL	ACAA	-	-	rs146936811		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137822004_137822007delACAA	uc003erq.2	-						DZIP1L_uc003err.1_Intron	NM_173543	NP_775814			DAZ interacting protein 1-like							intracellular	zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	139933295	139933296	+	Intron	INS	-	AA	AA	rs146668613	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139933295_139933296insAA	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414			calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7															HNSCC(16;0.037)			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	140052525	140052526	+	Intron	DEL	TG	-	-	rs144440469		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140052525_140052526delTG	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414			calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7															HNSCC(16;0.037)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	140422206	140422207	+	IGR	INS	-	A	A	rs151336303	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140422206_140422207insA								TRIM42 (2215 upstream) : SLC25A36 (238455 downstream)																																			---	---	---	---
SPSB4	92369	broad.mit.edu	37	3	140830196	140830197	+	Intron	INS	-	T	T	rs71627898		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140830196_140830197insT	uc003ett.2	+						SPSB4_uc010hum.2_Intron	NM_080862	NP_543138			splA/ryanodine receptor domain and SOCS box						intracellular signal transduction	cytoplasm	protein binding				0																		---	---	---	---
ZBTB38	253461	broad.mit.edu	37	3	141106093	141106094	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141106093_141106094insT	uc003etw.2	+						ZBTB38_uc010hun.2_5'Flank|ZBTB38_uc010huo.2_5'Flank	NM_001080412	NP_001073881			zinc finger and BTB domain containing 38						positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
GRK7	131890	broad.mit.edu	37	3	141523901	141523904	+	Intron	DEL	CACA	-	-	rs10545322		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141523901_141523904delCACA	uc011bnd.1	+							NM_139209	NP_631948			G-protein-coupled receptor kinase 7 precursor						visual perception	membrane	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5																		---	---	---	---
GRK7	131890	broad.mit.edu	37	3	141534514	141534514	+	Intron	DEL	A	-	-	rs5853050		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141534514delA	uc011bnd.1	+							NM_139209	NP_631948			G-protein-coupled receptor kinase 7 precursor						visual perception	membrane	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5																		---	---	---	---
TFDP2	7029	broad.mit.edu	37	3	141813147	141813148	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141813147_141813148insT	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																		---	---	---	---
SR140	23350	broad.mit.edu	37	3	142720221	142720222	+	5'Flank	INS	-	GGACAACGA	GGACAACGA	rs138803517	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142720221_142720222insGGACAACGA	uc003evh.1	+						SR140_uc003evi.1_5'Flank|SR140_uc011bnj.1_5'Flank|SR140_uc003evj.1_5'Flank|SR140_uc003evk.1_5'Flank	NM_001080415	NP_001073884			U2-associated SR140 protein						RNA processing	nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	142888590	142888590	+	IGR	DEL	C	-	-	rs143360269		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142888590delC								CHST2 (46780 upstream) : SLC9A9 (95475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146400819	146400819	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146400819delT								PLSCR5 (76816 upstream) : ZIC4 (703018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147019531	147019531	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147019531delA								PLSCR5 (695528 upstream) : ZIC4 (84306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147164368	147164369	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147164368_147164369insT								ZIC1 (29864 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147215378	147215379	+	IGR	DEL	AT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147215378_147215379delAT								ZIC1 (80874 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147491976	147491976	+	IGR	DEL	G	-	-	rs63597761		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147491976delG								ZIC1 (357472 upstream) : AGTR1 (923682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147704662	147704662	+	IGR	DEL	T	-	-	rs111517938		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147704662delT								ZIC1 (570158 upstream) : AGTR1 (710996 downstream)																																			---	---	---	---
GYG1	2992	broad.mit.edu	37	3	148708877	148708888	+	5'Flank	DEL	AGGAATGATTAT	-	-	rs11276429		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148708877_148708888delAGGAATGATTAT	uc003ewn.2	+						GYG1_uc011bnp.1_5'Flank|GYG1_uc003ewo.2_5'Flank|GYG1_uc003ewp.2_5'Flank	NM_004130	NP_004121			glycogenin 1						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	glycogenin glucosyltransferase activity|metal ion binding|protein binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)															---	---	---	---
RNF13	11342	broad.mit.edu	37	3	149643412	149643413	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149643412_149643413insT	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	150020285	150020286	+	IGR	INS	-	C	C	rs142438671	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150020285_150020286insC								PFN2 (331544 upstream) : TSC22D2 (106502 downstream)																																			---	---	---	---
TSC22D2	9819	broad.mit.edu	37	3	150144071	150144071	+	Intron	DEL	A	-	-	rs11346327		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150144071delA	uc003exv.2	+						TSC22D2_uc003exw.2_Intron|TSC22D2_uc003exx.2_Intron	NM_014779	NP_055594			TSC22 domain family, member 2								sequence-specific DNA binding transcription factor activity			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151014381	151014382	+	Intron	INS	-	C	C	rs139067916	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151014381_151014382insC	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|GPR87_uc003eyt.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	151050527	151050527	+	Intron	DEL	T	-	-	rs10710635		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151050527delT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	151383208	151383209	+	IGR	DEL	TT	-	-	rs34307578		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151383208_151383209delTT								IGSF10 (206711 upstream) : AADACL2 (68495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	151932848	151932849	+	IGR	DEL	AT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151932848_151932849delAT								SUCNR1 (333198 upstream) : LOC401093 (47564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	152421192	152421192	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152421192delA								MBNL1 (237624 upstream) : P2RY1 (131544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	152652910	152652910	+	IGR	DEL	A	-	-	rs36023924		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152652910delA								P2RY1 (97069 upstream) : RAP2B (227119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	152924010	152924011	+	IGR	INS	-	A	A	rs66523374		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152924010_152924011insA								RAP2B (37749 upstream) : C3orf79 (278273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	153076649	153076650	+	IGR	DEL	TC	-	-	rs148441930		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153076649_153076650delTC								RAP2B (190388 upstream) : C3orf79 (125634 downstream)																																			---	---	---	---
MME	4311	broad.mit.edu	37	3	154845738	154845739	+	Intron	INS	-	A	A	rs148979389	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154845738_154845739insA	uc010hvr.1	+						MME_uc003fab.1_Intron|MME_uc003fac.1_Intron|MME_uc003fad.1_Intron|MME_uc003fae.1_Intron	NM_007289	NP_009220			membrane metallo-endopeptidase						cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)													---	---	---	---
KCNAB1	7881	broad.mit.edu	37	3	156051359	156051360	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156051359_156051360delCA	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Intron|KCNAB1_uc010hvt.1_Intron	NM_172160	NP_751892			potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	156372024	156372025	+	IGR	DEL	AT	-	-	rs72107612		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156372024_156372025delAT								SSR3 (99089 upstream) : LOC100287227 (18939 downstream)																																			---	---	---	---
TIPARP	25976	broad.mit.edu	37	3	156419662	156419663	+	Intron	INS	-	CT	CT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156419662_156419663insCT	uc003fav.2	+						TIPARP_uc003faw.2_Intron	NM_015508	NP_056323			TCDD-inducible poly(ADP-ribose) polymerase								NAD+ ADP-ribosyltransferase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|breast(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
VEPH1	79674	broad.mit.edu	37	3	156998916	156998919	+	Intron	DEL	AGAC	-	-	rs112345347		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156998916_156998919delAGAC	uc003fbj.1	-						VEPH1_uc003fbk.1_Intron|VEPH1_uc010hvu.1_Intron	NM_024621	NP_078897			ventricular zone expressed PH domain homolog 1							plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	157462043	157462044	+	IGR	DEL	TA	-	-	rs138779307		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157462043_157462044delTA								C3orf55 (143024 upstream) : SHOX2 (351757 downstream)																																			---	---	---	---
RARRES1	5918	broad.mit.edu	37	3	158442618	158442618	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158442618delT	uc003fci.2	-						RARRES1_uc003fcj.2_Intron	NM_206963	NP_996846			retinoic acid receptor responder (tazarotene						negative regulation of cell proliferation	integral to membrane					0			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)													---	---	---	---
PPM1L	151742	broad.mit.edu	37	3	160491172	160491173	+	Intron	INS	-	A	A	rs141851154	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160491172_160491173insA	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)															---	---	---	---
PPM1L	151742	broad.mit.edu	37	3	160707950	160707951	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160707950_160707951insT	uc003fdr.2	+						PPM1L_uc003fds.2_Intron|PPM1L_uc003fdt.2_Intron|PPM1L_uc010hwf.2_Intron	NM_139245	NP_640338			protein phosphatase 1 (formerly 2C)-like						protein dephosphorylation|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(1)	1			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	161032157	161032157	+	IGR	DEL	A	-	-	rs72098956		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161032157delA								NMD3 (60838 upstream) : C3orf57 (30424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161776634	161776635	+	IGR	INS	-	T	T	rs147153968	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161776634_161776635insT								OTOL1 (554906 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162679463	162679463	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162679463delG	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	162716704	162716705	+	Intron	DEL	AT	-	-	rs142103849		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162716704_162716705delAT	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	162759451	162759452	+	Intron	INS	-	AA	AA	rs150344833	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162759451_162759452insAA	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	163119691	163119692	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163119691_163119692insT								None (None upstream) : MIR1263 (769567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	163162924	163162925	+	IGR	INS	-	T	T	rs63635360		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163162924_163162925insT								None (None upstream) : MIR1263 (726334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	163243619	163243619	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163243619delC								None (None upstream) : MIR1263 (645640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165232486	165232489	+	Intron	DEL	TTCC	-	-	rs56873284		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165232486_165232489delTTCC	uc003fel.2	-											full-length cDNA clone CS0DA002YJ24 of Neuroblastoma of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	165639617	165639618	+	IGR	INS	-	A	A	rs75551439		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165639617_165639618insA								BCHE (84364 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168128807	168128807	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168128807delA								GOLIM4 (315390 upstream) : MIR551B (140835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	169471284	169471284	+	IGR	DEL	G	-	-	rs7431994		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169471284delG								MECOM (89721 upstream) : TERC (11114 downstream)																																			---	---	---	---
GPR160	26996	broad.mit.edu	37	3	169768029	169768029	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169768029delT	uc003fgi.2	+						GPR160_uc010hwq.2_Intron	NM_014373	NP_055188			G protein-coupled receptor 160							integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)															---	---	---	---
SLC7A14	57709	broad.mit.edu	37	3	170188879	170188882	+	Intron	DEL	GTGT	-	-	rs59156901		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170188879_170188882delGTGT	uc003fgz.2	-						CLDN11_uc011bpt.1_Intron|uc003fha.1_Intron	NM_020949	NP_066000			solute carrier family 7 (cationic amino acid							integral to membrane	amino acid transmembrane transporter activity			ovary(2)|upper_aerodigestive_tract(1)|liver(1)|central_nervous_system(1)	5	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)															---	---	---	---
TNIK	23043	broad.mit.edu	37	3	171002397	171002398	+	Intron	INS	-	A	A	rs11375341		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171002397_171002398insA	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron	NM_015028	NP_055843			TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)															---	---	---	---
SPATA16	83893	broad.mit.edu	37	3	172697454	172697454	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172697454delA	uc003fin.3	-							NM_031955	NP_114161			spermatogenesis associated 16						cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding			ovary(2)|skin(1)	3	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)															---	---	---	---
SPATA16	83893	broad.mit.edu	37	3	172844959	172844960	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172844959_172844960delTG	uc003fin.3	-							NM_031955	NP_114161			spermatogenesis associated 16						cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding			ovary(2)|skin(1)	3	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	173069611	173069611	+	IGR	DEL	A	-	-	rs72066896		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173069611delA								SPATA16 (210579 upstream) : NLGN1 (46633 downstream)																																			---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173772178	173772178	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173772178delA	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747			neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173957155	173957155	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173957155delG	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747			neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	174240746	174240748	+	Intron	DEL	AAG	-	-	rs57653560		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174240746_174240748delAAG	uc003fiq.1	+						uc003fir.2_Intron|uc003fis.2_Intron|uc010hwx.1_Intron					Homo sapiens NAALADL2 gene, partial 5'UTR, variant 1.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	175558932	175558932	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175558932delT								NAALADL2 (35506 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176247070	176247071	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176247070_176247071delAC								NAALADL2 (723644 upstream) : TBL1XR1 (491472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176388553	176388554	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176388553_176388554delAC								NAALADL2 (865127 upstream) : TBL1XR1 (349989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176469810	176469811	+	IGR	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176469810_176469811delAG								NAALADL2 (946384 upstream) : TBL1XR1 (268732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176985865	176985866	+	IGR	INS	-	T	T	rs138412898	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176985865_176985866insT								TBL1XR1 (70817 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177251113	177251113	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177251113delA								TBL1XR1 (336065 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177531092	177531092	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177531092delG								TBL1XR1 (616044 upstream) : KCNMB2 (723132 downstream)																																			---	---	---	---
USP13	8975	broad.mit.edu	37	3	179382880	179382880	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179382880delA	uc003fkh.2	+						USP13_uc003fkf.2_Intron	NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
USP13	8975	broad.mit.edu	37	3	179425844	179425844	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179425844delT	uc003fkh.2	+						USP13_uc003fkf.2_Intron	NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
USP13	8975	broad.mit.edu	37	3	179503831	179503833	+	3'UTR	DEL	AGA	-	-	rs78667934		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179503831_179503833delAGA	uc003fkh.2	+	21						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	181059689	181059689	+	IGR	DEL	A	-	-	rs113172980		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181059689delA								DNAJC19 (352159 upstream) : SOX2OT (221820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182278252	182278253	+	IGR	INS	-	T	T	rs150580436	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182278252_182278253insT								SOX2OT (819249 upstream) : ATP11B (233038 downstream)																																			---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183413306	183413306	+	5'Flank	DEL	A	-	-	rs71849149		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183413306delA	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	183730729	183730729	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183730729delG	uc003fmg.2	-						ABCC5_uc011bqt.1_Intron|ABCC5_uc010hxl.2_Intron|ABCC5_uc003fmh.2_Intron|ABCC5_uc010hxm.2_Intron|ABCC5_uc010hxn.2_Intron|ABCC5_uc010hxo.2_Intron|ABCC5_uc003fmi.3_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	184266066	184266067	+	IGR	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184266066_184266067delCT								CHRD (158447 upstream) : EPHB3 (13520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	184976220	184976221	+	IGR	INS	-	GGT	GGT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184976220_184976221insGGT								EHHADH (4383 upstream) : MAP3K13 (24533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	186489325	186489326	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186489325_186489326insA								KNG1 (27584 upstream) : EIF4A2 (12035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	186538610	186538610	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186538610delT								RFC4 (14126 upstream) : ADIPOQ (21853 downstream)																																			---	---	---	---
ST6GAL1	6480	broad.mit.edu	37	3	186704913	186704914	+	Intron	INS	-	AAGG	AAGG	rs147208860	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186704913_186704914insAAGG	uc003frb.2	+						ST6GAL1_uc003frc.2_Intron	NM_173216	NP_775323			ST6 beta-galactosamide						humoral immune response|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			central_nervous_system(1)	1	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)														---	---	---	---
ST6GAL1	6480	broad.mit.edu	37	3	186704988	186704989	+	Intron	INS	-	AAGGA	AAGGA	rs144465329	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186704988_186704989insAAGGA	uc003frb.2	+						ST6GAL1_uc003frc.2_Intron	NM_173216	NP_775323			ST6 beta-galactosamide						humoral immune response|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			central_nervous_system(1)	1	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)														---	---	---	---
ST6GAL1	6480	broad.mit.edu	37	3	186753726	186753727	+	Intron	INS	-	A	A	rs138082077	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186753726_186753727insA	uc003frb.2	+						ST6GAL1_uc003frc.2_Intron|ST6GAL1_uc003frd.2_Intron	NM_173216	NP_775323			ST6 beta-galactosamide						humoral immune response|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			central_nervous_system(1)	1	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)														---	---	---	---
LPP	4026	broad.mit.edu	37	3	188006382	188006383	+	Intron	DEL	AT	-	-	rs71167088	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188006382_188006383delAT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
LPP	4026	broad.mit.edu	37	3	188500527	188500528	+	Intron	INS	-	AA	AA	rs66466869		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188500527_188500528insAA	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	188697351	188697352	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188697351_188697352insA	uc003frv.1	+							NM_198485	NP_940887			tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)														---	---	---	---
TP63	8626	broad.mit.edu	37	3	189495545	189495545	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189495545delT	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron	NM_003722	NP_003713			tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)										Hay-Wells_syndrome	HNSCC(45;0.13)			---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189705288	189705288	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189705288delG	uc011bsk.1	-						LEPREL1_uc003fsg.2_Intron	NM_018192	NP_060662			leprecan-like 1 isoform a						collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189793971	189793972	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189793971_189793972delCA	uc011bsk.1	-						LEPREL1_uc003fsg.2_Intron	NM_018192	NP_060662			leprecan-like 1 isoform a						collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
IL1RAP	3556	broad.mit.edu	37	3	190308047	190308047	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190308047delT	uc003fsm.1	+						IL1RAP_uc003fsk.2_Intron|IL1RAP_uc003fsl.2_Intron|IL1RAP_uc010hzf.2_Intron|IL1RAP_uc010hzg.1_Intron|IL1RAP_uc003fsn.1_Intron|IL1RAP_uc003fso.1_Intron|IL1RAP_uc003fsp.1_Intron|IL1RAP_uc003fsq.2_Intron	NM_002182	NP_002173			interleukin 1 receptor accessory protein isoform						inflammatory response|innate immune response|protein complex assembly	extracellular region|integral to plasma membrane				ovary(1)	1	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	190650834	190650834	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190650834delA								SNAR-I (54995 upstream) : OSTN (279488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191246273	191246274	+	IGR	INS	-	TC	TC	rs148860952		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191246273_191246274insTC								PYDC2 (67030 upstream) : FGF12 (613410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191477146	191477147	+	IGR	INS	-	GTAA	GTAA	rs142892660	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191477146_191477147insGTAA								PYDC2 (297903 upstream) : FGF12 (382537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191714773	191714774	+	IGR	INS	-	AGGA	AGGA	rs148328414	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191714773_191714774insAGGA								PYDC2 (535530 upstream) : FGF12 (144910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191831164	191831164	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191831164delT								PYDC2 (651921 upstream) : FGF12 (28520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	193708282	193708283	+	IGR	INS	-	TT	TT	rs55886145		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193708282_193708283insTT								OPA1 (292683 upstream) : LOC100128023 (2601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	193740061	193740062	+	IGR	DEL	AC	-	-	rs71967670		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193740061_193740062delAC								LOC100128023 (28034 upstream) : HES1 (113872 downstream)																																			---	---	---	---
ATP13A3	79572	broad.mit.edu	37	3	194142860	194142860	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194142860delA	uc003fty.3	-						ATP13A3_uc003ftx.3_Intron	NM_024524	NP_078800			ATPase type 13A3						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(1)	1	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	194506203	194506204	+	IGR	DEL	CT	-	-	rs150162574		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194506203_194506204delCT								FAM43A (96439 upstream) : C3orf21 (282811 downstream)																																			---	---	---	---
C3orf21	152002	broad.mit.edu	37	3	194802263	194802264	+	Intron	INS	-	C	C	rs144399388	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194802263_194802264insC	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)														---	---	---	---
MUC20	200958	broad.mit.edu	37	3	195448754	195448755	+	Intron	INS	-	G	G	rs144078556	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195448754_195448755insG	uc010hzo.2	+						MUC20_uc010hzp.2_5'Flank	NM_152673	NP_689886			mucin 20 isoform L						protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	195815192	195815203	+	IGR	DEL	TGTGTATGCGTG	-	-	rs36209346		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195815192_195815203delTGTGTATGCGTG								TFRC (6160 upstream) : ZDHHC19 (109121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	195891850	195891853	+	IGR	DEL	GTGT	-	-	rs111934138		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195891850_195891853delGTGT								TFRC (82818 upstream) : ZDHHC19 (32471 downstream)																																			---	---	---	---
PCYT1A	5130	broad.mit.edu	37	3	195973273	195973273	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195973273delT	uc003fwg.2	-						PCYT1A_uc003fwh.2_Intron	NM_005017	NP_005008			choline phosphate cytidylyltransferase 1 alpha							cytosol|soluble fraction	choline-phosphate cytidylyltransferase activity				0	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	196072073	196072079	+	IGR	DEL	CTGGAGT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196072073_196072079delCTGGAGT								TM4SF19 (6815 upstream) : UBXN7 (8292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	196185842	196185843	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196185842_196185843insA								UBXN7 (26497 upstream) : RNF168 (12786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	196332799	196332800	+	IGR	INS	-	A	A	rs71621273		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196332799_196332800insA								FBXO45 (16871 upstream) : LRRC33 (33856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	1125166	1125167	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1125166_1125167delGT								RNF212 (17584 upstream) : SPON2 (35555 downstream)																																			---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1911366	1911366	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1911366delT	uc003gdz.3	+						WHSC1_uc003geb.3_Intron|WHSC1_uc003gec.3_Intron|WHSC1_uc003ged.3_Intron|WHSC1_uc003gee.3_Intron|WHSC1_uc003gef.3_Intron|WHSC1_uc003gdx.2_Intron|WHSC1_uc003gdy.1_Intron|WHSC1_uc010icd.1_Intron|WHSC1_uc003gea.1_Intron|WHSC1_uc010ice.1_Intron|WHSC1_uc003geg.1_Intron|WHSC1_uc003geh.1_Intron	NM_001042424	NP_001035889			Wolf-Hirschhorn syndrome candidate 1 protein						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)				T	IGH@	MM								---	---	---	---
ZFYVE28	57732	broad.mit.edu	37	4	2351762	2351763	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2351762_2351763delAC	uc003gex.1	-						ZFYVE28_uc011bvk.1_Intron|ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gey.3_Intron|ZFYVE28_uc003gez.2_Intron	NM_020972	NP_066023			zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3																		---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3395889	3395889	+	Intron	DEL	T	-	-	rs77548109		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3395889delT	uc003ggw.2	+						RGS12_uc003ggu.2_Intron|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_Intron|RGS12_uc003ggv.2_Intron|RGS12_uc003ggy.1_Intron|RGS12_uc010ict.1_Intron|RGS12_uc003ggz.2_Intron|RGS12_uc010icu.1_Intron|RGS12_uc011bvs.1_Intron|RGS12_uc003gha.2_Intron|RGS12_uc010icv.2_Intron	NM_198229	NP_937872			regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
DOK7	285489	broad.mit.edu	37	4	3492409	3492412	+	Intron	DEL	TTCC	-	-	rs77173638		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3492409_3492412delTTCC	uc003ghd.2	+						DOK7_uc003ghe.2_Intron|DOK7_uc003ghf.2_Intron|DOK7_uc003ghg.1_5'Flank	NM_173660	NP_775931			downstream of tyrosine kinase 7 isoform 1						positive regulation of protein tyrosine kinase activity	cell junction|synapse	insulin receptor binding|protein kinase binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3589447	3589448	+	Intron	INS	-	GA	GA	rs144006715		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3589447_3589448insGA	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3627485	3627486	+	IGR	INS	-	T	T	rs141784691	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3627485_3627486insT								LRPAP1 (93261 upstream) : ADRA2C (140589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3634306	3634306	+	IGR	DEL	C	-	-	rs67244989		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3634306delC								LRPAP1 (100082 upstream) : ADRA2C (133769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	4622019	4622020	+	Intron	INS	-	TG	TG	rs145190268	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4622019_4622020insTG	uc003gid.2	+											Homo sapiens, clone IMAGE:5204729, mRNA.																														---	---	---	---
FLJ36777	730971	broad.mit.edu	37	4	7102438	7102438	+	Intron	DEL	T	-	-	rs112978811		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7102438delT	uc003gka.3	-							NR_027441				Homo sapiens, clone IMAGE:5767052, mRNA.												0																		---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7678551	7678552	+	Intron	INS	-	CTCC	CTCC	rs28460807		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7678551_7678552insCTCC	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																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7907436	7907436	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7907436delG	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	9640365	9640365	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9640365delA								MIR548I2 (82428 upstream) : DRD5 (142893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	10169775	10169776	+	IGR	INS	-	GA	GA	rs146658644	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10169775_10169776insGA								WDR1 (51202 upstream) : ZNF518B (271729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	10184236	10184239	+	IGR	DEL	ATAC	-	-	rs138729417		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10184236_10184239delATAC								WDR1 (65663 upstream) : ZNF518B (257266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11333692	11333692	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11333692delA								CLNK (647306 upstream) : MIR572 (36759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12088017	12088018	+	IGR	INS	-	A	A	rs151120637	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12088017_12088018insA								HS3ST1 (657480 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12557394	12557394	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12557394delA								None (None upstream) : HSP90AB2P (777643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12594275	12594282	+	IGR	DEL	TCTCTCTC	-	-	rs113298700		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12594275_12594282delTCTCTCTC								None (None upstream) : HSP90AB2P (740755 downstream)																																			---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13608630	13608630	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13608630delT	uc003gmz.1	-						BOD1L_uc010idr.1_Intron	NM_148894	NP_683692			biorientation of chromosomes in cell division								DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	14246588	14246591	+	IGR	DEL	TGTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14246588_14246591delTGTG								BOD1L (617260 upstream) : CPEB2 (758931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	16304923	16304924	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16304923_16304924delAC								FLJ39653 (45113 upstream) : LDB2 (198243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	19775944	19775945	+	IGR	INS	-	A	A	rs140037285	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19775944_19775945insA								None (None upstream) : SLIT2 (479290 downstream)																																			---	---	---	---
SLIT2	9353	broad.mit.edu	37	4	20433624	20433625	+	Intron	INS	-	TGTGTG	TGTGTG	rs137983627	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20433624_20433625insTGTGTG	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778			slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11																		---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21681002	21681002	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21681002delA	uc003gqh.1	-						KCNIP4_uc003gqi.1_Intron	NM_001035003	NP_001030175			Kv channel interacting protein 4 isoform 5							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)																---	---	---	---
LGI2	55203	broad.mit.edu	37	4	25009201	25009216	+	Intron	DEL	GTGTGTGTGTGTGTGT	-	-	rs68046456		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25009201_25009216delGTGTGTGTGTGTGTGT	uc003grf.2	-							NM_018176	NP_060646			leucine-rich repeat LGI family, member 2							extracellular region					0		Breast(46;0.173)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	25589703	25589704	+	IGR	DEL	AC	-	-	rs71639888		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25589703_25589704delAC								ANAPC4 (169584 upstream) : SLC34A2 (67731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	25710408	25710408	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25710408delT								SLC34A2 (30042 upstream) : SEL1L3 (38642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	27265637	27265637	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27265637delT								STIM2 (239829 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	27910304	27910304	+	IGR	DEL	C	-	-	rs151180118		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27910304delC								STIM2 (884496 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28587828	28587828	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28587828delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29009924	29009925	+	IGR	DEL	AT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29009924_29009925delAT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29229245	29229245	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29229245delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	30439498	30439498	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30439498delA								None (None upstream) : PCDH7 (282539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	30444672	30444673	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30444672_30444673delTG								None (None upstream) : PCDH7 (277364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32031338	32031338	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32031338delC								PCDH7 (882917 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32775099	32775105	+	IGR	DEL	CAGAATG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32775099_32775105delCAGAATG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32792806	32792809	+	IGR	DEL	TGTT	-	-	rs10570336		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32792806_32792809delTGTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33277945	33277952	+	IGR	DEL	ACACACAC	-	-	rs72339830		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33277945_33277952delACACACAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35432191	35432192	+	IGR	INS	-	TC	TC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35432191_35432192insTC								None (None upstream) : ARAP2 (517652 downstream)																																			---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36188285	36188285	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36188285delG	uc003gsq.1	-						ARAP2_uc003gsr.1_Intron	NM_015230	NP_056045			ArfGAP with RhoGAP domain, ankyrin repeat and PH						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	36542314	36542317	+	IGR	DEL	TGAT	-	-	rs141393751		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36542314_36542317delTGAT								MIR1255B-1 (114264 upstream) : KIAA1239 (704373 downstream)																																			---	---	---	---
TLR1	7096	broad.mit.edu	37	4	38807363	38807364	+	5'Flank	INS	-	T	T	rs147169812	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38807363_38807364insT	uc003gtl.2	-							NM_003263	NP_003254			toll-like receptor 1 precursor						cellular response to triacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|inflammatory response|innate immune response|macrophage activation|positive regulation of interleukin-6 biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	integral to plasma membrane|phagocytic vesicle membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	protein heterodimerization activity|transmembrane receptor activity			lung(2)|skin(2)|prostate(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	39803788	39803788	+	IGR	DEL	C	-	-	rs12511137		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39803788delC								UBE2K (19380 upstream) : PDS5A (20696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	40194206	40194207	+	IGR	INS	-	A	A	rs150858990	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40194206_40194207insA								N4BP2 (37189 upstream) : RHOH (4320 downstream)																																			---	---	---	---
RBM47	54502	broad.mit.edu	37	4	40568094	40568094	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40568094delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	42266715	42266715	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42266715delA								BEND4 (111820 upstream) : SHISA3 (133141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	45841278	45841278	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45841278delT								None (None upstream) : GABRG1 (196511 downstream)																																			---	---	---	---
GABRB1	2560	broad.mit.edu	37	4	47406506	47406507	+	Intron	INS	-	CACA	CACA	rs142486838	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47406506_47406507insCACA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	49248228	49248229	+	IGR	INS	-	A	A	rs71278346		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49248228_49248229insA								CWH43 (184135 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49653375	49653376	+	IGR	DEL	AT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49653375_49653376delAT								CWH43 (589282 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53175196	53175197	+	IGR	INS	-	T	T	rs77791484		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53175196_53175197insT								SPATA18 (211739 upstream) : USP46 (281932 downstream)																																			---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	55154269	55154269	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55154269delC	uc003han.3	+						PDGFRA_uc003haa.2_Intron	NM_006206	NP_006197			platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			---	---	---	---
PDCL2	132954	broad.mit.edu	37	4	56451691	56451692	+	Intron	INS	-	CA	CA	rs138999093	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56451691_56451692insCA	uc003hbb.2	-							NM_152401	NP_689614			phosducin-like 2												0	Lung NSC(11;0.00256)|Glioma(25;0.08)|all_epithelial(27;0.0863)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.69e-07)|Lung(4;1.03e-06)|Epithelial(7;0.00669)															---	---	---	---
CEP135	9662	broad.mit.edu	37	4	56890991	56890992	+	Intron	INS	-	T	T	rs113118558		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56890991_56890992insT	uc003hbi.2	+						CEP135_uc003hbj.2_Intron	NM_025009	NP_079285			centrosome protein 4						centriole replication|centriole-centriole cohesion|G2/M transition of mitotic cell cycle	centriole|cytosol	protein C-terminus binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
IGFBP7	3490	broad.mit.edu	37	4	57957326	57957327	+	Intron	DEL	CG	-	-	rs13128946	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57957326_57957327delCG	uc003hcn.2	-						IGFBP7_uc011cag.1_Intron	NM_001553	NP_001544			insulin-like growth factor binding protein 7						cell adhesion|negative regulation of cell proliferation|regulation of cell growth	extracellular space	insulin-like growth factor binding			lung(2)|central_nervous_system(1)	3	Glioma(25;0.08)|all_neural(26;0.181)				Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	60345749	60345750	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60345749_60345750delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61006350	61006351	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61006350_61006351insT								None (None upstream) : None (None downstream)																																			---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62092855	62092856	+	Intron	DEL	TT	-	-	rs74329640		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62092855_62092856delTT	uc003hcq.3	+						LPHN3_uc010ihg.1_Intron					RecName: Full=Latrophilin-3; AltName: Full=Calcium-independent alpha-latrotoxin receptor 3; AltName: Full=Lectomedin-3; Flags: Precursor;						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62444121	62444121	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62444121delA	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	62803119	62803119	+	Intron	DEL	T	-	-	rs33912206		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62803119delT	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hct.2_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	62980889	62980889	+	IGR	DEL	A	-	-	rs33949101		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62980889delA								LPHN3 (42722 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63132947	63132947	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63132947delA								LPHN3 (194780 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67525175	67525175	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67525175delA								MIR1269 (382529 upstream) : CENPC1 (812814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67682772	67682773	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67682772_67682773insT								MIR1269 (540126 upstream) : CENPC1 (655216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67748925	67748925	+	IGR	DEL	A	-	-	rs34762458		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67748925delA								MIR1269 (606279 upstream) : CENPC1 (589064 downstream)																																			---	---	---	---
STAP1	26228	broad.mit.edu	37	4	68449816	68449817	+	Intron	INS	-	AA	AA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68449816_68449817insAA	uc003hde.3	+						STAP1_uc003hdf.2_Intron	NM_012108	NP_036240			signal transducing adaptor family member 1						cellular membrane fusion|intracellular protein transport	cytoplasm					0																		---	---	---	---
UBA6	55236	broad.mit.edu	37	4	68498019	68498019	+	Intron	DEL	T	-	-	rs72185188		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68498019delT	uc003hdg.3	-							NM_018227	NP_060697			ubiquitin-activating enzyme E1-like 2						protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0																		---	---	---	---
TMPRSS11F	389208	broad.mit.edu	37	4	68921031	68921031	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68921031delA	uc003hdt.1	-						LOC550112_uc003hdl.3_Intron|uc011cak.1_Intron	NM_207407	NP_997290			transmembrane protease, serine 11F						proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	69368636	69368638	+	IGR	DEL	ATC	-	-	rs34266896		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69368636_69368638delATC								YTHDC1 (152812 upstream) : UGT2B15 (143678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	72742235	72742238	+	IGR	DEL	TCCT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72742235_72742238delTCCT								GC (72477 upstream) : NPFFR2 (155283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	72812913	72812916	+	IGR	DEL	TGTG	-	-	rs113784342		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72812913_72812916delTGTG								GC (143155 upstream) : NPFFR2 (84605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	73836939	73836940	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73836939_73836940insA								ADAMTS3 (402423 upstream) : COX18 (83476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	76325239	76325240	+	IGR	DEL	TA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76325239_76325240delTA								PARM1 (349916 upstream) : RCHY1 (79115 downstream)																																			---	---	---	---
CCDC158	339965	broad.mit.edu	37	4	77280250	77280251	+	Intron	DEL	TC	-	-	rs35311653		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77280250_77280251delTC	uc003hkb.3	-							NM_001042784	NP_001036249			coiled-coil domain containing 158											skin(3)|ovary(2)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	78036920	78036925	+	IGR	DEL	ACACAC	-	-	rs67154176		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78036920_78036925delACACAC								CCNI (39795 upstream) : CCNG2 (41432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	78277485	78277485	+	IGR	DEL	G	-	-	rs66735149		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78277485delG								CCNG2 (186275 upstream) : CXCL13 (155422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	79553399	79553402	+	IGR	DEL	TTCT	-	-	rs33991240		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79553399_79553402delTTCT								ANXA3 (21797 upstream) : BMP2K (144130 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	79943595	79943596	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79943595_79943596insA	uc003hlr.1	+											Homo sapiens full length insert cDNA clone YY75G10.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	80231202	80231202	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80231202delT								PAQR3 (370620 upstream) : NAA11 (7071 downstream)																																			---	---	---	---
ANTXR2	118429	broad.mit.edu	37	4	80832140	80832142	+	Intron	DEL	AAC	-	-	rs112051167		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80832140_80832142delAAC	uc003hly.3	-						ANTXR2_uc003hlx.1_Intron	NM_058172	NP_477520			anthrax toxin receptor 2 isoform 1							endoplasmic reticulum membrane|extracellular region|integral to membrane|plasma membrane	metal ion binding|protein binding|receptor activity			ovary(1)	1														Juvenile_Hyaline_Fibromatosis				---	---	---	---
Unknown	0	broad.mit.edu	37	4	81019888	81019891	+	IGR	DEL	GGAA	-	-	rs35134282		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81019888_81019891delGGAA								ANTXR2 (25411 upstream) : PRDM8 (85548 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	82409805	82409806	+	IGR	INS	-	TT	TT	rs142446219	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82409805_82409806insTT								RASGEF1B (16744 upstream) : HNRNPD (864661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	82589787	82589787	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82589787delA								RASGEF1B (196726 upstream) : HNRNPD (684680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	83167245	83167245	+	IGR	DEL	A	-	-	rs71666717		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83167245delA								RASGEF1B (774184 upstream) : HNRNPD (107222 downstream)																																			---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83773740	83773740	+	Intron	DEL	T	-	-	rs75606558		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83773740delT	uc003hnf.2	-						SEC31A_uc003hne.2_Intron|SEC31A_uc011ccl.1_Intron|SEC31A_uc003hnl.2_Intron|SEC31A_uc003hng.2_Intron|SEC31A_uc003hnh.2_Intron|SEC31A_uc003hni.2_Intron|SEC31A_uc003hnj.2_Intron|SEC31A_uc011ccm.1_Intron|SEC31A_uc011ccn.1_Intron|SEC31A_uc003hnk.2_Intron|SEC31A_uc003hnm.2_Intron|SEC31A_uc003hnn.1_Intron	NM_001077207	NP_001070675			SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)																---	---	---	---
LIN54	132660	broad.mit.edu	37	4	83885210	83885210	+	Intron	DEL	T	-	-	rs113845346		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83885210delT	uc003hnx.3	-						LIN54_uc003hnz.3_Intron|LIN54_uc003hny.3_Intron|LIN54_uc010ijt.2_Intron|LIN54_uc010iju.2_Intron|LIN54_uc010ijv.2_Intron	NM_194282	NP_919258			lin-54 homolog isoform a						cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Hepatocellular(203;0.114)																---	---	---	---
HPSE	10855	broad.mit.edu	37	4	84249896	84249907	+	Intron	DEL	GGGAAAGGCTTG	-	-	rs72079842		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84249896_84249907delGGGAAAGGCTTG	uc003hoj.3	-						HPSE_uc010ika.2_Intron|HPSE_uc011ccq.1_Intron|HPSE_uc011ccr.1_Intron|HPSE_uc011ccs.1_Intron|HPSE_uc011cct.1_Intron|HPSE_uc003hok.3_Intron	NM_001098540	NP_001092010			heparanase precursor						carbohydrate metabolic process|cell adhesion|proteoglycan metabolic process	extracellular region|lysosomal membrane|nucleus	beta-glucuronidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Heparin(DB01109)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	85488661	85488662	+	IGR	INS	-	A	A	rs71598405		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85488661_85488662insA								NKX6-1 (69274 upstream) : CDS1 (15395 downstream)																																			---	---	---	---
CDS1	1040	broad.mit.edu	37	4	85514659	85514660	+	Intron	INS	-	T	T	rs139601078	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85514659_85514660insT	uc011ccv.1	+							NM_001263	NP_001254			CDP-diacylglycerol synthase 1						signal transduction|visual perception	endoplasmic reticulum membrane|integral to membrane	diacylglycerol cholinephosphotransferase activity|phosphatidate cytidylyltransferase activity			large_intestine(2)|ovary(1)|breast(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85792040	85792040	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85792040delA	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)														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85806483	85806484	+	Intron	INS	-	TGTG	TGTG	rs149622391	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85806483_85806484insTGTG	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)														---	---	---	---
C4orf12	404201	broad.mit.edu	37	4	85896698	85896699	+	Intron	INS	-	CA	CA	rs142195208	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85896698_85896699insCA	uc003hph.2	+						C4orf12_uc003hpg.2_Intron	NR_015359				Homo sapiens C4ORF12 protein (C4ORF12) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	86351422	86351425	+	IGR	DEL	TTGG	-	-	rs113478640		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86351422_86351425delTTGG								C4orf12 (423254 upstream) : ARHGAP24 (44859 downstream)																																			---	---	---	---
ARHGAP24	83478	broad.mit.edu	37	4	86546851	86546851	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86546851delG	uc003hpk.2	+						ARHGAP24_uc003hpi.1_Intron|ARHGAP24_uc003hpj.2_Intron	NM_001025616	NP_001020787			Rho GTPase activating protein 24 isoform 1						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)														---	---	---	---
HSD17B13	345275	broad.mit.edu	37	4	88247006	88247008	+	5'Flank	DEL	TTG	-	-	rs113411868		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88247006_88247008delTTG	uc003hqo.2	-						HSD17B13_uc010ikk.2_5'Flank	NM_178135	NP_835236			hydroxysteroid (17-beta) dehydrogenase 13							extracellular region	binding|oxidoreductase activity				0		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.000308)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88780835	88780837	+	IGR	DEL	AAC	-	-	rs78775681		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88780835_88780837delAAC								MEPE (12893 upstream) : SPP1 (115965 downstream)																																			---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91176130	91176131	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91176130_91176131delAC	uc003hsv.3	+						FAM190A_uc003hsu.3_Intron|FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	92218535	92218536	+	Intron	DEL	TA	-	-	rs10573701		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92218535_92218536delTA	uc003hsv.3	+							NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94121717	94121718	+	Intron	INS	-	AAAC	AAAC	rs143243576	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94121717_94121718insAAAC	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	94291591	94291592	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94291591_94291592delCA	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	97688309	97688310	+	IGR	DEL	AT	-	-	rs33946251		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97688309_97688310delAT								PDHA2 (925685 upstream) : C4orf37 (791724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97693491	97693492	+	IGR	DEL	AC	-	-	rs149505894		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97693491_97693492delAC								PDHA2 (930867 upstream) : C4orf37 (786542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	99079364	99079365	+	IGR	INS	-	TC	TC	rs148827432	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99079364_99079365insTC								C4orf37 (14973 upstream) : RAP1GDS1 (103162 downstream)																																			---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102399384	102399385	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102399384_102399385insT	uc003hvx.3	+							NM_001083907	NP_001077376			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
SLC39A8	64116	broad.mit.edu	37	4	103188417	103188417	+	Intron	DEL	C	-	-	rs74650330		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103188417delC	uc003hwb.1	-						SLC39A8_uc011ceo.1_Intron|SLC39A8_uc003hwa.1_Intron|SLC39A8_uc003hwc.2_Intron	NM_022154	NP_071437			solute carrier family 39 (zinc transporter),							integral to membrane|organelle membrane|plasma membrane	zinc ion transmembrane transporter activity				0		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)														---	---	---	---
TACR3	6870	broad.mit.edu	37	4	104552026	104552027	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104552026_104552027delAC	uc003hxe.1	-							NM_001059	NP_001050			tachykinin receptor 3							integral to plasma membrane	tachykinin receptor activity			ovary(3)|lung(2)|breast(1)|skin(1)	7		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	105343455	105343456	+	IGR	INS	-	C	C	rs138052114	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105343455_105343456insC								TACR3 (702482 upstream) : CXXC4 (49889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	105823164	105823164	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105823164delT								CXXC4 (407106 upstream) : TET2 (244779 downstream)																																			---	---	---	---
TET2	54790	broad.mit.edu	37	4	106184186	106184188	+	Intron	DEL	AAA	-	-	rs71584294		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106184186_106184188delAAA	uc003hxk.2	+						TET2_uc011cez.1_Intron|TET2_uc003hxj.2_Intron	NM_001127208	NP_001120680			tet oncogene family member 2 isoform a						cell cycle|myeloid cell differentiation		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			haematopoietic_and_lymphoid_tissue(732)|pancreas(1)	733		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)				Mis N|F		MDS								---	---	---	---
PPA2	27068	broad.mit.edu	37	4	106317826	106317827	+	Intron	INS	-	G	G	rs144469298	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106317826_106317827insG	uc003hxl.2	-						PPA2_uc003hxm.2_Intron|PPA2_uc003hxn.2_Intron|PPA2_uc003hxo.2_Intron|PPA2_uc003hxp.2_Intron|PPA2_uc003hxq.2_Intron|PPA2_uc003hxr.2_Intron	NM_176869	NP_789845			inorganic pyrophosphatase 2 isoform 1 precursor						diphosphate metabolic process|tRNA aminoacylation for protein translation	mitochondrial matrix	inorganic diphosphatase activity|magnesium ion binding			pancreas(1)	1		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	109098850	109098851	+	IGR	INS	-	CA	CA	rs151020734		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109098850_109098851insCA								LEF1 (9272 upstream) : LOC285456 (360495 downstream)																																			---	---	---	---
RPL34	6164	broad.mit.edu	37	4	109545224	109545224	+	Intron	DEL	C	-	-	rs59330371		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109545224delC	uc003hyz.2	+						RPL34_uc003hza.2_Intron	NM_000995	NP_000986			ribosomal protein L34						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000286)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	110277209	110277210	+	Intron	DEL	CA	-	-	rs35812609		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110277209_110277210delCA	uc003hzi.1	-											Homo sapiens cDNA FLJ25407 fis, clone TST02904.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	111222580	111222580	+	IGR	DEL	C	-	-	rs34015583		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111222580delC								ELOVL6 (102760 upstream) : ENPEP (174649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111249132	111249132	+	IGR	DEL	G	-	-	rs35019526		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111249132delG								ELOVL6 (129312 upstream) : ENPEP (148097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111260224	111260225	+	IGR	INS	-	TT	TT	rs77074291		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111260224_111260225insTT								ELOVL6 (140404 upstream) : ENPEP (137004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111959399	111959400	+	IGR	DEL	AA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111959399_111959400delAA								MIR297 (177596 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111991873	111991874	+	IGR	DEL	GT	-	-	rs148372593		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111991873_111991874delGT								MIR297 (210070 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112741977	112741978	+	IGR	INS	-	A	A	rs145375097		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112741977_112741978insA								MIR297 (960174 upstream) : C4orf32 (324575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112797861	112797871	+	IGR	DEL	ATTGGATTTAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112797861_112797871delATTGGATTTAC								None (None upstream) : C4orf32 (268682 downstream)																																			---	---	---	---
CAMK2D	817	broad.mit.edu	37	4	114440116	114440116	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114440116delA	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	114448062	114448062	+	Intron	DEL	T	-	-	rs35641342		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114448062delT	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	114563893	114563893	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114563893delT	uc003ibi.2	-						CAMK2D_uc003ibj.2_Intron|CAMK2D_uc003ibk.2_Intron|CAMK2D_uc003ibo.3_Intron|CAMK2D_uc003ibm.2_Intron|CAMK2D_uc003ibn.2_Intron|CAMK2D_uc003ibl.2_Intron	NM_001221	NP_001212			calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|regulation of cell growth|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	116575161	116575161	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116575161delT								NDST4 (540129 upstream) : MIR1973 (645720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117232438	117232438	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117232438delA								MIR1973 (11514 upstream) : TRAM1L1 (772278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118480601	118480601	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118480601delT								TRAM1L1 (473865 upstream) : NDST3 (474172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118657898	118657899	+	IGR	INS	-	AACA	AACA	rs141140515	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118657898_118657899insAACA								TRAM1L1 (651162 upstream) : NDST3 (296874 downstream)																																			---	---	---	---
SEC24D	9871	broad.mit.edu	37	4	119749661	119749661	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119749661delT	uc003ici.3	-						SEC24D_uc003icj.3_Intron|SEC24D_uc003icl.2_Intron|SEC24D_uc010imz.1_Intron|SEC24D_uc011cgg.1_Intron	NM_014822	NP_055637			Sec24-related protein D						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0																		---	---	---	---
USP53	54532	broad.mit.edu	37	4	120208360	120208360	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120208360delT	uc003ics.3	+						USP53_uc003icr.3_Intron|USP53_uc003icu.3_Intron	NM_019050	NP_061923			ubiquitin specific protease 53						ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			ovary(1)|breast(1)|kidney(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	121851233	121851234	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121851233_121851234insA								PRDM5 (7220 upstream) : C4orf31 (105548 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	122194638	122194641	+	IGR	DEL	AGAA	-	-	rs10578617		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122194638_122194641delAGAA								TNIP3 (56856 upstream) : QRFPR (55156 downstream)																																			---	---	---	---
ADAD1	132612	broad.mit.edu	37	4	123297125	123297126	+	5'Flank	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123297125_123297126insA	uc003ieo.2	+							NM_139243	NP_640336			adenosine deaminase domain containing 1						multicellular organismal development|RNA processing	nucleus	adenosine deaminase activity|double-stranded RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	123391678	123391678	+	IGR	DEL	A	-	-	rs4833827	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123391678delA								IL2 (14028 upstream) : IL21 (142105 downstream)																																			---	---	---	---
SPATA5	166378	broad.mit.edu	37	4	123897704	123897704	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123897704delA	uc003iez.3	+						SPATA5_uc003iey.2_Intron	NM_145207	NP_660208			spermatogenesis associated 5						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	124425732	124425733	+	IGR	INS	-	GT	GT	rs146974629	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124425732_124425733insGT								SPRY1 (100825 upstream) : LOC285419 (145689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	124562154	124562161	+	IGR	DEL	GGAAGGAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124562154_124562161delGGAAGGAA								SPRY1 (237247 upstream) : LOC285419 (9261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126958016	126958017	+	IGR	INS	-	GGAA	GGAA	rs144099055	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126958016_126958017insGGAA								MIR2054 (529554 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	128173877	128173878	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128173877_128173878delTT								None (None upstream) : INTU (380242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	129642394	129642395	+	IGR	DEL	TT	-	-	rs68093533		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129642394_129642395delTT								PGRMC2 (433446 upstream) : PHF17 (88384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	130995935	130995935	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130995935delA								C4orf33 (962093 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134191200	134191200	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134191200delA								PCDH10 (78469 upstream) : PABPC4L (926291 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134374160	134374161	+	IGR	INS	-	CA	CA	rs150260013	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134374160_134374161insCA								PCDH10 (261429 upstream) : PABPC4L (743330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136643416	136643417	+	IGR	INS	-	TG	TG	rs139799828	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136643416_136643417insTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	137265484	137265487	+	IGR	DEL	AAAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137265484_137265487delAAAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138727873	138727874	+	IGR	DEL	CA	-	-	rs72208139		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138727873_138727874delCA								PCDH18 (274225 upstream) : SLC7A11 (357374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138970810	138970827	+	Intron	DEL	TAACCCTTCCTGCAAGTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138970810_138970827delTAACCCTTCCTGCAAGTG	uc003ihh.2	-											Homo sapiens hypothetical protein LOC641365, mRNA (cDNA clone IMAGE:5273182).																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	139974934	139974934	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139974934delG								CCRN4L (7843 upstream) : ELF2 (3937 downstream)																																			---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140896604	140896605	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140896604_140896605delCA	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187			mastermind-like 3						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
TBC1D9	23158	broad.mit.edu	37	4	141607093	141607095	+	Intron	DEL	AAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141607093_141607095delAAC	uc010ioj.2	-							NM_015130	NP_055945			TBC1 domain family, member 9 (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)																---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143227383	143227385	+	Intron	DEL	TTT	-	-	rs71586277		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143227383_143227385delTTT	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.1_5'Flank|INPP4B_uc011cho.1_Intron|INPP4B_uc011chp.1_5'Flank	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143465547	143465547	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143465547delG	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	145201257	145201257	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145201257delT								GYPA (139353 upstream) : HHIP (365916 downstream)																																			---	---	---	---
SLC10A7	84068	broad.mit.edu	37	4	147387546	147387546	+	Intron	DEL	C	-	-	rs5862758		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147387546delC	uc010ioz.2	-						SLC10A7_uc003ikr.2_Intron|SLC10A7_uc010ipa.2_Intron|SLC10A7_uc003iks.2_Intron|SLC10A7_uc003ikt.2_Intron	NM_001029998	NP_001025169			solute carrier family 10 (sodium/bile acid							integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)																	---	---	---	---
TTC29	83894	broad.mit.edu	37	4	147679077	147679078	+	Intron	INS	-	A	A	rs140669655	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147679077_147679078insA	uc003ikw.3	-						TTC29_uc010ipc.2_Intron|TTC29_uc003ikx.3_Intron|TTC29_uc010ipd.1_Intron	NM_031956	NP_114162			tetratricopeptide repeat domain 29								binding				0	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	147959351	147959354	+	IGR	DEL	AATA	-	-	rs67334132		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147959351_147959354delAATA								TTC29 (92317 upstream) : MIR548G (306427 downstream)																																			---	---	---	---
NR3C2	4306	broad.mit.edu	37	4	149062569	149062570	+	Intron	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149062569_149062570delTC	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	149728799	149728799	+	IGR	DEL	A	-	-	rs55707547		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149728799delA								NR3C2 (365156 upstream) : None (None downstream)																																			---	---	---	---
FAM160A1	729830	broad.mit.edu	37	4	152524465	152524465	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152524465delA	uc003imj.2	+							NM_001109977	NP_001103447			hypothetical protein LOC729830												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	152876910	152876911	+	5'Flank	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152876910_152876911insA	uc003imn.2	+						uc003imo.2_5'Flank					Homo sapiens cDNA clone IMAGE:5266192.																														---	---	---	---
FBXW7	55294	broad.mit.edu	37	4	153346798	153346799	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153346798_153346799insA	uc003ims.2	-						FBXW7_uc011cii.1_Intron|FBXW7_uc003imt.2_Intron|FBXW7_uc003imu.2_Intron	NM_033632	NP_361014			F-box and WD repeat domain containing 7 isoform						interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)						Mis|N|D|F		colorectal|endometrial|T-ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	4	155844706	155844706	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155844706delT								RBM46 (94742 upstream) : NPY2R (285075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	161018338	161018339	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161018338_161018339insA								RAPGEF2 (737039 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	161474584	161474587	+	IGR	DEL	GTGA	-	-	rs72387426		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161474584_161474587delGTGA								None (None upstream) : FSTL5 (830464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	161730764	161730765	+	IGR	DEL	AC	-	-	rs33963527		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161730764_161730765delAC								None (None upstream) : FSTL5 (574286 downstream)																																			---	---	---	---
FSTL5	56884	broad.mit.edu	37	4	162900216	162900216	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162900216delA	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	163897371	163897371	+	IGR	DEL	T	-	-	rs113732920		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163897371delT								FSTL5 (812185 upstream) : NAF1 (150489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	164231863	164231864	+	IGR	INS	-	TGTT	TGTT	rs148846621	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164231863_164231864insTGTT								NAF1 (143790 upstream) : NPY1R (13253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	164411815	164411815	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164411815delT								TKTL2 (16768 upstream) : C4orf43 (3858 downstream)																																			---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166863428	166863428	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166863428delT	uc003irh.1	+						TLL1_uc011cjn.1_Intron|TLL1_uc011cjo.1_Intron	NM_012464	NP_036596			tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	167155245	167155245	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167155245delG								TLL1 (130252 upstream) : SPOCK3 (499291 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	168852079	168852080	+	IGR	INS	-	A	A	rs143401907	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168852079_168852080insA								SPOCK3 (696338 upstream) : ANXA10 (161627 downstream)																																			---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169233176	169233176	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169233176delA	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)														---	---	---	---
SH3RF1	57630	broad.mit.edu	37	4	170182756	170182756	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170182756delA	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	170529267	170529268	+	Intron	INS	-	AC	AC	rs149552237	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170529267_170529268insAC	uc003isb.1	-						NEK1_uc003isc.1_Intron|NEK1_uc003isd.1_Intron|NEK1_uc003ise.1_Intron|NEK1_uc003isf.1_Intron	NM_012224	NP_036356			NIMA-related kinase 1						cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	170711784	170711785	+	IGR	INS	-	G	G	rs138975597	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170711784_170711785insG								C4orf27 (32691 upstream) : MFAP3L (195965 downstream)																																			---	---	---	---
AADAT	51166	broad.mit.edu	37	4	170987332	170987332	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170987332delT	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	171849178	171849179	+	IGR	DEL	GT	-	-	rs113865883	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171849178_171849179delGT								AADAT (837806 upstream) : GALNTL6 (885396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	172203798	172203798	+	IGR	DEL	C	-	-	rs10006806		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172203798delC								None (None upstream) : GALNTL6 (530777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	172306131	172306133	+	IGR	DEL	TCT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172306131_172306133delTCT								None (None upstream) : GALNTL6 (428442 downstream)																																			---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173631412	173631412	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173631412delT	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	174039608	174039608	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174039608delA								GALNTL6 (78052 upstream) : GALNT7 (50296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	175091999	175092000	+	Intron	DEL	AC	-	-	rs150663766		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175091999_175092000delAC	uc003ito.1	-											Homo sapiens cDNA FLJ43267 fis, clone IMR322007704.																														---	---	---	---
ADAM29	11086	broad.mit.edu	37	4	175852967	175852968	+	Intron	INS	-	CACA	CACA	rs138753312	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175852967_175852968insCACA	uc003iuc.2	+						ADAM29_uc003iud.2_Intron|ADAM29_uc010irr.2_Intron|ADAM29_uc011cki.1_Intron	NM_014269	NP_055084			ADAM metallopeptidase domain 29 preproprotein						proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)														---	---	---	---
GPM6A	2823	broad.mit.edu	37	4	176782136	176782136	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176782136delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	177344362	177344363	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177344362_177344363delTG								SPCS3 (90968 upstream) : VEGFC (260328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	179596856	179596857	+	IGR	INS	-	A	A	rs80077513		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179596856_179596857insA								LOC285501 (684953 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	179696074	179696074	+	IGR	DEL	C	-	-	rs34839229		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179696074delC								LOC285501 (784171 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180212026	180212027	+	IGR	INS	-	T	T	rs139997668	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180212026_180212027insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180712457	180712462	+	IGR	DEL	TGTGTG	-	-	rs72259963		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180712457_180712462delTGTGTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181207078	181207079	+	IGR	DEL	GT	-	-	rs67792079		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181207078_181207079delGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181351718	181351718	+	IGR	DEL	T	-	-	rs67049278		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181351718delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181642807	181642812	+	IGR	DEL	GTGTGG	-	-	rs113334076		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181642807_181642812delGTGTGG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181930590	181930591	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181930590_181930591insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	182707851	182707851	+	IGR	DEL	T	-	-	rs146629166		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182707851delT								None (None upstream) : MGC45800 (352308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	183022224	183022224	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183022224delA								None (None upstream) : MGC45800 (37935 downstream)																																			---	---	---	---
WWC2	80014	broad.mit.edu	37	4	184056533	184056534	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184056533_184056534insT	uc010irx.2	+							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)														---	---	---	---
ENPP6	133121	broad.mit.edu	37	4	185141166	185141167	+	5'Flank	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185141166_185141167insA	uc003iwc.2	-							NM_153343	NP_699174			ectonucleotide pyrophosphatase/phosphodiesterase						lipid catabolic process	extracellular region|integral to membrane|plasma membrane				central_nervous_system(1)	1		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	185214013	185214014	+	IGR	INS	-	GA	GA	rs138204534	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185214013_185214014insGA								ENPP6 (74899 upstream) : IRF2 (94864 downstream)																																			---	---	---	---
IRF2	3660	broad.mit.edu	37	4	185345218	185345219	+	Intron	DEL	AC	-	-	rs5864888		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185345218_185345219delAC	uc003iwf.3	-							NM_002199	NP_002190			interferon regulatory factor 2						blood coagulation|cell proliferation|interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	focal adhesion|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)														---	---	---	---
ACSL1	2180	broad.mit.edu	37	4	185712002	185712003	+	Intron	INS	-	AGC	AGC	rs145180185	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185712002_185712003insAGC	uc003iww.2	-						ACSL1_uc011ckm.1_Intron|ACSL1_uc003iwt.1_Intron|ACSL1_uc003iwu.1_Intron|ACSL1_uc011ckn.1_Intron|ACSL1_uc003iwv.1_Intron	NM_001995	NP_001986			acyl-CoA synthetase long-chain family member 1						digestion|fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|regulation of fatty acid oxidation|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			ovary(2)	2		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	186933976	186933977	+	IGR	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186933976_186933977delCA								SORBS2 (56106 upstream) : TLR3 (56332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	187396516	187396517	+	Intron	INS	-	AA	AA	rs75413796	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187396516_187396517insAA	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	187556464	187556465	+	Intron	INS	-	A	A	rs145871179	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187556464_187556465insA	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	187663674	187663674	+	IGR	DEL	T	-	-	rs67228121		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187663674delT								FAT1 (15824 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	188928313	188928313	+	IGR	DEL	A	-	-	rs10717034		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188928313delA								ZFP42 (2114 upstream) : TRIML2 (84114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190547515	190547516	+	IGR	INS	-	A	A	rs111951194		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190547515_190547516insA								None (None upstream) : FRG1 (314458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190667662	190667663	+	IGR	INS	-	A	A	rs139762060		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190667662_190667663insA								None (None upstream) : FRG1 (194311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	191033876	191033879	+	IGR	DEL	ATTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:191033876_191033879delATTG								LOC653545 (23700 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	576543	576543	+	IGR	DEL	C	-	-	rs67676324		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:576543delC								SLC9A3 (51994 upstream) : CEP72 (35862 downstream)																																			---	---	---	---
ZDHHC11	79844	broad.mit.edu	37	5	803135	803136	+	Intron	INS	-	A	A	rs150492590		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:803135_803136insA	uc011cma.1	-						ZDHHC11_uc010itc.2_Intron|ZDHHC11_uc003jbj.2_Intron	NM_024786	NP_079062			zinc finger, DHHC-type containing 11							integral to membrane	acyltransferase activity|zinc ion binding			skin(1)|pancreas(1)	2			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)															---	---	---	---
SLC6A3	6531	broad.mit.edu	37	5	1404032	1404033	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1404032_1404033delAC	uc003jck.2	-							NM_001044	NP_001035			solute carrier family 6 (neurotransmitter						cell death|neurotransmitter biosynthetic process	axon|cytoplasm|integral to plasma membrane|neuronal cell body				ovary(3)|breast(2)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amphetamine(DB00182)|Benztropine(DB00245)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Duloxetine(DB00476)|Fencamfamine(DB01463)|Mazindol(DB00579)|Methylphenidate(DB00422)|Modafinil(DB00745)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	2797633	2797633	+	IGR	DEL	T	-	-	rs55664037		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2797633delT								C5orf38 (42121 upstream) : IRX1 (798535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3249230	3249231	+	IGR	INS	-	T	T	rs147728881	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3249230_3249231insT								C5orf38 (493718 upstream) : IRX1 (346937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3323990	3323994	+	IGR	DEL	GTATC	-	-	rs148317105	by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3323990_3323994delGTATC								C5orf38 (568478 upstream) : IRX1 (272174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3382206	3382209	+	IGR	DEL	ACAA	-	-	rs66474822		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3382206_3382209delACAA								C5orf38 (626694 upstream) : IRX1 (213959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4766779	4766782	+	IGR	DEL	TGTG	-	-	rs71602183		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4766779_4766782delTGTG								None (None upstream) : LOC340094 (267690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5613293	5613294	+	IGR	INS	-	T	T	rs113895359		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5613293_5613294insT								KIAA0947 (122956 upstream) : FLJ33360 (697260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5629314	5629314	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5629314delG								KIAA0947 (138977 upstream) : FLJ33360 (681240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6185140	6185141	+	IGR	INS	-	TT	TT	rs71604173		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6185140_6185141insTT								KIAA0947 (694803 upstream) : FLJ33360 (125413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6571881	6571884	+	IGR	DEL	GAAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6571881_6571884delGAAG								UBE2QL1 (79176 upstream) : LOC255167 (10403 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6688695	6688696	+	IGR	DEL	TG	-	-	rs149598038		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6688695_6688696delTG								SRD5A1 (19022 upstream) : PAPD7 (26022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6891625	6891627	+	IGR	DEL	GAG	-	-	rs72262367		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6891625_6891627delGAG								PAPD7 (134464 upstream) : ADCY2 (504716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8038598	8038598	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8038598delT								MTRR (137365 upstream) : SEMA5A (996540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8062389	8062389	+	IGR	DEL	C	-	-	rs113943169		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8062389delC								MTRR (161156 upstream) : SEMA5A (972749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8451035	8451036	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8451035_8451036insT	uc003jeh.1	-											Homo sapiens cDNA clone IMAGE:5297486.																														---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9083699	9083702	+	Intron	DEL	CATC	-	-	rs78165962	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9083699_9083702delCATC	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9143066	9143069	+	Intron	DEL	ACAA	-	-	rs149901187		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9143066_9143069delACAA	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11036540	11036540	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11036540delT	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	11410987	11410987	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11410987delT	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	13389892	13389892	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13389892delA								None (None upstream) : DNAH5 (300545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13579918	13579918	+	IGR	DEL	C	-	-	rs233382		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13579918delC								None (None upstream) : DNAH5 (110519 downstream)																																			---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14275165	14275166	+	Intron	DEL	CG	-	-	rs74745926	byFrequency;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14275165_14275166delCG	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)																	---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15541160	15541161	+	Intron	DEL	TG	-	-	rs113578475		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15541160_15541161delTG	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	15760157	15760157	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15760157delT	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
MARCH11	441061	broad.mit.edu	37	5	16098877	16098877	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16098877delA	uc003jfo.2	-							NM_001102562	NP_001096032			membrane-associated ring finger (C3HC4) 11							cytoplasmic vesicle membrane|integral to membrane	ligase activity|zinc ion binding				0																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16792238	16792249	+	Intron	DEL	ACACAGAGAGAG	-	-	rs56343367	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16792238_16792249delACACAGAGAGAG	uc003jft.3	-						MYO10_uc003jfu.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	17099948	17099948	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17099948delT								MYO10 (163563 upstream) : LOC285696 (30189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17347808	17347809	+	IGR	DEL	AG	-	-	rs111593511		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17347808_17347809delAG								BASP1 (70873 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17381801	17381802	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17381801_17381802insA	uc003jga.2	-											Homo sapiens hypothetical gene supported by BC052942, mRNA (cDNA clone IMAGE:5268622).																														---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21513957	21513957	+	Intron	DEL	A	-	-	rs67316443		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21513957delA	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21539615	21539616	+	Intron	INS	-	TA	TA	rs143282782	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21539615_21539616insTA	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21556266	21556267	+	Intron	INS	-	A	A	rs141511148	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21556266_21556267insA	uc003jgh.3	+							NR_027026				Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21558318	21558322	+	Intron	DEL	GTTTA	-	-	rs139527968		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21558318_21558322delGTTTA	uc003jgh.3	+							NR_027026				Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21564551	21564554	+	Intron	DEL	AAAA	-	-	rs71706943		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21564551_21564554delAAAA	uc003jgh.3	+							NR_027026				Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21568113	21568114	+	Intron	INS	-	A	A	rs141608727	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21568113_21568114insA	uc003jgh.3	+							NR_027026				Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0																		---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22020664	22020664	+	Intron	DEL	A	-	-	rs113531853		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22020664delA	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron	NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22064098	22064099	+	Intron	DEL	AC	-	-	rs141174550		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22064098_22064099delAC	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron	NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22192041	22192041	+	Intron	DEL	T	-	-	rs67747789		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22192041delT	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron	NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
PRDM9	56979	broad.mit.edu	37	5	23514144	23514144	+	Intron	DEL	T	-	-	rs138160131	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23514144delT	uc003jgo.2	+							NM_020227	NP_064612			PR domain containing 9						meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6															HNSCC(3;0.000094)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23717343	23717347	+	IGR	DEL	AAAAG	-	-	rs72429036		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23717343_23717347delAAAAG								PRDM9 (188639 upstream) : CDH10 (769863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24037339	24037340	+	Intron	INS	-	T	T	rs148904072	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24037339_24037340insT	uc003jgq.1	+											Homo sapiens cDNA FLJ34836 fis, clone NT2NE2010400.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	24064420	24064421	+	Intron	INS	-	TG	TG	rs139050779	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24064420_24064421insTG	uc003jgq.1	+											Homo sapiens cDNA FLJ34836 fis, clone NT2NE2010400.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	27245412	27245413	+	IGR	INS	-	C	C	rs139109961	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27245412_27245413insC								CDH9 (206723 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28558279	28558280	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28558279_28558280delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29429286	29429287	+	IGR	INS	-	GGTA	GGTA	rs146728210	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29429286_29429287insGGTA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30265528	30265531	+	IGR	DEL	GAAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30265528_30265531delGAAA								None (None upstream) : CDH6 (928265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30898446	30898446	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30898446delG								None (None upstream) : CDH6 (295350 downstream)																																			---	---	---	---
RNASEN	29102	broad.mit.edu	37	5	31518248	31518250	+	Intron	DEL	ACA	-	-	rs148508712		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31518248_31518250delACA	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																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31908815	31908825	+	Intron	DEL	CCCCTTGCAAT	-	-	rs112636797		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31908815_31908825delCCCCTTGCAAT	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																		---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33545026	33545026	+	Intron	DEL	A	-	-	rs146911612		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33545026delA	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	34109932	34109934	+	IGR	DEL	TGT	-	-	rs78871010		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34109932_34109934delTGT								C1QTNF3 (66615 upstream) : RAI14 (546499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	36491942	36491942	+	IGR	DEL	A	-	-	rs76315388		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36491942delA								RANBP3L (189931 upstream) : SLC1A3 (114515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	38023607	38023608	+	IGR	INS	-	TG	TG	rs137954342	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38023607_38023608insTG								GDNF (183825 upstream) : EGFLAM (234925 downstream)																																			---	---	---	---
EGFLAM	133584	broad.mit.edu	37	5	38379931	38379931	+	Intron	DEL	A	-	-	rs34833258		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38379931delA	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron	NM_152403	NP_689616			EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)																	---	---	---	---
EGFLAM	133584	broad.mit.edu	37	5	38450926	38450926	+	Intron	DEL	T	-	-	rs113724457		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38450926delT	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	38661805	38661805	+	Intron	DEL	A	-	-	rs77509272		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38661805delA	uc003jlj.2	+											Homo sapiens cDNA clone IMAGE:4829282.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	38815863	38815864	+	Intron	DEL	CA	-	-	rs145433189		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38815863_38815864delCA	uc003jlk.1	-											full-length cDNA clone CS0DI053YO12 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
FYB	2533	broad.mit.edu	37	5	39115200	39115201	+	Intron	INS	-	T	T	rs10652993		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39115200_39115201insT	uc003jls.2	-						FYB_uc003jlt.2_Intron|FYB_uc003jlu.2_Intron|FYB_uc011cpl.1_Intron	NM_199335	NP_955367			FYN binding protein (FYB-120/130) isoform 2						cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	39494921	39494921	+	IGR	DEL	C	-	-	rs35768336		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39494921delC								DAB2 (69586 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40407992	40407993	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40407992_40407993insA								DAB2 (982657 upstream) : PTGER4 (272039 downstream)																																			---	---	---	---
PRKAA1	5562	broad.mit.edu	37	5	40795111	40795112	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40795111_40795112delAC	uc003jmc.2	-						PRKAA1_uc003jmb.2_Intron	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)													---	---	---	---
PLCXD3	345557	broad.mit.edu	37	5	41315517	41315517	+	Intron	DEL	A	-	-	rs71873562		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41315517delA	uc003jmm.1	-							NM_001005473	NP_001005473			phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6																		---	---	---	---
PLCXD3	345557	broad.mit.edu	37	5	41375263	41375264	+	Intron	INS	-	AG	AG	rs147961836	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41375263_41375264insAG	uc003jmm.1	-							NM_001005473	NP_001005473			phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6																		---	---	---	---
MGC42105	167359	broad.mit.edu	37	5	43248784	43248784	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43248784delC	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																		---	---	---	---
PAIP1	10605	broad.mit.edu	37	5	43526908	43526909	+	3'UTR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43526908_43526909insT	uc003job.2	-	11					PAIP1_uc003joa.2_3'UTR|PAIP1_uc010ivp.2_3'UTR|PAIP1_uc010ivo.2_RNA|PAIP1_uc003joc.2_3'UTR	NM_006451	NP_006442			poly(A) binding protein interacting protein 1						mRNA stabilization|nuclear-transcribed mRNA poly(A) tail shortening|translational initiation	cytosol	protein binding|RNA binding|translation activator activity			ovary(1)	1	Lung NSC(6;2.07e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	45740596	45740597	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45740596_45740597insT								HCN1 (44376 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	49616972	49616972	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49616972delA								None (None upstream) : EMB (75061 downstream)																																			---	---	---	---
PARP8	79668	broad.mit.edu	37	5	50001616	50001616	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50001616delA	uc003jon.3	+						PARP8_uc011cpz.1_Intron|PARP8_uc003joo.2_Intron|PARP8_uc003jop.2_Intron	NM_024615	NP_078891			poly (ADP-ribose) polymerase family, member 8							intracellular	NAD+ ADP-ribosyltransferase activity			lung(3)|large_intestine(1)|ovary(1)	5		Lung NSC(810;0.0305)|Breast(144;0.222)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	51578064	51578064	+	IGR	DEL	T	-	-	rs36035659		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51578064delT								ISL1 (887507 upstream) : ITGA1 (505710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	52823445	52823446	+	IGR	INS	-	TT	TT	rs142440818	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52823445_52823446insTT								FST (41543 upstream) : NDUFS4 (33019 downstream)																																			---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53511463	53511463	+	Intron	DEL	A	-	-	rs143565963		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53511463delA	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	53796047	53796047	+	IGR	DEL	G	-	-	rs35552845		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53796047delG								HSPB3 (43840 upstream) : SNX18 (17542 downstream)																																			---	---	---	---
DHX29	54505	broad.mit.edu	37	5	54576891	54576892	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54576891_54576892delAC	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)																---	---	---	---
GPBP1	65056	broad.mit.edu	37	5	56482058	56482059	+	Intron	INS	-	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56482058_56482059insC	uc003jrh.3	+						GPBP1_uc010iwg.2_Intron|GPBP1_uc003jri.3_Intron|GPBP1_uc003jrj.3_Intron	NM_022913	NP_075064			GC-rich promoter binding protein 1 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			large_intestine(1)|central_nervous_system(1)	2		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	57687752	57687753	+	IGR	INS	-	TTGTG	TTGTG	rs146824008	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57687752_57687753insTTGTG								ACTBL2 (909116 upstream) : PLK2 (62059 downstream)																																			---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59295984	59295984	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59295984delG	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron|PDE4D_uc003jse.1_Intron	NM_006203	NP_006194			phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59302137	59302137	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59302137delT	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron|PDE4D_uc003jse.1_Intron	NM_006203	NP_006194			phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59375138	59375139	+	Intron	INS	-	G	G	rs146249770	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59375138_59375139insG	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron|PDE4D_uc003jse.1_Intron	NM_006203	NP_006194			phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
ERCC8	1161	broad.mit.edu	37	5	60229766	60229767	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60229766_60229767delAC	uc003jsm.3	-						ERCC8_uc003jsl.3_Intron|ERCC8_uc011cqp.1_Intron|ERCC8_uc003jsn.3_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					---	---	---	---
IPO11	51194	broad.mit.edu	37	5	61753141	61753141	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61753141delC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	61945016	61945017	+	IGR	INS	-	AC	AC	rs146735357	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61945016_61945017insAC								IPO11 (20601 upstream) : ISCA1P1 (126185 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	63048824	63048825	+	IGR	DEL	GA	-	-	rs147418466		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63048824_63048825delGA								ISCA1P1 (975654 upstream) : HTR1A (207454 downstream)																																			---	---	---	---
RGS7BP	401190	broad.mit.edu	37	5	63872912	63872912	+	Intron	DEL	A	-	-	rs34745275		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63872912delA	uc003jtj.2	+						RGS7BP_uc011cqu.1_Intron	NM_001029875	NP_001025046			regulator of G-protein signaling 7 binding						negative regulation of signal transduction	cytoplasm|nucleus|plasma membrane					0		Lung NSC(810;0.000518)|Prostate(74;0.0435)|Ovarian(174;0.186)		Lung(70;0.147)														---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64570535	64570536	+	Intron	DEL	AG	-	-	rs34343508		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64570535_64570536delAG	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)														---	---	---	---
MAST4	375449	broad.mit.edu	37	5	65993849	65993850	+	Intron	INS	-	T	T	rs151274845	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65993849_65993850insT	uc003jur.3	+						MAST4_uc010iwz.2_Intron	NM_198828	NP_942123			microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66122494	66122495	+	5'Flank	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66122494_66122495insG	uc003jut.1	+						MAST4_uc003jur.3_Intron|MAST4_uc010iwz.2_Intron|MAST4_uc003jus.2_5'Flank	NM_015183	NP_055998			microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66290309	66290312	+	Intron	DEL	ATTT	-	-	rs3073600		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66290309_66290312delATTT	uc003jut.1	+						MAST4_uc003jus.2_Intron|MAST4_uc003juu.1_Intron|MAST4_uc011cra.1_Intron	NM_015183	NP_055998			microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	66635457	66635458	+	IGR	INS	-	CTTT	CTTT	rs150933394	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66635457_66635458insCTTT								CD180 (142840 upstream) : PIK3R1 (876146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67224857	67224857	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67224857delC								CD180 (732240 upstream) : PIK3R1 (286747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67639812	67639812	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67639812delG								PIK3R1 (42165 upstream) : SLC30A5 (750006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	68131146	68131146	+	IGR	DEL	G	-	-	rs34516107		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68131146delG								PIK3R1 (533499 upstream) : SLC30A5 (258672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	68305234	68305234	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68305234delT	uc003jvf.1	-											Homo sapiens cDNA FLJ46633 fis, clone TRACH2025705.																														---	---	---	---
MRPS27	23107	broad.mit.edu	37	5	71536388	71536389	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71536388_71536389insT	uc003kbz.3	-						MRPS27_uc003kca.3_Intron|MRPS27_uc011cse.1_Intron|MRPS27_uc010iza.2_Intron|MRPS27_uc010iyz.1_5'Flank	NM_015084	NP_055899			mitochondrial ribosomal protein S27							mitochondrion|ribosome					0		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-53)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	72880790	72880791	+	IGR	INS	-	T	T	rs11960117	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72880790_72880791insT								UTP15 (2996 upstream) : RGNEF (41192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73278607	73278608	+	IGR	INS	-	TG	TG	rs144779040	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73278607_73278608insTG								RGNEF (41194 upstream) : ENC1 (644627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73606074	73606074	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73606074delT								RGNEF (368661 upstream) : ENC1 (317161 downstream)																																			---	---	---	---
HEXB	3074	broad.mit.edu	37	5	73966295	73966295	+	Intron	DEL	C	-	-	rs113036475		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73966295delC	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	74365101	74365101	+	IGR	DEL	T	-	-	rs35258769		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74365101delT								GCNT4 (38377 upstream) : ANKRD31 (77961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	74436087	74436092	+	IGR	DEL	GGAAGG	-	-	rs56007035		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74436087_74436092delGGAAGG								GCNT4 (109363 upstream) : ANKRD31 (6970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	75348938	75348938	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75348938delA								POC5 (335625 upstream) : SV2C (30367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	76234293	76234294	+	IGR	DEL	AG	-	-	rs72097702		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76234293_76234294delAG								S100Z (17238 upstream) : CRHBP (14386 downstream)																																			---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76662985	76662986	+	Intron	INS	-	AG	AG	rs151326603	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76662985_76662986insAG	uc003kfa.2	+						PDE8B_uc003kfb.2_Intron|PDE8B_uc003kfc.2_Intron|PDE8B_uc003kfd.2_Intron|PDE8B_uc003kfe.2_Intron	NM_003719	NP_003710			phosphodiesterase 8B isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)														---	---	---	---
CMYA5	202333	broad.mit.edu	37	5	79064585	79064586	+	Intron	INS	-	T	T	rs145434755	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79064585_79064586insT	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	79612788	79612788	+	IGR	DEL	T	-	-	rs34998842		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79612788delT								LOC644936 (16491 upstream) : SPZ1 (3002 downstream)																																			---	---	---	---
RASGRF2	5924	broad.mit.edu	37	5	80270495	80270495	+	Intron	DEL	T	-	-	rs35446479		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80270495delT	uc003kha.1	+						RASGRF2_uc011ctn.1_Intron	NM_006909	NP_008840			Ras protein-specific guanine						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1)	12		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)														---	---	---	---
SSBP2	23635	broad.mit.edu	37	5	80965789	80965790	+	Intron	DEL	AG	-	-	rs34039360		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80965789_80965790delAG	uc003kho.2	-						SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578			single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)														---	---	---	---
EDIL3	10085	broad.mit.edu	37	5	83356437	83356437	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83356437delA	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	84564393	84564394	+	IGR	DEL	TG	-	-	rs111637119		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84564393_84564394delTG								EDIL3 (883782 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	85082369	85082370	+	IGR	INS	-	TT	TT	rs71607766		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85082369_85082370insTT								None (None upstream) : NBPF22P (495892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	85854454	85854455	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85854454_85854455insA								NBPF22P (261092 upstream) : COX7C (59329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86082514	86082543	+	IGR	DEL	ACACACACACACACACACACACACACACAC	-	-	rs148540710		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86082514_86082543delACACACACACACACACACACACACACACAC								COX7C (165933 upstream) : RASA1 (481608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86211873	86211873	+	IGR	DEL	G	-	-	rs34441366		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86211873delG								COX7C (295292 upstream) : RASA1 (352278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86475192	86475193	+	Intron	DEL	GA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86475192_86475193delGA	uc003kit.2	+											Homo sapiens cDNA clone IMAGE:5444809, **** WARNING: chimeric clone ****.																														---	---	---	---
POLR3G	10622	broad.mit.edu	37	5	89803177	89803177	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89803177delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	89833002	89833003	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89833002_89833003insA								LYSMD3 (7601 upstream) : GPR98 (21614 downstream)																																			---	---	---	---
GPR98	84059	broad.mit.edu	37	5	89922415	89922415	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89922415delA	uc003kju.2	+						GPR98_uc003kjt.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	89942593	89942593	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89942593delT	uc003kju.2	+						GPR98_uc003kjt.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90173402	90173403	+	Intron	INS	-	TT	TT	rs72003963		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90173402_90173403insTT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	90475765	90475772	+	IGR	DEL	GAAGGAAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90475765_90475772delGAAGGAAG								GPR98 (15733 upstream) : ARRDC3 (188769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	90871773	90871774	+	IGR	INS	-	A	A	rs113522796		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90871773_90871774insA								LOC100129716 (155242 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	92398241	92398241	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92398241delA								None (None upstream) : FLJ42709 (346824 downstream)																																			---	---	---	---
FAM172A	83989	broad.mit.edu	37	5	93338155	93338155	+	Intron	DEL	T	-	-	rs112863655		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93338155delT	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron|FAM172A_uc003kkm.3_Intron	NM_032042	NP_114431			hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	95861750	95861751	+	IGR	INS	-	TAGT	TAGT	rs141770784	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95861750_95861751insTAGT								PCSK1 (92798 upstream) : CAST (136026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	95883690	95883691	+	IGR	INS	-	GTAA	GTAA	rs142185064	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95883690_95883691insGTAA								PCSK1 (114738 upstream) : CAST (114086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	96996679	96996680	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96996679_96996680delGT								RIOK2 (477674 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97816334	97816335	+	IGR	DEL	TT	-	-	rs34168223		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97816334_97816335delTT								None (None upstream) : RGMB (288664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97834247	97834247	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97834247delA								None (None upstream) : RGMB (270752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97960192	97960194	+	IGR	DEL	ATG	-	-	rs74842666		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97960192_97960194delATG								None (None upstream) : RGMB (144805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	98486306	98486306	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98486306delA								CHD1 (224068 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	98909192	98909193	+	IGR	INS	-	TTTA	TTTA	rs140743003	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98909192_98909193insTTTA								CHD1 (646954 upstream) : LOC100133050 (806016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	100484895	100484895	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100484895delT								ST8SIA4 (245908 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	100667140	100667141	+	IGR	INS	-	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100667140_100667141insC								ST8SIA4 (428153 upstream) : SLCO4C1 (902553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101647783	101647784	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101647783_101647784insA								SLCO4C1 (15530 upstream) : SLCO6A1 (59866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	103352185	103352185	+	IGR	DEL	C	-	-	rs140208818	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103352185delC								NUDT12 (453695 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	104034266	104034266	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104034266delC								None (None upstream) : RAB9BP1 (400909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106388203	106388203	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106388203delG								None (None upstream) : EFNA5 (324388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	107049806	107049807	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107049806_107049807insA								EFNA5 (43210 upstream) : FBXL17 (144933 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	107103754	107103754	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107103754delC								EFNA5 (97158 upstream) : FBXL17 (90986 downstream)																																			---	---	---	---
FBXL17	64839	broad.mit.edu	37	5	107351624	107351624	+	Intron	DEL	T	-	-	rs79581448		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107351624delT	uc011cvc.1	-						FBXL17_uc003kon.3_Intron	NM_001163315	NP_001156787			F-box and leucine-rich repeat protein 17												0		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)														---	---	---	---
FBXL17	64839	broad.mit.edu	37	5	107507520	107507521	+	Intron	INS	-	G	G	rs140878304	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107507520_107507521insG	uc011cvc.1	-						FBXL17_uc003kon.3_Intron	NM_001163315	NP_001156787			F-box and leucine-rich repeat protein 17												0		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)														---	---	---	---
FER	2241	broad.mit.edu	37	5	108335728	108335728	+	Intron	DEL	G	-	-	rs80280300		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108335728delG	uc003kop.1	+						FER_uc011cvg.1_Intron	NM_005246	NP_005237			fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)														---	---	---	---
FER	2241	broad.mit.edu	37	5	108501295	108501298	+	Intron	DEL	GTGT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108501295_108501298delGTGT	uc003kop.1	+						FER_uc011cvg.1_Intron	NM_005246	NP_005237			fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)														---	---	---	---
MAN2A1	4124	broad.mit.edu	37	5	109030043	109030043	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109030043delT	uc003kou.1	+						MAN2A1_uc003kot.1_Intron	NM_002372	NP_002363			mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)														---	---	---	---
EPB41L4A	64097	broad.mit.edu	37	5	111625108	111625109	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111625108_111625109insT	uc003kpv.1	-						EPB41L4A_uc003kpw.1_Intron	NM_022140	NP_071423			erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	112263592	112263592	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112263592delT								REEP5 (5561 upstream) : DCP2 (48841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	115082567	115082567	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115082567delT								TMED7-TICAM2 (120697 upstream) : CDO1 (57865 downstream)																																			---	---	---	---
DMXL1	1657	broad.mit.edu	37	5	118434894	118434895	+	Intron	INS	-	TTTG	TTTG	rs138823497	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118434894_118434895insTTTG	uc003ksd.2	+						DMXL1_uc010jcl.1_Intron|DMXL1_uc003ksc.1_Intron	NM_005509	NP_005500			Dmx-like 1											ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)														---	---	---	---
TNFAIP8	25816	broad.mit.edu	37	5	118651060	118651060	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118651060delT	uc003ksg.2	+						TNFAIP8_uc003ksf.1_Intron	NM_001077654	NP_001071122			tumor necrosis factor, alpha-induced protein 8						anti-apoptosis|apoptosis|negative regulation of anti-apoptosis	cytoplasm	caspase inhibitor activity|protein binding			ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)														---	---	---	---
TNFAIP8	25816	broad.mit.edu	37	5	118707831	118707832	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118707831_118707832insA	uc003ksh.2	+						TNFAIP8_uc003ksf.1_Intron|TNFAIP8_uc003ksg.2_Intron|TNFAIP8_uc011cwf.1_Intron|TNFAIP8_uc003ksi.2_Intron	NM_014350	NP_055165			tumor necrosis factor, alpha-induced protein 8						anti-apoptosis|apoptosis|negative regulation of anti-apoptosis	cytoplasm	caspase inhibitor activity|protein binding			ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	118892723	118892723	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118892723delC								HSD17B4 (14696 upstream) : FAM170A (72531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121151680	121151681	+	IGR	DEL	AC	-	-	rs35044749		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121151680_121151681delAC								None (None upstream) : FTMT (35969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121153436	121153437	+	IGR	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121153436_121153437delTC								None (None upstream) : FTMT (34213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121892402	121892403	+	IGR	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121892402_121892403delCA								SNCAIP (92608 upstream) : SNX2 (218347 downstream)																																			---	---	---	---
SNX2	6643	broad.mit.edu	37	5	122148295	122148295	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122148295delT	uc003kte.2	+						SNX2_uc011cwn.1_Intron	NM_003100	NP_003091			sorting nexin 2						cell communication|endocytosis|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding|protein transporter activity			kidney(1)	1		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)														---	---	---	---
PRDM6	93166	broad.mit.edu	37	5	122510729	122510730	+	Intron	INS	-	TTAT	TTAT	rs138075950	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122510729_122510730insTTAT	uc003kti.2	+						PRDM6_uc003ktj.2_Intron	NM_001136239	NP_001129711			PR domain containing 6						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding				0																		---	---	---	---
CEP120	153241	broad.mit.edu	37	5	122691850	122691851	+	Intron	INS	-	A	A	rs138090276		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122691850_122691851insA	uc003ktk.2	-						CEP120_uc011cwq.1_Intron	NM_153223	NP_694955			coiled-coil domain containing 100							centrosome				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	123020607	123020609	+	IGR	DEL	AAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123020607_123020609delAAA								CSNK1G3 (68145 upstream) : ZNF608 (952001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123020622	123020623	+	IGR	DEL	AC	-	-	rs139060273	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123020622_123020623delAC								CSNK1G3 (68160 upstream) : ZNF608 (951987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123423427	123423427	+	IGR	DEL	T	-	-	rs113758040		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123423427delT								CSNK1G3 (470965 upstream) : ZNF608 (549183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124305898	124305899	+	IGR	INS	-	C	C	rs145956579	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124305898_124305899insC								ZNF608 (221398 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124562210	124562215	+	IGR	DEL	TCTGTA	-	-	rs35261652		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124562210_124562215delTCTGTA								ZNF608 (477710 upstream) : None (None downstream)																																			---	---	---	---
FBN2	2201	broad.mit.edu	37	5	127640206	127640206	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127640206delA	uc003kuu.2	-							NM_001999	NP_001990			fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)														---	---	---	---
LYRM7	90624	broad.mit.edu	37	5	130533726	130533726	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130533726delT	uc003kvg.1	+							NM_181705	NP_859056			Lyrm7 homolog												0		all_cancers(142;0.0377)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
CDC42SE2	56990	broad.mit.edu	37	5	130610992	130610992	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130610992delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	131424307	131424308	+	IGR	DEL	AA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131424307_131424308delAA								CSF2 (12449 upstream) : P4HA2 (103998 downstream)																																			---	---	---	---
UQCRQ	27089	broad.mit.edu	37	5	132204448	132204448	+	3'UTR	DEL	G	-	-	rs78523057		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132204448delG	uc003kya.1	+	3					GDF9_uc011cxj.1_5'Flank	NM_014402	NP_055217			ubiquinol-cytochrome c reductase, complex III						respiratory electron transport chain	mitochondrial inner membrane|respiratory chain	ubiquinol-cytochrome-c reductase activity				0		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
FSTL4	23105	broad.mit.edu	37	5	132917978	132917978	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132917978delA	uc003kyn.1	-							NM_015082	NP_055897			follistatin-like 4 precursor							extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	133131314	133131314	+	IGR	DEL	G	-	-	rs36077092		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133131314delG								FSTL4 (183091 upstream) : C5orf15 (159885 downstream)																																			---	---	---	---
CDKL3	51265	broad.mit.edu	37	5	133647589	133647589	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133647589delA	uc003kzf.3	-						CDKL3_uc011cxm.1_Intron|CDKL3_uc011cxn.1_Intron|CDKL3_uc010jdw.2_Intron|CDKL3_uc011cxo.1_Intron|CDKL3_uc011cxp.1_Intron|CDKL3_uc011cxq.1_Intron|CDKL3_uc003kzg.3_Intron	NM_001113575	NP_001107047			cyclin-dependent kinase-like 3 isoform 1							cytoplasm	ATP binding|cyclin-dependent protein kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
PHF15	23338	broad.mit.edu	37	5	133876090	133876090	+	Intron	DEL	T	-	-	rs63047361		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133876090delT	uc003kzo.1	+						PHF15_uc011cxt.1_Intron|PHF15_uc003kzk.2_Intron|PHF15_uc003kzl.2_Intron|PHF15_uc003kzm.2_Intron|PHF15_uc003kzn.2_Intron	NM_015288	NP_056103			PHD finger protein 15						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	134195531	134195531	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134195531delT								C5orf24 (107 upstream) : TXNDC15 (13929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	134410620	134410625	+	Intron	DEL	AATGAT	-	-	rs5871549		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134410620_134410625delAATGAT	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																														---	---	---	---
TRPC7	57113	broad.mit.edu	37	5	135667871	135667872	+	Intron	INS	-	G	G	rs111593354		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135667871_135667872insG	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	135944109	135944112	+	IGR	DEL	CACA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135944109_135944112delCACA								TRPC7 (251036 upstream) : SPOCK1 (366876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	136134564	136134565	+	IGR	INS	-	A	A	rs144476124	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136134564_136134565insA								TRPC7 (441491 upstream) : SPOCK1 (176423 downstream)																																			---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136410383	136410385	+	Intron	DEL	TTG	-	-	rs71845125		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-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	136457929	136457930	+	Intron	INS	-	AC	AC	rs140564261		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136457929_136457930insAC	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589			sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	136927580	136927580	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136927580delA								SPOCK1 (92562 upstream) : KLHL3 (25610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	137615240	137615240	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137615240delA								GFRA3 (4987 upstream) : CDC25C (5719 downstream)																																			---	---	---	---
EGR1	1958	broad.mit.edu	37	5	137804475	137804475	+	3'UTR	DEL	C	-	-	rs113788672		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137804475delC	uc003ldb.1	+	2						NM_001964	NP_001955			early growth response 1						cellular response to heparin|cellular response to mycophenolic acid|glomerular mesangial cell proliferation|interleukin-1-mediated signaling pathway|positive regulation of glomerular metanephric mesangial cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of protein sumoylation|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytoplasm|nucleus	histone acetyltransferase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)															---	---	---	---
LRRTM2	26045	broad.mit.edu	37	5	138207717	138207720	+	3'UTR	DEL	GTGT	-	-	rs6149266		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138207717_138207720delGTGT	uc011cyz.1	-	2					CTNNA1_uc003ldh.2_Intron|CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron	NM_015564	NP_056379			leucine rich repeat transmembrane neuronal 2							cell junction|integral to membrane|postsynaptic membrane					0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
SIL1	64374	broad.mit.edu	37	5	138317521	138317521	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138317521delT	uc003ldm.2	-						SIL1_uc003ldn.2_Intron|SIL1_uc003ldo.2_Intron|SIL1_uc003ldp.2_Intron|SIL1_uc003ldq.1_Intron	NM_022464	NP_071909			SIL1 protein precursor						intracellular protein transport|protein folding|transmembrane transport	endoplasmic reticulum lumen	unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)											Marinesco-Sj_gren_syndrome				---	---	---	---
MATR3	9782	broad.mit.edu	37	5	138623307	138623308	+	Intron	INS	-	A	A	rs139718775		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138623307_138623308insA	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)															---	---	---	---
C5orf32	84418	broad.mit.edu	37	5	139596473	139596474	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139596473_139596474delAC	uc003lfd.2	+						C5orf32_uc010jfi.2_Intron	NM_032412	NP_115788			hypothetical protein LOC84418												0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHAC2	56134	broad.mit.edu	37	5	140366187	140366187	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140366187delG	uc003lii.2	+						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_Intron	NM_018899	NP_061722			protocadherin alpha subfamily C, 2 isoform 1						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
NR3C1	2908	broad.mit.edu	37	5	142748100	142748101	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142748100_142748101delAC	uc003lmz.2	-						NR3C1_uc003lmy.2_Intron|NR3C1_uc003lna.2_Intron|NR3C1_uc003lnb.2_Intron|NR3C1_uc011dbk.1_Intron|NR3C1_uc003lnc.2_Intron|NR3C1_uc003lnd.2_Intron|NR3C1_uc003lne.2_Intron|NR3C1_uc003lnf.2_Intron	NM_000176	NP_000167			glucocorticoid receptor isoform alpha						chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter	mitochondrial matrix|nucleoplasm	glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Amcinonide(DB00288)|Betamethasone(DB00443)|Budesonide(DB01222)|Dexamethasone(DB01234)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluticasone Propionate(DB00588)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Prednisone(DB00635)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	142929969	142929969	+	IGR	DEL	T	-	-	rs11290314		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142929969delT								NR3C1 (114892 upstream) : HMHB1 (261757 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	143245686	143245686	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143245686delC								HMHB1 (45404 upstream) : YIPF5 (292045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	144417632	144417633	+	IGR	INS	-	T	T	rs71799692		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144417632_144417633insT								KCTD16 (560688 upstream) : PRELID2 (720949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	145047928	145047929	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145047928_145047929insA								None (None upstream) : PRELID2 (90653 downstream)																																			---	---	---	---
RBM27	54439	broad.mit.edu	37	5	145654995	145654996	+	Intron	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145654995_145654996insG	uc003lnz.3	+							NM_018989	NP_061862			RNA binding motif protein 27						mRNA processing	cytoplasm|nuclear speck	nucleotide binding|RNA binding|zinc ion binding			central_nervous_system(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
STK32A	202374	broad.mit.edu	37	5	146690346	146690347	+	Intron	INS	-	T	T	rs143407578	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146690346_146690347insT	uc010jgn.1	+						STK32A_uc003lol.3_Intron|STK32A_uc003lom.2_Intron|STK32A_uc011dbw.1_Intron	NM_001112724	NP_001106195			serine/threonine kinase 32A isoform 1								ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	146938430	146938431	+	5'Flank	DEL	TT	-	-	rs5872027		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146938430_146938431delTT	uc003lop.1	+											Homo sapiens cDNA FLJ14672 fis, clone NT2RP2003687.																														---	---	---	---
JAKMIP2	9832	broad.mit.edu	37	5	147014740	147014741	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147014740_147014741insA	uc003loq.1	-						JAKMIP2_uc011dbx.1_Intron|JAKMIP2_uc003lor.1_Intron|uc003lop.1_Intron|JAKMIP2_uc010jgo.1_Intron	NM_014790	NP_055605			janus kinase and microtubule interacting protein							Golgi apparatus				large_intestine(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	148836218	148836221	+	IGR	DEL	AGAG	-	-	rs143911630		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148836218_148836221delAGAG								LOC728264 (23819 upstream) : CSNK1A1 (36728 downstream)																																			---	---	---	---
ARHGEF37	389337	broad.mit.edu	37	5	148982056	148982056	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148982056delT	uc003lra.1	+							NM_001001669	NP_001001669			hypothetical protein LOC389337						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
PDGFRB	5159	broad.mit.edu	37	5	149497091	149497094	+	Intron	DEL	GCGC	-	-	rs10638772		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149497091_149497094delGCGC	uc003lro.2	-						PDGFRB_uc010jhd.2_Intron	NM_002609	NP_002600			platelet-derived growth factor receptor beta						aorta morphogenesis|cardiac myofibril assembly|hemopoiesis|metanephric glomerular capillary formation|metanephric glomerular mesangial cell proliferation involved in metanephros development|peptidyl-tyrosine phosphorylation|positive regulation of calcium ion import|positive regulation of chemotaxis|positive regulation of DNA biosynthetic process|positive regulation of ERK1 and ERK2 cascade|positive regulation of MAP kinase activity|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of mitosis|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|protein autophosphorylation|regulation of actin cytoskeleton organization|retina vasculature development in camera-type eye|smooth muscle cell chemotaxis	apical plasma membrane|cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|vascular endothelial growth factor receptor activity			central_nervous_system(4)|lung(4)|breast(3)|stomach(2)|prostate(2)|large_intestine(1)|ovary(1)	17		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)			T	ETV6|TRIP11|HIP1|RAB5EP|H4|NIN|HCMOGT-1|PDE4DIP	MPD|AML|CMML|CML								---	---	---	---
Unknown	0	broad.mit.edu	37	5	150477180	150477181	+	IGR	INS	-	T	T	rs113676778		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150477180_150477181insT								TNIP1 (10461 upstream) : ANXA6 (3087 downstream)																																			---	---	---	---
SLC36A2	153201	broad.mit.edu	37	5	150719728	150719729	+	Intron	INS	-	GAA	GAA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150719728_150719729insGAA	uc003lty.2	-						GM2A_uc011dcs.1_Intron|SLC36A2_uc003ltz.2_Intron|SLC36A2_uc003lua.2_Intron|SLC36A2_uc010jhv.2_Intron|SLC36A2_uc011dct.1_Intron	NM_181776	NP_861441			solute carrier family 36, member 2						cellular nitrogen compound metabolic process	cytoplasm|integral to membrane|plasma membrane	glycine transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
SLC36A1	206358	broad.mit.edu	37	5	150842442	150842442	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150842442delT	uc003luc.2	+						GM2A_uc011dcs.1_Intron|SLC36A1_uc003lub.1_Intron|SLC36A1_uc010jhw.1_Intron	NM_078483	NP_510968			solute carrier family 36 member 1						cellular nitrogen compound metabolic process|ion transport	endoplasmic reticulum|integral to membrane|lysosomal membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			skin(1)	1		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)|all_neural(839;0.138)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glycine(DB00145)|L-Alanine(DB00160)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	151566695	151566695	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151566695delT	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	151727616	151727617	+	IGR	DEL	AC	-	-	rs112050420		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151727616_151727617delAC								GLRA1 (423219 upstream) : NMUR2 (43485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	151864002	151864002	+	IGR	DEL	A	-	-	rs150511731		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151864002delA								NMUR2 (79162 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	152501861	152501862	+	IGR	INS	-	AA	AA	rs67399495		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152501861_152501862insAA								NMUR2 (717021 upstream) : GRIA1 (367313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	153369625	153369630	+	IGR	DEL	CACACA	-	-	rs113686922		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153369625_153369630delCACACA								GRIA1 (176197 upstream) : FAM114A2 (1641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	154406711	154406712	+	IGR	INS	-	A	A	rs111631250		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154406711_154406712insA								KIF4B (9026 upstream) : SGCD (728351 downstream)																																			---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155195302	155195303	+	Intron	INS	-	T	T	rs141747376	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155195302_155195303insT	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	155270415	155270418	+	Intron	DEL	CACA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155270415_155270418delCACA	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	155683209	155683210	+	Intron	DEL	TG	-	-	rs140075227		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155683209_155683210delTG	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)															---	---	---	---
HAVCR2	84868	broad.mit.edu	37	5	156518458	156518458	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156518458delA	uc003lwk.1	-							NM_032782	NP_116171			T cell immunoglobulin mucin 3 precursor							integral to membrane					0	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
CYFIP2	26999	broad.mit.edu	37	5	156799905	156799906	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156799905_156799906delAC	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	156903649	156903649	+	Intron	DEL	T	-	-	rs147434648		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156903649delT	uc003lww.1	-											SubName: Full=cDNA FLJ34145 fis, clone FCBBF3011867, highly similar to ADAM 19 (EC 3.4.24.-);						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)															---	---	---	---
CLINT1	9685	broad.mit.edu	37	5	157236506	157236506	+	Intron	DEL	A	-	-	rs72318416		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157236506delA	uc003lxj.1	-						CLINT1_uc003lxi.1_Intron|CLINT1_uc011ddv.1_Intron	NM_014666	NP_055481			epsin 4						endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
CLINT1	9685	broad.mit.edu	37	5	157258414	157258414	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157258414delG	uc003lxj.1	-						CLINT1_uc003lxi.1_Intron|CLINT1_uc011ddv.1_Intron	NM_014666	NP_055481			epsin 4						endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	157737302	157737303	+	IGR	INS	-	TCTT	TCTT	rs138749619	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157737302_157737303insTCTT								CLINT1 (451134 upstream) : EBF1 (385621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	157999497	157999498	+	IGR	INS	-	TTTG	TTTG	rs150388208	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157999497_157999498insTTTG								CLINT1 (713329 upstream) : EBF1 (123426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	160401632	160401652	+	IGR	DEL	GGTCAAGGGGAGAGAAAACAC	-	-	rs66664769		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160401632_160401652delGGTCAAGGGGAGAGAAAACAC								LOC285629 (35999 upstream) : GABRB2 (313784 downstream)																																			---	---	---	---
GABRB2	2561	broad.mit.edu	37	5	160879699	160879699	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160879699delT	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	161135026	161135026	+	IGR	DEL	A	-	-	rs33934994		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161135026delA								GABRA6 (5428 upstream) : GABRA1 (139171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162339862	162339863	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162339862_162339863insT								GABRG2 (757318 upstream) : CCNG1 (524714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166460865	166460865	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166460865delC								None (None upstream) : ODZ2 (250978 downstream)																																			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167130908	167130909	+	Intron	INS	-	C	C	rs141497929	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167130908_167130909insC	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
FGF18	8817	broad.mit.edu	37	5	170871063	170871064	+	Intron	INS	-	C	C	rs139681382	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170871063_170871064insC	uc003mbk.2	+							NM_003862	NP_003853			fibroblast growth factor 18 precursor						cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of cell proliferation	extracellular space|nucleolus	growth factor activity|type 1 fibroblast growth factor receptor binding|type 2 fibroblast growth factor receptor binding				0	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	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	172178243	172178244	+	IGR	INS	-	AAGG	AAGG	rs28532090		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172178243_172178244insAAGG								NEURL1B (59712 upstream) : DUSP1 (16858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172178287	172178288	+	IGR	INS	-	GAAG	GAAG	rs138846286		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172178287_172178288insGAAG								NEURL1B (59756 upstream) : DUSP1 (16814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172628615	172628615	+	IGR	DEL	A	-	-	rs11338538		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172628615delA								BNIP1 (37226 upstream) : NKX2-5 (30523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173029775	173029776	+	IGR	INS	-	T	T	rs35321544		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173029775_173029776insT								LOC285593 (17701 upstream) : BOD1 (4372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173811757	173811762	+	IGR	DEL	GGTGTG	-	-	rs72317627		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173811757_173811762delGGTGTG								HMP19 (275576 upstream) : MSX2 (339813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174074922	174074922	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174074922delA								HMP19 (538741 upstream) : MSX2 (76653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	176233023	176233024	+	IGR	INS	-	A	A	rs71591840		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176233023_176233024insA								TSPAN17 (146965 upstream) : UNC5A (4536 downstream)																																			---	---	---	---
UIMC1	51720	broad.mit.edu	37	5	176399266	176399266	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176399266delG	uc011dfp.1	-						UIMC1_uc003mfc.1_Intron|UIMC1_uc003mfd.1_Intron|UIMC1_uc003mfg.1_Intron|UIMC1_uc003mfh.1_Intron|UIMC1_uc010jkj.1_Intron|UIMC1_uc011dfq.1_Intron|UIMC1_uc003mff.1_5'Flank	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	176586275	176586275	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176586275delT	uc003mfr.3	+						NSD1_uc003mft.3_Intron|NSD1_uc003mfs.1_Intron|NSD1_uc011dfx.1_Intron|NSD1_uc003mfp.2_Intron	NM_022455	NP_071900			nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	177362810	177362812	+	IGR	DEL	CCT	-	-	rs113173559		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177362810_177362812delCCT								LOC728554 (51543 upstream) : PROP1 (56424 downstream)																																			---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177672019	177672021	+	Intron	DEL	CAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177672019_177672021delCAT	uc003mje.2	-						COL23A1_uc010jkt.2_Intron	NM_173465	NP_775736			collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177906101	177906102	+	Intron	INS	-	ATG	ATG	rs144013344	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177906101_177906102insATG	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	178129615	178129616	+	IGR	INS	-	C	C	rs141870446	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178129615_178129616insC								CLK4 (71999 upstream) : ZNF354A (8915 downstream)																																			---	---	---	---
BTNL8	79908	broad.mit.edu	37	5	180368087	180368090	+	Intron	DEL	AGGG	-	-	rs144370596		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180368087_180368090delAGGG	uc003mmp.2	+						BTNL8_uc003mmq.2_Intron|BTNL8_uc011dhg.1_Intron|BTNL8_uc010jll.2_Intron|BTNL8_uc010jlm.2_Intron|BTNL8_uc011dhh.1_Intron	NM_001040462	NP_001035552			butyrophilin-like 8 isoform 2 precursor							integral to membrane				upper_aerodigestive_tract(1)|skin(1)	2	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
DUSP22	56940	broad.mit.edu	37	6	316281	316281	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:316281delT	uc003msx.2	+						DUSP22_uc011dhn.1_Intron|DUSP22_uc003msy.1_Intron	NM_020185	NP_064570			dual specificity phosphatase 22						apoptosis|cell proliferation|inactivation of MAPK activity|multicellular organismal development|positive regulation of JNK cascade|regulation of cell proliferation|transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	885946	885951	+	IGR	DEL	GAGTGT	-	-	rs111704891	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:885946_885951delGAGTGT								EXOC2 (192837 upstream) : LOC285768 (75291 downstream)																																			---	---	---	---
GMDS	2762	broad.mit.edu	37	6	2209804	2209805	+	Intron	INS	-	ACACAC	ACACAC	rs144499295	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2209804_2209805insACACAC	uc003mtq.2	-							NM_001500	NP_001491			GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	2653787	2653788	+	IGR	DEL	GA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2653787_2653788delGA								C6orf195 (18489 upstream) : MYLK4 (10076 downstream)																																			---	---	---	---
NQO2	4835	broad.mit.edu	37	6	3016764	3016764	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3016764delG	uc003mus.2	+						NQO2_uc003mut.2_Intron	NM_000904	NP_000895			NAD(P)H dehydrogenase, quinone 2							cytoplasm|nucleus	coenzyme binding|dihydronicotinamide riboside quinone reductase activity|electron carrier activity|metal ion binding|NADPH dehydrogenase (quinone) activity			ovary(1)	1	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Menadione(DB00170)|NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	3696363	3696364	+	IGR	INS	-	CA	CA	rs148179380	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3696363_3696364insCA								SLC22A23 (239570 upstream) : C6orf145 (26472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	3930257	3930257	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3930257delA								FAM50B (78707 upstream) : PRPF4B (91312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	3942545	3942546	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3942545_3942546insA								FAM50B (90995 upstream) : PRPF4B (79023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4529562	4529562	+	IGR	DEL	T	-	-	rs138412535		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4529562delT								PECI (393731 upstream) : CDYL (176831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	6020560	6020561	+	IGR	INS	-	GT	GT	rs144921588	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6020560_6020561insGT								NRN1 (12927 upstream) : F13A1 (123751 downstream)																																			---	---	---	---
LOC285780	285780	broad.mit.edu	37	6	6536743	6536743	+	Intron	DEL	T	-	-	rs34369168		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6536743delT	uc003mww.3	-						LOC285780_uc003mwx.2_Intron	NR_026970				Homo sapiens cDNA FLJ33708 fis, clone BRAWH2007862.												0																		---	---	---	---
LOC285780	285780	broad.mit.edu	37	6	6576719	6576720	+	Intron	DEL	AA	-	-	rs66829876		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6576719_6576720delAA	uc003mww.3	-						LOC285780_uc003mwx.2_Intron	NR_026970				Homo sapiens cDNA FLJ33708 fis, clone BRAWH2007862.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	6711723	6711732	+	IGR	DEL	GAGATGCATC	-	-	rs143310364		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6711723_6711732delGAGATGCATC								LY86 (56507 upstream) : RREB1 (396456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	6730463	6730463	+	IGR	DEL	A	-	-	rs67490800		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6730463delA								LY86 (75247 upstream) : RREB1 (377725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	6741388	6741389	+	IGR	INS	-	G	G	rs142471936	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6741388_6741389insG								LY86 (86172 upstream) : RREB1 (366799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	6851144	6851144	+	IGR	DEL	A	-	-	rs71793963		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6851144delA								LY86 (195928 upstream) : RREB1 (257044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	7086072	7086072	+	IGR	DEL	T	-	-	rs78753067		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7086072delT								LY86 (430856 upstream) : RREB1 (22116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	8486031	8486032	+	Intron	INS	-	AA	AA	rs140812309	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8486031_8486032insAA	uc003mye.2	+											Homo sapiens, clone IMAGE:5539086, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	8680077	8680078	+	Intron	INS	-	A	A	rs147881253	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8680077_8680078insA	uc003mye.2	+											Homo sapiens, clone IMAGE:5539086, mRNA.																														---	---	---	---
GCNT2	2651	broad.mit.edu	37	6	10498206	10498207	+	Intron	INS	-	A	A	rs111685852		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10498206_10498207insA	uc010jol.2	+						GCNT2_uc010jom.2_Intron					SubName: Full=Glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group); SubName: Full=Putative uncharacterized protein GCNT2;							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)														---	---	---	---
SYCP2L	221711	broad.mit.edu	37	6	10863684	10863684	+	Intron	DEL	A	-	-	rs35054043		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10863684delA	uc011dim.1	+											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)															---	---	---	---
SYCP2L	221711	broad.mit.edu	37	6	10974449	10974450	+	3'UTR	INS	-	T	T	rs142397019	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10974449_10974450insT	uc003mzo.2	+	30					SYCP2L_uc010jow.2_3'UTR	NM_001040274	NP_001035364			synaptonemal complex protein 2-like							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	11434663	11434663	+	Intron	DEL	T	-	-	rs148065014		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11434663delT	uc003mzy.2	+											Homo sapiens cDNA clone IMAGE:4812340.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	11491999	11492000	+	Intron	INS	-	TGA	TGA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11491999_11492000insTGA	uc003mzz.1	+											Homo sapiens cDNA clone IMAGE:5269873.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	11614655	11614656	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11614655_11614656insA								TMEM170B (30899 upstream) : C6orf105 (99234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	12246884	12246885	+	IGR	INS	-	T	T	rs147475528	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12246884_12246885insT								HIVEP1 (81653 upstream) : EDN1 (43644 downstream)																																			---	---	---	---
TBC1D7	51256	broad.mit.edu	37	6	13314437	13314437	+	Intron	DEL	A	-	-	rs34405450		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13314437delA	uc003naj.2	-						TBC1D7_uc011dis.1_Intron|TBC1D7_uc003nan.2_Intron|TBC1D7_uc003nal.2_Intron|TBC1D7_uc003nam.2_Intron|TBC1D7_uc003nao.2_Intron|TBC1D7_uc010jpd.2_Intron|TBC1D7_uc003nap.2_Intron	NM_016495	NP_057579			TBC1 domain family, member 7 isoform a						positive regulation of protein ubiquitination	cytoplasmic membrane-bounded vesicle	protein binding|Rab GTPase activator activity			ovary(1)	1	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	13905867	13905868	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13905867_13905868insT								CCDC90A (91078 upstream) : RNF182 (19335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14622155	14622156	+	IGR	INS	-	A	A	rs145660654		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14622155_14622156insA								CD83 (485009 upstream) : JARID2 (623578 downstream)																																			---	---	---	---
DTNBP1	84062	broad.mit.edu	37	6	15523793	15523794	+	Intron	INS	-	T	T	rs5874516		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15523793_15523794insT	uc003nbm.2	-						DTNBP1_uc003nbl.2_Intron|DTNBP1_uc003nbn.2_Intron|DTNBP1_uc003nbo.2_Intron	NM_032122	NP_115498			dystrobrevin binding protein 1 isoform a						actin cytoskeleton reorganization|cellular membrane organization|neuron projection morphogenesis|post-Golgi vesicle-mediated transport|regulation of dopamine receptor signaling pathway	axon part|BLOC-1 complex|cell junction|dendritic spine|endoplasmic reticulum membrane|endosome membrane|growth cone|melanosome membrane|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|synaptic vesicle membrane|synaptosome	identical protein binding				0	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)											Hermansky-Pudlak_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	6	15970139	15970140	+	IGR	INS	-	AA	AA	rs151078252	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15970139_15970140insAA								DTNBP1 (306868 upstream) : MYLIP (159177 downstream)																																			---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16571200	16571201	+	Intron	INS	-	GA	GA	rs147754285	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16571200_16571201insGA	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron|ATXN1_uc003nbu.1_Intron	NM_000332	NP_000323			ataxin 1						cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	17048086	17048086	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17048086delA								ATXN1 (286365 upstream) : RBM24 (233723 downstream)																																			---	---	---	---
CAP2	10486	broad.mit.edu	37	6	17515428	17515428	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17515428delA	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357			adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)															---	---	---	---
NUP153	9972	broad.mit.edu	37	6	17689303	17689303	+	Intron	DEL	A	-	-	rs34922440		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17689303delA	uc003ncd.1	-						NUP153_uc011dje.1_Intron|NUP153_uc010jpl.1_Intron	NM_005124	NP_005115			nucleoporin 153kDa						carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm	DNA binding|protein binding|transporter activity|zinc ion binding			lung(4)|ovary(2)|breast(2)|skin(1)	9	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	18697664	18697673	+	Intron	DEL	TGTGTGTGTG	-	-	rs142278840		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18697664_18697673delTGTGTGTGTG	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	19006604	19006605	+	IGR	INS	-	T	T	rs148128976	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19006604_19006605insT								MIR548A1 (434493 upstream) : ID4 (831012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19449010	19449011	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19449010_19449011delTG								MIR548A1 (876899 upstream) : ID4 (388606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19633027	19633027	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19633027delA								None (None upstream) : ID4 (204590 downstream)																																			---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20620222	20620222	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20620222delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	21615725	21615726	+	IGR	INS	-	ACAC	ACAC	rs139701800	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21615725_21615726insACAC								SOX4 (16878 upstream) : FLJ22536 (49277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	22878818	22878818	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22878818delG								HDGFL1 (308069 upstream) : None (None downstream)																																			---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25506088	25506089	+	Intron	INS	-	GAG	GAG	rs151165183	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25506088_25506089insGAG	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	26484030	26484031	+	5'Flank	INS	-	A	A	rs34417103		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26484030_26484031insA	uc003nie.1	-											Homo sapiens cDNA FLJ40220 fis, clone TESTI2021667.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	26705269	26705270	+	IGR	INS	-	AA	AA	rs28689790	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26705269_26705270insAA								ZNF322A (45306 upstream) : GUSBL1 (133996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27745747	27745749	+	IGR	DEL	TTT	-	-	rs140969962		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27745747_27745749delTTT								ZNF184 (304850 upstream) : HIST1H2BL (29509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	28100842	28100842	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28100842delA	uc010jqw.1	-						uc003nkk.1_Intron|uc003nkl.1_Intron					SubName: Full=cDNA FLJ45995 fis, clone SKNMC2003639;																														---	---	---	---
TRIM15	89870	broad.mit.edu	37	6	30134410	30134410	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30134410delC	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	30341717	30341720	+	IGR	DEL	TTCT	-	-	rs3130367		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30341717_30341720delTTCT								TRIM39 (27085 upstream) : HLA-E (115551 downstream)																																			---	---	---	---
HCG22	285834	broad.mit.edu	37	6	31023092	31023099	+	RNA	DEL	AAGGAAGG	-	-	rs71815275		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31023092_31023099delAAGGAAGG	uc010jsi.1	+	1		c.1109_1116delAAGGAAGG			HCG22_uc003nsj.1_Intron	NR_003948				Homo sapiens HLA complex group 22 (HCG22), non-coding RNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	31066737	31066737	+	IGR	DEL	A	-	-	rs34308896		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31066737delA								HCG22 (39084 upstream) : C6orf15 (12263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	31184394	31184395	+	IGR	INS	-	GAC	GAC	rs144902597	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31184394_31184395insGAC								HCG27 (12650 upstream) : HLA-C (52135 downstream)																																			---	---	---	---
HLA-B	3106	broad.mit.edu	37	6	31275455	31275456	+	Intron	INS	-	AGG	AGG	rs147714295	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31275455_31275456insAGG	uc003ntf.2	-						HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron					SubName: Full=MHC class I antigen;						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	6	31331446	31331447	+	IGR	INS	-	T	T	rs141655453	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31331446_31331447insT								HLA-B (6457 upstream) : MICA (36114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	31363459	31363460	+	IGR	DEL	AC	-	-	rs71723266		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31363459_31363460delAC								HLA-B (38470 upstream) : MICA (4101 downstream)																																			---	---	---	---
LSM2	57819	broad.mit.edu	37	6	31767016	31767016	+	Intron	DEL	T	-	-	rs71690229		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31767016delT	uc003nxg.2	-							NM_021177	NP_067000			LSM2 homolog, U6 small nuclear RNA associated						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|cytosol|nucleoplasm	U6 snRNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	32381268	32381269	+	IGR	INS	-	C	C	rs145262523	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32381268_32381269insC								BTNL2 (6368 upstream) : HLA-DRA (26378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	32416735	32416736	+	IGR	DEL	TG	-	-	rs28892608	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32416735_32416736delTG								HLA-DRA (3914 upstream) : HLA-DRB1 (68427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	32446426	32446428	+	IGR	DEL	AAT	-	-	rs113525829		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32446426_32446428delAAT								HLA-DRA (33605 upstream) : HLA-DRB1 (38735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	32450271	32450273	+	IGR	DEL	CTT	-	-	rs142138359		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32450271_32450273delCTT								HLA-DRA (37450 upstream) : HLA-DRB1 (34890 downstream)																																			---	---	---	---
HLA-DRB5	3127	broad.mit.edu	37	6	32555946	32555947	+	Intron	INS	-	T	T	rs148048368	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32555946_32555947insT	uc003obk.3	-						HLA-DRB1_uc003obp.3_Intron	NM_002125	NP_002116			major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	32851046	32851046	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32851046delT								PPP1R2P1 (3197 upstream) : HLA-DMB (51364 downstream)																																			---	---	---	---
CUTA	51596	broad.mit.edu	37	6	33385527	33385527	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33385527delC	uc003oej.1	-						CUTA_uc003oek.1_5'UTR|CUTA_uc003oel.1_Intron|CUTA_uc003oem.1_5'UTR|CUTA_uc003oen.1_Intron|SYNGAP1_uc003oeo.1_5'Flank|SYNGAP1_uc011dri.1_5'Flank|SYNGAP1_uc010juy.2_5'Flank	NM_001014840	NP_001014840			cutA divalent cation tolerance homolog isoform						protein localization|response to metal ion	membrane	enzyme binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	33440941	33440941	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33440941delA								ZBTB9 (15623 upstream) : BAK1 (99383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	33918368	33918369	+	IGR	INS	-	TT	TT	rs147700351		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33918368_33918369insTT								MLN (146575 upstream) : MIR1275 (49380 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	34550235	34550235	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34550235delT								SPDEF (26144 upstream) : C6orf106 (4831 downstream)																																			---	---	---	---
FKBP5	2289	broad.mit.edu	37	6	35659355	35659356	+	5'Flank	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35659355_35659356insT	uc011dte.1	-						FKBP5_uc003okx.2_5'Flank|FKBP5_uc011dtf.1_5'Flank|FKBP5_uc003oky.2_Intron|FKBP5_uc003okz.2_5'Flank	NM_001145776	NP_001139248			FK506 binding protein 5 isoform 1						protein folding	cytoplasm|membrane|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1																		---	---	---	---
BTBD9	114781	broad.mit.edu	37	6	38272335	38272336	+	Intron	INS	-	C	C	rs10947730		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38272335_38272336insC	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																		---	---	---	---
C6orf64	55776	broad.mit.edu	37	6	39074016	39074017	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39074016_39074017insA	uc003ook.1	-						C6orf64_uc011dty.1_Intron|C6orf64_uc003oom.1_Intron	NM_018322	NP_060792			hypothetical protein LOC55776							integral to membrane					0																		---	---	---	---
LRFN2	57497	broad.mit.edu	37	6	40557857	40557857	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40557857delT	uc003oph.1	-							NM_020737	NP_065788			leucine rich repeat and fibronectin type III							cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
TREM1	54210	broad.mit.edu	37	6	41246394	41246395	+	Intron	INS	-	A	A	rs145638846		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41246394_41246395insA	uc003oqf.1	-						TREM1_uc003oqg.1_Intron	NM_018643	NP_061113			triggering receptor expressed on myeloid cells 1						blood coagulation|humoral immune response|intracellular signal transduction|leukocyte migration	extracellular region|integral to membrane|intracellular|plasma membrane	receptor activity			breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)				Glutathione(DB00143)													---	---	---	---
CCND3	896	broad.mit.edu	37	6	41945822	41945823	+	Intron	INS	-	T	T	rs141456746	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41945822_41945823insT	uc003orp.2	-						CCND3_uc011duk.1_Intron|CCND3_uc011dum.1_Intron	NM_001136017	NP_001129489			cyclin D3 isoform 1						cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation	cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus	protein kinase binding				0	Colorectal(47;0.121)		Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)					T	IGH@	MM								---	---	---	---
TAF8	129685	broad.mit.edu	37	6	42039371	42039371	+	Intron	DEL	T	-	-	rs112569860		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42039371delT	uc003ors.2	+						TAF8_uc003ort.2_Intron|TAF8_uc003oru.1_Intron|TAF8_uc003orv.1_Intron|TAF8_uc011dun.1_Intron	NM_138572	NP_612639			TBP-associated factor 8						cell differentiation|maintenance of protein location in nucleus|positive regulation of transcription, DNA-dependent|regulation of fat cell differentiation|transcription, DNA-dependent	perinuclear region of cytoplasm|transcription factor TFIID complex	DNA binding|protein binding			ovary(1)	1	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00179)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	42192081	42192082	+	IGR	INS	-	AA	AA	rs34806499		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42192081_42192082insAA								MRPS10 (6448 upstream) : TRERF1 (587 downstream)																																			---	---	---	---
TRERF1	55809	broad.mit.edu	37	6	42379738	42379739	+	Intron	INS	-	TT	TT	rs34959367		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42379738_42379739insTT	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)															---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42548929	42548930	+	Intron	INS	-	T	T	rs111289516		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42548929_42548930insT	uc011dur.1	+						UBR2_uc003osf.2_Intron	NM_015255	NP_056070			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	43705849	43705849	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43705849delT								MRPS18A (50321 upstream) : VEGFA (32104 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	43705991	43705992	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43705991_43705992delTG								MRPS18A (50463 upstream) : VEGFA (31961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	43710121	43710124	+	IGR	DEL	TCAA	-	-	rs147191481		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43710121_43710124delTCAA								MRPS18A (54593 upstream) : VEGFA (27829 downstream)																																			---	---	---	---
CAPN11	11131	broad.mit.edu	37	6	44135653	44135654	+	Intron	INS	-	A	A	rs143026637	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44135653_44135654insA	uc003owt.1	+							NM_007058	NP_008989			calpain 11						proteolysis	acrosomal vesicle	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)|breast(1)	2	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
CAPN11	11131	broad.mit.edu	37	6	44149212	44149215	+	Intron	DEL	ACAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44149212_44149215delACAG	uc003owt.1	+						CAPN11_uc011dvn.1_Intron	NM_007058	NP_008989			calpain 11						proteolysis	acrosomal vesicle	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)|breast(1)	2	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	44755194	44755195	+	IGR	INS	-	CTGT	CTGT	rs148897939	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44755194_44755195insCTGT								CDC5L (340415 upstream) : SUPT3H (21859 downstream)																																			---	---	---	---
SUPT3H	8464	broad.mit.edu	37	6	45178829	45178830	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45178829_45178830insT	uc003oxo.2	-						SUPT3H_uc003oxn.1_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron	NM_181356	NP_852001			suppressor of Ty 3 homolog isoform 2						histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3																		---	---	---	---
SUPT3H	8464	broad.mit.edu	37	6	45235569	45235569	+	Intron	DEL	C	-	-	rs113477245		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45235569delC	uc003oxo.2	-						SUPT3H_uc003oxn.1_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron	NM_181356	NP_852001			suppressor of Ty 3 homolog isoform 2						histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	45746382	45746383	+	IGR	INS	-	GAGA	GAGA	rs146309660	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45746382_45746383insGAGA								RUNX2 (227564 upstream) : CLIC5 (119807 downstream)																																			---	---	---	---
C6orf138	442213	broad.mit.edu	37	6	48005940	48005941	+	Intron	INS	-	A	A	rs138515654	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48005940_48005941insA	uc011dwm.1	-						C6orf138_uc011dwn.1_Intron|C6orf138_uc003ozf.2_Intron	NM_001013732	NP_001013754			hypothetical protein LOC442213							integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1																		---	---	---	---
C6orf138	442213	broad.mit.edu	37	6	48073707	48073708	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48073707_48073708insA	uc011dwn.1	-							NM_001013732	NP_001013754			hypothetical protein LOC442213							integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	48140560	48140561	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48140560_48140561delGT								C6orf138 (61617 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	48144081	48144082	+	IGR	INS	-	C	C	rs150986922	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48144081_48144082insC								C6orf138 (65138 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	49344109	49344109	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49344109delT								None (None upstream) : MUT (54885 downstream)																																			---	---	---	---
CENPQ	55166	broad.mit.edu	37	6	49442280	49442281	+	Intron	DEL	AA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49442280_49442281delAA	uc003ozh.1	+							NM_018132	NP_060602			centromere protein Q						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2	Lung NSC(77;0.0128)																	---	---	---	---
GLYATL3	389396	broad.mit.edu	37	6	49493810	49493810	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49493810delT	uc003ozi.2	+							NM_001010904	NP_001010904			glycine N-acyltransferase-like protein 3							mitochondrion	glycine N-acyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	50365026	50365026	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50365026delA								DEFB112 (348662 upstream) : TFAP2D (316231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	51119688	51119689	+	IGR	INS	-	T	T	rs144901523	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51119688_51119689insT								TFAP2B (304363 upstream) : PKHD1 (360456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	51136733	51136734	+	IGR	INS	-	G	G	rs141871397		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51136733_51136734insG								TFAP2B (321408 upstream) : PKHD1 (343411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	52171784	52171784	+	IGR	DEL	A	-	-	rs34143892		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52171784delA								MCM3 (22202 upstream) : PAQR8 (55142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	52587599	52587600	+	IGR	INS	-	A	A	rs138445796		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52587599_52587600insA								TMEM14A (36216 upstream) : GSTA2 (27288 downstream)																																			---	---	---	---
HMGCLL1	54511	broad.mit.edu	37	6	55310456	55310457	+	Intron	DEL	AT	-	-	rs147378069		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55310456_55310457delAT	uc003pcn.2	-						HMGCLL1_uc003pco.2_Intron|HMGCLL1_uc010jzx.2_Intron|HMGCLL1_uc011dxc.1_Intron|HMGCLL1_uc011dxd.1_Intron|HMGCLL1_uc011dxe.1_Intron	NM_019036	NP_061909			3-hydroxymethyl-3-methylglutaryl-Coenzyme A								hydroxymethylglutaryl-CoA lyase activity|metal ion binding			skin(2)|ovary(1)|pancreas(1)	4	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)															---	---	---	---
BMP5	653	broad.mit.edu	37	6	55720945	55720945	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55720945delC	uc003pcq.2	-						BMP5_uc011dxf.1_Intron	NM_021073	NP_066551			bone morphogenetic protein 5 preproprotein						cartilage development|cell differentiation|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity			ovary(2)	2	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)															---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	56056489	56056490	+	Intron	INS	-	A	A	rs145559926	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56056489_56056490insA	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)															---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57207700	57207701	+	Intron	DEL	TT	-	-	rs33966680		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57207700_57207701delTT	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	57325103	57325111	+	Intron	DEL	CTGTTGGCC	-	-	rs61216240	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57325103_57325111delCTGTTGGCC	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	57340797	57340798	+	Intron	INS	-	TGT	TGT	rs112489174		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57340797_57340798insTGT	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	57347209	57347209	+	Intron	DEL	G	-	-	rs66791500		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57347209delG	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	57352202	57352202	+	Intron	DEL	C	-	-	rs67188531		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57352202delC	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57360568	57360569	+	Intron	DEL	AT	-	-	rs140251188		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57360568_57360569delAT	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57369333	57369334	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57369333_57369334insA	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	57379495	57379496	+	Intron	INS	-	TA	TA	rs146172325		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57379495_57379496insTA	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	57432404	57432405	+	Intron	INS	-	TT	TT	rs147084165		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57432404_57432405insTT	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	57461972	57461973	+	Intron	INS	-	T	T	rs138866737		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57461972_57461973insT	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57485672	57485673	+	Intron	INS	-	C	C	rs151109620	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57485672_57485673insC	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57495582	57495583	+	Intron	DEL	AA	-	-	rs66476328		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57495582_57495583delAA	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57503262	57503262	+	Intron	DEL	C	-	-	rs66721860		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57503262delC	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-4284-01A-01D-1126-08	TCGA-BR-4284-11A-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	57515229	57515233	+	IGR	DEL	TTTGA	-	-	rs67538111		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57515229_57515233delTTTGA								PRIM2 (1854 upstream) : GUSBL2 (730926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57527818	57527818	+	IGR	DEL	G	-	-	rs67858073		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57527818delG								PRIM2 (14443 upstream) : GUSBL2 (718341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57544113	57544116	+	IGR	DEL	AAAG	-	-	rs78073104		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57544113_57544116delAAAG								PRIM2 (30738 upstream) : GUSBL2 (702043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57551912	57551912	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57551912delA								PRIM2 (38537 upstream) : GUSBL2 (694247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57561231	57561232	+	IGR	INS	-	A	A	rs71549759		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57561231_57561232insA								PRIM2 (47856 upstream) : GUSBL2 (684927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57562229	57562229	+	IGR	DEL	G	-	-	rs67409233		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57562229delG								PRIM2 (48854 upstream) : GUSBL2 (683930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57563307	57563307	+	IGR	DEL	G	-	-	rs67382068		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57563307delG								PRIM2 (49932 upstream) : GUSBL2 (682852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57655199	57655200	+	IGR	INS	-	T	T	rs143759651	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57655199_57655200insT								PRIM2 (141824 upstream) : GUSBL2 (590959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	58461280	58461280	+	IGR	DEL	T	-	-	rs67271877		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58461280delT								GUSBL2 (173556 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	62220412	62220412	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62220412delG								None (None upstream) : KHDRBS2 (169453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63207128	63207128	+	IGR	DEL	A	-	-	rs140485152		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63207128delA								KHDRBS2 (211028 upstream) : LGSN (778729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	64188392	64188392	+	IGR	DEL	A	-	-	rs34940581		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64188392delA								LGSN (158510 upstream) : PTP4A1 (43259 downstream)																																			---	---	---	---
EYS	346007	broad.mit.edu	37	6	66151506	66151507	+	Intron	DEL	TC	-	-	rs35754722		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66151506_66151507delTC	uc011dxu.1	-						EYS_uc003peq.2_Intron|EYS_uc003per.1_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
EYS	346007	broad.mit.edu	37	6	66379909	66379911	+	Intron	DEL	ATT	-	-	rs71959272	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66379909_66379911delATT	uc011dxu.1	-						EYS_uc003peq.2_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	67457643	67457643	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67457643delT								MCART3P (958268 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68165493	68165504	+	IGR	DEL	TGTGTTCTAGGG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68165493_68165504delTGTGTTCTAGGG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68480137	68480138	+	IGR	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68480137_68480138delTC								None (None upstream) : BAI3 (865494 downstream)																																			---	---	---	---
COL19A1	1310	broad.mit.edu	37	6	70737450	70737451	+	Intron	DEL	TG	-	-	rs67202657		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70737450_70737451delTG	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849			alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4																		---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	73107751	73107751	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73107751delA	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	73732334	73732334	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73732334delA	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)														---	---	---	---
CD109	135228	broad.mit.edu	37	6	74504961	74504962	+	Intron	DEL	AT	-	-	rs149757450		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74504961_74504962delAT	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000			CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4																		---	---	---	---
FILIP1	27145	broad.mit.edu	37	6	76075421	76075421	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76075421delT	uc003pia.2	-						FILIP1_uc003phy.1_Intron|FILIP1_uc003phz.2_5'Flank|FILIP1_uc010kbe.2_Intron	NM_015687	NP_056502			filamin A interacting protein 1											skin(3)|ovary(1)	4																		---	---	---	---
MYO6	4646	broad.mit.edu	37	6	76516105	76516105	+	Intron	DEL	A	-	-	rs144743862		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76516105delA	uc003pih.1	+						MYO6_uc003pig.1_Intron	NM_004999	NP_004990			myosin VI						actin filament-based movement|DNA damage response, signal transduction by p53 class mediator|endocytosis|intracellular protein transport|positive regulation of transcription from RNA polymerase II promoter|regulation of secretion|sensory perception of sound|synaptic transmission	cell cortex|clathrin coated vesicle membrane|coated pit|cytosol|DNA-directed RNA polymerase II, holoenzyme|filamentous actin|Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|ruffle membrane|unconventional myosin complex	actin filament binding|ADP binding|ATP binding|calmodulin binding|minus-end directed microfilament motor activity|protein binding			kidney(1)|pancreas(1)	2		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	77655782	77655782	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77655782delA								IMPG1 (873447 upstream) : HTR1B (516166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	77690608	77690608	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77690608delC								IMPG1 (908273 upstream) : HTR1B (481340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	77826977	77826977	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77826977delG								None (None upstream) : HTR1B (344971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78997681	78997681	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78997681delC								HTR1B (824561 upstream) : IRAK1BP1 (579508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82972712	82972715	+	IGR	DEL	AAGG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82972712_82972715delAAGG								IBTK (15264 upstream) : TPBG (100208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	85720460	85720460	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85720460delG								TBX18 (246561 upstream) : NT5E (438842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86411921	86411922	+	IGR	INS	-	C	C	rs147926490	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86411921_86411922insC								SNHG5 (23470 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86955283	86955310	+	IGR	DEL	TCCTTCTAACCTCCCCTCTTATCACCCT	-	-	rs12209680	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86955283_86955310delTCCTTCTAACCTCCCCTCTTATCACCCT								SNHG5 (566832 upstream) : HTR1E (691714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87752250	87752251	+	IGR	INS	-	AG	AG	rs149642477	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87752250_87752251insAG								HTR1E (25860 upstream) : CGA (42971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87754055	87754056	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87754055_87754056insA								HTR1E (27665 upstream) : CGA (41166 downstream)																																			---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87918823	87918823	+	Intron	DEL	C	-	-	rs5878022		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87918823delC	uc003plm.3	+						ZNF292_uc003pll.1_Intron	NM_015021	NP_055836			zinc finger protein 292						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
C6orf162	57150	broad.mit.edu	37	6	88045746	88045746	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88045746delA	uc003plp.1	+						C6orf164_uc003plr.2_Intron|C6orf162_uc003plq.1_Intron	NM_001042493	NP_001035958			hypothetical protein LOC57150							integral to membrane					0		all_cancers(76;3.81e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.15e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.3e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0164)														---	---	---	---
ORC3L	23595	broad.mit.edu	37	6	88301108	88301108	+	Intron	DEL	A	-	-	rs75781438		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88301108delA	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|RARS2_uc003pmb.2_5'Flank|RARS2_uc003pmc.2_5'Flank|RARS2_uc003pmd.2_5'Flank|RARS2_uc003pme.2_5'Flank|RARS2_uc003pmf.2_5'Flank	NM_012381	NP_036513			origin recognition complex, subunit 3 isoform 2						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	88453785	88453788	+	IGR	DEL	CTTT	-	-	rs10544587		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88453785_88453788delCTTT								AKIRIN2 (41800 upstream) : SPACA1 (303719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	88670996	88670997	+	IGR	DEL	AA	-	-	rs71554764		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88670996_88670997delAA								AKIRIN2 (259011 upstream) : SPACA1 (86510 downstream)																																			---	---	---	---
UBE2J1	51465	broad.mit.edu	37	6	90060309	90060309	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90060309delT	uc010kcb.2	-						UBE2J1_uc003pnc.2_Intron	NM_016021	NP_057105			ubiquitin-conjugating enzyme E2, J1							endoplasmic reticulum membrane|integral to membrane	ATP binding|ubiquitin-protein ligase activity				0		all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0139)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90446346	90446346	+	Intron	DEL	A	-	-	rs67132672		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90446346delA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	90532649	90532650	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90532649_90532650insT								MDN1 (3207 upstream) : CASP8AP2 (6969 downstream)																																			---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90668817	90668824	+	Intron	DEL	CACACACA	-	-	rs71774380		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90668817_90668824delCACACACA	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	90928226	90928226	+	Intron	DEL	T	-	-	rs148823934		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90928226delT	uc011eab.1	-						BACH2_uc003pnw.2_Intron|BACH2_uc010kch.2_Intron	NM_021813	NP_068585			BTB and CNC homology 1, basic leucine zipper							nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	91377314	91377315	+	IGR	DEL	AG	-	-	rs151298520		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91377314_91377315delAG								MAP3K7 (80407 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92639020	92639021	+	IGR	INS	-	C	C	rs149280929	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92639020_92639021insC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93586390	93586393	+	IGR	DEL	GAAG	-	-	rs28811888		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93586390_93586393delGAAG								None (None upstream) : EPHA7 (363349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93595190	93595190	+	IGR	DEL	A	-	-	rs77471930		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93595190delA								None (None upstream) : EPHA7 (354552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93637148	93637149	+	IGR	INS	-	AC	AC	rs148197665	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93637148_93637149insAC								None (None upstream) : EPHA7 (312593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93686494	93686495	+	IGR	INS	-	T	T	rs140194299	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93686494_93686495insT								None (None upstream) : EPHA7 (263247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93864319	93864319	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93864319delT								None (None upstream) : EPHA7 (85423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	95079208	95079209	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:95079208_95079209insA								TSG1 (593009 upstream) : MANEA (946204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	95174232	95174233	+	IGR	INS	-	C	C	rs149789380	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:95174232_95174233insC								TSG1 (688033 upstream) : MANEA (851180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	97122779	97122780	+	IGR	INS	-	A	A	rs147934869	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97122779_97122780insA								FHL5 (58267 upstream) : GPR63 (123109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	97950867	97950868	+	Intron	DEL	TC	-	-	rs9384988	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97950867_97950868delTC	uc003ppd.1	+											Homo sapiens cDNA FLJ34046 fis, clone FCBBF2007610.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	98462625	98462625	+	IGR	DEL	T	-	-	rs67519294		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98462625delT								C6orf167 (731564 upstream) : MIR2113 (9782 downstream)																																			---	---	---	---
USP45	85015	broad.mit.edu	37	6	99897014	99897016	+	Intron	DEL	CAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99897014_99897016delCAT	uc003ppx.2	-						USP45_uc003ppv.2_Intron|USP45_uc003ppw.2_Intron	NM_001080481	NP_001073950			ubiquitin specific peptidase 45						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|breast(1)	2		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101261349	101261350	+	Intron	INS	-	A	A	rs9498393		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101261349_101261350insA	uc003pqk.2	-						ASCC3_uc011eai.1_Intron|ASCC3_uc003pql.2_Intron	NM_006828	NP_006819			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	101716919	101716919	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101716919delG								ASCC3 (387695 upstream) : GRIK2 (129986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	103079957	103079957	+	IGR	DEL	T	-	-	rs35882192		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103079957delT								GRIK2 (562000 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	103904041	103904042	+	IGR	INS	-	TTTCTTTC	TTTCTTTC	rs140923549	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103904041_103904042insTTTCTTTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104880088	104880089	+	IGR	INS	-	A	A	rs72180653		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104880088_104880089insA								None (None upstream) : HACE1 (295879 downstream)																																			---	---	---	---
LIN28B	389421	broad.mit.edu	37	6	105432335	105432335	+	Intron	DEL	T	-	-	rs61375518		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105432335delT	uc003pqv.1	+						LIN28B_uc010kda.1_Intron	NM_001004317	NP_001004317			lin-28 homolog B						miRNA catabolic process|pre-miRNA processing|regulation of transcription, DNA-dependent|RNA 3'-end processing	cytoplasm|nucleus	DNA binding|protein binding|RNA binding|zinc ion binding				0		all_cancers(87;0.00346)|Acute lymphoblastic leukemia(125;2.26e-08)|all_hematologic(75;2.79e-06)|all_epithelial(87;0.204)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	105957582	105957583	+	IGR	DEL	TG	-	-	rs71707516		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105957582_105957583delTG								PREP (106613 upstream) : PRDM1 (576612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106602642	106602642	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106602642delT								PRDM1 (44828 upstream) : ATG5 (29712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	107126822	107126823	+	IGR	INS	-	CACA	CACA	rs140663928	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107126822_107126823insCACA								QRSL1 (10532 upstream) : MIR587 (105177 downstream)																																			---	---	---	---
SESN1	27244	broad.mit.edu	37	6	109312270	109312272	+	Intron	DEL	AAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109312270_109312272delAAA	uc003pst.3	-						SESN1_uc003psu.2_Intron	NM_014454	NP_055269			sestrin 1						cell cycle arrest|negative regulation of cell proliferation|response to DNA damage stimulus	nucleus				ovary(1)	1		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)														---	---	---	---
C6orf182	285753	broad.mit.edu	37	6	109419342	109419343	+	Intron	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109419342_109419343delTC	uc010kdk.2	+						C6orf182_uc003psv.3_Intron|C6orf182_uc003psw.3_Intron|C6orf182_uc003psx.3_Intron|C6orf182_uc010kdl.2_Intron	NM_001083535	NP_001077004			hypothetical protein LOC285753							microtubule|microtubule organizing center					0		all_cancers(87;4.45e-07)|Acute lymphoblastic leukemia(125;2.15e-10)|all_hematologic(75;3.25e-08)|all_epithelial(87;0.000254)|Colorectal(196;0.0293)|all_lung(197;0.11)		BRCA - Breast invasive adenocarcinoma(108;0.00123)|Epithelial(106;0.0022)|all cancers(137;0.00405)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)														---	---	---	---
C6orf182	285753	broad.mit.edu	37	6	109419820	109419820	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109419820delT	uc010kdk.2	+						C6orf182_uc003psv.3_Intron|C6orf182_uc003psw.3_Intron|C6orf182_uc003psx.3_Intron|C6orf182_uc010kdl.2_Intron	NM_001083535	NP_001077004			hypothetical protein LOC285753							microtubule|microtubule organizing center					0		all_cancers(87;4.45e-07)|Acute lymphoblastic leukemia(125;2.15e-10)|all_hematologic(75;3.25e-08)|all_epithelial(87;0.000254)|Colorectal(196;0.0293)|all_lung(197;0.11)		BRCA - Breast invasive adenocarcinoma(108;0.00123)|Epithelial(106;0.0022)|all cancers(137;0.00405)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)														---	---	---	---
PPIL6	285755	broad.mit.edu	37	6	109739752	109739752	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109739752delT	uc003ptg.3	-						PPIL6_uc010kdo.2_Intron|PPIL6_uc010kdp.2_Intron	NM_173672	NP_775943			peptidylprolyl isomerase-like 6 isoform 1						protein folding		peptidyl-prolyl cis-trans isomerase activity				0		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.00684)|BRCA - Breast invasive adenocarcinoma(108;0.00889)|all cancers(137;0.0106)|OV - Ovarian serous cystadenocarcinoma(136;0.0259)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	110360641	110360642	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110360641_110360642delAC								GPR6 (58720 upstream) : WASF1 (60380 downstream)																																			---	---	---	---
DDO	8528	broad.mit.edu	37	6	110731093	110731093	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110731093delC	uc003puc.2	-						C6orf186_uc003pub.2_Intron|DDO_uc003pud.2_Intron	NM_003649	NP_003640			D-aspartate oxidase isoform a						aspartate catabolic process	peroxisome	binding|D-amino-acid oxidase activity|D-aspartate oxidase activity			ovary(2)|breast(1)	3		all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327)		all cancers(137;2.54e-48)|Epithelial(106;3.11e-44)|OV - Ovarian serous cystadenocarcinoma(136;2.08e-24)|BRCA - Breast invasive adenocarcinoma(108;0.000141)|GBM - Glioblastoma multiforme(226;0.00046)														---	---	---	---
TRAF3IP2	10758	broad.mit.edu	37	6	111907207	111907208	+	Intron	INS	-	ATGGT	ATGGT	rs149529683	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111907207_111907208insATGGT	uc011ebc.1	-						TRAF3IP2_uc003pvg.2_Intron|TRAF3IP2_uc003pvf.2_Intron|TRAF3IP2_uc010kdw.2_Intron|TRAF3IP2_uc010kdx.2_Intron	NM_147686	NP_679211			TRAF3 interacting protein 2 isoform 2						intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular				ovary(2)|central_nervous_system(1)	3		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)														---	---	---	---
FYN	2534	broad.mit.edu	37	6	112082054	112082054	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112082054delC	uc003pvj.2	-						FYN_uc003pvi.2_5'Flank|FYN_uc003pvk.2_Intron	NM_002037	NP_002028			protein-tyrosine kinase fyn isoform a						axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	112201272	112201273	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112201272_112201273insA								FYN (6645 upstream) : WISP3 (174005 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	112799806	112799807	+	IGR	DEL	TG	-	-	rs66566229		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112799806_112799807delTG								RFPL4B (127308 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	113434962	113434962	+	IGR	DEL	A	-	-	rs5879202		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113434962delA								RFPL4B (762464 upstream) : MARCKS (743565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114714426	114714427	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114714426_114714427insT								HS3ST5 (50886 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116080226	116080226	+	IGR	DEL	T	-	-	rs146555923		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116080226delT								None (None upstream) : FRK (182467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116224385	116224386	+	IGR	DEL	AC	-	-	rs143567384		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116224385_116224386delAC								None (None upstream) : FRK (38307 downstream)																																			---	---	---	---
DSE	29940	broad.mit.edu	37	6	116642501	116642501	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116642501delT	uc003pws.2	+						DSE_uc011ebf.1_Intron|DSE_uc003pwq.1_Intron|DSE_uc003pwr.2_Intron	NM_001080976	NP_001074445			dermatan sulfate epimerase precursor						dermatan sulfate biosynthetic process	endoplasmic reticulum|Golgi apparatus|integral to membrane	chondroitin-glucuronate 5-epimerase activity			ovary(1)	1		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)														---	---	---	---
GPRC6A	222545	broad.mit.edu	37	6	117132995	117132995	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117132995delA	uc003pxj.1	-						GPRC6A_uc003pxk.1_Intron|GPRC6A_uc003pxl.1_Intron	NM_148963	NP_683766			G protein-coupled receptor, family C, group 6,						response to amino acid stimulus		G-protein coupled receptor activity			ovary(4)|skin(2)	6		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	117275772	117275773	+	IGR	INS	-	G	G	rs150193495	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117275772_117275773insG								RFX6 (22464 upstream) : VGLL2 (310948 downstream)																																			---	---	---	---
GOPC	57120	broad.mit.edu	37	6	117767247	117767247	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117767247delA	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								---	---	---	---
Unknown	0	broad.mit.edu	37	6	119910995	119910998	+	IGR	DEL	ATCA	-	-	rs149756682		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119910995_119910998delATCA								MAN1A1 (240069 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	123278321	123278322	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123278321_123278322insA								SMPDL3A (147459 upstream) : CLVS2 (39260 downstream)																																			---	---	---	---
CLVS2	134829	broad.mit.edu	37	6	123373247	123373248	+	Intron	INS	-	A	A	rs140357597	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123373247_123373248insA	uc003pzi.1	+							NM_001010852	NP_001010852			retinaldehyde binding protein 1-like 2						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124710862	124710865	+	Intron	DEL	TGTG	-	-	rs148565355		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124710862_124710865delTGTG	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304			T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	125713613	125713614	+	IGR	INS	-	A	A	rs71541268	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125713613_125713614insA								HDDC2 (90331 upstream) : HEY2 (355166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	126097976	126097976	+	IGR	DEL	T	-	-	rs13220179		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126097976delT								HEY2 (15562 upstream) : NCOA7 (4352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	126986437	126986437	+	Intron	DEL	G	-	-	rs66526406		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126986437delG	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127032134	127032135	+	Intron	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127032134_127032135delAG	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
ECHDC1	55862	broad.mit.edu	37	6	127633204	127633204	+	Intron	DEL	A	-	-	rs111435615		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127633204delA	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	128901158	128901158	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128901158delT								PTPRK (59288 upstream) : LAMA2 (303128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	128903333	128903333	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128903333delT								PTPRK (61463 upstream) : LAMA2 (300953 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	129082444	129082444	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129082444delG								PTPRK (240574 upstream) : LAMA2 (121842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	130253501	130253504	+	IGR	DEL	AAAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130253501_130253504delAAAG								C6orf191 (71085 upstream) : L3MBTL3 (86230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	131004317	131004318	+	IGR	DEL	AC	-	-	rs138613477		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131004317_131004318delAC								TMEM200A (240109 upstream) : LOC285733 (144006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	131430139	131430139	+	IGR	DEL	G	-	-	rs67750482		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131430139delG								EPB41L2 (45677 upstream) : AKAP7 (26732 downstream)																																			---	---	---	---
STX7	8417	broad.mit.edu	37	6	132804117	132804117	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132804117delA	uc003qdg.2	-						STX7_uc011ecg.1_Intron|STX7_uc011ech.1_Intron	NM_003569	NP_003560			syntaxin 7						intracellular protein transport|post-Golgi vesicle-mediated transport	early endosome membrane|integral to membrane	SNAP receptor activity				0	Breast(56;0.0615)			OV - Ovarian serous cystadenocarcinoma(155;0.00532)|GBM - Glioblastoma multiforme(226;0.0114)														---	---	---	---
EYA4	2070	broad.mit.edu	37	6	133749037	133749037	+	Intron	DEL	A	-	-	rs71743373		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133749037delA	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	133979295	133979296	+	Intron	INS	-	TG	TG	rs146613308	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133979295_133979296insTG	uc003qeg.1	-											Homo sapiens cDNA FLJ36194 fis, clone TESTI2027615.																														---	---	---	---
C6orf217	100131814	broad.mit.edu	37	6	135966413	135966413	+	Intron	DEL	A	-	-	rs78760145		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135966413delA	uc003qgn.2	+						C6orf217_uc003qgo.2_Intron|C6orf217_uc010kgo.2_Intron					Homo sapiens cDNA clone IMAGE:4795512.												0																		---	---	---	---
PDE7B	27115	broad.mit.edu	37	6	136367371	136367371	+	Intron	DEL	A	-	-	rs34990837		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136367371delA	uc003qgp.2	+						uc003qgq.1_Intron|PDE7B_uc003qgr.2_Intron|uc003qgs.1_Intron	NM_018945	NP_061818			phosphodiesterase 7B						signal transduction|synaptic transmission	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(1)	1	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Dyphylline(DB00651)|Ketotifen(DB00920)													---	---	---	---
PDE7B	27115	broad.mit.edu	37	6	136387185	136387189	+	Intron	DEL	TTTGT	-	-	rs66714948		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136387185_136387189delTTTGT	uc003qgp.2	+						uc003qgq.1_Intron|PDE7B_uc003qgr.2_Intron|uc003qgs.1_Intron	NM_018945	NP_061818			phosphodiesterase 7B						signal transduction|synaptic transmission	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(1)	1	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Dyphylline(DB00651)|Ketotifen(DB00920)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	136534965	136534966	+	Intron	INS	-	AC	AC	rs144908316	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136534965_136534966insAC	uc003qgq.1	-											Homo sapiens cDNA clone IMAGE:5266948.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	137851885	137851885	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137851885delT								OLIG3 (36354 upstream) : TNFAIP3 (336696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138125374	138125375	+	IGR	DEL	AC	-	-	rs112243361		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138125374_138125375delAC								OLIG3 (309843 upstream) : TNFAIP3 (63206 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138156071	138156072	+	Intron	INS	-	GGAA	GGAA	rs7766931	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138156071_138156072insGGAA	uc003qhq.1	-											Homo sapiens cDNA FLJ42179 fis, clone THYMU2030796.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	140245749	140245750	+	IGR	INS	-	TTC	TTC	rs71892306		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140245749_140245750insTTC								CITED2 (549964 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	140702708	140702711	+	IGR	DEL	CACA	-	-	rs112286795	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140702708_140702711delCACA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141427633	141427634	+	IGR	INS	-	TGTG	TGTG	rs142224058	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141427633_141427634insTGTG								None (None upstream) : NMBR (969112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	142232095	142232095	+	Intron	DEL	A	-	-	rs147734905		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142232095delA	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																														---	---	---	---
VTA1	51534	broad.mit.edu	37	6	142536577	142536578	+	Intron	INS	-	A	A	rs145881910		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142536577_142536578insA	uc003qiw.2	+						VTA1_uc011edt.1_Intron|VTA1_uc011edu.1_Intron	NM_016485	NP_057569			Vps20-associated 1 homolog						cellular membrane organization|endosome transport|protein transport	cytosol|endosome membrane	protein binding				0	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;1.34e-05)|GBM - Glioblastoma multiforme(68;0.00182)														---	---	---	---
HIVEP2	3097	broad.mit.edu	37	6	143124703	143124704	+	Intron	INS	-	ACAC	ACAC	rs148800522	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143124703_143124704insACAC	uc003qjd.2	-							NM_006734	NP_006725			human immunodeficiency virus type I enhancer						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)														---	---	---	---
AIG1	51390	broad.mit.edu	37	6	143469956	143469957	+	Intron	INS	-	A	A	rs75465637		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143469956_143469957insA	uc003qjh.2	+						AIG1_uc003qjf.2_Intron|AIG1_uc003qji.2_Intron|AIG1_uc011edw.1_Intron|AIG1_uc003qjg.2_Intron	NM_016108	NP_057192			androgen-induced 1							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(155;2.34e-05)|GBM - Glioblastoma multiforme(68;0.0246)														---	---	---	---
PHACTR2	9749	broad.mit.edu	37	6	144077223	144077223	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144077223delA	uc003qjq.3	+						PHACTR2_uc010khh.2_Intron|PHACTR2_uc010khi.2_Intron|PHACTR2_uc003qjr.3_Intron	NM_014721	NP_055536			phosphatase and actin regulator 2 isoform 3								actin binding|protein phosphatase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146241631	146241632	+	Intron	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146241631_146241632delTC	uc003qlf.2	-						SHPRH_uc003qld.2_Intron|SHPRH_uc003qle.2_Intron|SHPRH_uc003qlg.1_Intron|SHPRH_uc003qlh.2_Intron|SHPRH_uc003qli.1_Intron	NM_001042683	NP_001036148			SNF2 histone linker PHD RING helicase isoform a						DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)														---	---	---	---
STXBP5	134957	broad.mit.edu	37	6	147531532	147531533	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147531532_147531533insT	uc003qlz.2	+						STXBP5_uc010khz.1_Intron|STXBP5_uc003qlx.2_Intron|STXBP5_uc003qly.2_Intron	NM_001127715	NP_001121187			syntaxin binding protein 5 (tomosyn) isoform b						exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	148434350	148434351	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148434350_148434351insT								SAMD5 (543193 upstream) : SASH1 (229378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	148644002	148644005	+	IGR	DEL	TCTT	-	-	rs67436106		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148644002_148644005delTCTT								SAMD5 (752845 upstream) : SASH1 (19724 downstream)																																			---	---	---	---
SASH1	23328	broad.mit.edu	37	6	148870950	148870951	+	3'UTR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148870950_148870951insT	uc003qme.1	+	20					SASH1_uc003qmf.1_3'UTR	NM_015278	NP_056093			SAM and SH3 domain containing 1								protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	149458064	149458064	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149458064delG								UST (59939 upstream) : TAB2 (81695 downstream)																																			---	---	---	---
PCMT1	5110	broad.mit.edu	37	6	150073339	150073339	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150073339delT	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	150088394	150088395	+	Intron	INS	-	T	T	rs75871516		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150088394_150088395insT	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	150098975	150098978	+	Intron	DEL	TCCT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150098975_150098978delTCCT	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)														---	---	---	---
RAET1E	135250	broad.mit.edu	37	6	150212620	150212621	+	5'Flank	INS	-	TGTG	TGTG	rs145898636	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150212620_150212621insTGTG	uc003qnl.1	-						uc003qni.1_Intron|RAET1E_uc003qnj.2_Intron|RAET1E_uc003qnk.1_5'Flank|RAET1E_uc010kih.1_5'Flank	NM_139165	NP_631904			retinoic acid early transcript 1E precursor						antigen processing and presentation|immune response|regulation of immune response	integral to membrane|MHC class I protein complex	protein binding				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)														---	---	---	---
PLEKHG1	57480	broad.mit.edu	37	6	150931224	150931224	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150931224delT	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron	NM_001029884	NP_001025055			pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)														---	---	---	---
PLEKHG1	57480	broad.mit.edu	37	6	150964079	150964079	+	Intron	DEL	A	-	-	rs77269211		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150964079delA	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron	NM_001029884	NP_001025055			pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)														---	---	---	---
PLEKHG1	57480	broad.mit.edu	37	6	151132409	151132410	+	Intron	INS	-	T	T	rs34705005		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151132409_151132410insT	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)														---	---	---	---
AKAP12	9590	broad.mit.edu	37	6	151599341	151599344	+	Intron	DEL	TTTG	-	-	rs112508328		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151599341_151599344delTTTG	uc011eep.1	+						AKAP12_uc003qoe.2_Intron	NM_005100	NP_005091			A kinase (PRKA) anchor protein 12 isoform 1						G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting	cell cortex|cytoskeleton|plasma membrane	adenylate cyclase binding|protein kinase A binding			large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	8		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	153268506	153268506	+	IGR	DEL	T	-	-	rs67924730		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153268506delT								VIP (187608 upstream) : FBXO5 (23154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153469781	153469782	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153469781_153469782insA								RGS17 (17392 upstream) : OPRM1 (861854 downstream)																																			---	---	---	---
IPCEF1	26034	broad.mit.edu	37	6	154538567	154538567	+	Intron	DEL	G	-	-	rs66900674		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154538567delG	uc003qpx.2	-						OPRM1_uc003qpt.1_Intron|IPCEF1_uc003qpw.2_Intron|IPCEF1_uc010kjh.2_Intron	NM_015553	NP_056368			phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0																		---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155444319	155444320	+	Intron	INS	-	T	T	rs71801312		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155444319_155444320insT	uc003qqb.2	+						TIAM2_uc003qqe.2_Intron	NM_012454	NP_036586			T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	156147442	156147443	+	IGR	DEL	AA	-	-	rs148457516		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156147442_156147443delAA								NOX3 (370405 upstream) : MIR1202 (120488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156362842	156362843	+	IGR	INS	-	A	A	rs61683313		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156362842_156362843insA								MIR1202 (94829 upstream) : ARID1B (736243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156879644	156879644	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156879644delA								MIR1202 (611631 upstream) : ARID1B (219442 downstream)																																			---	---	---	---
SYNJ2	8871	broad.mit.edu	37	6	158511575	158511575	+	Intron	DEL	T	-	-	rs66516903		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158511575delT	uc003qqx.1	+						SYNJ2_uc003qqw.1_Intron|SYNJ2_uc003qqy.1_Intron|SYNJ2_uc003qqz.1_Intron|SYNJ2_uc003qra.1_Intron|SYNJ2_uc010kjp.1_Intron	NM_003898	NP_003889			synaptojanin 2								nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)														---	---	---	---
FNDC1	84624	broad.mit.edu	37	6	159646224	159646227	+	Intron	DEL	CACG	-	-	rs149700143	by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159646224_159646227delCACG	uc010kjv.2	+						FNDC1_uc010kjw.1_Intron	NM_032532	NP_115921			fibronectin type III domain containing 1							extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	160179288	160179288	+	IGR	DEL	A	-	-	rs113734462		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160179288delA								WTAP (1939 upstream) : ACAT2 (3701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	160356319	160356320	+	IGR	DEL	CA	-	-	rs71854069		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160356319_160356320delCA								MAS1 (27214 upstream) : IGF2R (33811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	161248207	161248207	+	IGR	DEL	G	-	-	rs13212550	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161248207delG								PLG (73862 upstream) : MAP3K4 (164615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	161276362	161276364	+	IGR	DEL	CAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161276362_161276364delCAT								PLG (102017 upstream) : MAP3K4 (136458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	161278570	161278571	+	IGR	INS	-	T	T	rs143722280	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161278570_161278571insT								PLG (104225 upstream) : MAP3K4 (134251 downstream)																																			---	---	---	---
AGPAT4	56895	broad.mit.edu	37	6	161613066	161613066	+	Intron	DEL	C	-	-	rs113602351		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161613066delC	uc003qtr.1	-						AGPAT4_uc003qts.1_Intron|AGPAT4_uc011egb.1_Intron|AGPAT4_uc003qtt.1_Intron|AGPAT4_uc011egc.1_Intron|AGPAT4_uc011egd.1_Intron|AGPAT4_uc011ege.1_Intron	NM_020133	NP_064518			1-acylglycerol-3-phosphate O-acyltransferase 4						phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	161812469	161812469	+	Intron	DEL	T	-	-	rs72102149		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161812469delT	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	161846135	161846136	+	Intron	INS	-	CT	CT	rs148007611	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161846135_161846136insCT	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	161887095	161887096	+	Intron	DEL	TG	-	-	rs113714185		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161887095_161887096delTG	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)														---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163655280	163655281	+	Intron	INS	-	GGTGTGT	GGTGTGT	rs145634457	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163655280_163655281insGGTGTGT	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623			parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	163771674	163771676	+	IGR	DEL	TAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163771674_163771676delTAT								LOC285796 (26180 upstream) : QKI (63999 downstream)																																			---	---	---	---
QKI	9444	broad.mit.edu	37	6	163887483	163887484	+	Intron	INS	-	AGAA	AGAA	rs140526739	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163887483_163887484insAGAA	uc003qui.2	+						QKI_uc003que.2_Intron|QKI_uc003quf.2_Intron|QKI_uc003qug.2_Intron|QKI_uc003quh.2_Intron|QKI_uc003quj.2_Intron	NM_006775	NP_006766			quaking homolog, KH domain RNA binding isoform						mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	164225143	164225143	+	IGR	DEL	A	-	-	rs34541824		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164225143delA								QKI (230251 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164349740	164349741	+	IGR	INS	-	GCTCC	GCTCC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164349740_164349741insGCTCC								QKI (354848 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164695424	164695424	+	IGR	DEL	T	-	-	rs67415547		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164695424delT								QKI (700532 upstream) : C6orf118 (997731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	166305210	166305212	+	Intron	DEL	TTC	-	-	rs67224922		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166305210_166305212delTTC	uc003qup.1	-											Homo sapiens cDNA FLJ33369 fis, clone BRACE2005904.																														---	---	---	---
C6orf176	90632	broad.mit.edu	37	6	166366347	166366347	+	Intron	DEL	A	-	-	rs34934698		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166366347delA	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	166433495	166433496	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166433495_166433496insA								LOC441177 (30392 upstream) : T (137590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	167860180	167860181	+	IGR	INS	-	A	A	rs77349029		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167860180_167860181insA								TCP10 (62182 upstream) : C6orf123 (325040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168052560	168052561	+	IGR	DEL	GA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168052560_168052561delGA								TCP10 (254562 upstream) : C6orf123 (132660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168128646	168128646	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168128646delA								TCP10 (330648 upstream) : C6orf123 (56575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168659356	168659356	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168659356delT								FRMD1 (179517 upstream) : DACT2 (48230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	169121050	169121051	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169121050_169121051insT								SMOC2 (52379 upstream) : THBS2 (494825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	169297916	169297917	+	IGR	DEL	TC	-	-	rs66578710		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169297916_169297917delTC								SMOC2 (229245 upstream) : THBS2 (317959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	184435	184436	+	IGR	INS	-	T	T	rs149802465	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:184435_184436insT								None (None upstream) : FAM20C (8533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	534287	534288	+	IGR	INS	-	C	C	rs151031139	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:534287_534288insC								FAM20C (233576 upstream) : PDGFA (2611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1323122	1323123	+	IGR	INS	-	TT	TT	rs139796883	by1000genomes;byFrequency	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1323122_1323123insTT								UNCX (46510 upstream) : MICALL2 (150873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1375834	1375835	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1375834_1375835insA								UNCX (99222 upstream) : MICALL2 (98161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1552662	1552663	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1552662_1552663delTT								INTS1 (8644 upstream) : MAFK (17705 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1735913	1735914	+	5'Flank	INS	-	GA	GA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1735913_1735914insGA	uc003slc.1	-											SubName: Full=LOC401296 protein;																														---	---	---	---
MAD1L1	8379	broad.mit.edu	37	7	1889435	1889436	+	Intron	INS	-	GGCAGC	GGCAGC	rs141924718	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1889435_1889436insGGCAGC	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc003sld.1_Intron|uc003slj.1_RNA	NM_001013836	NP_001013858			MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)														---	---	---	---
MAD1L1	8379	broad.mit.edu	37	7	2060398	2060398	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2060398delT	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc010ksj.2_Intron	NM_001013836	NP_001013858			MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	2435270	2435277	+	IGR	DEL	GATAGATG	-	-	rs3074531		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2435270_2435277delGATAGATG								EIF3B (14895 upstream) : CHST12 (7946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	2889946	2889951	+	IGR	DEL	ATCACC	-	-	rs138485369		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2889946_2889951delATCACC								GNA12 (5987 upstream) : CARD11 (55818 downstream)																																			---	---	---	---
CARD11	84433	broad.mit.edu	37	7	3004358	3004359	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3004358_3004359delTG	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								---	---	---	---
Unknown	0	broad.mit.edu	37	7	3285121	3285131	+	IGR	DEL	ACTGAAGCCTT	-	-	rs58267150		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3285121_3285131delACTGAAGCCTT								CARD11 (201542 upstream) : SDK1 (55949 downstream)																																			---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3953614	3953614	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3953614delT	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	3954337	3954337	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3954337delC	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)														---	---	---	---
RADIL	55698	broad.mit.edu	37	7	4847611	4847612	+	Intron	INS	-	CTC	CTC	rs149677631	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4847611_4847612insCTC	uc003snj.1	-						RADIL_uc003sng.1_Intron|RADIL_uc003sni.1_Intron|RADIL_uc011jwc.1_Intron|RADIL_uc011jwd.1_Intron	NM_018059	NP_060529			Rap GTPase interactor						cell adhesion|multicellular organismal development|signal transduction		protein binding			lung(2)|central_nervous_system(2)|pancreas(2)|breast(1)	7		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	5175150	5175150	+	5'Flank	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5175150delA	uc003snu.1	-						uc010ksu.1_5'Flank|uc011jwf.1_Intron					SubName: Full=cDNA FLJ60262, weakly similar to Zinc finger protein 81;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	5194816	5194817	+	IGR	INS	-	AAAG	AAAG	rs140035954	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5194816_5194817insAAAG								LOC389458 (81963 upstream) : WIPI2 (35018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	5281239	5281240	+	IGR	DEL	TT	-	-	rs71891793		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5281239_5281240delTT								WIPI2 (7754 upstream) : SLC29A4 (41321 downstream)																																			---	---	---	---
SLC29A4	222962	broad.mit.edu	37	7	5340894	5340894	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5340894delA	uc003sod.2	+						SLC29A4_uc003soc.2_Intron|SLC29A4_uc003soe.2_Intron|SLC29A4_uc010ksw.2_Intron	NM_153247	NP_694979			solute carrier family 29 (nucleoside						nucleobase, nucleoside and nucleotide metabolic process	apical plasma membrane|integral to membrane	nucleoside transmembrane transporter activity			liver(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)														---	---	---	---
FBXL18	80028	broad.mit.edu	37	7	5533230	5533230	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5533230delT	uc003soo.2	-						FBXL18_uc003son.3_Intron	NM_024963	NP_079239			F-box and leucine-rich repeat protein 18											central_nervous_system(2)|ovary(1)	3		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	5579707	5579708	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5579707_5579708insA								ACTB (9475 upstream) : FSCN1 (52746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	6107411	6107412	+	IGR	INS	-	T	T	rs139623058	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6107411_6107412insT								EIF2AK1 (8551 upstream) : USP42 (37138 downstream)																																			---	---	---	---
USP42	84132	broad.mit.edu	37	7	6199760	6199764	+	Intron	DEL	GAAAG	-	-	rs74541050		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6199760_6199764delGAAAG	uc011jwp.1	+						USP42_uc011jwq.1_Intron	NM_032172	NP_115548			ubiquitin specific peptidase 42						cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)												OREG0017860	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	7	6954620	6954621	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6954620_6954621insT								C7orf28B (88759 upstream) : C1GALT1 (267625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	7982518	7982518	+	IGR	DEL	T	-	-	rs35521476		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7982518delT								RPA3 (224280 upstream) : GLCCI1 (25905 downstream)																																			---	---	---	---
GLCCI1	113263	broad.mit.edu	37	7	8033419	8033420	+	Intron	INS	-	A	A	rs75430388		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8033419_8033420insA	uc003srk.2	+							NM_138426	NP_612435			glucocorticoid induced transcript 1												0		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)														---	---	---	---
GLCCI1	113263	broad.mit.edu	37	7	8080156	8080159	+	Intron	DEL	ACAC	-	-	rs112264935		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8080156_8080159delACAC	uc003srk.2	+							NM_138426	NP_612435			glucocorticoid induced transcript 1												0		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)														---	---	---	---
ICA1	3382	broad.mit.edu	37	7	8207656	8207657	+	Intron	INS	-	AG	AG	rs149474890	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8207656_8207657insAG	uc003srm.2	-						ICA1_uc010ktr.2_Intron|ICA1_uc003srl.2_Intron|ICA1_uc003srn.3_Intron|ICA1_uc003srp.3_Intron|ICA1_uc010kts.2_Intron|ICA1_uc003srq.2_Intron|ICA1_uc003srr.2_Intron|ICA1_uc003sro.3_Intron|ICA1_uc011jxg.1_Intron|ICA1_uc003srs.1_Intron	NM_022307	NP_071682			islet cell autoantigen 1						neurotransmitter transport	cell junction|cytosol|Golgi membrane|nucleus|secretory granule membrane|synaptic vesicle membrane|transport vesicle membrane				central_nervous_system(1)	1		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)														---	---	---	---
ICA1	3382	broad.mit.edu	37	7	8272666	8272666	+	Intron	DEL	C	-	-	rs71545885		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8272666delC	uc003srm.2	-						ICA1_uc010ktr.2_Intron|ICA1_uc003srl.2_Intron|ICA1_uc003srn.3_Intron|ICA1_uc003srp.3_Intron|ICA1_uc010kts.2_Intron|ICA1_uc003srq.2_Intron|ICA1_uc003srr.2_Intron|ICA1_uc003sro.3_Intron|ICA1_uc011jxg.1_Intron|ICA1_uc003srs.1_Intron	NM_022307	NP_071682			islet cell autoantigen 1						neurotransmitter transport	cell junction|cytosol|Golgi membrane|nucleus|secretory granule membrane|synaptic vesicle membrane|transport vesicle membrane				central_nervous_system(1)	1		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	8378262	8378262	+	Intron	DEL	C	-	-	rs35032386		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8378262delC	uc003srt.1	+											full-length cDNA clone CS0DC002YA18 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	9299469	9299476	+	IGR	DEL	AGAGAGAG	-	-	rs71547634		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9299469_9299476delAGAGAGAG								NXPH1 (506877 upstream) : PER4 (374424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9866704	9866705	+	IGR	INS	-	A	A	rs33948402		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9866704_9866705insA								PER4 (191257 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10179204	10179204	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10179204delT								PER4 (503757 upstream) : NDUFA4 (793611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10510701	10510712	+	IGR	DEL	ACACACACACAC	-	-	rs111285329		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10510701_10510712delACACACACACAC								PER4 (835254 upstream) : NDUFA4 (462103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10915832	10915835	+	IGR	DEL	AAAG	-	-	rs76362644		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10915832_10915835delAAAG								None (None upstream) : NDUFA4 (56980 downstream)																																			---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11188211	11188214	+	Intron	DEL	TTAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11188211_11188214delTTAT	uc003srz.2	+						PHF14_uc011jxj.1_Intron|PHF14_uc003ssa.2_Intron	NM_001007157	NP_001007158			PHD finger protein 14 isoform 1								zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)														---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11553567	11553568	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11553567_11553568delCA	uc003ssf.3	-							NM_015204	NP_056019			thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	12758275	12758276	+	IGR	DEL	CT	-	-	rs113310219		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12758275_12758276delCT								ARL4A (27719 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	12774095	12774096	+	IGR	INS	-	T	T	rs137938267	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12774095_12774096insT								ARL4A (43539 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	12887376	12887379	+	IGR	DEL	TTTC	-	-	rs141286153		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12887376_12887379delTTTC								ARL4A (156820 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13205847	13205848	+	IGR	INS	-	AA	AA	rs148608699	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13205847_13205848insAA								ARL4A (475291 upstream) : ETV1 (725010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13351149	13351150	+	IGR	INS	-	TACCTTAGGA	TACCTTAGGA	rs148833138	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13351149_13351150insTACCTTAGGA								ARL4A (620593 upstream) : ETV1 (579708 downstream)																																			---	---	---	---
ETV1	2115	broad.mit.edu	37	7	13958500	13958501	+	Intron	DEL	AA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13958500_13958501delAA	uc011jxq.1	-						ETV1_uc011jxn.1_Intron|ETV1_uc011jxo.1_Intron|ETV1_uc011jxp.1_Intron|ETV1_uc003ssw.3_Intron|ETV1_uc003ssx.2_Intron|ETV1_uc011jxr.1_Intron|ETV1_uc011jxs.1_Intron|ETV1_uc010ktv.2_Intron	NM_004956	NP_004947			ets variant gene 1 isoform a						transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		TMPRSS2/ETV1(24)|EWSR1/ETV1(7)	prostate(24)|soft_tissue(4)|bone(3)|lung(2)|central_nervous_system(1)|ovary(1)	35								T	EWSR1|TMPRSS2|SLC45A3|C15orf21|HNRNPA2B1. ACSL3	Ewing sarcoma|prostate								---	---	---	---
Unknown	0	broad.mit.edu	37	7	15035197	15035200	+	IGR	DEL	TCTC	-	-	rs139020036		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15035197_15035200delTCTC								DGKB (92647 upstream) : TMEM195 (204743 downstream)																																			---	---	---	---
MEOX2	4223	broad.mit.edu	37	7	15711726	15711727	+	Intron	INS	-	A	A	rs68131578		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15711726_15711727insA	uc003stc.2	-						MEOX2_uc011jxw.1_Intron|uc003ste.2_Intron	NM_005924	NP_005915			mesenchyme homeobox 2						blood circulation|multicellular organismal development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)														---	---	---	---
ISPD	729920	broad.mit.edu	37	7	16386146	16386147	+	Intron	INS	-	A	A	rs138016674	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16386146_16386147insA	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	16922973	16922974	+	5'Flank	INS	-	CCTC	CCTC	rs150943300	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16922973_16922974insCCTC	uc003sts.2	-							NM_176813	NP_789783			breast cancer membrane protein 11 precursor							extracellular region					0	Lung NSC(10;0.0376)|all_lung(11;0.0721)|all_epithelial(12;0.202)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	17330378	17330381	+	IGR	DEL	ACAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17330378_17330381delACAC								AGR3 (408765 upstream) : AHR (7895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	17602001	17602002	+	IGR	INS	-	T	T	rs143193115	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17602001_17602002insT								AHR (216226 upstream) : SNX13 (228384 downstream)																																			---	---	---	---
SNX13	23161	broad.mit.edu	37	7	17884777	17884780	+	Intron	DEL	ACAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17884777_17884780delACAC	uc003stw.1	-						SNX13_uc003stv.2_Intron|SNX13_uc010kuc.2_Intron					SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;						cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)																	---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18137088	18137089	+	Intron	INS	-	T	T	rs34184774		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18137088_18137089insT	uc011jya.1	+							NM_014707	NP_055522			histone deacetylase 9 isoform 3						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18225868	18225868	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18225868delT	uc011jya.1	+							NM_014707	NP_055522			histone deacetylase 9 isoform 3						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18767068	18767068	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18767068delT	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc011jyd.1_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003sua.1_Intron|HDAC9_uc010kue.1_Intron	NM_058176	NP_478056			histone deacetylase 9 isoform 1						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	19251345	19251345	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19251345delT								FERD3L (66301 upstream) : TWISTNB (483740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20086005	20086005	+	IGR	DEL	C	-	-	rs34391590		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20086005delC								TMEM196 (272789 upstream) : MACC1 (88283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20293685	20293686	+	IGR	INS	-	T	T	rs150932879	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20293685_20293686insT								MACC1 (36672 upstream) : ITGB8 (76639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20523470	20523470	+	IGR	DEL	C	-	-	rs36071306		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20523470delC								ITGB8 (68092 upstream) : ABCB5 (131775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20831745	20831745	+	IGR	DEL	C	-	-	rs34168465		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20831745delC								SP8 (5237 upstream) : RPL23P8 (35172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	21036435	21036435	+	IGR	DEL	T	-	-	rs35846964		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21036435delT								RPL23P8 (168996 upstream) : SP4 (431254 downstream)																																			---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21584302	21584302	+	Intron	DEL	T	-	-	rs72103781		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21584302delT	uc003svc.2	+							NM_003777	NP_003768			dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21653553	21653553	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21653553delT	uc003svc.2	+							NM_003777	NP_003768			dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	22423867	22423868	+	IGR	INS	-	G	G	rs11768870		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22423867_22423868insG								RAPGEF5 (27334 upstream) : MGC87042 (35198 downstream)																																			---	---	---	---
MGC87042	256227	broad.mit.edu	37	7	22538351	22538351	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22538351delA	uc003svh.2	-						MGC87042_uc010kum.1_Intron					SubName: Full=cDNA FLJ60218, highly similar to Six transmembrane epithelial antigen ofprostate 1;							integral to membrane	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	22722002	22722003	+	IGR	INS	-	GGA	GGA	rs144180327	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22722002_22722003insGGA								MGC87042 (182204 upstream) : IL6 (43500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	22882991	22882999	+	IGR	DEL	TGGTGTTGT	-	-	rs58631719	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22882991_22882999delTGGTGTTGT								TOMM7 (20570 upstream) : SNORD93 (13233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	23243791	23243792	+	5'Flank	INS	-	T	T	rs142310028	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23243791_23243792insT	uc003svz.1	+											Homo sapiens cDNA FLJ25144 fis, clone CBR07272.																														---	---	---	---
IGF2BP3	10643	broad.mit.edu	37	7	23396013	23396014	+	Intron	INS	-	AA	AA	rs75189758		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23396013_23396014insAA	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	24234699	24234700	+	IGR	INS	-	TAA	TAA	rs148677912	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24234699_24234700insTAA								STK31 (290334 upstream) : NPY (89109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	24239750	24239750	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24239750delA								STK31 (295385 upstream) : NPY (84059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25286950	25286950	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25286950delG								NPVF (18845 upstream) : MIR148A (702589 downstream)																																			---	---	---	---
JAZF1	221895	broad.mit.edu	37	7	28142217	28142218	+	Intron	INS	-	A	A	rs142911060	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28142217_28142218insA	uc003szn.2	-							NM_175061	NP_778231			JAZF zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcriptional repressor complex	nucleic acid binding|transcription corepressor activity|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131								T	SUZ12	endometrial stromal tumours								---	---	---	---
CHN2	1124	broad.mit.edu	37	7	29253504	29253505	+	Intron	INS	-	A	A	rs141768623	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29253504_29253505insA	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron	NM_004067	NP_004058			beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2																		---	---	---	---
CHN2	1124	broad.mit.edu	37	7	29359055	29359056	+	Intron	INS	-	T	T	rs143515231	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29359055_29359056insT	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron	NM_004067	NP_004058			beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2																		---	---	---	---
CHN2	1124	broad.mit.edu	37	7	29473458	29473458	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29473458delA	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron	NM_004067	NP_004058			beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2																		---	---	---	---
CHN2	1124	broad.mit.edu	37	7	29511197	29511197	+	Intron	DEL	A	-	-	rs3842624		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29511197delA	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron	NM_004067	NP_004058			beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2																		---	---	---	---
FAM188B	84182	broad.mit.edu	37	7	30807056	30807057	+	Intron	DEL	AT	-	-	rs72281152		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30807056_30807057delAT	uc010kwe.2	+							NM_032222	NP_115598			hypothetical protein LOC84182												0																		---	---	---	---
GHRHR	2692	broad.mit.edu	37	7	31006257	31006258	+	Intron	INS	-	T	T	rs142835664	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31006257_31006258insT	uc003tbx.2	+						GHRHR_uc003tbw.1_Intron|GHRHR_uc003tby.2_5'Flank|GHRHR_uc003tbz.2_5'Flank	NM_000823	NP_000814			growth hormone releasing hormone receptor						activation of adenylate cyclase activity by G-protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of cell proliferation|positive regulation of growth hormone secretion|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of multicellular organism growth|response to estrogen stimulus|response to glucocorticoid stimulus	cell surface|integral to membrane|nuclear inner membrane|nuclear matrix|nuclear outer membrane|plasma membrane|stored secretory granule	growth factor binding|growth hormone-releasing hormone receptor activity|peptide hormone binding			ovary(2)|lung(1)|breast(1)|large_intestine(1)	5					Sermorelin(DB00010)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	31148360	31148361	+	RNA	INS	-	TG	TG	rs146476306	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31148360_31148361insTG	uc003tcg.2	+	1		c.919_920insTG								Homo sapiens cDNA FLJ39226 fis, clone OCBBF2007232.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	31328413	31328413	+	IGR	DEL	T	-	-	rs5883275		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31328413delT								ADCYAP1R1 (182102 upstream) : NEUROD6 (48669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	31330852	31330853	+	IGR	INS	-	T	T	rs147673881	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31330852_31330853insT								ADCYAP1R1 (184541 upstream) : NEUROD6 (46229 downstream)																																			---	---	---	---
PDE1C	5137	broad.mit.edu	37	7	32041151	32041152	+	Intron	INS	-	A	A	rs148169948	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32041151_32041152insA	uc003tcm.1	-						PDE1C_uc003tcn.1_Intron|PDE1C_uc003tco.1_Intron|PDE1C_uc003tcr.2_Intron|PDE1C_uc003tcs.2_Intron	NM_005020	NP_005011			phosphodiesterase 1C						activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)															---	---	---	---
PDE1C	5137	broad.mit.edu	37	7	32290873	32290880	+	Intron	DEL	AGCCCAGG	-	-	rs72360042		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32290873_32290880delAGCCCAGG	uc003tco.1	-							NM_005020	NP_005011			phosphodiesterase 1C						activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)															---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32668807	32668808	+	Intron	DEL	GT	-	-	rs74825116		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32668807_32668808delGT	uc011kai.1	+						uc003tcw.2_Intron	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32906427	32906427	+	Intron	DEL	A	-	-	rs113617669		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32906427delA	uc011kai.1	+							NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33601892	33601892	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33601892delA	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				---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	35045423	35045423	+	Intron	DEL	A	-	-	rs5883491		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35045423delA	uc003tem.3	-							NM_015283	NP_056098			dpy-19-like 1							integral to membrane					0																		---	---	---	---
TBX20	57057	broad.mit.edu	37	7	35258536	35258536	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35258536delC	uc011kas.1	-							NM_001077653	NP_001071121			T-box transcription factor TBX20							nucleus	DNA binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	36084910	36084910	+	IGR	DEL	T	-	-	rs2700936	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36084910delT								SEPT7 (139995 upstream) : EEPD1 (107926 downstream)																																			---	---	---	---
EEPD1	80820	broad.mit.edu	37	7	36210924	36210925	+	Intron	INS	-	AT	AT	rs146673998	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36210924_36210925insAT	uc003tfa.2	+							NM_030636	NP_085139			endonuclease/exonuclease/phosphatase family						DNA repair		DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	36845108	36845108	+	IGR	DEL	T	-	-	rs111285035		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36845108delT								AOAH (80955 upstream) : ELMO1 (48853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	37618204	37618207	+	IGR	DEL	TGCT	-	-	rs140401006		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37618204_37618207delTGCT								ELMO1 (129674 upstream) : GPR141 (161789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	37837732	37837740	+	Intron	DEL	CCTCTCCCA	-	-	rs150715076		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37837732_37837740delCCTCTCCCA	uc003tfl.2	+											Homo sapiens, clone IMAGE:3881224, mRNA.																														---	---	---	---
EPDR1	54749	broad.mit.edu	37	7	37989210	37989211	+	Intron	DEL	TA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37989210_37989211delTA	uc003tfp.2	+						EPDR1_uc003tfq.2_Intron|EPDR1_uc010kxh.2_Intron	NM_017549	NP_060019			ependymin related protein 1 precursor						cell-matrix adhesion	extracellular region	calcium ion binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
AMPH	273	broad.mit.edu	37	7	38588495	38588496	+	Intron	DEL	GT	-	-	rs57068643		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38588495_38588496delGT	uc003tgu.2	-						AMPH_uc003tgv.2_Intron	NM_001635	NP_001626			amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	39003414	39003415	+	IGR	INS	-	TTT	TTT	rs71558143		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39003414_39003415insTTT								VPS41 (54614 upstream) : POU6F2 (42993 downstream)																																			---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39295737	39295737	+	Intron	DEL	T	-	-	rs36038117		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39295737delT	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	40401187	40401187	+	Intron	DEL	G	-	-	rs6462978	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40401187delG	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	40488182	40488182	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40488182delC	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	41298015	41298016	+	IGR	INS	-	T	T	rs149017303	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41298015_41298016insT								C7orf10 (397658 upstream) : INHBA (430587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41578181	41578182	+	IGR	INS	-	A	A	rs66890613		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41578181_41578182insA								C7orf10 (677824 upstream) : INHBA (150421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41872030	41872030	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41872030delT								LOC285954 (53056 upstream) : GLI3 (128520 downstream)																																			---	---	---	---
BLVRA	644	broad.mit.edu	37	7	43846348	43846349	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43846348_43846349insA	uc003tir.2	+						BLVRA_uc010kxv.2_Intron	NM_000712	NP_000703			biliverdin reductase A precursor						heme catabolic process	cytosol	biliverdin reductase activity|zinc ion binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
POLR2J4	84820	broad.mit.edu	37	7	44052476	44052477	+	Intron	INS	-	A	A	rs148166677		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44052476_44052477insA	uc010kxw.2	-						POLR2J4_uc003tjc.2_Intron|POLR2J4_uc003tjd.2_Intron|POLR2J4_uc003tje.3_Intron					SubName: Full=cDNA FLJ58900, weakly similar to Uroplakin-3B;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	44063278	44063278	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44063278delA								POLR2J4 (4530 upstream) : RASA4P (5208 downstream)																																			---	---	---	---
GCK	2645	broad.mit.edu	37	7	44230941	44230942	+	5'Flank	INS	-	A	A	rs139763106	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44230941_44230942insA	uc003tkl.2	-							NM_000162	NP_000153			glucokinase isoform 1						cellular response to insulin stimulus|cellular response to leptin stimulus|detection of glucose|endocrine pancreas development|glucose homeostasis|glucose transport|glycolysis|negative regulation of gluconeogenesis|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|regulation of glucose transport|regulation of glycolysis|transmembrane transport	cytosol|nucleoplasm	ATP binding|glucokinase activity|glucose binding|protein binding			skin(3)|lung(1)	4																		---	---	---	---
PPIA	5478	broad.mit.edu	37	7	44842433	44842434	+	3'UTR	DEL	AA	-	-	rs66472348		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44842433_44842434delAA	uc003tlw.2	+	5					PPIA_uc003tlx.2_RNA|PPIA_uc010kyl.2_RNA	NM_021130	NP_066953			peptidylprolyl isomerase A						entry into host cell|leukocyte migration|platelet activation|platelet degranulation|protein folding|provirus integration|regulation of viral genome replication|RNA-dependent DNA replication|uncoating of virus	cytosol|extracellular region|nucleus	peptide binding|peptidyl-prolyl cis-trans isomerase activity|unfolded protein binding|virion binding				0					Cyclosporine(DB00091)|L-Proline(DB00172)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	45245826	45245827	+	IGR	INS	-	T	T	rs71565960		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45245826_45245827insT								RAMP3 (21979 upstream) : ADCY1 (367912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	45339363	45339364	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45339363_45339364insA								RAMP3 (115516 upstream) : ADCY1 (274375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	45541666	45541667	+	IGR	INS	-	AACT	AACT	rs144014096	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45541666_45541667insAACT								RAMP3 (317819 upstream) : ADCY1 (72072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46179005	46179005	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46179005delT								IGFBP3 (218134 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	47226680	47226681	+	IGR	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47226680_47226681delTC								None (None upstream) : TNS3 (88072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	48968019	48968019	+	IGR	DEL	T	-	-	rs113397357	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48968019delT								CDC14C (970 upstream) : VWC2 (845238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49697473	49697473	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49697473delA								CDC14C (730424 upstream) : VWC2 (115784 downstream)																																			---	---	---	---
GRB10	2887	broad.mit.edu	37	7	50701406	50701407	+	Intron	INS	-	AACAAC	AACAAC	rs141632476	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50701406_50701407insAACAAC	uc003tpi.2	-						GRB10_uc003tph.3_Intron|GRB10_uc003tpj.2_Intron|GRB10_uc003tpk.2_Intron|GRB10_uc010kzb.2_Intron|GRB10_uc003tpl.2_Intron|GRB10_uc003tpm.2_Intron|GRB10_uc003tpn.2_Intron	NM_005311	NP_005302			growth factor receptor-bound protein 10 isoform						insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			lung(3)|ovary(2)|upper_aerodigestive_tract(1)	6	Glioma(55;0.08)|all_neural(89;0.245)													Russell-Silver_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	52553922	52553923	+	IGR	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52553922_52553923delCA								None (None upstream) : POM121L12 (549426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53311701	53311701	+	IGR	DEL	A	-	-	rs67088403		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53311701delA								POM121L12 (207084 upstream) : HPVC1 (957216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53392613	53392614	+	IGR	INS	-	C	C	rs146282324	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53392613_53392614insC								POM121L12 (287996 upstream) : HPVC1 (876303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53449098	53449098	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53449098delA								POM121L12 (344481 upstream) : HPVC1 (819819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53791282	53791282	+	IGR	DEL	A	-	-	rs75302107		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53791282delA								POM121L12 (686665 upstream) : HPVC1 (477635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54754692	54754692	+	IGR	DEL	A	-	-	rs36079469		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54754692delA								VSTM2A (116505 upstream) : SEC61G (65249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54848836	54848836	+	IGR	DEL	A	-	-	rs113058219		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54848836delA								SEC61G (21897 upstream) : EGFR (237889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54859723	54859723	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54859723delA								SEC61G (32784 upstream) : EGFR (227002 downstream)																																			---	---	---	---
EGFR	1956	broad.mit.edu	37	7	55271158	55271161	+	Intron	DEL	ACAC	-	-	rs141162488		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55271158_55271161delACAC	uc003tqk.2	+						EGFR_uc011kco.1_Intron	NM_005228	NP_005219			epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			---	---	---	---
MRPS17	51373	broad.mit.edu	37	7	56015302	56015302	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56015302delT	uc003trb.2	+							NM_015969	NP_057053			mitochondrial ribosomal protein S17 precursor						translation	mitochondrial small ribosomal subunit	rRNA binding|structural constituent of ribosome				0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	56804254	56804256	+	IGR	DEL	CTT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-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	57553336	57553340	+	IGR	DEL	AGTGG	-	-	rs146767663	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57553336_57553340delAGTGG								ZNF716 (20071 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57609986	57609986	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57609986delG								ZNF716 (76721 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57651750	57651751	+	IGR	INS	-	T	T	rs148924254		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57651750_57651751insT								ZNF716 (118485 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57726740	57726740	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57726740delT								ZNF716 (193475 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57737520	57737525	+	IGR	DEL	ATAATT	-	-	rs111496547		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57737520_57737525delATAATT								ZNF716 (204255 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57914934	57914935	+	IGR	DEL	CC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57914934_57914935delCC								ZNF716 (381669 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61084918	61084919	+	IGR	INS	-	A	A	rs76827969		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61084918_61084919insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61096393	61096393	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61096393delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61763563	61763564	+	IGR	INS	-	TCTT	TCTT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61763563_61763564insTCTT								None (None upstream) : LOC643955 (988108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61859537	61859538	+	IGR	DEL	TG	-	-	rs140811137		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61859537_61859538delTG								None (None upstream) : LOC643955 (892134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63551991	63551992	+	IGR	INS	-	GTGT	GTGT	rs10671953		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63551991_63551992insGTGT								ZNF727 (13066 upstream) : ZNF735 (115589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63633747	63633748	+	IGR	DEL	AA	-	-	rs79924981		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63633747_63633748delAA								ZNF727 (94822 upstream) : ZNF735 (33833 downstream)																																			---	---	---	---
LOC168474	168474	broad.mit.edu	37	7	64314549	64314551	+	5'Flank	DEL	CTT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64314549_64314551delCTT	uc003ttj.1	-							NR_002789				SubName: Full=Selenophosphate synthetase 1; SubName: Full=Selenophosphate synthetase 1, isoform CRA_a;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	65658789	65658790	+	IGR	INS	-	T	T	rs112838689		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65658789_65658790insT								CRCP (39238 upstream) : TPST1 (11469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65964054	65964054	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65964054delA								NCRNA00174 (98659 upstream) : LOC493754 (29392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	66846145	66846146	+	IGR	INS	-	GT	GT	rs139984947	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66846145_66846146insGT								STAG3L4 (59633 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67599360	67599360	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67599360delA								STAG3L4 (812848 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67675359	67675362	+	IGR	DEL	GATA	-	-	rs112648331		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67675359_67675362delGATA								STAG3L4 (888847 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68515377	68515378	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68515377_68515378insT								None (None upstream) : AUTS2 (548527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68626141	68626142	+	IGR	INS	-	AG	AG	rs145924309		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68626141_68626142insAG								None (None upstream) : AUTS2 (437763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68671564	68671564	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68671564delT								None (None upstream) : AUTS2 (392341 downstream)																																			---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69487845	69487846	+	Intron	INS	-	T	T	rs111831842		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69487845_69487846insT	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	69734388	69734389	+	Intron	INS	-	G	G	rs145781363	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69734388_69734389insG	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	70008518	70008518	+	Intron	DEL	A	-	-	rs34091149		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70008518delA	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	70195666	70195666	+	Intron	DEL	T	-	-	rs112099139		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70195666delT	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	70196733	70196734	+	Intron	DEL	CT	-	-	rs34970993		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70196733_70196734delCT	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	70467775	70467775	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70467775delT								AUTS2 (209891 upstream) : WBSCR17 (130014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	70587906	70587907	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70587906_70587907insT								AUTS2 (330022 upstream) : WBSCR17 (9882 downstream)																																			---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	70667979	70667980	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70667979_70667980delCA	uc003tvy.2	+							NM_022479	NP_071924			UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)																---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71593368	71593368	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71593368delA	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)																---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72032118	72032118	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72032118delT	uc011keh.1	-							NM_001145441	NP_001138913			tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0																		---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72284592	72284593	+	Intron	INS	-	A	A	rs113955633		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72284592_72284593insA	uc011kej.1	-						TYW1B_uc011keh.1_Intron|TYW1B_uc011kek.1_Intron	NM_001145440	NP_001138912			tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0																		---	---	---	---
BCL7B	9275	broad.mit.edu	37	7	72960998	72960998	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72960998delA	uc003tyf.1	-						BCL7B_uc003tye.1_Intron|BCL7B_uc003tyg.1_Intron	NM_001707	NP_001698			B-cell CLL/lymphoma 7B								actin binding			ovary(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
TBL2	26608	broad.mit.edu	37	7	72984537	72984538	+	3'UTR	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72984537_72984538delTC	uc003tyh.2	-	7					TBL2_uc011kex.1_3'UTR|TBL2_uc010lbg.2_3'UTR|TBL2_uc003tyi.2_3'UTR|TBL2_uc011key.1_3'UTR|TBL2_uc010lbh.2_3'UTR	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	73015507	73015510	+	Intron	DEL	GTGT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73015507_73015510delGTGT	uc003tyn.1	-						MLXIPL_uc003tyk.1_Intron|MLXIPL_uc003tyl.1_Intron|MLXIPL_uc003tym.1_Intron|MLXIPL_uc003tyo.1_Intron|MLXIPL_uc003typ.1_Intron|MLXIPL_uc003tyq.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)																---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73341194	73341194	+	Intron	DEL	G	-	-	rs67953567		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73341194delG	uc011kfa.1	-							NM_181471				replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73416588	73416588	+	Intron	DEL	T	-	-	rs66780858		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73416588delT	uc011kfa.1	-							NM_181471				replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
EIF4H	7458	broad.mit.edu	37	7	73600242	73600243	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73600242_73600243insA	uc003uad.1	+						RFC2_uc011kfa.1_Intron|EIF4H_uc011kfg.1_Intron|EIF4H_uc010lbm.2_Intron|EIF4H_uc003uae.1_Intron|EIF4H_uc003uaf.1_Intron	NM_022170	NP_071496			eukaryotic translation initiation factor 4H						interspecies interaction between organisms|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex|perinuclear region of cytoplasm	nucleotide binding|protein binding|translation initiation factor activity				0																		---	---	---	---
CLIP2	7461	broad.mit.edu	37	7	73739149	73739151	+	Intron	DEL	AAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73739149_73739151delAAA	uc003uam.2	+						CLIP2_uc003uan.2_Intron	NM_003388	NP_003379			CAP-GLY domain containing linker protein 2							microtubule associated complex				skin(3)	3																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	74011996	74011996	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74011996delA	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
POR	5447	broad.mit.edu	37	7	75586868	75586868	+	Intron	DEL	T	-	-	rs41295414		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75586868delT	uc003udy.2	+							NM_000941	NP_000932			cytochrome P450 reductase						cellular organofluorine metabolic process|positive regulation of monooxygenase activity	endoplasmic reticulum membrane	iron ion binding|NADPH-hemoprotein reductase activity			central_nervous_system(1)	1					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Lipoic Acid(DB00166)|Menadione(DB00170)|Methoxyflurane(DB01028)|Mitomycin(DB00305)|Nilutamide(DB00665)													---	---	---	---
SRRM3	222183	broad.mit.edu	37	7	75868854	75868854	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75868854delA	uc010ldi.2	+							NM_001110199	NP_001103669			serine/arginine repetitive matrix 3												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	76005872	76005872	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76005872delT								YWHAG (17530 upstream) : SRCRB4D (12775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	76072238	76072239	+	IGR	INS	-	ATG	ATG			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76072238_76072239insATG								ZP3 (851 upstream) : DTX2 (18733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	76184341	76184341	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76184341delT	uc003ufs.1	+											Homo sapiens hypothetical LOC554248, mRNA (cDNA clone MGC:87732 IMAGE:5768316), complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	76208541	76208541	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76208541delC	uc003ufs.1	+											Homo sapiens hypothetical LOC554248, mRNA (cDNA clone MGC:87732 IMAGE:5768316), complete cds.																														---	---	---	---
PMS2L11	441263	broad.mit.edu	37	7	76634275	76634280	+	Intron	DEL	TGCTGT	-	-	rs67390349		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-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																		---	---	---	---
PION	54103	broad.mit.edu	37	7	77043174	77043175	+	Intron	INS	-	T	T	rs139450909	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77043174_77043175insT	uc003ugf.2	-							NM_017439	NP_059135			pigeon homolog						beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1																		---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77821840	77821841	+	Intron	INS	-	T	T	rs80229655		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77821840_77821841insT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77867851	77867852	+	Intron	INS	-	AA	AA	rs144481558	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77867851_77867852insAA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	78085305	78085305	+	Intron	DEL	T	-	-	rs112813962		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78085305delT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	78533048	78533049	+	Intron	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78533048_78533049delGT	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	78571049	78571050	+	Intron	INS	-	ACACACAA	ACACACAA	rs148076593	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78571049_78571050insACACACAA	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	79123418	79123418	+	IGR	DEL	T	-	-	rs71518934		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79123418delT								MAGI2 (40528 upstream) : GNAI1 (640722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79506696	79506698	+	IGR	DEL	ATG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79506696_79506698delATG								MAGI2 (423806 upstream) : GNAI1 (257442 downstream)																																			---	---	---	---
GNAI1	2770	broad.mit.edu	37	7	79834907	79834907	+	Intron	DEL	T	-	-	rs11344814		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79834907delT	uc003uhb.1	+						GNAI1_uc011kgt.1_Intron	NM_002069	NP_002060			guanine nucleotide binding protein (G protein),						cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	81825384	81825385	+	Intron	INS	-	G	G	rs148886464	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81825384_81825385insG	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)													---	---	---	---
SEMA3E	9723	broad.mit.edu	37	7	83029712	83029712	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83029712delT	uc003uhy.1	-							NM_012431	NP_036563			semaphorin 3E precursor						axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)																---	---	---	---
SEMA3A	10371	broad.mit.edu	37	7	83795592	83795593	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83795592_83795593insA	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	83889130	83889131	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83889130_83889131insA								SEMA3A (64913 upstream) : SEMA3D (735743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85590294	85590295	+	IGR	INS	-	TGTA	TGTA	rs140032188	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85590294_85590295insTGTA								SEMA3D (774123 upstream) : GRM3 (682935 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85632340	85632340	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85632340delC								SEMA3D (816169 upstream) : GRM3 (640890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85725911	85725912	+	IGR	INS	-	TTGTT	TTGTT	rs146317032	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85725911_85725912insTTGTT								SEMA3D (909740 upstream) : GRM3 (547318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	87109238	87109239	+	IGR	DEL	TC	-	-	rs45555137		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87109238_87109239delTC								ABCB4 (4219 upstream) : ABCB1 (23709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	87961072	87961073	+	IGR	INS	-	AAGTA	AAGTA	rs139710765	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87961072_87961073insAAGTA								STEAP4 (24863 upstream) : ZNF804B (427680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	87982968	87982969	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87982968_87982969delTG								STEAP4 (46759 upstream) : ZNF804B (405784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	88288455	88288456	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88288455_88288456insA								STEAP4 (352246 upstream) : ZNF804B (100297 downstream)																																			---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88740759	88740761	+	Intron	DEL	TTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88740759_88740761delTTG	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	89463754	89463755	+	IGR	INS	-	A	A	rs147846047	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89463754_89463755insA								ZNF804B (497410 upstream) : DPY19L2P4 (284959 downstream)																																			---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90398789	90398789	+	Intron	DEL	C	-	-	rs79512772		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90398789delC	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.1_Intron|CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90405096	90405098	+	Intron	DEL	CTC	-	-	rs78340354		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90405096_90405098delCTC	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.1_Intron|CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	91367417	91367418	+	IGR	INS	-	GCGTGT	GCGTGT	rs139634336		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91367417_91367418insGCGTGT								FZD1 (469286 upstream) : MTERF (64042 downstream)																																			---	---	---	---
ANKIB1	54467	broad.mit.edu	37	7	91956940	91956940	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91956940delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	92694233	92694234	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92694233_92694234delTT								CDK6 (228292 upstream) : SAMD9 (34598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	93017572	93017573	+	IGR	INS	-	A	A	rs150383860	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93017572_93017573insA								CCDC132 (29235 upstream) : CALCR (36226 downstream)																																			---	---	---	---
CALCR	799	broad.mit.edu	37	7	93140923	93140923	+	Intron	DEL	A	-	-	rs71825455		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93140923delA	uc003umv.1	-						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)													---	---	---	---
CALCR	799	broad.mit.edu	37	7	93184991	93184992	+	Intron	INS	-	AAAA	AAAA	rs150493694	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93184991_93184992insAAAA	uc003umv.1	-						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	93401891	93401891	+	Intron	DEL	A	-	-	rs11320596		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93401891delA	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)															---	---	---	---
GNGT1	2792	broad.mit.edu	37	7	93449285	93449286	+	Intron	INS	-	TGTG	TGTG	rs149954579	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93449285_93449286insTGTG	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)															---	---	---	---
GNGT1	2792	broad.mit.edu	37	7	93475785	93475785	+	Intron	DEL	T	-	-	rs143178820		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93475785delT	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)															---	---	---	---
CASD1	64921	broad.mit.edu	37	7	94168980	94168981	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94168980_94168981insA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	94508433	94508434	+	IGR	INS	-	AGAG	AGAG	rs145936827	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94508433_94508434insAGAG								PEG10 (209429 upstream) : PPP1R9A (28515 downstream)																																			---	---	---	---
PON1	5444	broad.mit.edu	37	7	94931944	94931945	+	Intron	INS	-	A	A	rs151197485	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94931944_94931945insA	uc003uns.2	-						PON1_uc011kih.1_Intron	NM_000446	NP_000437			paraoxonase 1 precursor						aromatic compound catabolic process|carboxylic acid catabolic process|organophosphate catabolic process|phosphatidylcholine metabolic process|positive regulation of binding|positive regulation of cholesterol efflux|positive regulation of transporter activity|response to external stimulus	spherical high-density lipoprotein particle	aryldialkylphosphatase activity|arylesterase activity|calcium ion binding|phospholipid binding|protein homodimerization activity			pancreas(1)	1	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Atorvastatin(DB01076)|Cefazolin(DB01327)													---	---	---	---
DYNC1I1	1780	broad.mit.edu	37	7	95479411	95479411	+	Intron	DEL	T	-	-	rs148725818		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95479411delT	uc003uoc.3	+						DYNC1I1_uc003uod.3_Intron|DYNC1I1_uc003uob.2_Intron|DYNC1I1_uc003uoe.3_Intron|DYNC1I1_uc010lfl.2_Intron	NM_004411	NP_004402			dynein, cytoplasmic 1, intermediate chain 1						vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole|vesicle	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)															---	---	---	---
DYNC1I1	1780	broad.mit.edu	37	7	95510686	95510686	+	Intron	DEL	A	-	-	rs72080368		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95510686delA	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	96005813	96005814	+	IGR	DEL	AT	-	-	rs55663634		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96005813_96005814delAT								SLC25A13 (54354 upstream) : SHFM1 (296423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96377119	96377130	+	IGR	DEL	CTTCCTTCCTTT	-	-	rs71956221		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96377119_96377130delCTTCCTTCCTTT								SHFM1 (37916 upstream) : DLX6AS (220698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97281292	97281292	+	IGR	DEL	A	-	-	rs35031887		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97281292delA								ACN9 (470219 upstream) : TAC1 (79979 downstream)																																			---	---	---	---
BAIAP2L1	55971	broad.mit.edu	37	7	97998118	97998118	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97998118delT	uc003upj.2	-							NM_018842	NP_061330			BAI1-associated protein 2-like 1						filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	98177600	98177603	+	IGR	DEL	CTAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98177600_98177603delCTAT								BAIAP2L1 (147173 upstream) : NPTX2 (68994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	99586068	99586068	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99586068delC	uc003usi.2	+											RecName: Full=Putative zinc-alpha-2-glycoprotein-like 2; Flags: Precursor;																														---	---	---	---
ZSCAN21	7589	broad.mit.edu	37	7	99657042	99657043	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99657042_99657043insA	uc003uso.2	+						ZSCAN21_uc003usn.1_Intron	NM_145914	NP_666019			zinc finger protein 38						positive regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	99734764	99734764	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99734764delT								MBLAC1 (8645 upstream) : C7orf59 (11766 downstream)																																			---	---	---	---
STAG3	10734	broad.mit.edu	37	7	99782538	99782538	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99782538delT	uc003utx.1	+						STAG3_uc010lgs.1_Intron|STAG3_uc011kjk.1_Intron	NM_012447	NP_036579			stromal antigen 3						chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100372454	100372454	+	Intron	DEL	A	-	-	rs79958454		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100372454delA	uc003uwj.2	+						ZAN_uc003uwk.2_Intron|ZAN_uc003uwl.2_Intron|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_Intron|ZAN_uc011kke.1_Intron	NM_003386	NP_003377			zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)															---	---	---	---
EPHB4	2050	broad.mit.edu	37	7	100418493	100418494	+	Intron	INS	-	T	T	rs111457037		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100418493_100418494insT	uc003uwn.1	-						EPHB4_uc003uwm.1_Intron|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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100439738	100439739	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100439738_100439739insA								EPHB4 (14595 upstream) : SLC12A9 (10619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	100970298	100970298	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100970298delT								RABL5 (5205 upstream) : EMID2 (35824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	100981677	100981677	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100981677delA								RABL5 (16584 upstream) : EMID2 (24445 downstream)																																			---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101150210	101150210	+	Intron	DEL	T	-	-	rs67323485		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101150210delT	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101182626	101182626	+	Intron	DEL	C	-	-	rs7804329	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101182626delC	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	102794393	102794396	+	IGR	DEL	ACAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102794393_102794396delACAG								NAPEPLD (4386 upstream) : DPY19L2P2 (21068 downstream)																																			---	---	---	---
RELN	5649	broad.mit.edu	37	7	103159218	103159218	+	Intron	DEL	T	-	-	rs35224913		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103159218delT	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	104500626	104500647	+	Intron	DEL	CACACACACACACACACACACA	-	-	rs150295832		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104500626_104500647delCACACACACACACACACACACA	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105357112	105357119	+	Intron	DEL	CACACACA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105357112_105357119delCACACACA	uc003vde.2	-							NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	106104677	106104680	+	IGR	DEL	CAGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106104677_106104680delCAGA								NAMPT (179039 upstream) : FLJ36031 (194470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	106187508	106187509	+	Intron	INS	-	GT	GT	rs147491242	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106187508_106187509insGT	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	107513960	107513961	+	IGR	INS	-	T	T	rs34287847		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107513960_107513961insT								SLC26A3 (70282 upstream) : DLD (17625 downstream)																																			---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	110492255	110492256	+	Intron	INS	-	GGAT	GGAT	rs143076567	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110492255_110492256insGGAT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	111286077	111286077	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111286077delA								IMMP2L (83539 upstream) : DOCK4 (80088 downstream)																																			---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111844937	111844938	+	Intron	INS	-	AC	AC	rs141780551	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111844937_111844938insAC	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron|DOCK4_uc010ljt.1_Intron|ZNF277_uc003vgd.2_5'Flank|ZNF277_uc003vge.2_5'Flank|ZNF277_uc003vgf.2_5'Flank|ZNF277_uc003vgc.2_5'Flank	NM_014705	NP_055520			dedicator of cytokinesis 4						cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	114368923	114368923	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114368923delT								FOXP2 (37831 upstream) : MDFIC (193286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	114379547	114379547	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114379547delT								FOXP2 (48455 upstream) : MDFIC (182662 downstream)																																			---	---	---	---
MDFIC	29969	broad.mit.edu	37	7	114616912	114616912	+	Intron	DEL	T	-	-	rs36014646		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114616912delT	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																		---	---	---	---
TES	26136	broad.mit.edu	37	7	115877898	115877899	+	Intron	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115877898_115877899delGT	uc003vho.2	+						TES_uc011kmx.1_Intron|TES_uc011kmy.1_Intron|TES_uc010lka.1_Intron|TES_uc003vhp.2_Intron	NM_015641	NP_056456			testin isoform 1						negative regulation of cell proliferation	cytoplasm|focal adhesion|nucleus|protein complex	zinc ion binding				0	Lung NSC(10;0.0137)|all_lung(10;0.0148)	Breast(660;0.0602)	STAD - Stomach adenocarcinoma(10;0.00878)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	117345251	117345251	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117345251delT								CFTR (36535 upstream) : CTTNBP2 (5457 downstream)																																			---	---	---	---
CTTNBP2	83992	broad.mit.edu	37	7	117408145	117408146	+	Intron	INS	-	CA	CA	rs149334068	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117408145_117408146insCA	uc003vjf.2	-							NM_033427	NP_219499			cortactin binding protein 2											ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	118278502	118278503	+	IGR	INS	-	T	T	rs139177322	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118278502_118278503insT								ANKRD7 (395720 upstream) : None (None downstream)																																			---	---	---	---
KCND2	3751	broad.mit.edu	37	7	119956908	119956909	+	Intron	INS	-	G	G	rs11760877	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119956908_119956909insG	uc003vjj.1	+							NM_012281	NP_036413			potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
KCND2	3751	broad.mit.edu	37	7	119995603	119995604	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119995603_119995604insA	uc003vjj.1	+							NM_012281	NP_036413			potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	121197318	121197319	+	IGR	INS	-	GT	GT	rs150003700	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121197318_121197319insGT								FAM3C (160896 upstream) : PTPRZ1 (315840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	121442073	121442074	+	IGR	INS	-	T	T	rs149339406	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121442073_121442074insT								FAM3C (405651 upstream) : PTPRZ1 (71085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	124704544	124704545	+	Intron	INS	-	T	T	rs140257081	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124704544_124704545insT	uc010lkx.1	+						uc003vlp.2_Intron|uc003vlq.1_Intron					Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	124970679	124970679	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124970679delT								POT1 (400642 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	125473055	125473056	+	IGR	DEL	TC	-	-	rs71756574		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125473055_125473056delTC								POT1 (903018 upstream) : GRM8 (605596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	126061680	126061681	+	IGR	INS	-	T	T	rs72177290		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126061680_126061681insT								None (None upstream) : GRM8 (16971 downstream)																																			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126303335	126303335	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126303335delA	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	127102564	127102564	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127102564delT								ZNF800 (69797 upstream) : GCC1 (118119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	127107163	127107165	+	IGR	DEL	AAG	-	-	rs73233069		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127107163_127107165delAAG								ZNF800 (74396 upstream) : GCC1 (113518 downstream)																																			---	---	---	---
LEP	3952	broad.mit.edu	37	7	127897322	127897322	+	3'UTR	DEL	A	-	-	rs112344366		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127897322delA	uc003vml.2	+	3						NM_000230	NP_000221			leptin precursor						adult feeding behavior|energy reserve metabolic process|negative regulation of appetite|placenta development|positive regulation of developmental growth	extracellular space					0																		---	---	---	---
NRF1	4899	broad.mit.edu	37	7	129384776	129384777	+	Intron	INS	-	GGGG	GGGG	rs140830308	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129384776_129384777insGGGG	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																		---	---	---	---
CPA5	93979	broad.mit.edu	37	7	130003878	130003879	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130003878_130003879insT	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)																	---	---	---	---
MKLN1	4289	broad.mit.edu	37	7	130803313	130803313	+	Intron	DEL	A	-	-	rs35721483		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130803313delA	uc011kpl.1	+							NM_001145354	NP_001138826			muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
MKLN1	4289	broad.mit.edu	37	7	131140804	131140804	+	Intron	DEL	C	-	-	rs66826457		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131140804delC	uc011kpm.1	+						MKLN1_uc011kpl.1_Intron|MKLN1_uc010lmh.2_Intron|MKLN1_uc003vqs.2_Intron	NM_013255	NP_037387			muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	132382934	132382934	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132382934delA	uc003vrd.1	+											Homo sapiens cDNA FLJ40288 fis, clone TESTI2028098.																														---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	132989824	132989825	+	Intron	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132989824_132989825delTT	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	133031999	133031999	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133031999delT	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)																---	---	---	---
SLC35B4	84912	broad.mit.edu	37	7	133978946	133978946	+	3'UTR	DEL	A	-	-	rs112171997		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133978946delA	uc003vrn.2	-	10					SLC35B4_uc010lmk.2_3'UTR|SLC35B4_uc010lml.1_Intron	NM_032826	NP_116215			solute carrier family 35, member B4							Golgi membrane|integral to membrane	UDP-N-acetylglucosamine transmembrane transporter activity|UDP-xylose transmembrane transporter activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	134018850	134018856	+	IGR	DEL	AATCCAC	-	-	rs137951272		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134018850_134018856delAATCCAC								SLC35B4 (17023 upstream) : AKR1B1 (108251 downstream)																																			---	---	---	---
BPGM	669	broad.mit.edu	37	7	134353643	134353644	+	Intron	INS	-	AC	AC	rs149915145	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134353643_134353644insAC	uc003vrv.2	+						BPGM_uc003vrw.2_Intron|BPGM_uc003vrx.2_Intron	NM_199186	NP_954655			bisphosphoglycerate mutase						glycolysis|respiratory gaseous exchange		2,3-bisphospho-D-glycerate 2-phosphohydrolase activity|bisphosphoglycerate mutase activity|phosphoglycerate mutase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	134456375	134456375	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134456375delT								BPGM (91810 upstream) : CALD1 (7796 downstream)																																			---	---	---	---
CALD1	800	broad.mit.edu	37	7	134607836	134607837	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134607836_134607837delAC	uc003vrz.2	+						CALD1_uc003vry.2_Intron|CALD1_uc003vsa.2_Intron|CALD1_uc003vsb.2_Intron|CALD1_uc010lmm.2_Intron|CALD1_uc011kpt.1_Intron|CALD1_uc003vsc.2_Intron|CALD1_uc003vsd.2_Intron|CALD1_uc011kpu.1_Intron	NM_033138	NP_149129			caldesmon 1 isoform 1						cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding				0																		---	---	---	---
C7orf49	78996	broad.mit.edu	37	7	134829348	134829349	+	Intron	INS	-	A	A	rs7791732	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134829348_134829349insA	uc003vsh.2	-						uc003vsg.2_Intron					Homo sapiens cDNA: FLJ22450 fis, clone HRC09626.							cytoplasm				large_intestine(1)|ovary(1)	2																		---	---	---	---
CNOT4	4850	broad.mit.edu	37	7	135189043	135189044	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135189043_135189044insT	uc003vsv.1	-						CNOT4_uc003vss.2_Intron|CNOT4_uc011kpz.1_Intron|CNOT4_uc003vst.2_Intron|CNOT4_uc003vsu.1_Intron	NM_001008225	NP_001008226			CCR4-NOT transcription complex, subunit 4						nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135332966	135332966	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135332966delA	uc003vsw.2	+						NUP205_uc003vsx.2_Intron	NM_015135	NP_055950			nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	135785101	135785102	+	IGR	INS	-	C	C	rs150626195	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135785101_135785102insC								LUZP6 (122897 upstream) : CHRM2 (768297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136412097	136412098	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136412097_136412098insA								LUZP6 (749893 upstream) : CHRM2 (141301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	138095360	138095363	+	IGR	DEL	ATAT	-	-	rs144279509	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138095360_138095363delATAT								AKR1D1 (292310 upstream) : TRIM24 (49716 downstream)																																			---	---	---	---
UBN2	254048	broad.mit.edu	37	7	138953039	138953039	+	Intron	DEL	T	-	-	rs76764215		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138953039delT	uc011kqr.1	+						UBN2_uc003vuv.2_Intron	NM_173569	NP_775840			ubinuclein 2											ovary(1)|skin(1)	2																		---	---	---	---
UBN2	254048	broad.mit.edu	37	7	138969521	138969521	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138969521delT	uc011kqr.1	+							NM_173569	NP_775840			ubinuclein 2											ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	139113609	139113612	+	IGR	DEL	CTTA	-	-	rs140329952		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139113609_139113612delCTTA								LUC7L2 (5411 upstream) : KLRG2 (24477 downstream)																																			---	---	---	---
HIPK2	28996	broad.mit.edu	37	7	139334296	139334297	+	Intron	DEL	TG	-	-	rs66465535		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139334296_139334297delTG	uc003vvf.3	-						HIPK2_uc003vvd.3_Intron	NM_022740	NP_073577			homeodomain interacting protein kinase 2 isoform						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	140825962	140825963	+	IGR	INS	-	AAGA	AAGA	rs151042086	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140825962_140825963insAAGA								MRPS33 (111181 upstream) : AGK (425115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	141235808	141235809	+	IGR	INS	-	A	A	rs35695551		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141235808_141235809insA								MRPS33 (521027 upstream) : AGK (15269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	143493856	143493856	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143493856delA	uc011ktn.1	+						uc011kto.1_Intron|uc011ktp.1_Intron|LOC154761_uc011ktq.1_Intron|LOC154761_uc011ktr.1_Intron|LOC154761_uc011kts.1_Intron|LOC154761_uc003wdj.1_Intron	NM_001130026	NP_001123498			hypothetical protein LOC285966 isoform B																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	144610227	144610228	+	IGR	INS	-	AA	AA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144610227_144610228insAA								TPK1 (77081 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	144796333	144796334	+	IGR	INS	-	T	T	rs151129586	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144796333_144796334insT								TPK1 (263187 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145569410	145569411	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145569410_145569411insT								None (None upstream) : CNTNAP2 (244042 downstream)																																			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	147891797	147891797	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147891797delG	uc003weu.1	+							NM_014141	NP_054860			cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148451845	148451845	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148451845delT	uc010lpg.2	+						CUL1_uc003wey.2_Intron|CUL1_uc003wez.2_Intron	NM_003592	NP_003583			cullin 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	149200619	149200620	+	IGR	DEL	AG	-	-	rs10582498		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149200619_149200620delAG								ZNF746 (5721 upstream) : ZNF767 (43625 downstream)																																			---	---	---	---
ZNF767	79970	broad.mit.edu	37	7	149304725	149304725	+	Intron	DEL	C	-	-	rs35434259		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149304725delC	uc003wfy.3	-						ZNF767_uc003wfx.2_Intron|ZNF767_uc011kuq.1_Intron	NR_027789				Homo sapiens cDNA FLJ12700 fis, clone NT2RP1000721.											central_nervous_system(1)	1	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00434)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	149791695	149791695	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149791695delC								ATP6V0E2 (213909 upstream) : ACTR3C (152607 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	150177010	150177011	+	IGR	INS	-	TTTA	TTTA	rs139150240	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150177010_150177011insTTTA								GIMAP8 (528 upstream) : GIMAP7 (34934 downstream)																																			---	---	---	---
PRKAG2	51422	broad.mit.edu	37	7	151303095	151303095	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151303095delT	uc003wkk.2	-						PRKAG2_uc003wki.2_Intron|PRKAG2_uc011kvl.1_Intron|PRKAG2_uc003wkj.2_Intron|PRKAG2_uc010lqe.1_Intron	NM_016203	NP_057287			AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151944708	151944708	+	Intron	DEL	T	-	-	rs113407913		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151944708delT	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	151955584	151955586	+	Intron	DEL	TTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151955584_151955586delTTG	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	152099302	152099302	+	Intron	DEL	G	-	-	rs67270422		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152099302delG	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	152111381	152111382	+	Intron	INS	-	GGGTC	GGGTC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152111381_152111382insGGGTC	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								---	---	---	---
ACTR3B	57180	broad.mit.edu	37	7	152498092	152498092	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152498092delT	uc003wle.1	+						ACTR3B_uc003wlf.1_Intron|ACTR3B_uc003wlg.1_Intron|ACTR3B_uc011kvp.1_Intron	NM_020445	NP_065178			actin-related protein 3-beta isoform 1						regulation of actin filament polymerization	cell projection|cytoplasm|cytoskeleton	actin binding|ATP binding				0		all_hematologic(28;0.0592)|Prostate(32;0.191)	OV - Ovarian serous cystadenocarcinoma(82;0.0287)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0434)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	152697387	152697389	+	IGR	DEL	CTT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152697387_152697389delCTT								ACTR3B (144924 upstream) : DPP6 (887030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	152839496	152839499	+	IGR	DEL	AGAC	-	-	rs112966816		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152839496_152839499delAGAC								ACTR3B (287033 upstream) : DPP6 (744920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	153235755	153235756	+	IGR	INS	-	T	T	rs149761724	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153235755_153235756insT								ACTR3B (683292 upstream) : DPP6 (348663 downstream)																																			---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154555066	154555067	+	Intron	DEL	GA	-	-	rs34214003		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154555066_154555067delGA	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	154859403	154859406	+	3'UTR	DEL	GAGT	-	-	rs35536331		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154859403_154859406delGAGT	uc011kvt.1	-	3					uc003wlt.2_3'UTR					SubName: Full=cDNA FLJ50038;																														---	---	---	---
RBM33	155435	broad.mit.edu	37	7	155486329	155486332	+	Intron	DEL	TTCT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155486329_155486332delTTCT	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	156180309	156180310	+	IGR	INS	-	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156180309_156180310insC								SHH (575342 upstream) : C7orf4 (152875 downstream)																																			---	---	---	---
NOM1	64434	broad.mit.edu	37	7	156749716	156749716	+	Intron	DEL	T	-	-	rs80241547		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156749716delT	uc003wmy.2	+							NM_138400	NP_612409			nucleolar protein with MIF4G domain 1						RNA metabolic process	nucleolus	protein binding				0	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)														---	---	---	---
DNAJB6	10049	broad.mit.edu	37	7	157186914	157186915	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157186914_157186915insT	uc003wnk.2	+						DNAJB6_uc003wnl.2_Intron|DNAJB6_uc011kvy.1_Intron|DNAJB6_uc011kvz.1_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)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157717806	157717806	+	Intron	DEL	T	-	-	rs60818843		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157717806delT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	2130401	2130402	+	IGR	INS	-	ACAC	ACAC	rs67628111		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2130401_2130402insACAC								MYOM2 (37022 upstream) : CSMD1 (662474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2271344	2271345	+	IGR	INS	-	G	G	rs139341315		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2271344_2271345insG								MYOM2 (177965 upstream) : CSMD1 (521531 downstream)																																			---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2963744	2963745	+	Intron	INS	-	A	A	rs146336179		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2963744_2963745insA	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	3737359	3737360	+	Intron	DEL	GT	-	-	rs66793205		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3737359_3737360delGT	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	5288575	5288576	+	IGR	INS	-	AAAG	AAAG	rs138276795	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5288575_5288576insAAAG								CSMD1 (436247 upstream) : MCPH1 (975545 downstream)																																			---	---	---	---
ERI1	90459	broad.mit.edu	37	8	8884658	8884659	+	Intron	DEL	TA	-	-	rs140641752	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8884658_8884659delTA	uc011kwu.1	+						ERI1_uc003wsk.2_Intron	NM_153332	NP_699163			three prime histone mRNA exonuclease 1						gene silencing by RNA|rRNA 3'-end processing	cytoplasm|histone pre-mRNA 3'end processing complex|nucleolus	3'-5' exonuclease activity|histone pre-mRNA stem-loop binding|metal ion binding|ribosome binding|rRNA binding				0					Adenosine monophosphate(DB00131)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	9823611	9823612	+	IGR	INS	-	T	T	rs140853547	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9823611_9823612insT								MIR124-1 (62629 upstream) : MSRA (88218 downstream)																																			---	---	---	---
SOX7	83595	broad.mit.edu	37	8	10624919	10624919	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10624919delA	uc011kwz.1	-						PINX1_uc003wth.2_Intron|PINX1_uc003wti.2_Intron	NM_031439	NP_113627			SRY-box 7						endoderm formation|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of caspase activity|regulation of canonical Wnt receptor signaling pathway	cytoplasm|nucleus	transcription regulatory region DNA binding			breast(1)	1				COAD - Colon adenocarcinoma(149;0.0732)														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	10772255	10772256	+	Intron	INS	-	ACAGAAGA	ACAGAAGA	rs144004651	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10772255_10772256insACAGAAGA	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	11136213	11136214	+	IGR	INS	-	AG	AG	rs149636132	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11136213_11136214insAG								XKR6 (77338 upstream) : MTMR9 (5786 downstream)																																			---	---	---	---
MTMR9	66036	broad.mit.edu	37	8	11177526	11177526	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11177526delT	uc003wtm.2	+						MTMR9_uc010lrx.2_Intron|MTMR9_uc011kxa.1_Intron|uc003wtn.1_5'Flank|uc003wto.1_RNA	NM_015458	NP_056273			myotubularin related protein 9							cytoplasm	phosphatase activity|protein binding				0			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)														---	---	---	---
C8orf12	83656	broad.mit.edu	37	8	11239297	11239298	+	Intron	INS	-	AT	AT	rs146545095	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11239297_11239298insAT	uc003wtu.2	+							NR_026814				Homo sapiens mRNA for hypothetical protein (C8orf12 gene).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	12448061	12448061	+	Intron	DEL	T	-	-	rs147215813		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12448061delT	uc003wvy.3	-											Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
C8orf79	57604	broad.mit.edu	37	8	12845202	12845203	+	Intron	DEL	AA	-	-	rs111727856		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12845202_12845203delAA	uc010lsq.2	+						C8orf79_uc011kxw.1_Intron	NM_020844	NP_065895			hypothetical protein LOC57604 isoform 1								methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	13769744	13769747	+	IGR	DEL	TTAT	-	-	rs72132347		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13769744_13769747delTTAT								C8orf48 (343948 upstream) : SGCZ (177627 downstream)																																			---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14657668	14657668	+	Intron	DEL	T	-	-	rs34437259		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14657668delT	uc003wwq.2	-							NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14672970	14672971	+	Intron	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14672970_14672971delAG	uc003wwq.2	-							NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14984761	14984770	+	Intron	DEL	ACACAAACAA	-	-	rs66716379	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14984761_14984770delACACAAACAA	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)														---	---	---	---
ZDHHC2	51201	broad.mit.edu	37	8	17045880	17045881	+	Intron	INS	-	AAT	AAT	rs140602273	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17045880_17045881insAAT	uc003wxe.2	+							NM_016353	NP_057437			zinc finger, DHHC-type containing 2							integral to membrane	acyltransferase activity|zinc ion binding				0				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)														---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17520354	17520355	+	Intron	DEL	AA	-	-	rs67375722		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17520354_17520355delAA	uc003wxv.2	-						MTUS1_uc003wxt.2_Intron|MTUS1_uc011kyg.1_Intron|MTUS1_uc010lsy.2_Intron|MTUS1_uc003wxw.2_Intron|MTUS1_uc003wxs.2_Intron	NM_001001924	NP_001001924			mitochondrial tumor suppressor 1 isoform 1							Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	17980689	17980690	+	IGR	INS	-	G	G	rs60550153		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17980689_17980690insG								ASAH1 (38182 upstream) : NAT1 (47281 downstream)																																			---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18629906	18629906	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18629906delT	uc003wza.2	-						PSD3_uc003wyy.2_Intron|PSD3_uc003wyz.2_Intron	NM_015310	NP_056125			ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18779344	18779344	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18779344delG	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)														---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19509155	19509158	+	Intron	DEL	TTTC	-	-	rs5889881		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19509155_19509158delTTTC	uc011kyo.1	-						CSGALNACT1_uc003wzg.2_Intron|CSGALNACT1_uc011kyp.1_Intron	NM_018371	NP_060841			chondroitin sulfate						anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	20242092	20242092	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20242092delG								LZTS1 (129289 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21963499	21963500	+	IGR	INS	-	T	T	rs144961583	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21963499_21963500insT								FAM160B2 (1609 upstream) : NUDT18 (883 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	22564090	22564090	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22564090delT								EGR3 (13275 upstream) : PEBP4 (6675 downstream)																																			---	---	---	---
PEBP4	157310	broad.mit.edu	37	8	22775144	22775145	+	Intron	INS	-	C	C	rs139644070	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22775144_22775145insC	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)														---	---	---	---
CHMP7	91782	broad.mit.edu	37	8	23101514	23101515	+	Intron	INS	-	T	T	rs146249994	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23101514_23101515insT	uc003xdc.2	+						CHMP7_uc011kzs.1_5'Flank|CHMP7_uc003xdd.2_5'Flank	NM_152272	NP_689485			CHMP family, member 7						cellular membrane organization|late endosome to vacuole transport	cytosol|ESCRT III complex	protein transporter activity				0		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)														---	---	---	---
LOXL2	4017	broad.mit.edu	37	8	23202191	23202192	+	Intron	INS	-	TGTG	TGTG	rs142528723	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23202191_23202192insTGTG	uc003xdh.1	-						uc003xdj.2_Intron	NM_002318	NP_002309			lysyl oxidase-like 2 precursor						aging|cell adhesion|protein modification process	extracellular space|membrane	copper ion binding|electron carrier activity|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor|scavenger receptor activity			breast(2)|ovary(1)	3		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	24288180	24288181	+	IGR	INS	-	A	A	rs143194188	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24288180_24288181insA								ADAMDEC1 (24654 upstream) : ADAM7 (10328 downstream)																																			---	---	---	---
EBF2	64641	broad.mit.edu	37	8	25770036	25770037	+	Intron	DEL	AA	-	-	rs71715063		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25770036_25770037delAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	26315331	26315332	+	IGR	INS	-	AGAG	AGAG			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26315331_26315332insAGAG								BNIP3L (44687 upstream) : PNMA2 (46864 downstream)																																			---	---	---	---
ADRA1A	148	broad.mit.edu	37	8	26615678	26615678	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26615678delG	uc003xfc.1	-						ADRA1A_uc010lul.1_Intron|ADRA1A_uc003xfd.1_Intron|ADRA1A_uc003xfe.1_Intron|ADRA1A_uc010lum.1_Intron|ADRA1A_uc003xff.1_Intron	NM_033303	NP_150646			alpha-1A-adrenergic receptor isoform 2						activation of phospholipase C activity|aging|apoptosis|calcium ion transport into cytosol|cell-cell signaling|intracellular protein kinase cascade|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of synaptic transmission, GABAergic|positive regulation of action potential|positive regulation of cardiac muscle contraction|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase C signaling cascade|positive regulation of vasoconstriction|response to drug|response to hormone stimulus|response to stress|smooth muscle contraction	integral to plasma membrane	alpha1-adrenergic receptor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amphetamine(DB00182)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Carvedilol(DB01136)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Maprotiline(DB00934)|Mephentermine(DB01365)|Metaraminol(DB00610)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Nefazodone(DB01149)|Nicergoline(DB00699)|Nilutamide(DB00665)|Norepinephrine(DB00368)|Norgestrel(DB00506)|Oxymetazoline(DB00935)|Perphenazine(DB00850)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Prazosin(DB00457)|Promazine(DB00420)|Promethazine(DB01069)|Propericiazine(DB01608)|Propiomazine(DB00777)|Pseudoephedrine(DB00852)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioridazine(DB00679)|Tolazoline(DB00797)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Ziprasidone(DB00246)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	26764857	26764857	+	IGR	DEL	C	-	-	rs116879808	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26764857delC								ADRA1A (41935 upstream) : MIR548H-4 (141513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	27427498	27427499	+	IGR	INS	-	GGATGGATGGAT	GGATGGATGGAT	rs13258678		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27427498_27427499insGGATGGATGGAT								EPHX2 (25014 upstream) : CLU (26952 downstream)																																			---	---	---	---
ESCO2	157570	broad.mit.edu	37	8	27667137	27667139	+	Intron	DEL	CTT	-	-	rs140644411		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27667137_27667139delCTT	uc010luy.1	+											Homo sapiens clone 305-4G mRNA sequence.						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				---	---	---	---
ZNF395	55893	broad.mit.edu	37	8	28253476	28253477	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28253476_28253477delAC	uc003xgt.2	-							NM_018660	NP_061130			zinc finger protein 395						transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	30107759	30107760	+	IGR	INS	-	T	T	rs111908470		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30107759_30107760insT								DCTN6 (66700 upstream) : RBPMS (134184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30137683	30137683	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30137683delC								DCTN6 (96624 upstream) : RBPMS (104261 downstream)																																			---	---	---	---
RBPMS	11030	broad.mit.edu	37	8	30269964	30269964	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30269964delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	31269129	31269130	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31269129_31269130delAC								WRN (237853 upstream) : NRG1 (228138 downstream)																																			---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32118874	32118875	+	Intron	INS	-	GTGT	GTGT	rs145925059	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32118874_32118875insGTGT	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	32328318	32328318	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32328318delT	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	32504164	32504164	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32504164delG	uc003xiv.2	+						NRG1_uc003xip.2_Intron|NRG1_uc003xir.2_Intron|NRG1_uc010lvl.2_Intron|NRG1_uc010lvm.2_Intron|NRG1_uc010lvn.2_Intron|NRG1_uc003xis.2_Intron|NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc003xix.2_Intron|NRG1_uc003xiy.2_5'Flank|NRG1_uc010lvt.2_5'Flank	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	35676184	35676186	+	IGR	DEL	GAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35676184_35676186delGAT								UNC5D (24004 upstream) : KCNU1 (965656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37312305	37312305	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37312305delA								KCNU1 (518664 upstream) : ZNF703 (240996 downstream)																																			---	---	---	---
RAB11FIP1	80223	broad.mit.edu	37	8	37750190	37750190	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37750190delA	uc003xkm.1	-						RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Intron	NM_001002814	NP_001002814			RAB11 family interacting protein 1 isoform 3						protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)															---	---	---	---
GOT1L1	137362	broad.mit.edu	37	8	37798621	37798631	+	5'Flank	DEL	TTTTTTTTTTT	-	-	rs71216641		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37798621_37798631delTTTTTTTTTTT	uc011lbj.1	-							NM_152413	NP_689626			glutamic-oxaloacetic transaminase 1-like 1						biosynthetic process|cellular amino acid metabolic process	cytoplasm	pyridoxal phosphate binding|transaminase activity			ovary(1)	1	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)															---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38232586	38232586	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38232586delA	uc003xli.2	-						WHSC1L1_uc011lbm.1_Intron|WHSC1L1_uc010lwe.2_Intron|WHSC1L1_uc003xlj.2_Intron	NM_023034	NP_075447			WHSC1L1 protein isoform long						cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)					T	NUP98	AML								---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38590821	38590822	+	Intron	INS	-	T	T	rs113616267		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38590821_38590822insT	uc011lbz.1	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc003xmb.3_Intron	NM_006283	NP_006274			transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
ADAM9	8754	broad.mit.edu	37	8	38902929	38902930	+	Intron	DEL	GC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38902929_38902930delGC	uc003xmr.2	+						ADAM9_uc011lcf.1_Intron|ADAM9_uc011lcg.1_Intron|ADAM9_uc010lwr.2_Intron	NM_003816	NP_003807			ADAM metallopeptidase domain 9 isoform 1						activation of MAPKK activity|cell-cell adhesion mediated by integrin|cell-matrix adhesion|keratinocyte differentiation|monocyte activation|PMA-inducible membrane protein ectodomain proteolysis|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell adhesion mediated by integrin|positive regulation of keratinocyte migration|positive regulation of macrophage fusion|positive regulation of membrane protein ectodomain proteolysis|positive regulation of protein secretion|response to calcium ion|response to glucocorticoid stimulus|response to hydrogen peroxide|response to manganese ion|response to tumor necrosis factor|transforming growth factor beta receptor signaling pathway	extracellular space|extracellular space|integral to membrane|intrinsic to external side of plasma membrane	collagen binding|integrin binding|laminin binding|metalloendopeptidase activity|protein kinase C binding|SH3 domain binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)															---	---	---	---
ADAM18	8749	broad.mit.edu	37	8	39446154	39446154	+	Intron	DEL	T	-	-	rs75364245		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39446154delT	uc003xni.2	+						ADAM18_uc003xnh.2_Intron|ADAM18_uc010lww.2_Intron|ADAM18_uc010lwx.2_Intron	NM_014237	NP_055052			a disintegrin and metalloprotease domain 18						cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	39767236	39767237	+	IGR	INS	-	A	A	rs138778629	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39767236_39767237insA								ADAM2 (71457 upstream) : IDO1 (4091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40241861	40241862	+	IGR	INS	-	T	T	rs145271065	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40241861_40241862insT								C8orf4 (229040 upstream) : ZMAT4 (146254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41291451	41291452	+	IGR	INS	-	ATCT	ATCT	rs141442451	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41291451_41291452insATCT								SFRP1 (124471 upstream) : GOLGA7 (56629 downstream)																																			---	---	---	---
ANK1	286	broad.mit.edu	37	8	41739352	41739353	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41739352_41739353insT	uc003xom.2	-							NM_001142446	NP_001135918			ankyrin 1 isoform 9						axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	41964107	41964107	+	IGR	DEL	T	-	-	rs67112236		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41964107delT								MYST3 (54602 upstream) : AP3M2 (46357 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42430054	42430055	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42430054_42430055insA								C8orf40 (21915 upstream) : CHRNB3 (122507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42660085	42660086	+	IGR	INS	-	TCCCTCACCCCA	TCCCTCACCCCA	rs140667165	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42660085_42660086insTCCCTCACCCCA								CHRNA6 (36466 upstream) : THAP1 (31732 downstream)																																	OREG0018750	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RNF170	81790	broad.mit.edu	37	8	42731801	42731801	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42731801delT	uc003xpo.2	-						RNF170_uc011lcx.1_Intron|RNF170_uc010lxp.2_Intron|RNF170_uc003xpm.2_Intron|RNF170_uc003xpp.2_Intron|RNF170_uc003xpn.2_Intron|RNF170_uc003xpq.3_Intron	NM_001160223	NP_001153695			ring finger protein 170 isoform a							integral to membrane	zinc ion binding				0	all_lung(13;1.25e-11)|Lung NSC(13;3.55e-10)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00645)|Lung NSC(58;0.0176)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	46958601	46958601	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46958601delT								None (None upstream) : BEYLA (793907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47419989	47419989	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47419989delA								None (None upstream) : BEYLA (332519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47729974	47729974	+	IGR	DEL	A	-	-	rs71548409		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47729974delA								None (None upstream) : BEYLA (22534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47929843	47929844	+	IGR	INS	-	G	G	rs139965331	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47929843_47929844insG								BEYLA (162436 upstream) : KIAA0146 (243698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49086677	49086678	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49086677_49086678insT								UBE2V2 (112225 upstream) : EFCAB1 (536673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49297743	49297743	+	IGR	DEL	A	-	-	rs140564135		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49297743delA								UBE2V2 (323291 upstream) : EFCAB1 (325608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50170033	50170033	+	IGR	DEL	A	-	-	rs35041014		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50170033delA								C8orf22 (181392 upstream) : SNTG1 (652316 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50177746	50177747	+	IGR	DEL	CC	-	-	rs1825005		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50177746_50177747delCC								C8orf22 (189105 upstream) : SNTG1 (644602 downstream)																																			---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51264957	51264958	+	Intron	INS	-	T	T	rs72249719		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51264957_51264958insT	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	53950749	53950750	+	IGR	INS	-	CG	CG	rs147124493		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53950749_53950750insCG								NPBWR1 (97296 upstream) : OPRK1 (187526 downstream)																																			---	---	---	---
RGS20	8601	broad.mit.edu	37	8	54802669	54802669	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54802669delT	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	54876665	54876666	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54876665_54876666insT								RGS20 (4804 upstream) : TCEA1 (2451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55941524	55941525	+	IGR	DEL	AT	-	-	rs67980207		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55941524_55941525delAT								RP1 (258993 upstream) : XKR4 (73492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56440064	56440065	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56440064_56440065delTG								XKR4 (1356 upstream) : TMEM68 (211255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56477821	56477821	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56477821delT								XKR4 (39113 upstream) : TMEM68 (173499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56603262	56603262	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56603262delC								XKR4 (164554 upstream) : TMEM68 (48058 downstream)																																			---	---	---	---
TGS1	96764	broad.mit.edu	37	8	56722013	56722013	+	Intron	DEL	T	-	-	rs35319904		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56722013delT	uc003xsj.3	+						TGS1_uc010lyh.2_Intron	NM_024831	NP_079107			trimethylguanosine synthase homolog						cellular lipid metabolic process|ncRNA metabolic process|regulation of transcription, DNA-dependent|RNA capping|spliceosomal snRNP assembly|transcription, DNA-dependent	Cajal body|cytosol	RNA trimethylguanosine synthase activity			ovary(1)|lung(1)|breast(1)	3		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	56949070	56949071	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56949070_56949071delGT								LYN (25134 upstream) : RPS20 (31668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58116712	58116712	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58116712delG								IMPAD1 (210285 upstream) : C8orf71 (75390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58254269	58254270	+	5'Flank	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58254269_58254270delTG	uc003xth.2	+											Homo sapiens cDNA clone IMAGE:5267652.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	58532964	58532964	+	IGR	DEL	A	-	-	rs79252672		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58532964delA								C8orf71 (335676 upstream) : FAM110B (374149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58665518	58665518	+	IGR	DEL	A	-	-	rs34502604		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58665518delA								C8orf71 (468230 upstream) : FAM110B (241595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58815239	58815239	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58815239delA								C8orf71 (617951 upstream) : FAM110B (91874 downstream)																																			---	---	---	---
TOX	9760	broad.mit.edu	37	8	59789027	59789028	+	Intron	INS	-	A	A	rs148291510	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59789027_59789028insA	uc003xtw.1	-							NM_014729	NP_055544			thymus high mobility group box protein TOX							nucleus	DNA binding			kidney(2)|lung(1)|skin(1)	4		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	60312089	60312091	+	IGR	DEL	GTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60312089_60312091delGTG								TOX (280322 upstream) : CA8 (789332 downstream)																																			---	---	---	---
CA8	767	broad.mit.edu	37	8	61165907	61165907	+	Intron	DEL	T	-	-	rs80321949		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61165907delT	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)																---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61497842	61497856	+	Intron	DEL	TTTTGTTTTGTTTTG	-	-	rs36005117		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61497842_61497856delTTTTGTTTTGTTTTG	uc003xud.1	+						RAB2A_uc011lef.1_Intron	NM_002865	NP_002856			RAB2A, member RAS oncogene family						ER to Golgi vesicle-mediated transport|protein transport|small GTPase mediated signal transduction	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|melanosome	GDP binding|GTP binding|GTPase activity				0			BRCA - Breast invasive adenocarcinoma(89;0.0805)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	62021773	62021773	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62021773delT								CHD7 (242310 upstream) : CLVS1 (178752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62119913	62119914	+	IGR	INS	-	G	G	rs141379376	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62119913_62119914insG								CHD7 (340450 upstream) : CLVS1 (80611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65814768	65814768	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65814768delT								CYP7B1 (103420 upstream) : ARMC1 (700304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66828467	66828467	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66828467delA								PDE7A (74712 upstream) : DNAJC5B (105324 downstream)																																			---	---	---	---
SGK3	23678	broad.mit.edu	37	8	67595608	67595609	+	Intron	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67595608_67595609insG	uc003xwp.2	+							NM_013257	NP_037389			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	67807635	67807636	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67807635_67807636insT	uc003xwz.3	+						C8orf45_uc011lev.1_Intron|C8orf45_uc011lew.1_Intron|C8orf45_uc011lex.1_Intron|C8orf45_uc003xwy.3_Intron	NM_173518	NP_775789			minichromosome maintenance complex						DNA replication		ATP binding|DNA binding			ovary(1)	1	Breast(64;0.186)		Epithelial(68;0.00384)|OV - Ovarian serous cystadenocarcinoma(28;0.00913)|all cancers(69;0.0175)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68104309	68104310	+	Intron	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68104309_68104310insG	uc003xxi.2	+						ARFGEF1_uc003xxl.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron|CSPP1_uc010lyw.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68920674	68920676	+	Intron	DEL	AGA	-	-	rs68110557		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68920674_68920676delAGA	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146			DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
PREX2	80243	broad.mit.edu	37	8	69018457	69018459	+	Intron	DEL	CTT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69018457_69018459delCTT	uc003xxv.1	+						PREX2_uc011lez.1_Intron	NM_024870	NP_079146			DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69725605	69725605	+	Intron	DEL	T	-	-	rs67642782		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69725605delT	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190			hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	69843073	69843074	+	Intron	DEL	AT	-	-	rs57209811	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69843073_69843074delAT	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	69844930	69844939	+	Intron	DEL	AAACAAAACA	-	-	rs36215198		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69844930_69844939delAAACAAAACA	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	70276545	70276546	+	IGR	INS	-	GAGA	GAGA	rs147235724	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70276545_70276546insGAGA								C8orf34 (545289 upstream) : SULF1 (102313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	70345709	70345709	+	IGR	DEL	G	-	-	rs35808925		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70345709delG								C8orf34 (614453 upstream) : SULF1 (33150 downstream)																																			---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70472574	70472575	+	Intron	INS	-	T	T	rs34692406		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70472574_70472575insT	uc010lza.1	+						SULF1_uc003xyd.2_Intron|SULF1_uc003xye.2_Intron|SULF1_uc003xyf.2_Intron|SULF1_uc003xyg.2_Intron	NM_015170	NP_055985			sulfatase 1 precursor						apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)															---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70552418	70552421	+	Intron	DEL	AAAG	-	-	rs112130640		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70552418_70552421delAAAG	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	73099615	73099616	+	IGR	INS	-	A	A	rs143756643		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73099615_73099616insA								TRPA1 (111796 upstream) : KCNB2 (350010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	73106418	73106419	+	IGR	INS	-	CTT	CTT	rs142746383	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73106418_73106419insCTT								TRPA1 (118599 upstream) : KCNB2 (343207 downstream)																																			---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73603091	73603091	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73603091delA	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	73856588	73856589	+	IGR	INS	-	T	T	rs139326982	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73856588_73856589insT								KCNB2 (6006 upstream) : TERF1 (64508 downstream)																																	OREG0018830	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
UBE2W	55284	broad.mit.edu	37	8	74739456	74739456	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74739456delT	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)															---	---	---	---
LY96	23643	broad.mit.edu	37	8	74927047	74927048	+	Intron	INS	-	AC	AC	rs150039538	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74927047_74927048insAC	uc003yad.2	+							NM_015364	NP_056179			MD-2 protein precursor						cellular defense response|detection of lipopolysaccharide|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	extracellular space|lipopolysaccharide receptor complex|plasma membrane	coreceptor activity|lipopolysaccharide receptor activity|protein binding				0	Breast(64;0.0311)		Epithelial(68;0.0208)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0619)															---	---	---	---
HNF4G	3174	broad.mit.edu	37	8	76432074	76432075	+	Intron	INS	-	GT	GT	rs142842410	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76432074_76432075insGT	uc003yaq.2	+						HNF4G_uc003yap.1_Intron	NM_004133	NP_004124			hepatocyte nuclear factor 4, gamma						endocrine pancreas development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	77220953	77220954	+	IGR	INS	-	CTGT	CTGT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77220953_77220954insCTGT								HNF4G (741894 upstream) : LOC100192378 (302161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78552603	78552603	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78552603delT								PEX2 (640079 upstream) : PKIA (875733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78870576	78870577	+	IGR	INS	-	A	A	rs138301056	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78870576_78870577insA								PEX2 (958052 upstream) : PKIA (557759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79980015	79980016	+	IGR	INS	-	A	A	rs143028382	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79980015_79980016insA								IL7 (262257 upstream) : STMN2 (543364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80118703	80118704	+	IGR	DEL	GT	-	-	rs34146088		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80118703_80118704delGT								IL7 (400945 upstream) : STMN2 (404676 downstream)																																			---	---	---	---
TPD52	7163	broad.mit.edu	37	8	81054849	81054850	+	Intron	INS	-	GG	GG	rs143697849	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81054849_81054850insGG	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)															---	---	---	---
TPD52	7163	broad.mit.edu	37	8	81067241	81067242	+	Intron	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81067241_81067242insG	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	81473922	81473922	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81473922delA								ZBTB10 (39314 upstream) : ZNF704 (76847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81531858	81531858	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81531858delT								ZBTB10 (97250 upstream) : ZNF704 (18911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82213874	82213875	+	IGR	INS	-	AC	AC	rs148011736	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82213874_82213875insAC								FABP5 (16866 upstream) : PMP2 (138689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82691836	82691836	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82691836delC								CHMP4C (20090 upstream) : SNX16 (19984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83656988	83656989	+	IGR	INS	-	A	A	rs137917348	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83656988_83656989insA								SNX16 (902467 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83815837	83815838	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83815837_83815838delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84301439	84301440	+	IGR	INS	-	A	A	rs141510360	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84301439_84301440insA								None (None upstream) : RALYL (794013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84354104	84354104	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84354104delT								None (None upstream) : RALYL (741349 downstream)																																			---	---	---	---
CPNE3	8895	broad.mit.edu	37	8	87566456	87566456	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87566456delA	uc003ydv.2	+						CPNE3_uc003ydw.1_Intron	NM_003909	NP_003900			copine III						lipid metabolic process|vesicle-mediated transport	cytosol	calcium-dependent phospholipid binding|protein serine/threonine kinase activity|transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	89041883	89041885	+	IGR	DEL	AAT	-	-	rs10588057		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89041883_89041885delAAT								DCAF4L2 (155587 upstream) : MMP16 (7577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90902771	90902772	+	IGR	DEL	AA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90902771_90902772delAA								RIPK2 (99480 upstream) : OSGIN2 (11324 downstream)																																			---	---	---	---
NECAB1	64168	broad.mit.edu	37	8	91833898	91833898	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91833898delT	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)															---	---	---	---
OTUD6B	51633	broad.mit.edu	37	8	92083176	92083177	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92083176_92083177insT	uc003yeu.3	+						uc003yet.2_5'Flank|OTUD6B_uc011lgh.1_Intron	NM_016023	NP_057107			OTU domain containing 6B											ovary(2)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(11;0.0187)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	93262976	93262976	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93262976delT								RUNX1T1 (155270 upstream) : C8orf83 (632889 downstream)																																			---	---	---	---
C8orf83	286144	broad.mit.edu	37	8	93964647	93964648	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93964647_93964648delAC	uc003yfk.3	-						C8orf83_uc003yfr.3_Intron|C8orf83_uc010map.2_Intron|C8orf83_uc003yfo.3_Intron|C8orf83_uc003yfn.3_Intron|C8orf83_uc003yfq.3_Intron|C8orf83_uc003yfl.3_Intron|C8orf83_uc003yfm.3_Intron	NR_015339				RecName: Full=UPF0599 protein C8orf83;							endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	94141932	94141932	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94141932delA								C8orf83 (112031 upstream) : FAM92A1 (570841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94402458	94402459	+	IGR	INS	-	C	C	rs28451055		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94402458_94402459insC								C8orf83 (372557 upstream) : FAM92A1 (310314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94453162	94453162	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94453162delA								C8orf83 (423261 upstream) : FAM92A1 (259611 downstream)																																			---	---	---	---
KIAA1429	25962	broad.mit.edu	37	8	95533271	95533271	+	Intron	DEL	T	-	-	rs34659944		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95533271delT	uc003ygo.1	-						KIAA1429_uc003ygp.2_Intron|KIAA1429_uc010maz.1_Intron	NM_015496	NP_056311			hypothetical protein LOC25962 isoform 1						mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)															---	---	---	---
DPY19L4	286148	broad.mit.edu	37	8	95765237	95765237	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95765237delA	uc003ygx.2	+							NM_181787	NP_861452			dpy-19-like 4							integral to membrane				ovary(2)	2	Breast(36;3.85e-06)																	---	---	---	---
INTS8	55656	broad.mit.edu	37	8	95846591	95846592	+	Intron	DEL	GT	-	-	rs139513040		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95846591_95846592delGT	uc003yhb.2	+						INTS8_uc003yha.1_Intron|INTS8_uc011lgq.1_Intron|INTS8_uc011lgr.1_Intron|INTS8_uc010mba.2_Intron	NM_017864	NP_060334			integrator complex subunit 8						snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	97037506	97037507	+	IGR	INS	-	T	T	rs149669383	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97037506_97037507insT								C8orf37 (756069 upstream) : GDF6 (117053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	97190592	97190592	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97190592delT								GDF6 (17572 upstream) : UQCRB (48718 downstream)																																			---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97742083	97742084	+	Intron	INS	-	TG	TG	rs142087422	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97742083_97742084insTG	uc003yhw.2	+							NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97997498	97997498	+	Intron	DEL	T	-	-	rs35640819		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97997498delT	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)																	---	---	---	---
HRSP12	10247	broad.mit.edu	37	8	99124423	99124424	+	Intron	INS	-	AC	AC	rs144555285	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99124423_99124424insAC	uc003yii.1	-							NM_005836	NP_005827			heat-responsive protein 12						regulation of translational termination	nucleus	endonuclease activity			ovary(1)	1	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)															---	---	---	---
KCNS2	3788	broad.mit.edu	37	8	99437557	99437560	+	5'Flank	DEL	ACAC	-	-	rs72444718		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99437557_99437560delACAC	uc003yin.2	+							NM_020697	NP_065748			potassium voltage-gated channel,							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)															---	---	---	---
STK3	6788	broad.mit.edu	37	8	99471213	99471214	+	Intron	INS	-	A	A	rs148806082	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99471213_99471214insA	uc003yip.2	-						STK3_uc003yio.2_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100224888	100224889	+	Intron	INS	-	TTCTCTTCCTACC	TTCTCTTCCTACC	rs141294294	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100224888_100224889insTTCTCTTCCTACC	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)															---	---	---	---
RGS22	26166	broad.mit.edu	37	8	101039465	101039465	+	Intron	DEL	A	-	-	rs77774164		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101039465delA	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron|RGS22_uc011lgz.1_Intron|RGS22_uc010mbo.1_Intron	NM_015668	NP_056483			regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	102353922	102353923	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102353922_102353923insT								ZNF706 (135962 upstream) : NACAP1 (20099 downstream)																																			---	---	---	---
GRHL2	79977	broad.mit.edu	37	8	102502835	102502836	+	5'Flank	INS	-	G	G	rs4562283	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102502835_102502836insG	uc010mbu.2	+						GRHL2_uc010mbt.1_5'Flank|GRHL2_uc011lhi.1_5'Flank	NM_024915	NP_079191			transcription factor CP2-like 3							cytoplasm|nucleus	DNA binding			ovary(2)|skin(1)	3	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	103948667	103948667	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103948667delT								AZIN1 (72270 upstream) : ATP6V1C1 (84581 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103995520	103995521	+	IGR	INS	-	T	T	rs144747551	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103995520_103995521insT								AZIN1 (119123 upstream) : ATP6V1C1 (37727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	104303105	104303105	+	IGR	DEL	C	-	-	rs34745072		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104303105delC								BAALC (60575 upstream) : FZD6 (7562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107064229	107064234	+	IGR	DEL	CACACG	-	-	rs66805605		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107064229_107064234delCACACG								ZFPM2 (247464 upstream) : OXR1 (218239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109299636	109299636	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109299636delA								EIF3E (38677 upstream) : TTC35 (156217 downstream)																																			---	---	---	---
TMEM74	157753	broad.mit.edu	37	8	109769028	109769031	+	Intron	DEL	AGGA	-	-	rs112425656		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109769028_109769031delAGGA	uc003ymx.2	-											Homo sapiens cDNA FLJ30668 fis, clone FCBBF1000675.						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	110180734	110180734	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110180734delT								TRHR (48924 upstream) : NUDCD1 (72415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110219871	110219872	+	IGR	INS	-	AAC	AAC	rs145525771	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110219871_110219872insAAC								TRHR (88061 upstream) : NUDCD1 (33277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111971303	111971303	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111971303delC								KCNV1 (983227 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	113176663	113176663	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113176663delT								None (None upstream) : CSMD3 (58498 downstream)																																			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113335377	113335378	+	Intron	INS	-	AAAC	AAAC	rs138412366	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113335377_113335378insAAAC	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc003ynw.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	114713494	114713494	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114713494delT								CSMD3 (264252 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	114733880	114733881	+	IGR	DEL	AT	-	-	rs10099174		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114733880_114733881delAT								CSMD3 (284638 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	114809149	114809149	+	IGR	DEL	A	-	-	rs75923252		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114809149delA								CSMD3 (359907 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	114837624	114837624	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114837624delA								CSMD3 (388382 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	114974966	114974967	+	IGR	INS	-	AG	AG	rs138418803	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114974966_114974967insAG								CSMD3 (525724 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115424864	115424865	+	IGR	INS	-	ACAC	ACAC	rs151129275	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115424864_115424865insACAC								CSMD3 (975622 upstream) : TRPS1 (995860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116270151	116270151	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116270151delA								None (None upstream) : TRPS1 (150574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117225133	117225134	+	IGR	INS	-	CA	CA	rs139477483	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117225133_117225134insCA								TRPS1 (543905 upstream) : EIF3H (431922 downstream)																																			---	---	---	---
SLC30A8	169026	broad.mit.edu	37	8	118068770	118068771	+	Intron	INS	-	TTTC	TTTC	rs145969216	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118068770_118068771insTTTC	uc010mcz.2	+						SLC30A8_uc011lia.1_Intron|SLC30A8_uc003yog.2_Intron	NM_173851	NP_776250			solute carrier family 30 member 8						insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)															---	---	---	---
SLC30A8	169026	broad.mit.edu	37	8	118139462	118139463	+	Intron	DEL	AT	-	-	rs10549939		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118139462_118139463delAT	uc010mcz.2	+						SLC30A8_uc011lia.1_Intron|SLC30A8_uc003yog.2_Intron	NM_173851	NP_776250			solute carrier family 30 member 8						insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	118654707	118654707	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118654707delA								MED30 (102208 upstream) : EXT1 (156895 downstream)																																			---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118914821	118914822	+	Intron	INS	-	ATG	ATG	rs10674196		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118914821_118914822insATG	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	118919282	118919283	+	Intron	DEL	CA	-	-	rs142610371		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118919282_118919283delCA	uc003yok.1	-							NM_000127	NP_000118			exostosin 1						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)					Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	8	120181588	120181595	+	IGR	DEL	ACACACAC	-	-	rs33914422		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120181588_120181595delACACACAC								COLEC10 (62393 upstream) : MAL2 (39015 downstream)																																			---	---	---	---
TAF2	6873	broad.mit.edu	37	8	120780490	120780491	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120780490_120780491insT	uc003you.2	-							NM_003184	NP_003175			TBP-associated factor 2						G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121165320	121165321	+	Intron	INS	-	A	A	rs151029825	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121165320_121165321insA	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)															---	---	---	---
SNTB1	6641	broad.mit.edu	37	8	121767412	121767413	+	Intron	DEL	GA	-	-	rs35817960		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121767412_121767413delGA	uc010mdg.2	-						SNTB1_uc003ype.2_Intron	NM_021021	NP_066301			basic beta 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	122191954	122191971	+	IGR	DEL	TATTTGTGTAAATGACTG	-	-	rs144051959		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122191954_122191971delTATTTGTGTAAATGACTG								SNTB1 (367645 upstream) : HAS2 (433300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123440659	123440659	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123440659delC								HAS2AS (783726 upstream) : ZHX2 (353242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123659401	123659401	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123659401delT								None (None upstream) : ZHX2 (134500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123756012	123756013	+	IGR	INS	-	GC	GC	rs149296000	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123756012_123756013insGC								None (None upstream) : ZHX2 (37888 downstream)																																			---	---	---	---
WDYHV1	55093	broad.mit.edu	37	8	124450912	124450913	+	Intron	INS	-	A	A	rs146956459		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124450912_124450913insA	uc003yqn.1	+						WDYHV1_uc011lij.1_Intron|WDYHV1_uc003yqo.1_Intron	NM_018024	NP_060494			WDYHV motif containing 1						protein modification process	cytosol|nucleus	protein binding|protein N-terminal glutamine amidohydrolase activity			ovary(1)|skin(1)	2																		---	---	---	---
TATDN1	83940	broad.mit.edu	37	8	125501644	125501645	+	Intron	INS	-	T	T	rs150856509	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125501644_125501645insT	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	126506424	126506424	+	IGR	DEL	A	-	-	rs142310073		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126506424delA								TRIB1 (55782 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127595667	127595668	+	IGR	INS	-	A	A	rs150436534	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127595667_127595668insA								FAM84B (25201 upstream) : LOC727677 (706394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127808836	127808839	+	IGR	DEL	AGAG	-	-	rs34289913		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127808836_127808839delAGAG								FAM84B (238370 upstream) : LOC727677 (493223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127836865	127836865	+	IGR	DEL	G	-	-	rs59376372		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127836865delG								FAM84B (266399 upstream) : LOC727677 (465197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128028370	128028373	+	IGR	DEL	CACA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128028370_128028373delCACA								FAM84B (457904 upstream) : LOC727677 (273689 downstream)																																			---	---	---	---
LOC727677	727677	broad.mit.edu	37	8	128463297	128463297	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128463297delT	uc003yse.1	-						LOC727677_uc011liv.1_Intron					Homo sapiens isolate DGPc1_8_exons1-2-3-4-5 unknown mRNA, alternatively spliced.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	128710238	128710239	+	Intron	DEL	CA	-	-	rs34141920		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128710238_128710239delCA	uc003ysg.2	-											Homo sapiens, clone IMAGE:5554747, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	128798039	128798040	+	IGR	INS	-	AAAC	AAAC	rs139313316	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128798039_128798040insAAAC								MYC (44361 upstream) : PVT1 (8739 downstream)																																			---	---	---	---
PVT1	5820	broad.mit.edu	37	8	128982535	128982536	+	Intron	INS	-	TTTT	TTTT	rs149339863		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128982535_128982536insTTTT	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	129184682	129184682	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129184682delT								MIR1208 (22248 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130292457	130292457	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130292457delA								None (None upstream) : GSDMC (467986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130431662	130431664	+	IGR	DEL	CTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130431662_130431664delCTG								None (None upstream) : GSDMC (328779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130564224	130564225	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130564224_130564225delGT								None (None upstream) : GSDMC (196218 downstream)																																			---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131192213	131192214	+	Intron	INS	-	AGAGAA	AGAGAA	rs149057640	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131192213_131192214insAGAGAA	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|ASAP1_uc011liw.1_Intron	NM_018482	NP_060952			development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131290317	131290318	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131290317_131290318insA	uc003yta.1	-						ASAP1_uc011liw.1_Intron	NM_018482	NP_060952			development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131412869	131412869	+	Intron	DEL	A	-	-	rs113187171		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131412869delA	uc003yta.1	-						ASAP1_uc011liw.1_Intron	NM_018482	NP_060952			development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	132709364	132709365	+	IGR	INS	-	AC	AC	rs138895487	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132709364_132709365insAC								ADCY8 (656529 upstream) : EFR3A (206994 downstream)																																			---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133240236	133240236	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133240236delA	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	133929633	133929634	+	Intron	INS	-	TG	TG	rs141561412	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133929633_133929634insTG	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_5'Flank|TG_uc003ytx.1_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	134597995	134597995	+	IGR	DEL	C	-	-	rs35063284		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134597995delC								ST3GAL1 (13812 upstream) : ZFAT (892038 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	134675694	134675695	+	IGR	INS	-	T	T	rs139449809		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134675694_134675695insT								ST3GAL1 (91511 upstream) : ZFAT (814338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135016760	135016766	+	IGR	DEL	AAAAAAG	-	-	rs67221246		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135016760_135016766delAAAAAAG								ST3GAL1 (432577 upstream) : ZFAT (473267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137944564	137944565	+	IGR	INS	-	AC	AC	rs150354269	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137944564_137944565insAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138736050	138736053	+	IGR	DEL	ACGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138736050_138736053delACGA								None (None upstream) : FAM135B (406215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	139140100	139140100	+	IGR	DEL	A	-	-	rs67513464		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139140100delA								None (None upstream) : FAM135B (2168 downstream)																																			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139237780	139237781	+	Intron	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139237780_139237781delGT	uc003yuy.2	-						FAM135B_uc003yux.2_Intron|FAM135B_uc003yuz.2_Intron	NM_015912	NP_056996			hypothetical protein LOC51059											ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)												HNSCC(54;0.14)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140037272	140037273	+	IGR	INS	-	C	C	rs146649411	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140037272_140037273insC								COL22A1 (111036 upstream) : KCNK9 (575809 downstream)																																			---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	141242529	141242532	+	Intron	DEL	TCTC	-	-	rs145796550		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141242529_141242532delTCTC	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844			trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
EIF2C2	27161	broad.mit.edu	37	8	141546426	141546426	+	Intron	DEL	T	-	-	rs33930625		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141546426delT	uc003yvn.2	-						EIF2C2_uc010men.2_Intron|EIF2C2_uc010meo.2_Intron	NM_012154	NP_036286			argonaute 2 isoform 1						mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	142357767	142357768	+	IGR	INS	-	ACTC	ACTC	rs56311139		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142357767_142357768insACTC								LOC731779 (3048 upstream) : GPR20 (8821 downstream)																																			---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143303830	143303833	+	Intron	DEL	CATC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143303830_143303833delCATC	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron	NM_145003	NP_659440			t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143410180	143410180	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143410180delG	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron|TSNARE1_uc003ywl.3_Intron	NM_145003	NP_659440			t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	144931503	144931503	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144931503delT								NRBP2 (7303 upstream) : EPPK1 (8409 downstream)																																			---	---	---	---
PARP10	84875	broad.mit.edu	37	8	145055219	145055219	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145055219delA	uc003zal.3	-						PARP10_uc003zak.3_Intron|PARP10_uc011lku.1_Intron|PARP10_uc011lkv.1_Intron|PARP10_uc003zam.2_Intron	NM_032789	NP_116178			poly (ADP-ribose) polymerase family, member 10							Golgi apparatus|nucleolus	NAD+ ADP-ribosyltransferase activity|nucleotide binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)|pancreas(1)	6	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
SPATC1	375686	broad.mit.edu	37	8	145088566	145088567	+	Intron	INS	-	AAG	AAG	rs144039966	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145088566_145088567insAAG	uc011lkw.1	+						SPATC1_uc011lkx.1_Intron	NM_198572	NP_940974			spermatogenesis and centriole associated 1											ovary(1)|central_nervous_system(1)	2	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	146284585	146284585	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146284585delT								C8orf33 (3170 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	2360378	2360378	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2360378delT								SMARCA2 (166757 upstream) : FLJ35024 (62324 downstream)																																			---	---	---	---
FLJ35024	401491	broad.mit.edu	37	9	2570217	2570218	+	Intron	DEL	AT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2570217_2570218delAT	uc003zhh.1	-						FLJ35024_uc003zhi.2_Intron|FLJ35024_uc003zhj.3_Intron					Homo sapiens cDNA FLJ35024 fis, clone OCBBF2015233.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	2986345	2986346	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2986345_2986346insT								KIAA0020 (142215 upstream) : RFX3 (238303 downstream)																																			---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	4297120	4297121	+	Intron	INS	-	A	A	rs111499278		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4297120_4297121insA	uc003zhx.1	-						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_uc003zii.1_Intron	NM_001042413	NP_001035878			GLIS family zinc finger 3 isoform a						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	4418269	4418269	+	IGR	DEL	A	-	-	rs35868409		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4418269delA								GLIS3 (118234 upstream) : SLC1A1 (72175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	5318008	5318009	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5318008_5318009delGT								RLN2 (13428 upstream) : RLN1 (16960 downstream)																																			---	---	---	---
C9orf46	55848	broad.mit.edu	37	9	5484538	5484539	+	Intron	INS	-	AGA	AGA	rs150962993	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5484538_5484539insAGA	uc003zjd.2	-							NM_018465	NP_060935			hypothetical protein LOC55848							integral to membrane				ovary(1)	1	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.00106)|Lung(218;0.125)														---	---	---	---
C9orf46	55848	broad.mit.edu	37	9	5620084	5620085	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5620084_5620085insT	uc003zjd.2	-							NM_018465	NP_060935			hypothetical protein LOC55848							integral to membrane				ovary(1)	1	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.00106)|Lung(218;0.125)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	7600259	7600259	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7600259delA								KDM4C (424612 upstream) : C9orf123 (196234 downstream)																																			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8734748	8734748	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8734748delT	uc003zkk.2	-						PTPRD_uc003zkp.2_5'Flank|PTPRD_uc003zkq.2_5'Flank|PTPRD_uc003zkr.2_5'Flank|PTPRD_uc003zks.2_5'Flank|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8832105	8832106	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8832105_8832106delTG	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	12430491	12430492	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12430491_12430492delTG								None (None upstream) : TYRP1 (262894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	13458875	13458875	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13458875delT								MPDZ (179312 upstream) : NFIB (622973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	15375343	15375344	+	IGR	INS	-	C	C	rs7871488	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15375343_15375344insC								TTC39B (68099 upstream) : SNAPC3 (47438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	16255204	16255205	+	IGR	INS	-	A	A	rs138960619	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16255204_16255205insA								C9orf93 (283309 upstream) : BNC2 (154297 downstream)																																			---	---	---	---
BNC2	54796	broad.mit.edu	37	9	16737546	16737547	+	Intron	INS	-	T	T	rs34557388		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16737546_16737547insT	uc003zml.2	-						BNC2_uc011lmw.1_Intron|BNC2_uc003zmm.2_Intron|BNC2_uc003zmq.1_Intron|BNC2_uc003zmr.1_Intron|BNC2_uc003zmp.1_Intron|BNC2_uc010mij.1_Intron|BNC2_uc003zmu.1_Intron|BNC2_uc010mim.1_Intron|BNC2_uc010min.1_Intron	NM_017637	NP_060107			basonuclin 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	17095798	17095799	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17095798_17095799delGT								BNC2 (225012 upstream) : CNTLN (39239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	18015906	18015906	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18015906delC								SH3GL2 (218786 upstream) : ADAMTSL1 (458198 downstream)																																			---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18884941	18884941	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18884941delG	uc003zne.3	+						ADAMTSL1_uc003znf.3_Intron	NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	19231541	19231542	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19231541_19231542insT								PLIN2 (103968 upstream) : DENND4C (59160 downstream)																																			---	---	---	---
KIAA1797	54914	broad.mit.edu	37	9	20901192	20901193	+	Intron	DEL	TG	-	-	rs72059031		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20901192_20901193delTG	uc003zog.1	+						KIAA1797_uc003zoh.1_Intron	NM_017794	NP_060264			hypothetical protein LOC54914							integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	21049452	21049453	+	IGR	INS	-	TGTGTGTGTG	TGTGTGTGTG	rs35156893		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21049452_21049453insTGTGTGTGTG								PTPLAD2 (17817 upstream) : IFNB1 (27652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	21346866	21346867	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21346866_21346867insA								KLHL9 (11437 upstream) : IFNA6 (3452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25769170	25769170	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25769170delA								TUSC1 (90314 upstream) : None (None downstream)																																			---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28182975	28182975	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28182975delA	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)														---	---	---	---
ACO1	48	broad.mit.edu	37	9	32396646	32396656	+	Intron	DEL	CTGCTTTTGCC	-	-	rs138768297		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32396646_32396656delCTGCTTTTGCC	uc003zqw.3	+						ACO1_uc010mjh.1_Intron|ACO1_uc003zqx.3_Intron|ACO1_uc003zqy.3_Intron	NM_002197	NP_002188			aconitase 1						citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	33104821	33104822	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33104821_33104822delTT								SMU1 (28107 upstream) : B4GALT1 (5817 downstream)																																			---	---	---	---
KIF24	347240	broad.mit.edu	37	9	34321307	34321308	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34321307_34321308insA	uc003zua.3	-						KIF24_uc010mkb.2_Intron	NM_194313	NP_919289			kinesin family member 24						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0107)															---	---	---	---
CNTFR	1271	broad.mit.edu	37	9	34571559	34571560	+	Intron	INS	-	AC	AC	rs145378339	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34571559_34571560insAC	uc003zup.1	-						CNTFR_uc003zuq.1_Intron|LOC415056_uc003zut.2_Intron|LOC415056_uc003zur.2_Intron|LOC415056_uc003zus.2_Intron	NM_147164	NP_671693			ciliary neurotrophic factor receptor						nervous system development	anchored to membrane|extrinsic to membrane|plasma membrane	ciliary neurotrophic factor receptor activity|receptor binding			ovary(3)|central_nervous_system(1)|skin(1)	5	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)														---	---	---	---
UNC13B	10497	broad.mit.edu	37	9	35293035	35293036	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35293035_35293036insT	uc003zwq.2	+						UNC13B_uc010mkl.1_Intron|UNC13B_uc003zwr.2_Intron	NM_006377	NP_006368			UNC13 (C. elegans)-like						excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
SHB	6461	broad.mit.edu	37	9	38024540	38024541	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38024540_38024541delCA	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	38136422	38136423	+	IGR	DEL	GA	-	-	rs35196223		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38136422_38136423delGA								SHB (67212 upstream) : ALDH1B1 (256279 downstream)																																			---	---	---	---
FAM74A3	728495	broad.mit.edu	37	9	40715911	40715944	+	RNA	DEL	GAGAAGACGTGGAAAGAGCTCAGAGGCTGTCCCA	-	-	rs62565542		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40715911_40715944delGAGAAGACGTGGAAAGAGCTCAGAGGCTGTCCCA	uc010mmk.2	+	1		c.388_421delGAGAAGACGTGGAAAGAGCTCAGAGGCTGTCCCA				NR_026801				Homo sapiens family with sequence similarity 74, member A3 (FAM74A3), non-coding RNA.											skin(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	42523654	42523654	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:42523654delA								FAM95B1 (49417 upstream) : FOXD4L2 (193580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	43401739	43401739	+	IGR	DEL	C	-	-	rs142652528		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43401739delC								LOC642929 (256255 upstream) : FAM75A6 (222765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66537754	66537755	+	Intron	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66537754_66537755delGT	uc010mnh.1	-						uc004aef.2_Intron					Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	66774039	66774039	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66774039delG								LOC442421 (271012 upstream) : AQP7P1 (480228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66823200	66823200	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66823200delT								LOC442421 (320173 upstream) : AQP7P1 (431067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66977084	66977084	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66977084delA								LOC442421 (474057 upstream) : AQP7P1 (277183 downstream)																																			---	---	---	---
AQP7P1	375719	broad.mit.edu	37	9	67290547	67290547	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67290547delT	uc004aen.1	-						AQP7P1_uc004aeo.1_5'Flank|AQP7P1_uc004aep.1_5'Flank					Homo sapiens cDNA FLJ46364 fis, clone TESTI4051015.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	68432901	68432901	+	IGR	DEL	A	-	-	rs111743052		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68432901delA								FAM27B (638712 upstream) : MIR1299 (569338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68721177	68721177	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68721177delC								FAM27B (926988 upstream) : MIR1299 (281062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68989138	68989141	+	IGR	DEL	CCCT	-	-	rs138958079		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68989138_68989141delCCCT								None (None upstream) : MIR1299 (13098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69492863	69492865	+	IGR	DEL	ATC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69492863_69492865delATC								ANKRD20A4 (67755 upstream) : LOC100133920 (158496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69814659	69814660	+	IGR	INS	-	T	T	rs147599302	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69814659_69814660insT								LOC100133920 (149710 upstream) : FOXD4L5 (361049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69816366	69816366	+	IGR	DEL	A	-	-	rs146173549		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69816366delA								LOC100133920 (151417 upstream) : FOXD4L5 (359343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	70117457	70117458	+	IGR	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70117457_70117458insG								LOC100133920 (452508 upstream) : FOXD4L5 (58251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	72870617	72870617	+	Intron	DEL	A	-	-	rs35306519		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72870617delA	uc004ahq.1	-											Homo sapiens cDNA FLJ42142 fis, clone TESTI2045155.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	73058555	73058555	+	IGR	DEL	A	-	-	rs140322977		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73058555delA								KLF9 (28982 upstream) : TRPM3 (91413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	73143780	73143781	+	IGR	INS	-	A	A	rs78489198		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73143780_73143781insA								KLF9 (114207 upstream) : TRPM3 (6187 downstream)																																			---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73211645	73211645	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73211645delG	uc004aid.2	-						TRPM3_uc004ahu.2_Intron|TRPM3_uc004ahv.2_Intron|TRPM3_uc004ahw.2_Intron|TRPM3_uc004ahx.2_Intron|TRPM3_uc004ahy.2_Intron|TRPM3_uc004ahz.2_Intron|TRPM3_uc004aia.2_Intron|TRPM3_uc004aib.2_Intron|TRPM3_uc004aic.2_Intron	NM_001007471	NP_001007472			transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73674594	73674594	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73674594delA	uc004aid.2	-						TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron|TRPM3_uc004aii.2_Intron	NM_001007471	NP_001007472			transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73739223	73739223	+	5'Flank	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73739223delA	uc004aid.2	-						TRPM3_uc004aic.2_5'Flank|TRPM3_uc010mor.2_5'Flank|TRPM3_uc004aii.2_Intron	NM_001007471	NP_001007472			transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
C9orf85	138241	broad.mit.edu	37	9	74575830	74575830	+	Intron	DEL	T	-	-	rs111315320		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74575830delT	uc004ain.2	+						C9orf85_uc004aio.2_Intron|C9orf85_uc010mou.2_Intron|C9orf85_uc010mov.2_Intron	NM_182505	NP_872311			hypothetical protein LOC138241												0																		---	---	---	---
GDA	9615	broad.mit.edu	37	9	74840905	74840906	+	Intron	DEL	GT	-	-	rs35524358		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74840905_74840906delGT	uc004aiq.2	+						GDA_uc011lse.1_Intron|GDA_uc011lsf.1_Intron|GDA_uc004air.2_Intron|GDA_uc010mow.1_Intron|GDA_uc004ais.2_Intron|GDA_uc004ait.1_Intron	NM_004293	NP_004284			guanine deaminase						nervous system development|purine base metabolic process|purine nucleotide catabolic process	cytosol	guanine deaminase activity|zinc ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	75476920	75476920	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75476920delA								TMC1 (25653 upstream) : ALDH1A1 (38668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76142313	76142313	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76142313delT								ANXA1 (357006 upstream) : RORB (969939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76381628	76381629	+	IGR	INS	-	AA	AA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76381628_76381629insAA								ANXA1 (596321 upstream) : RORB (730623 downstream)																																			---	---	---	---
TRPM6	140803	broad.mit.edu	37	9	77360379	77360380	+	Intron	DEL	GT	-	-	rs71861907		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77360379_77360380delGT	uc004ajl.1	-						TRPM6_uc004ajk.1_Intron|TRPM6_uc010mpb.1_Intron|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajj.1_Intron	NM_017662	NP_060132			transient receptor potential cation channel,						response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	78100286	78100286	+	IGR	DEL	A	-	-	rs11342601		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78100286delA								OSTF1 (338173 upstream) : PCSK5 (405274 downstream)																																			---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79383500	79383501	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79383500_79383501delTG	uc010mpk.2	-						PCA3_uc010mpm.1_Intron|PCA3_uc004akm.2_Intron|PCA3_uc010mpn.1_Intron	NM_015225	NP_056040			prune homolog 2						apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	79647179	79647180	+	IGR	INS	-	C	C	rs149926932	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79647179_79647180insC								FOXB2 (11310 upstream) : VPS13A (145181 downstream)																																			---	---	---	---
GNAQ	2776	broad.mit.edu	37	9	80439696	80439697	+	Intron	INS	-	A	A	rs142186672	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80439696_80439697insA	uc004akw.2	-						GNAQ_uc011lso.1_5'Flank	NM_002072	NP_002063			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity			eye(136)|skin(44)|meninges(11)|ovary(1)|kidney(1)	193								Mis		uveal melanoma								---	---	---	---
Unknown	0	broad.mit.edu	37	9	80744201	80744202	+	IGR	INS	-	A	A	rs34382015		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80744201_80744202insA								GNAQ (98009 upstream) : CEP78 (106789 downstream)																																			---	---	---	---
CEP78	84131	broad.mit.edu	37	9	80864140	80864141	+	Intron	INS	-	TTGTTGTTG	TTGTTGTTG	rs142548300	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80864140_80864141insTTGTTGTTG	uc004akx.2	+						CEP78_uc004aky.3_Intron|CEP78_uc010mpp.2_Intron|CEP78_uc011lsp.1_3'UTR	NM_032171	NP_115547			centrosomal protein 78kDa isoform b						G2/M transition of mitotic cell cycle	centrosome|cytosol				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	81568801	81568802	+	IGR	INS	-	A	A	rs142353224	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81568801_81568802insA								PSAT1 (623794 upstream) : TLE4 (618076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82116418	82116419	+	IGR	DEL	CA	-	-	rs71504953		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82116418_82116419delCA								None (None upstream) : TLE4 (70459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82503338	82503338	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82503338delG								TLE4 (161681 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83682645	83682650	+	IGR	DEL	TTGTTG	-	-	rs141713884		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83682645_83682650delTTGTTG								None (None upstream) : TLE1 (515950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84054963	84054963	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84054963delA								None (None upstream) : TLE1 (143637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84108516	84108516	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84108516delA								None (None upstream) : TLE1 (90084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84983376	84983377	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84983376_84983377delGT								FLJ46321 (373206 upstream) : RASEF (613940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85064078	85064079	+	IGR	DEL	TG	-	-	rs72497426		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85064078_85064079delTG								FLJ46321 (453908 upstream) : RASEF (533238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85847714	85847714	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85847714delC								RASEF (169671 upstream) : FRMD3 (10191 downstream)																																			---	---	---	---
FRMD3	257019	broad.mit.edu	37	9	86006496	86006497	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86006496_86006497insT	uc004ams.1	-						FRMD3_uc004amr.1_Intron	NM_174938	NP_777598			FERM domain containing 3							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
UBQLN1	29979	broad.mit.edu	37	9	86277183	86277184	+	Intron	DEL	AC	-	-	rs7030866		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86277183_86277184delAC	uc004amv.2	-						UBQLN1_uc004amw.2_Intron	NM_013438	NP_038466			ubiquilin 1 isoform 1						apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0																		---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87332523	87332523	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87332523delA	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)			---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87570934	87570934	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87570934delC	uc004aoa.1	+						NTRK2_uc004any.1_3'UTR|NTRK2_uc004anz.1_Intron	NM_001018064	NP_001018074			neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16															TSP Lung(25;0.17)			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87723319	87723319	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87723319delT								NTRK2 (84814 upstream) : AGTPBP1 (438136 downstream)																																			---	---	---	---
GOLM1	51280	broad.mit.edu	37	9	88686594	88686594	+	Intron	DEL	A	-	-	rs113944849		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88686594delA	uc004aol.2	-						GOLM1_uc010mqd.1_Intron|GOLM1_uc004aom.2_Intron	NM_016548	NP_057632			golgi membrane protein 1							Golgi apparatus|integral to plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	89327343	89327344	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89327343_89327344insT								ZCCHC6 (357965 upstream) : GAS1 (231935 downstream)																																			---	---	---	---
DAPK1	1612	broad.mit.edu	37	9	90297344	90297344	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90297344delT	uc004apc.2	+						DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_Intron|DAPK1_uc011lth.1_Intron|DAPK1_uc004apf.1_3'UTR	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	90790091	90790092	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90790091_90790092delAC								CDK20 (200424 upstream) : SPIN1 (212748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91323829	91323829	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91323829delA								LOC286238 (56754 upstream) : C9orf47 (281949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	92725701	92725714	+	IGR	DEL	CACACACACAGCCA	-	-	rs72295161		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92725701_92725714delCACACACACAGCCA								LOC100129066 (391027 upstream) : DIRAS2 (646400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	92773151	92773152	+	IGR	INS	-	G	G	rs141787751	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92773151_92773152insG								LOC100129066 (438477 upstream) : DIRAS2 (598962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	92782741	92782743	+	IGR	DEL	AGA	-	-	rs151286151		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92782741_92782743delAGA								LOC100129066 (448067 upstream) : DIRAS2 (589371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	93295606	93295606	+	Intron	DEL	G	-	-	rs7866106	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93295606delG	uc004aqt.1	-											Homo sapiens cDNA FLJ46333 fis, clone TESTI4045701.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	93509195	93509195	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93509195delG								DIRAS2 (104087 upstream) : SYK (54817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	93533404	93533404	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93533404delA								DIRAS2 (128296 upstream) : SYK (30608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	94238854	94238854	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94238854delA								NFIL3 (52710 upstream) : ROR2 (86519 downstream)																																			---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94334695	94334695	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94334695delC	uc004ari.1	-							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	94382687	94382688	+	Intron	INS	-	A	A	rs140392824	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94382687_94382688insA	uc004ari.1	-							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	94779168	94779168	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94779168delT								ROR2 (66724 upstream) : SPTLC1 (14252 downstream)																																			---	---	---	---
BICD2	23299	broad.mit.edu	37	9	95496249	95496249	+	Intron	DEL	A	-	-	rs35019242		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95496249delA	uc004aso.1	-						BICD2_uc004asp.1_Intron	NM_015250	NP_056065			bicaudal D homolog 2 isoform 2						microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule	cytoplasmic vesicle|cytoskeleton|Golgi apparatus|plasma membrane	Rab GTPase binding			skin(1)	1																		---	---	---	---
PHF2	5253	broad.mit.edu	37	9	96394085	96394086	+	Intron	INS	-	GGG	GGG	rs148327848	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96394085_96394086insGGG	uc004aub.2	+						PHF2_uc011lug.1_Intron	NM_005392	NP_005383			PHD finger protein 2						liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	96887773	96887773	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96887773delA								PTPDC1 (15637 upstream) : MIRLET7A1 (50466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	96889529	96889529	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96889529delA								PTPDC1 (17393 upstream) : MIRLET7A1 (48710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	97860610	97860627	+	IGR	DEL	CTAGCTCCCATTTCTGTC	-	-	rs72074456		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97860610_97860627delCTAGCTCCCATTTCTGTC								C9orf3 (11170 upstream) : FANCC (711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98144019	98144020	+	IGR	INS	-	CTAA	CTAA	rs112063401		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98144019_98144020insCTAA								FANCC (64028 upstream) : PTCH1 (61246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98847337	98847338	+	Intron	INS	-	A	A	rs7034468	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98847337_98847338insA	uc004avy.3	+											Homo sapiens cDNA clone IMAGE:3638298.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	99578000	99578001	+	IGR	INS	-	AGAG	AGAG	rs139157616	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99578000_99578001insAGAG								ZNF510 (37662 upstream) : ZNF782 (1272 downstream)																																			---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101111631	101111631	+	Intron	DEL	G	-	-	rs58706340		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101111631delG	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)													---	---	---	---
GALNT12	79695	broad.mit.edu	37	9	101596408	101596408	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101596408delT	uc004ayz.2	+							NM_024642	NP_078918			N-acetylgalactosaminyltransferase 12							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	102228318	102228319	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102228318_102228319delTT								SEC61B (235418 upstream) : NR4A3 (355818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	102577180	102577180	+	Intron	DEL	T	-	-	rs112662104		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102577180delT	uc004bad.1	-											Homo sapiens cDNA FLJ32889 fis, clone TESTI2004560.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	102739057	102739057	+	IGR	DEL	A	-	-	rs11304213		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102739057delA								STX17 (2240 upstream) : ERP44 (2408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	103718181	103718182	+	IGR	INS	-	TA	TA	rs10640056		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103718181_103718182insTA								MURC (368010 upstream) : LPPR1 (72849 downstream)																																			---	---	---	---
LPPR1	54886	broad.mit.edu	37	9	103835765	103835766	+	Intron	INS	-	A	A	rs144350888	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103835765_103835766insA	uc004bbb.2	+						LPPR1_uc011lvi.1_Intron	NM_207299	NP_997182			plasticity related gene 3							integral to membrane	catalytic activity				0																		---	---	---	---
LPPR1	54886	broad.mit.edu	37	9	104060065	104060065	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104060065delT	uc004bbb.2	+						LPPR1_uc011lvi.1_Intron|LPPR1_uc004bbc.2_Intron|LPPR1_uc010mtc.2_Intron	NM_207299	NP_997182			plasticity related gene 3							integral to membrane	catalytic activity				0																		---	---	---	---
GRIN3A	116443	broad.mit.edu	37	9	104434448	104434460	+	Intron	DEL	CTTGAACAATTTA	-	-	rs67340874		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104434448_104434460delCTTGAACAATTTA	uc004bbp.1	-						GRIN3A_uc004bbq.1_Intron	NM_133445	NP_597702			glutamate receptor, ionotropic,						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740)													---	---	---	---
GRIN3A	116443	broad.mit.edu	37	9	104466439	104466439	+	Intron	DEL	A	-	-	rs147206111		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104466439delA	uc004bbp.1	-						GRIN3A_uc004bbq.1_Intron	NM_133445	NP_597702			glutamate receptor, ionotropic,						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	104630183	104630184	+	IGR	INS	-	ATCCTGTT	ATCCTGTT	rs140276454	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104630183_104630184insATCCTGTT								GRIN3A (129321 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105394231	105394232	+	IGR	INS	-	T	T	rs5899503		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105394231_105394232insT								GRIN3A (893369 upstream) : CYLC2 (363361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	106349823	106349824	+	IGR	INS	-	C	C	rs140284665	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106349823_106349824insC								CYLC2 (569053 upstream) : SMC2 (506717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107092078	107092079	+	IGR	DEL	AA	-	-	rs34756850		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107092078_107092079delAA								SMC2 (188385 upstream) : OR13F1 (174465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107411402	107411403	+	IGR	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107411402_107411403delCA								OR13C9 (30917 upstream) : OR13D1 (45300 downstream)																																			---	---	---	---
NIPSNAP3B	55335	broad.mit.edu	37	9	107538677	107538678	+	Intron	INS	-	C	C	rs141949279	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107538677_107538678insC	uc004bcj.1	+						LOC286367_uc004bck.3_RNA					Homo sapiens cDNA FLJ11275 fis, clone PLACE1009375.											pancreas(1)|skin(1)	2																		---	---	---	---
NIPSNAP3B	55335	broad.mit.edu	37	9	107540095	107540096	+	Intron	INS	-	T	T	rs137863935	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107540095_107540096insT	uc004bcj.1	+											Homo sapiens cDNA FLJ11275 fis, clone PLACE1009375.											pancreas(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	108729048	108729048	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108729048delA								TMEM38B (191604 upstream) : ZNF462 (896330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	109887073	109887074	+	IGR	INS	-	A	A	rs144991708	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109887073_109887074insA								ZNF462 (113284 upstream) : RAD23B (158470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110003891	110003894	+	IGR	DEL	GAAG	-	-	rs140386387		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110003891_110003894delGAAG								ZNF462 (230102 upstream) : RAD23B (41650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110567672	110567672	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110567672delT								KLF4 (315625 upstream) : None (None downstream)																																	OREG0007559	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	---	---	---	---
Unknown	0	broad.mit.edu	37	9	110893721	110893724	+	IGR	DEL	TATT	-	-	rs146329802		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110893721_110893724delTATT								KLF4 (641674 upstream) : ACTL7B (723147 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110925739	110925740	+	IGR	INS	-	TG	TG	rs140798611	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110925739_110925740insTG								KLF4 (673692 upstream) : ACTL7B (691131 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111484689	111484690	+	IGR	INS	-	GA	GA	rs149291401	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111484689_111484690insGA								None (None upstream) : ACTL7B (132181 downstream)																																			---	---	---	---
PALM2	114299	broad.mit.edu	37	9	112526142	112526143	+	Intron	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112526142_112526143delGT	uc004beg.2	+						PALM2_uc004bef.2_Intron	NM_001037293	NP_001032370			paralemmin 2 isoform b						regulation of cell shape	plasma membrane				ovary(2)	2																		---	---	---	---
MUSK	4593	broad.mit.edu	37	9	113512095	113512095	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113512095delT	uc004bey.2	+							NM_005592	NP_005583			skeletal muscle receptor tyrosine kinase						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|ovary(2)|central_nervous_system(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	113603230	113603230	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113603230delA								MUSK (39952 upstream) : LPAR1 (32826 downstream)																																			---	---	---	---
LPAR1	1902	broad.mit.edu	37	9	113719484	113719485	+	Intron	INS	-	A	A	rs148381793	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113719484_113719485insA	uc004bfa.2	-						LPAR1_uc011lwm.1_Intron|LPAR1_uc004bfb.2_Intron|LPAR1_uc004bfc.2_Intron|LPAR1_uc011lwn.1_Intron|LPAR1_uc011lwo.1_Intron|LPAR1_uc010mub.2_Intron	NM_057159	NP_476500			lysophosphatidic acid receptor 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane				ovary(2)	2																		---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114170786	114170786	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114170786delA	uc004bfe.1	-							NM_001080398	NP_001073867			KIAA0368 protein												0																		---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114234921	114234921	+	Intron	DEL	A	-	-	rs77662929		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114234921delA	uc004bfe.1	-						KIAA0368_uc010muc.1_Intron	NM_001080398	NP_001073867			KIAA0368 protein												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	114370096	114370096	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114370096delT	uc004bfk.3	-											Homo sapiens chromosome 9 open reading frame 29, mRNA (cDNA clone MGC:39589 IMAGE:4838739), complete cds.																														---	---	---	---
HSDL2	84263	broad.mit.edu	37	9	115168447	115168447	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115168447delA	uc004bga.1	+						HSDL2_uc011lwv.1_Intron|HSDL2_uc004bgb.1_Intron|HSDL2_uc004bgc.1_Intron|HSDL2_uc011lww.1_Intron	NM_032303	NP_115679			hydroxysteroid dehydrogenase like 2							peroxisome	oxidoreductase activity|sterol binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	115658578	115658579	+	IGR	INS	-	A	A	rs139390273	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115658578_115658579insA								SLC46A2 (5385 upstream) : ZNF883 (100823 downstream)																																			---	---	---	---
FKBP15	23307	broad.mit.edu	37	9	116019141	116019142	+	Intron	DEL	AA	-	-	rs10705989		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116019141_116019142delAA	uc010muu.1	-						SLC31A1_uc004bgu.2_Intron|SLC31A1_uc004bgv.3_Intron	NM_015258	NP_056073			FK506 binding protein 15, 133kDa						endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3																		---	---	---	---
RGS3	5998	broad.mit.edu	37	9	116287413	116287414	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116287413_116287414delTG	uc004bhq.2	+						RGS3_uc004bhr.2_Intron|RGS3_uc004bhs.2_Intron|RGS3_uc004bht.2_Intron|RGS3_uc010muy.2_Intron|RGS3_uc004bhu.2_Intron	NM_144488	NP_652759			regulator of G-protein signalling 3 isoform 6						inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	116500308	116500309	+	IGR	DEL	TC	-	-	rs141875626	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116500308_116500309delTC								RGS3 (140291 upstream) : ZNF618 (138253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	116885173	116885174	+	IGR	INS	-	TC	TC	rs141205964	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116885173_116885174insTC								KIF12 (23666 upstream) : COL27A1 (33057 downstream)																																			---	---	---	---
COL27A1	85301	broad.mit.edu	37	9	117040680	117040682	+	Intron	DEL	CGA	-	-	rs149815057	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117040680_117040682delCGA	uc011lxl.1	+						COL27A1_uc004bii.2_Intron	NM_032888	NP_116277			collagen, type XXVII, alpha 1 precursor						cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4																		---	---	---	---
DEC1	50514	broad.mit.edu	37	9	117952843	117952845	+	Intron	DEL	AAA	-	-	rs112821652		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117952843_117952845delAAA	uc004bjk.1	+							NM_017418	NP_059114			deleted in esophageal cancer 1						negative regulation of cell proliferation					ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	120420093	120420093	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120420093delT								ASTN2 (242776 upstream) : TLR4 (46367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	120967118	120967119	+	IGR	DEL	AC	-	-	rs140762168		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120967118_120967119delAC								TLR4 (487354 upstream) : DBC1 (961789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121357715	121357716	+	IGR	INS	-	T	T	rs150868919	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121357715_121357716insT								TLR4 (877951 upstream) : DBC1 (571192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121784695	121784695	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121784695delA								None (None upstream) : DBC1 (144213 downstream)																																			---	---	---	---
DBC1	1620	broad.mit.edu	37	9	122066154	122066154	+	Intron	DEL	T	-	-	rs11292229		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122066154delT	uc004bkc.2	-						DBC1_uc004bkd.2_Intron	NM_014618	NP_055433			deleted in bladder cancer 1 precursor						cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	122795980	122795982	+	IGR	DEL	CAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122795980_122795982delCAA								DBC1 (664241 upstream) : MIR147 (211275 downstream)																																			---	---	---	---
PSMD5	5711	broad.mit.edu	37	9	123586582	123586582	+	Intron	DEL	A	-	-	rs35903891		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123586582delA	uc004bko.2	-						PSMD5_uc011lye.1_Intron	NM_005047	NP_005038			proteasome 26S non-ATPase subunit 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|proteasome regulatory particle assembly|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	123663473	123663474	+	IGR	INS	-	T	T	rs148408818	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123663473_123663474insT								PHF19 (23867 upstream) : TRAF1 (1198 downstream)																																			---	---	---	---
GSN	2934	broad.mit.edu	37	9	123996441	123996441	+	Intron	DEL	C	-	-	rs34728869		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123996441delC	uc004bld.1	+							NM_198252	NP_937895			gelsolin isoform b						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3																		---	---	---	---
GSN	2934	broad.mit.edu	37	9	124004772	124004772	+	Intron	DEL	A	-	-	rs35925722		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124004772delA	uc004bld.1	+							NM_198252	NP_937895			gelsolin isoform b						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126247936	126247943	+	Intron	DEL	CACACACA	-	-	rs62579172	by1000genomes;by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126247936_126247943delCACACACA	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																		---	---	---	---
GOLGA1	2800	broad.mit.edu	37	9	127666373	127666373	+	Intron	DEL	A	-	-	rs35994785		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127666373delA	uc004bpc.2	-						GOLGA1_uc010mws.2_Intron	NM_002077	NP_002068			golgin 97							Golgi cisterna membrane				ovary(1)	1																		---	---	---	---
MAPKAP1	79109	broad.mit.edu	37	9	128456608	128456608	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128456608delA	uc004bpv.2	-						MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Intron|MAPKAP1_uc004bpz.2_Intron|MAPKAP1_uc010mxa.2_Intron|MAPKAP1_uc004bqa.2_Intron	NM_001006617	NP_001006618			mitogen-activated protein kinase associated						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|response to stress|T cell costimulation	cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	Ras GTPase binding			ovary(2)|lung(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	128848535	128848535	+	IGR	DEL	T	-	-	rs35073670		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128848535delT								PBX3 (118882 upstream) : FAM125B (240593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128915792	128915793	+	IGR	INS	-	TCCA	TCCA	rs143999533	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128915792_128915793insTCCA								PBX3 (186139 upstream) : FAM125B (173335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128990917	128990918	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128990917_128990918delAC								PBX3 (261264 upstream) : FAM125B (98210 downstream)																																	OREG0019490	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	9	129006945	129006945	+	IGR	DEL	T	-	-	rs66755741		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129006945delT								PBX3 (277292 upstream) : FAM125B (82183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	129477299	129477299	+	IGR	DEL	T	-	-	rs34302034		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129477299delT								LMX1B (13988 upstream) : ZBTB43 (89986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	129563441	129563441	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129563441delT								LMX1B (100130 upstream) : ZBTB43 (3844 downstream)																																			---	---	---	---
ZBTB43	23099	broad.mit.edu	37	9	129599383	129599383	+	3'UTR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129599383delA	uc004bql.2	+	3					ZBTB43_uc010mxf.2_3'UTR	NM_014007	NP_054726			zinc finger and BTB domain containing 43						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	129653888	129653889	+	IGR	INS	-	A	A	rs139008911	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129653888_129653889insA								ZBTB34 (5734 upstream) : RALGPS1 (23164 downstream)																																			---	---	---	---
ENG	2022	broad.mit.edu	37	9	130619584	130619585	+	5'Flank	DEL	TG	-	-	rs57160067		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130619584_130619585delTG	uc004bsj.3	-						ENG_uc004bsk.3_5'Flank	NM_001114753	NP_001108225			endoglin isoform 1 precursor						artery morphogenesis|BMP signaling pathway|cell adhesion|cell chemotaxis|central nervous system vasculogenesis|chronological cell aging|detection of hypoxia|extracellular matrix disassembly|heart looping|negative regulation of endothelial cell proliferation|negative regulation of nitric-oxide synthase activity|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of protein autophosphorylation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|patterning of blood vessels|positive regulation of BMP signaling pathway|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of systemic arterial blood pressure|positive regulation of transcription from RNA polymerase II promoter|regulation of cell adhesion|regulation of cell proliferation|regulation of transcription, DNA-dependent|regulation of transforming growth factor beta receptor signaling pathway|smooth muscle tissue development|transforming growth factor beta receptor signaling pathway|venous blood vessel morphogenesis|wound healing	cell surface|external side of plasma membrane|extracellular space|membrane fraction	activin binding|galactose binding|glycosaminoglycan binding|protein homodimerization activity|transforming growth factor beta binding|transforming growth factor beta receptor activity|transforming growth factor beta receptor, cytoplasmic mediator activity|transmembrane receptor activity|type I transforming growth factor beta receptor binding|type II transforming growth factor beta receptor binding				0														Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				---	---	---	---
Unknown	0	broad.mit.edu	37	9	130896942	130896943	+	IGR	INS	-	T	T	rs138659103	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130896942_130896943insT								LOC389791 (4031 upstream) : LCN2 (14789 downstream)																																			---	---	---	---
GLE1	2733	broad.mit.edu	37	9	131294317	131294317	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131294317delT	uc004bvj.2	+						GLE1_uc004bvi.2_Intron|GLE1_uc010myd.2_Intron	NM_001003722	NP_001003722			GLE1 RNA export mediator homolog isoform 1						poly(A)+ mRNA export from nucleus|protein transport|transmembrane transport	cytoplasm|nuclear pore	protein binding				0																		---	---	---	---
NUP188	23511	broad.mit.edu	37	9	131736596	131736597	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131736596_131736597insT	uc004bws.1	+							NM_015354	NP_056169			nucleoporin 188kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|kidney(1)|breast(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	131959102	131959105	+	IGR	DEL	CCTT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131959102_131959105delCCTT								IER5L (18562 upstream) : C9orf106 (124190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132303659	132303660	+	IGR	INS	-	GAAACAGG	GAAACAGG	rs144228541	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132303659_132303660insGAAACAGG								C9orf106 (218777 upstream) : C9orf50 (70846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	133447393	133447393	+	IGR	DEL	T	-	-	rs113392792		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133447393delT								ASS1 (70733 upstream) : LOC100272217 (5346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	134432029	134432029	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134432029delT								UCK1 (25367 upstream) : RAPGEF1 (20129 downstream)																																			---	---	---	---
RAPGEF1	2889	broad.mit.edu	37	9	134611304	134611304	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134611304delA	uc004cbc.2	-						RAPGEF1_uc010mzn.2_Intron|RAPGEF1_uc004cbd.2_Intron	NM_005312	NP_005303			guanine nucleotide-releasing factor 2 isoform a						activation of MAPKK activity|nerve growth factor receptor signaling pathway|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome	guanyl-nucleotide exchange factor activity|SH3 domain binding			lung(3)|ovary(2)|breast(1)|skin(1)	7		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	135011009	135011010	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135011009_135011010insT								MED27 (55756 upstream) : NTNG2 (26324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	135129019	135129019	+	IGR	DEL	A	-	-	rs34611392		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135129019delA								NTNG2 (10799 upstream) : SETX (7809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	136465847	136465848	+	IGR	INS	-	G	G	rs142057255	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136465847_136465848insG								FAM163B (20502 upstream) : DBH (35637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	137415518	137415519	+	IGR	INS	-	T	T	rs141862754	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137415518_137415519insT								RXRA (83087 upstream) : COL5A1 (118133 downstream)																																			---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137693635	137693635	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137693635delA	uc004cfe.2	+							NM_000093	NP_000084			alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
UBAC1	10422	broad.mit.edu	37	9	138819807	138819808	+	Intron	INS	-	CA	CA	rs150121424		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138819807_138819808insCA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	139021862	139021862	+	IGR	DEL	T	-	-	rs142558414		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139021862delT								C9orf69 (11131 upstream) : LHX3 (66236 downstream)																																			---	---	---	---
PNPLA7	375775	broad.mit.edu	37	9	140367413	140367413	+	Intron	DEL	G	-	-	rs28835969	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140367413delG	uc004cnf.2	-						C9orf167_uc011mew.1_Intron|PNPLA7_uc004cnd.1_Intron|PNPLA7_uc004cne.1_Intron|PNPLA7_uc011mfa.1_Intron|PNPLA7_uc010ncj.1_Intron	NM_152286	NP_689499			patatin-like phospholipase domain containing 7						lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity			skin(1)	1	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	951601	951619	+	IGR	DEL	GGGAGGAGCTGAGGAGCAA	-	-	rs72388873		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:951601_951619delGGGAGGAGCTGAGGAGCAA								LARP4B (19899 upstream) : GTPBP4 (82730 downstream)																																			---	---	---	---
IDI1	3422	broad.mit.edu	37	10	1102094	1102094	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1102094delA	uc001igc.2	-						WDR37_uc001ige.2_5'Flank|WDR37_uc001igf.1_5'Flank|WDR37_uc009xhm.1_5'Flank|WDR37_uc009xhn.1_5'Flank	NM_004508	NP_004499			isopentenyl-diphosphate delta isomerase						carotenoid biosynthetic process|cholesterol biosynthetic process	cytosol|peroxisome	hydrolase activity|isopentenyl-diphosphate delta-isomerase activity|metal ion binding				0		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.221)	Epithelial(11;0.0972)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	1210990	1210992	+	IGR	DEL	CAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1210990_1210992delCAT								NCRNA00200 (378 upstream) : ADARB2 (17082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3336331	3336332	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3336331_3336332insA								PITRM1 (121328 upstream) : KLF6 (481857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4037345	4037346	+	IGR	INS	-	TT	TT	rs112606351		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4037345_4037346insTT								KLF6 (209872 upstream) : LOC100216001 (584098 downstream)																																			---	---	---	---
AKR1C3	8644	broad.mit.edu	37	10	5102834	5102834	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5102834delT	uc001ihr.2	+							NM_003739	NP_003730			aldo-keto reductase family 1, member C3						prostaglandin metabolic process	cytoplasm	aldo-keto reductase (NADP) activity|androsterone dehydrogenase (A-specific) activity|indanol dehydrogenase activity|prostaglandin-F synthase activity|testosterone 17-beta-dehydrogenase (NAD+) activity|testosterone 17-beta-dehydrogenase (NADP+) activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			skin(1)	1					Dimethyl sulfoxide(DB01093)|NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	6301212	6301215	+	IGR	DEL	CATT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6301212_6301215delCATT								PFKFB3 (23707 upstream) : PRKCQ (167890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	6332462	6332463	+	IGR	INS	-	T	T	rs144991198		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6332462_6332463insT								PFKFB3 (54957 upstream) : PRKCQ (136642 downstream)																																			---	---	---	---
PRKCQ	5588	broad.mit.edu	37	10	6483433	6483433	+	Intron	DEL	C	-	-	rs5782899		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6483433delC	uc001ijj.1	-						PRKCQ_uc009xim.1_Intron|PRKCQ_uc001iji.1_Intron|PRKCQ_uc009xin.1_Intron|PRKCQ_uc010qax.1_Intron	NM_006257	NP_006248			protein kinase C, theta						axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6																		---	---	---	---
PRKCQ	5588	broad.mit.edu	37	10	6512251	6512251	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6512251delC	uc001ijj.1	-						PRKCQ_uc009xim.1_Intron|PRKCQ_uc001iji.1_Intron|PRKCQ_uc009xin.1_Intron|PRKCQ_uc010qax.1_Intron	NM_006257	NP_006248			protein kinase C, theta						axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6																		---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7382255	7382257	+	Intron	DEL	GAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7382255_7382257delGAG	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	8222667	8222668	+	IGR	INS	-	T	T	rs112235991		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8222667_8222668insT								GATA3 (105505 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8545236	8545236	+	IGR	DEL	A	-	-	rs76162998		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8545236delA								GATA3 (428074 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8582569	8582569	+	IGR	DEL	T	-	-	rs67649852		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8582569delT								GATA3 (465407 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8723799	8723800	+	IGR	INS	-	T	T	rs111955196		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8723799_8723800insT								GATA3 (606637 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9689915	9689916	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9689915_9689916delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10036839	10036839	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10036839delG								None (None upstream) : SFTA1P (789563 downstream)																																			---	---	---	---
CELF2	10659	broad.mit.edu	37	10	11199356	11199357	+	Intron	DEL	CA	-	-	rs35476826	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11199356_11199357delCA	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																		---	---	---	---
CELF2	10659	broad.mit.edu	37	10	11242079	11242083	+	Intron	DEL	GAGAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11242079_11242083delGAGAA	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|CELF2_uc010qbk.1_Intron|CELF2_uc010qbl.1_Intron|CELF2_uc010qbm.1_Intron|CELF2_uc001iko.3_Intron|CELF2_uc001ikp.3_Intron|CELF2_uc010qbn.1_Intron|CELF2_uc009xiw.1_Intron|CELF2_uc010qbo.1_Intron|CELF2_uc010qbp.1_Intron	NM_001025077	NP_001020248			CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	11762965	11762965	+	IGR	DEL	A	-	-	rs66692584		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11762965delA								USP6NL (109286 upstream) : ECHDC3 (21391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	11845878	11845879	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11845878_11845879delTT								ECHDC3 (39814 upstream) : C10orf47 (19518 downstream)																																			---	---	---	---
C10orf47	254427	broad.mit.edu	37	10	11871580	11871581	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11871580_11871581insA	uc001ikx.2	+							NM_153256	NP_694988			hypothetical protein LOC254427											central_nervous_system(1)	1																		---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12442833	12442833	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12442833delG	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718			calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)														---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12503687	12503688	+	Intron	DEL	AA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12503687_12503688delAA	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	12905757	12905757	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12905757delT								LOC283070 (28213 upstream) : CCDC3 (32868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	13577180	13577180	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13577180delA								BEND7 (32204 upstream) : PRPF18 (51759 downstream)																																			---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	14025838	14025838	+	Intron	DEL	A	-	-	rs35270555		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14025838delA	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497			FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3																		---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	14477491	14477492	+	Intron	DEL	AG	-	-	rs76393363		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14477491_14477492delAG	uc001imv.2	-						FRMD4A_uc001imw.1_Intron|MIR1265_hsa-mir-1265|MI0006401_5'Flank					Homo sapiens mRNA for KIAA1294 protein, partial cds.							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	14524081	14524082	+	IGR	INS	-	TTG	TTG			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14524081_14524082insTTG								FRMD4A (19938 upstream) : FAM107B (36477 downstream)																																			---	---	---	---
DCLRE1C	64421	broad.mit.edu	37	10	14943544	14943545	+	Intron	INS	-	T	T	rs55801071	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14943544_14943545insT	uc010qbx.1	-						SUV39H2_uc001ing.2_Intron|SUV39H2_uc001inh.2_Intron|SUV39H2_uc001ini.2_Intron|SUV39H2_uc001inj.2_Intron	NM_001033855	NP_001029027			artemis protein isoform a						DNA recombination	nucleus	5'-3' exonuclease activity|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)	1													Involved_in_tolerance_or_repair_of_DNA_crosslinks|NHEJ					---	---	---	---
OLAH	55301	broad.mit.edu	37	10	15096612	15096612	+	Intron	DEL	T	-	-	rs5783429		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15096612delT	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																		---	---	---	---
FAM188A	80013	broad.mit.edu	37	10	15859564	15859565	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15859564_15859565delTG	uc001iod.1	-						FAM188A_uc001ioe.1_Intron|FAM188A_uc001iof.1_Intron	NM_024948	NP_079224			chromosome 10 open reading frame 97						apoptosis	nucleus	calcium ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	16331684	16331685	+	IGR	INS	-	A	A	rs111441784		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16331684_16331685insA								FAM188A (429165 upstream) : PTER (147282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	16350586	16350587	+	IGR	INS	-	A	A	rs7475541		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16350586_16350587insA								FAM188A (448067 upstream) : PTER (128380 downstream)																																			---	---	---	---
CACNB2	783	broad.mit.edu	37	10	18469381	18469381	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18469381delT	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	18522429	18522429	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18522429delA	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	18642340	18642340	+	Intron	DEL	A	-	-	rs138882939		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18642340delA	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc010qcl.1_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron|CACNB2_uc001ipw.2_Intron|CACNB2_uc001ipx.2_Intron|CACNB2_uc009xkb.1_Intron|CACNB2_uc010qcm.1_Intron|CACNB2_uc001ipz.2_Intron|CACNB2_uc001ipy.2_Intron	NM_201596	NP_963890			calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	19000534	19000534	+	IGR	DEL	A	-	-	rs113602193		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19000534delA								ARL5B (33594 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19112417	19112417	+	IGR	DEL	G	-	-	rs5783628		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19112417delG								ARL5B (145477 upstream) : PLXDC2 (992955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19253613	19253613	+	IGR	DEL	T	-	-	rs72012065		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19253613delT								ARL5B (286673 upstream) : PLXDC2 (851759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19904871	19904872	+	Intron	DEL	TT	-	-	rs10580913		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19904871_19904872delTT	uc010qcr.1	+											Homo sapiens cDNA FLJ60310 complete cds.																														---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20374138	20374139	+	Intron	INS	-	A	A	rs10633088		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20374138_20374139insA	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	21334935	21334936	+	Intron	INS	-	AC	AC	rs146442559	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21334935_21334936insAC	uc001iqk.2	-							NM_213569	NP_998734			nebulette non-muscle isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21828878	21828878	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21828878delA	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc001iqr.1_Intron|MLLT10_uc001iqq.1_Intron|MLLT10_uc001iqu.1_Intron|MLLT10_uc009xke.1_Intron|MLLT10_uc001iqw.1_Intron|MLLT10_uc001iqx.1_Intron|MLLT10_uc009xkf.1_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
DNAJC1	64215	broad.mit.edu	37	10	22066433	22066433	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22066433delC	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	23767789	23767789	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23767789delT								OTUD1 (36481 upstream) : KIAA1217 (215886 downstream)																																			---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24284380	24284385	+	Intron	DEL	TGTGTG	-	-	rs148298139		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24284380_24284385delTGTGTG	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	24497051	24497051	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24497051delT	uc001iru.3	+						KIAA1217_uc001irs.2_Intron|KIAA1217_uc001irt.3_5'Flank|KIAA1217_uc010qcy.1_5'Flank|KIAA1217_uc010qcz.1_5'Flank	NM_019590	NP_062536			sickle tail isoform 1						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24528115	24528115	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24528115delA	uc001iru.3	+						KIAA1217_uc001irs.2_Intron|KIAA1217_uc001irt.3_Intron|KIAA1217_uc010qcy.1_Intron|KIAA1217_uc010qcz.1_Intron|KIAA1217_uc001irv.1_5'Flank	NM_019590	NP_062536			sickle tail isoform 1						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
GPR158	57512	broad.mit.edu	37	10	25497780	25497780	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25497780delT	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	25857067	25857068	+	Intron	INS	-	A	A	rs74556613	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25857067_25857068insA	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																		---	---	---	---
GAD2	2572	broad.mit.edu	37	10	26536848	26536849	+	Intron	INS	-	A	A	rs66469560		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26536848_26536849insA	uc001isp.2	+						GAD2_uc001isq.2_Intron	NM_001134366	NP_001127838			glutamate decarboxylase 2						glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion	cell junction|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|Golgi membrane|presynaptic membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	26654079	26654079	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26654079delC								GAD2 (60588 upstream) : APBB1IP (73187 downstream)																																			---	---	---	---
APBB1IP	54518	broad.mit.edu	37	10	26724526	26724527	+	5'Flank	INS	-	TTGT	TTGT	rs146354052	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26724526_26724527insTTGT	uc001iss.2	+						APBB1IP_uc001isr.2_5'Flank|APBB1IP_uc009xks.1_5'Flank	NM_019043	NP_061916			amyloid beta (A4) precursor protein-binding,						blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7																		---	---	---	---
APBB1IP	54518	broad.mit.edu	37	10	26784310	26784311	+	Intron	INS	-	CCTGTTC	CCTGTTC	rs143423534	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26784310_26784311insCCTGTTC	uc001iss.2	+						APBB1IP_uc001isr.2_Intron|APBB1IP_uc009xks.1_Intron	NM_019043	NP_061916			amyloid beta (A4) precursor protein-binding,						blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7																		---	---	---	---
ABI1	10006	broad.mit.edu	37	10	27131413	27131414	+	Intron	INS	-	A	A	rs150682956	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27131413_27131414insA	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	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																		---	---	---	---
ABI1	10006	broad.mit.edu	37	10	27143949	27143950	+	Intron	INS	-	T	T	rs144026225	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27143949_27143950insT	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	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	27156134	27156135	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27156134_27156135insT								ABI1 (6175 upstream) : NCRNA00202 (64000 downstream)																																			---	---	---	---
ANKRD26	22852	broad.mit.edu	37	10	27378822	27378826	+	Intron	DEL	ATTCT	-	-	rs112167562		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27378822_27378826delATTCT	uc001ith.2	-						ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730			ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	27735743	27735746	+	IGR	DEL	TCTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27735743_27735746delTCTC								PTCHD3 (32446 upstream) : RAB18 (57503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	28295178	28295178	+	IGR	DEL	A	-	-	rs11333048		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28295178delA								ARMC4 (7201 upstream) : MPP7 (44745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	28327378	28327379	+	IGR	INS	-	GTGTGT	GTGTGT	rs149023957	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28327378_28327379insGTGTGT								ARMC4 (39401 upstream) : MPP7 (12544 downstream)																																			---	---	---	---
MPP7	143098	broad.mit.edu	37	10	28444527	28444528	+	Intron	INS	-	AAAAAAAAA	AAAAAAAAA	rs76018652		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28444527_28444528insAAAAAAAAA	uc001iua.1	-						MPP7_uc009xkz.1_Intron|MPP7_uc001iub.1_Intron|MPP7_uc009xla.2_Intron|MPP7_uc010qdv.1_Intron	NM_173496	NP_775767			palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1																		---	---	---	---
MPP7	143098	broad.mit.edu	37	10	28544349	28544349	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28544349delT	uc001iua.1	-						MPP7_uc001iub.1_Intron|MPP7_uc009xla.2_Intron|MPP7_uc010qdv.1_Intron	NM_173496	NP_775767			palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1																		---	---	---	---
WAC	51322	broad.mit.edu	37	10	28863916	28863916	+	Intron	DEL	G	-	-	rs77432070		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28863916delG	uc001iuf.2	+						WAC_uc001iud.2_Intron|WAC_uc001iue.2_Intron|WAC_uc009xlb.2_Intron|WAC_uc001iug.2_Intron|WAC_uc001iuh.2_Intron	NM_016628	NP_057712			WW domain-containing adapter with a coiled-coil						cell cycle checkpoint|histone H2B conserved C-terminal lysine ubiquitination|histone monoubiquitination|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nuclear speck	chromatin binding|RNA polymerase II core binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	29282441	29282441	+	IGR	DEL	T	-	-	rs67167114		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29282441delT								BAMBI (310573 upstream) : LYZL1 (295549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29386857	29386858	+	IGR	INS	-	TT	TT	rs3069106		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29386857_29386858insTT								BAMBI (414989 upstream) : LYZL1 (191132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29655338	29655338	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29655338delT								LYZL1 (55181 upstream) : LOC387647 (43145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29661306	29661307	+	IGR	DEL	CC	-	-	rs113610862		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29661306_29661307delCC								LYZL1 (61149 upstream) : LOC387647 (37176 downstream)																																			---	---	---	---
LOC387647	387647	broad.mit.edu	37	10	29703734	29703735	+	Intron	INS	-	T	T	rs112940700		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29703734_29703735insT	uc001ium.2	+						LOC387647_uc001iuo.1_Intron|LOC387647_uc001iup.2_Intron|LOC387647_uc001iuq.1_Intron|LOC387647_uc001iun.2_Intron					Homo sapiens cDNA FLJ31518 fis, clone NT2RI2000064.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	30773885	30773886	+	IGR	INS	-	A	A	rs5784203		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30773885_30773886insA								MAP3K8 (23124 upstream) : LYZL2 (126823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	31459051	31459051	+	IGR	DEL	A	-	-	rs67673325		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31459051delA								ZNF438 (138185 upstream) : LOC220930 (146407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	31895056	31895056	+	IGR	DEL	T	-	-	rs113993572		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31895056delT								ZEB1 (76929 upstream) : ARHGAP12 (200169 downstream)																																			---	---	---	---
ARHGAP12	94134	broad.mit.edu	37	10	32164981	32164982	+	Intron	DEL	AC	-	-	rs72486850		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32164981_32164982delAC	uc001ivz.1	-						ARHGAP12_uc001ivy.1_Intron|ARHGAP12_uc009xls.2_Intron|ARHGAP12_uc001iwb.1_Intron|ARHGAP12_uc001iwc.1_Intron|ARHGAP12_uc009xlq.1_Intron|ARHGAP12_uc001iwd.1_Intron|ARHGAP12_uc009xlr.1_Intron	NM_018287	NP_060757			Rho GTPase activating protein 12						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		Prostate(175;0.0199)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	32495496	32495497	+	IGR	INS	-	A	A	rs11394328		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32495496_32495497insA								KIF5B (150125 upstream) : EPC1 (62362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	32509579	32509580	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32509579_32509580insA								KIF5B (164208 upstream) : EPC1 (48279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	32517171	32517172	+	IGR	INS	-	A	A	rs61633570		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32517171_32517172insA								KIF5B (171800 upstream) : EPC1 (40687 downstream)																																			---	---	---	---
ITGB1	3688	broad.mit.edu	37	10	33242473	33242474	+	Intron	INS	-	AA	AA	rs35171776		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33242473_33242474insAA	uc001iws.3	-						ITGB1_uc001iwt.3_Intron	NM_133376	NP_596867			integrin beta 1 isoform 1A precursor						axon guidance|blood coagulation|cell-cell adhesion mediated by integrin|cell-matrix adhesion|cellular defense response|homophilic cell adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|leukocyte migration|positive regulation of apoptosis|regulation of immune response	cell surface|cleavage furrow|focal adhesion|melanosome|neuromuscular junction|ruffle|sarcolemma	identical protein binding|protein heterodimerization activity|receptor activity			upper_aerodigestive_tract(1)|ovary(1)	2		Ovarian(717;1.34e-05)|Breast(68;0.0634)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	33277811	33277812	+	IGR	INS	-	TTT	TTT	rs33943614		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33277811_33277812insTTT								ITGB1 (30518 upstream) : NRP1 (188608 downstream)																																			---	---	---	---
NRP1	8829	broad.mit.edu	37	10	33467411	33467412	+	3'UTR	INS	-	T	T	rs138880492	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33467411_33467412insT	uc001iwx.3	-	17					NRP1_uc001iwv.3_3'UTR|NRP1_uc009xlz.2_3'UTR|NRP1_uc001iww.3_3'UTR|NRP1_uc001iwy.3_3'UTR	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)													---	---	---	---
NRP1	8829	broad.mit.edu	37	10	33602442	33602442	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33602442delA	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	34086292	34086292	+	IGR	DEL	A	-	-	rs112947192		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34086292delA								NRP1 (462286 upstream) : PARD3 (313806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34293377	34293378	+	IGR	INS	-	TTGTT	TTGTT	rs139015336	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34293377_34293378insTTGTT								NRP1 (669371 upstream) : PARD3 (106720 downstream)																																			---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34633209	34633210	+	Intron	DEL	TT	-	-	rs10542056		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34633209_34633210delTT	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixo.1_Intron|PARD3_uc001ixp.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron|PARD3_uc001ixs.1_Intron	NM_019619	NP_062565			partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)																---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34866778	34866779	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34866778_34866779insT	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565			partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)																---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34929806	34929806	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34929806delA	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	35181007	35181008	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35181007_35181008insT								PARD3 (77084 upstream) : CUL2 (117800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	35956143	35956145	+	IGR	DEL	CAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35956143_35956145delCAC								FZD8 (25781 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36502383	36502383	+	IGR	DEL	T	-	-	rs5784489		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36502383delT								FZD8 (572021 upstream) : ANKRD30A (912402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36594206	36594207	+	IGR	INS	-	GTGTGT	GTGTGT	rs140319150	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36594206_36594207insGTGTGT								FZD8 (663844 upstream) : ANKRD30A (820578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36835092	36835092	+	IGR	DEL	A	-	-	rs78985865		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36835092delA								FZD8 (904730 upstream) : ANKRD30A (579693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	37235417	37235418	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37235417_37235418insT								None (None upstream) : ANKRD30A (179367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	37541611	37541611	+	IGR	DEL	T	-	-	rs1750617	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37541611delT								ANKRD30A (20116 upstream) : ZNF248 (548836 downstream)																																			---	---	---	---
LOC100129055	100129055	broad.mit.edu	37	10	38502830	38502830	+	RNA	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38502830delA	uc001izn.2	+	7		c.2332delA				NR_024524				Homo sapiens cDNA clone IMAGE:4825074.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	38562146	38562147	+	IGR	DEL	AC	-	-	rs35392190	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38562146_38562147delAC								LOC100129055 (58874 upstream) : HSD17B7P2 (83161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38873885	38873899	+	IGR	DEL	AACTGGAATGGACTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38873885_38873899delAACTGGAATGGACTC								LOC399744 (132805 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38877438	38877438	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38877438delG								LOC399744 (136358 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	39091666	39091667	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39091666_39091667insT								LOC399744 (350586 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	39091887	39091887	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39091887delA								LOC399744 (350807 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42602922	42602923	+	IGR	DEL	AA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42602922_42602923delAA								None (None upstream) : LOC441666 (224392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42605152	42605153	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42605152_42605153insA								None (None upstream) : LOC441666 (222162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	43169816	43169817	+	Intron	INS	-	A	A	rs140982273		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43169816_43169817insA	uc001jah.1	-											Homo sapiens cDNA FLJ41072 fis, clone 3NB692005439.																														---	---	---	---
BMS1	9790	broad.mit.edu	37	10	43330077	43330077	+	3'UTR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43330077delT	uc001jaj.2	+	23						NM_014753	NP_055568			BMS1-like, ribosome assembly protein						ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	43334543	43334544	+	IGR	INS	-	T	T	rs138700186	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43334543_43334544insT								BMS1 (4160 upstream) : RET (237973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44192072	44192073	+	IGR	INS	-	GA	GA	rs10626755		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44192072_44192073insGA								ZNF32 (47746 upstream) : HNRNPA3P1 (90787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44553892	44553893	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44553892_44553893delGT								HNRNPA3P1 (268027 upstream) : CXCL12 (311714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44672047	44672048	+	IGR	INS	-	AC	AC	rs140612749	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44672047_44672048insAC								HNRNPA3P1 (386182 upstream) : CXCL12 (193559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44708749	44708751	+	IGR	DEL	AAC	-	-	rs3979462		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44708749_44708751delAAC								HNRNPA3P1 (422884 upstream) : CXCL12 (156856 downstream)																																			---	---	---	---
ALOX5	240	broad.mit.edu	37	10	45902840	45902840	+	Intron	DEL	T	-	-	rs66922872		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45902840delT	uc001jce.2	+						ALOX5_uc009xmt.2_Intron|ALOX5_uc010qfg.1_Intron	NM_000698	NP_000689			arachidonate 5-lipoxygenase						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	cytosol|nuclear envelope lumen|nuclear matrix|nuclear membrane	arachidonate 5-lipoxygenase activity|iron ion binding|lipoxygenase activity|protein binding			ovary(1)|pancreas(1)	2		Lung SC(717;0.0257)			Diethylcarbamazine(DB00711)|Hydrocortisone(DB00741)|Leflunomide(DB01097)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Minocycline(DB01017)|Montelukast(DB00471)|Quinacrine(DB01103)|Vitamin E(DB00163)|Zileuton(DB00744)													---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47104413	47104414	+	Intron	INS	-	A	A	rs77544885		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47104413_47104414insA	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	47109102	47109102	+	Intron	DEL	C	-	-	rs11318568		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47109102delC	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																		---	---	---	---
ANTXRL	195977	broad.mit.edu	37	10	47669755	47669756	+	Intron	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47669755_47669756delGT	uc001jel.2	+							NR_003601				Homo sapiens cDNA FLJ32754 fis, clone TESTI2001671.												0																		---	---	---	---
WDFY4	57705	broad.mit.edu	37	10	50029471	50029471	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50029471delA	uc001jha.3	+						WDFY4_uc001jhb.1_Intron	NM_020945	NP_065996			WDFY family member 4							integral to membrane	binding				0																		---	---	---	---
C10orf72	196740	broad.mit.edu	37	10	50313008	50313009	+	Intron	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50313008_50313009delAG	uc001jhf.2	-						C10orf72_uc001jhh.2_Intron	NM_001031746	NP_001026916			hypothetical protein LOC196740 isoform 1							integral to membrane|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	50917991	50917992	+	IGR	INS	-	TG	TG	rs147584592	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50917991_50917992insTG								C10orf53 (1035 upstream) : OGDHL (24696 downstream)																																			---	---	---	---
SGMS1	259230	broad.mit.edu	37	10	52346991	52346991	+	Intron	DEL	T	-	-	rs36030853		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52346991delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	52489829	52489829	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52489829delA								SGMS1 (104906 upstream) : ASAH2B (9867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	52542210	52542211	+	IGR	INS	-	TG	TG	rs146359090	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52542210_52542211insTG								ASAH2B (27643 upstream) : A1CF (24116 downstream)																																			---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	52816143	52816143	+	Intron	DEL	C	-	-	rs150712416		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52816143delC	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	52990547	52990547	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52990547delA	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53004068	53004069	+	Intron	INS	-	T	T	rs72521448		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53004068_53004069insT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53360757	53360757	+	Intron	DEL	G	-	-	rs112201340		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53360757delG	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	54672024	54672025	+	IGR	INS	-	T	T	rs145008506	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54672024_54672025insT								MBL2 (140564 upstream) : PCDH15 (890510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	54823546	54823546	+	IGR	DEL	T	-	-	rs34075951		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54823546delT								MBL2 (292086 upstream) : PCDH15 (738989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	55300564	55300564	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55300564delA								MBL2 (769104 upstream) : PCDH15 (261971 downstream)																																			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	56102385	56102386	+	Intron	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56102385_56102386delTC	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045			protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	56844222	56844223	+	Intron	INS	-	A	A	rs148357517	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56844222_56844223insA	uc001jjv.1	-							NM_001142770	NP_001136242			protocadherin 15 isoform CD2-2 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	57152740	57152741	+	Intron	DEL	TG	-	-	rs34723306		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57152740_57152741delTG	uc001jjv.1	-							NM_001142770	NP_001136242			protocadherin 15 isoform CD2-2 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	57165828	57165829	+	Intron	INS	-	A	A	rs34959833		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57165828_57165829insA	uc001jjv.1	-							NM_001142770	NP_001136242			protocadherin 15 isoform CD2-2 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58001391	58001392	+	IGR	INS	-	GTGT	GTGT	rs139723028	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58001391_58001392insGTGT								PCDH15 (613689 upstream) : ZWINT (115807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58498786	58498786	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58498786delT								ZWINT (377752 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58544197	58544200	+	IGR	DEL	TCTT	-	-	rs139235224		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58544197_58544200delTCTT								ZWINT (423163 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	60784362	60784362	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60784362delT								BICC1 (195517 upstream) : PHYHIPL (151986 downstream)																																			---	---	---	---
ARID5B	84159	broad.mit.edu	37	10	63662461	63662462	+	Intron	DEL	TA	-	-	rs71019002		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63662461_63662462delTA	uc001jlt.1	+						ARID5B_uc010qil.1_Intron	NM_032199	NP_115575			AT rich interactive domain 5B (MRF1-like)						liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)																	---	---	---	---
ZNF365	22891	broad.mit.edu	37	10	64329480	64329480	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64329480delA	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	64626751	64626752	+	IGR	INS	-	TAAAGTA	TAAAGTA	rs145341724	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64626751_64626752insTAAAGTA								EGR2 (47824 upstream) : NRBF2 (266255 downstream)																																			---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	65150334	65150336	+	Intron	DEL	ACA	-	-	rs34365599		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65150334_65150336delACA	uc001jmn.2	-						JMJD1C_uc001jmr.1_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	65243985	65244012	+	IGR	DEL	GATGGATGGATGGATAGATAGATAGATA	-	-	rs71025181	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65243985_65244012delGATGGATGGATGGATAGATAGATAGATA								LOC84989 (17665 upstream) : REEP3 (37111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	65627373	65627374	+	IGR	INS	-	T	T	rs144041533	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65627373_65627374insT								REEP3 (245402 upstream) : ANXA2P3 (957911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66548429	66548429	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66548429delA								None (None upstream) : ANXA2P3 (36856 downstream)																																			---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68120687	68120688	+	Intron	INS	-	TC	TC	rs139544295	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68120687_68120688insTC	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	69070470	69070470	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69070470delA	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|CTNNA3_uc001jna.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	69174381	69174383	+	Intron	DEL	ACA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69174381_69174383delACA	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																		---	---	---	---
HERC4	26091	broad.mit.edu	37	10	69705574	69705578	+	Intron	DEL	AACAT	-	-	rs35496892		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69705574_69705578delAACAT	uc001jng.3	-						HERC4_uc009xpq.2_Intron|HERC4_uc001jnf.3_Intron|HERC4_uc001jnh.3_Intron|HERC4_uc009xpr.2_Intron|HERC4_uc001jni.3_Intron	NM_022079	NP_071362			hect domain and RLD 4 isoform a						cell differentiation|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	cytosol	ubiquitin-protein ligase activity			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
DNA2	1763	broad.mit.edu	37	10	70208690	70208691	+	Intron	DEL	GT	-	-	rs10544469		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70208690_70208691delGT	uc001jof.2	-						DNA2_uc001jog.1_Intron|DNA2_uc001joh.1_Intron	NM_001080449	NP_001073918			DNA replication helicase 2 homolog						base-excision repair|DNA replication, removal of RNA primer|mitochondrial DNA repair|mitochondrial DNA replication|positive regulation of DNA replication|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	mitochondrial nucleoid|nucleoplasm	5'-flap endonuclease activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|site-specific endodeoxyribonuclease activity, specific for altered base				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70576041	70576041	+	IGR	DEL	C	-	-	rs2490178		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70576041delC								CCAR1 (24734 upstream) : STOX1 (11253 downstream)																																			---	---	---	---
VPS26A	9559	broad.mit.edu	37	10	70921751	70921751	+	Intron	DEL	T	-	-	rs36040871		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70921751delT	uc001jpb.2	+						VPS26A_uc001jpc.2_Intron|VPS26A_uc009xqa.2_Intron|VPS26A_uc001jpd.2_Intron	NM_004896	NP_004887			vacuolar protein sorting 26 A isoform 1						retrograde transport, endosome to Golgi|vacuolar transport	cytosol|endosome membrane|retromer complex|vesicle	protein binding|protein transporter activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	72720211	72720212	+	IGR	DEL	GA	-	-	rs71881002		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72720211_72720212delGA								PCBD1 (71670 upstream) : UNC5B (252086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	72749057	72749058	+	IGR	INS	-	GTCTTTCC	GTCTTTCC	rs140093403	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72749057_72749058insGTCTTTCC								PCBD1 (100516 upstream) : UNC5B (223240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	72889058	72889059	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72889058_72889059delAC								PCBD1 (240517 upstream) : UNC5B (83239 downstream)																																			---	---	---	---
UNC5B	219699	broad.mit.edu	37	10	73008606	73008607	+	Intron	DEL	TC	-	-	rs71480570		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73008606_73008607delTC	uc001jro.2	+						UNC5B_uc001jrp.2_Intron	NM_170744	NP_734465			unc-5 homolog B precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane				ovary(2)|lung(1)	3																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73920943	73920943	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73920943delA	uc001jst.1	-						ASCC1_uc001jsr.1_Intron|ASCC1_uc001jss.1_Intron|ASCC1_uc001jsu.1_Intron|ASCC1_uc010qju.1_Intron					RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	73999184	73999185	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73999184_73999185insA								ANAPC16 (3568 upstream) : DDIT4 (34492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	74027197	74027197	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74027197delA								ANAPC16 (31581 upstream) : DDIT4 (6480 downstream)																																			---	---	---	---
CBARA1	10367	broad.mit.edu	37	10	74210782	74210783	+	Intron	INS	-	TT	TT	rs34430004		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74210782_74210783insTT	uc001jtb.1	-						CBARA1_uc010qjw.1_Intron|CBARA1_uc010qjx.1_Intron|CBARA1_uc009xqo.1_Intron	NM_006077	NP_006068			calcium binding atopy-related autoantigen 1						calcium ion import|defense response|elevation of mitochondrial calcium ion concentration	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	75707718	75707718	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75707718delA								C10orf55 (25183 upstream) : VCL (47233 downstream)																																			---	---	---	---
ADK	132	broad.mit.edu	37	10	76207942	76207943	+	Intron	INS	-	AA	AA	rs141029644	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76207942_76207943insAA	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	76238975	76238976	+	Intron	INS	-	A	A	rs146779078	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76238975_76238976insA	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	76340333	76340333	+	Intron	DEL	A	-	-	rs35565783		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76340333delA	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	78113088	78113089	+	Intron	INS	-	TG	TG	rs138242972	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78113088_78113089insTG	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	79015358	79015359	+	Intron	INS	-	A	A	rs139221713	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79015358_79015359insA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	79200752	79200753	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79200752_79200753insT	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	79709932	79709932	+	IGR	DEL	T	-	-	rs66532312		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79709932delT								LOC100128292 (20350 upstream) : POLR3A (25974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	79923655	79923655	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79923655delA								RPS24 (107085 upstream) : LOC283050 (779429 downstream)																																			---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	80998904	80998905	+	Intron	INS	-	GGTC	GGTC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80998904_80998905insGGTC	uc001kaf.2	+							NM_020338	NP_065071			retinoic acid induced 17						transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	81364530	81364531	+	IGR	DEL	TT	-	-	rs4253472		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81364530_81364531delTT								SFTPA2 (44367 upstream) : SFTPA1 (6181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	83280598	83280599	+	IGR	INS	-	G	G	rs149296981	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83280598_83280599insG								SH2D4B (874282 upstream) : NRG3 (354471 downstream)																																			---	---	---	---
NRG3	10718	broad.mit.edu	37	10	83998084	83998084	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83998084delA	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	84261921	84261921	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84261921delT	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	84508089	84508090	+	Intron	INS	-	A	A	rs138217779	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84508089_84508090insA	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	84712182	84712183	+	Intron	DEL	AA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84712182_84712183delAA	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	85252889	85252889	+	IGR	DEL	T	-	-	rs113684564		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85252889delT								NRG3 (505954 upstream) : GHITM (646296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85634204	85634209	+	IGR	DEL	ATCATC	-	-	rs139285969		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85634204_85634209delATCATC								NRG3 (887269 upstream) : GHITM (264976 downstream)																																			---	---	---	---
FAM190B	54462	broad.mit.edu	37	10	86122168	86122168	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86122168delG	uc001kdh.1	+						FAM190B_uc001kdg.1_Intron|FAM190B_uc010qmd.1_Intron	NM_018999	NP_061872			granule cell antiserum positive 14											ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	86931761	86931761	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86931761delA								FAM190B (653485 upstream) : GRID1 (427551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	87094777	87094777	+	IGR	DEL	C	-	-	rs59549790	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87094777delC								FAM190B (816501 upstream) : GRID1 (264535 downstream)																																			---	---	---	---
LDB3	11155	broad.mit.edu	37	10	88447845	88447848	+	Intron	DEL	TGTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88447845_88447848delTGTC	uc001kdv.2	+						LDB3_uc010qml.1_Intron|LDB3_uc010qmm.1_Intron|LDB3_uc001kdu.2_Intron|LDB3_uc009xsz.2_Intron|LDB3_uc001kdr.2_Intron|LDB3_uc009xsy.2_Intron|LDB3_uc001kds.2_Intron|LDB3_uc001kdt.2_Intron	NM_007078	NP_009009			LIM domain binding 3 isoform 1							cytoskeleton|perinuclear region of cytoplasm|pseudopodium	zinc ion binding			ovary(1)	1																		---	---	---	---
AGAP11	119385	broad.mit.edu	37	10	88767879	88767880	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88767879_88767880insT	uc001kee.2	+						AGAP11_uc001kef.2_Intron	NM_133447	NP_597704			ankyrin repeat and GTPase domain Arf GTPase						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
LOC728190	728190	broad.mit.edu	37	10	89078962	89078964	+	Intron	DEL	TTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89078962_89078964delTTG	uc009xtc.2	-						LOC728190_uc009xtd.2_Intron|LOC728190_uc010qmq.1_Intron|LOC728190_uc001kem.3_Intron					Homo sapiens cDNA FLJ34397 fis, clone HCHON2001110.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	89871732	89871732	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89871732delC								PTEN (143201 upstream) : RNLS (20325 downstream)																																			---	---	---	---
RNLS	55328	broad.mit.edu	37	10	89935931	89935931	+	Intron	DEL	T	-	-	rs143790919		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89935931delT	uc010qms.1	-											SubName: Full=cDNA FLJ55083, highly similar to Renalase (EC 1.4.-.-);							extracellular region	oxidoreductase activity			ovary(1)	1																		---	---	---	---
RNLS	55328	broad.mit.edu	37	10	90264601	90264602	+	Intron	INS	-	GT	GT	rs76349017		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90264601_90264602insGT	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																		---	---	---	---
RNLS	55328	broad.mit.edu	37	10	90320699	90320700	+	Intron	DEL	AC	-	-	rs72167105		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90320699_90320700delAC	uc001kfe.2	-						RNLS_uc010qms.1_Intron|RNLS_uc001kfd.2_Intron	NM_001031709	NP_001026879			renalase isoform 1							extracellular region	oxidoreductase activity			ovary(1)	1																		---	---	---	---
RNLS	55328	broad.mit.edu	37	10	90329078	90329078	+	Intron	DEL	T	-	-	rs5786828		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90329078delT	uc001kfe.2	-						RNLS_uc010qms.1_Intron|RNLS_uc001kfd.2_Intron	NM_001031709	NP_001026879			renalase isoform 1							extracellular region	oxidoreductase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	90516749	90516749	+	IGR	DEL	A	-	-	rs35647140		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90516749delA								LIPK (4238 upstream) : LIPN (4414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	90813666	90813667	+	IGR	INS	-	A	A	rs149845387	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90813666_90813667insA								FAS (38125 upstream) : CH25H (152029 downstream)																																			---	---	---	---
SLC16A12	387700	broad.mit.edu	37	10	91252977	91252977	+	Intron	DEL	T	-	-	rs113828440		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91252977delT	uc001kgm.2	-							NM_213606	NP_998771			solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	91604897	91604898	+	IGR	INS	-	CA	CA	rs146001068	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91604897_91604898insCA								KIF20B (70197 upstream) : HTR7 (895680 downstream)																																			---	---	---	---
LOC100188947	100188947	broad.mit.edu	37	10	93345793	93345794	+	Intron	INS	-	T	T	rs146150101	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93345793_93345794insT	uc010qnl.1	-							NR_024467				Homo sapiens, clone IMAGE:6063621, mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	93443361	93443361	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93443361delA								PPP1R3C (50503 upstream) : TNKS2 (114790 downstream)																																			---	---	---	---
MARCH5	54708	broad.mit.edu	37	10	94082490	94082490	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94082490delT	uc001khx.1	+						MARCH5_uc010qno.1_Intron	NM_017824	NP_060294			membrane-associated ring finger (C3HC4) 5						cell aging|protein autoubiquitination|protein localization in mitochondrion|protein polyubiquitination|regulation of mitochondrial fission	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane	GTPase binding|ubiquitin-protein ligase activity|zinc ion binding			skin(1)	1																		---	---	---	---
KIF11	3832	broad.mit.edu	37	10	94352395	94352396	+	5'Flank	INS	-	CA	CA	rs117386379	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94352395_94352396insCA	uc001kic.2	+						KIF11_uc010qnq.1_5'Flank	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																		---	---	---	---
KIF11	3832	broad.mit.edu	37	10	94389055	94389056	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94389055_94389056insA	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																		---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95164875	95164876	+	Intron	INS	-	TCTT	TCTT	rs67277463		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95164875_95164876insTCTT	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc001kip.3_Intron|MYOF_uc009xuf.2_Intron	NM_013451	NP_038479			myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
PDE6C	5146	broad.mit.edu	37	10	95382406	95382407	+	Intron	DEL	TG	-	-	rs67350128		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95382406_95382407delTG	uc001kiu.3	+							NM_006204	NP_006195			phosphodiesterase 6C						visual perception	plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|metal ion binding			ovary(2)|kidney(1)|skin(1)	4		Colorectal(252;0.123)																---	---	---	---
PDE6C	5146	broad.mit.edu	37	10	95417500	95417501	+	Intron	DEL	TA	-	-	rs147167151		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95417500_95417501delTA	uc001kiu.3	+							NM_006204	NP_006195			phosphodiesterase 6C						visual perception	plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|metal ion binding			ovary(2)|kidney(1)|skin(1)	4		Colorectal(252;0.123)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	96918462	96918462	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96918462delT								CYP2C8 (89208 upstream) : C10orf129 (35495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	97327295	97327302	+	IGR	DEL	GGCAGGCA	-	-	rs113174768		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97327295_97327302delGGCAGGCA								SORBS1 (6124 upstream) : ALDH18A1 (38385 downstream)																																			---	---	---	---
ALDH18A1	5832	broad.mit.edu	37	10	97367284	97367284	+	Intron	DEL	G	-	-	rs149687230		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97367284delG	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)													---	---	---	---
C10orf12	26148	broad.mit.edu	37	10	98672818	98672818	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98672818delT	uc009xvg.1	+						LCOR_uc001kmr.2_Intron|LCOR_uc001kms.1_Intron|LCOR_uc001kmt.1_Intron|LCOR_uc001kmu.1_Intron	NM_015652	NP_056467			hypothetical protein LOC26148											skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	99481237	99481238	+	IGR	INS	-	T	T	rs113772884		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99481237_99481238insT								MARVELD1 (3332 upstream) : ZFYVE27 (15642 downstream)																																			---	---	---	---
HPSE2	60495	broad.mit.edu	37	10	100311906	100311906	+	Intron	DEL	G	-	-	rs66924333		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100311906delG	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	100706230	100706230	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100706230delA	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	100804448	100804449	+	Intron	INS	-	A	A	rs144392167	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100804448_100804449insA	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)														---	---	---	---
DNMBP	23268	broad.mit.edu	37	10	101681450	101681450	+	Intron	DEL	A	-	-	rs148561071		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101681450delA	uc001kqj.2	-						DNMBP_uc001kqh.2_Intron	NM_015221	NP_056036			dynamin binding protein						intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)|skin(1)	6		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)														---	---	---	---
DNMBP	23268	broad.mit.edu	37	10	101704479	101704479	+	Intron	DEL	C	-	-	rs67382282		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101704479delC	uc001kqj.2	-						NCRNA00093_uc001kqk.1_Intron	NM_015221	NP_056036			dynamin binding protein						intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)|skin(1)	6		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	102104857	102104857	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102104857delT								PKD2L1 (14614 upstream) : SCD (1915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	102768112	102768112	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102768112delG								LZTS2 (527 upstream) : PDZD7 (2685 downstream)																																			---	---	---	---
PDZD7	79955	broad.mit.edu	37	10	102774481	102774482	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102774481_102774482delCA	uc001ksn.2	-							NM_024895	NP_079171			PDZ domain containing 7							cilium|nucleus	protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)												OREG0020452	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
BTRC	8945	broad.mit.edu	37	10	103246201	103246201	+	Intron	DEL	A	-	-	rs34815375		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103246201delA	uc001kta.2	+						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)														---	---	---	---
C10orf76	79591	broad.mit.edu	37	10	103749956	103749956	+	Intron	DEL	C	-	-	rs6584468		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103749956delC	uc009xwy.1	-						C10orf76_uc009xwx.1_Intron	NM_024541	NP_078817			hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)														---	---	---	---
C10orf76	79591	broad.mit.edu	37	10	103766916	103766917	+	Intron	INS	-	AAAAAAAAAA	AAAAAAAAAA	rs80151019		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103766916_103766917insAAAAAAAAAA	uc009xwy.1	-							NM_024541	NP_078817			hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)														---	---	---	---
SUFU	51684	broad.mit.edu	37	10	104266548	104266548	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104266548delC	uc001kvy.1	+						SUFU_uc001kvw.1_Intron|SUFU_uc001kvx.2_Intron	NM_016169	NP_057253			suppressor of fused						negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding			central_nervous_system(4)|skin(2)|breast(1)	7		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)				D|F|S		medulloblastoma	medulloblastoma			Medulloblastoma_associated_with_Germline_SUFU_Mutation				---	---	---	---
AS3MT	57412	broad.mit.edu	37	10	104649371	104649372	+	Intron	INS	-	CCTT	CCTT	rs78246259		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104649371_104649372insCCTT	uc001kwk.2	+						AS3MT_uc001kwj.2_Intron|AS3MT_uc009xxh.2_Intron	NM_020682	NP_065733			arsenic (+3 oxidation state) methyltransferase						arsonoacetate metabolic process|toxin metabolic process	cytosol	arsenite methyltransferase activity|methylarsonite methyltransferase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)														---	---	---	---
AS3MT	57412	broad.mit.edu	37	10	104654956	104654956	+	Intron	DEL	T	-	-	rs112372288		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104654956delT	uc001kwk.2	+						AS3MT_uc001kwj.2_Intron	NM_020682	NP_065733			arsenic (+3 oxidation state) methyltransferase						arsonoacetate metabolic process|toxin metabolic process	cytosol	arsenite methyltransferase activity|methylarsonite methyltransferase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)														---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104735226	104735227	+	Intron	INS	-	A	A	rs57482469		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104735226_104735227insA	uc001kwm.2	+						CNNM2_uc001kwn.2_Intron	NM_017649	NP_060119			cyclin M2 isoform 1						ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104789222	104789225	+	Intron	DEL	AAAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104789222_104789225delAAAT	uc001kwm.2	+						CNNM2_uc001kwn.2_Intron	NM_017649	NP_060119			cyclin M2 isoform 1						ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
SH3PXD2A	9644	broad.mit.edu	37	10	105375241	105375262	+	Intron	DEL	GTGTGTGTGTGTGTGTGTGTGT	-	-	rs72232193	by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105375241_105375262delGTGTGTGTGTGTGTGTGTGTGT	uc001kxj.1	-						SH3PXD2A_uc010qqr.1_Intron|SH3PXD2A_uc010qqs.1_Intron|SH3PXD2A_uc010qqt.1_Intron|SH3PXD2A_uc009xxn.1_Intron|SH3PXD2A_uc010qqu.1_Intron	NM_014631	NP_055446			SH3 multiple domains 1						cell communication|superoxide metabolic process	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol binding|protein binding				0		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	108134770	108134771	+	IGR	INS	-	ACAC	ACAC	rs144760024	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108134770_108134771insACAC								None (None upstream) : SORCS1 (198651 downstream)																																			---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108362270	108362271	+	Intron	INS	-	AC	AC	rs66699179		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108362270_108362271insAC	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	108686579	108686580	+	Intron	DEL	AT	-	-	rs78358063		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108686579_108686580delAT	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	109192076	109192076	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109192076delT								SORCS1 (267784 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	109339726	109339727	+	IGR	INS	-	A	A	rs146034178		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109339726_109339727insA								SORCS1 (415434 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110976408	110976409	+	IGR	INS	-	T	T	rs147647204	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110976408_110976409insT								None (None upstream) : XPNPEP1 (648115 downstream)																																			---	---	---	---
XPNPEP1	7511	broad.mit.edu	37	10	111656191	111656192	+	Intron	INS	-	T	T	rs142432969		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111656191_111656192insT	uc001kyp.1	-						XPNPEP1_uc009xxt.1_Intron|XPNPEP1_uc001kyq.1_Intron|XPNPEP1_uc010qrb.1_Intron	NM_020383	NP_065116			X-prolyl aminopeptidase (aminopeptidase P) 1,						bradykinin catabolic process|proteolysis		manganese ion binding|metalloaminopeptidase activity|protein homodimerization activity			ovary(3)|pancreas(1)	4		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)														---	---	---	---
RBM20	282996	broad.mit.edu	37	10	112428366	112428366	+	Intron	DEL	A	-	-	rs66563682		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112428366delA	uc001kzf.2	+							NM_001134363	NP_001127835			RNA binding motif protein 20							nucleus	nucleotide binding|RNA binding|zinc ion binding				0																		---	---	---	---
SHOC2	8036	broad.mit.edu	37	10	112715951	112715951	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112715951delT	uc001kzl.3	+						SHOC2_uc009xxx.2_Intron|SHOC2_uc010qrg.1_Intron	NM_007373	NP_031399			soc-2 suppressor of clear homolog						fibroblast growth factor receptor signaling pathway|positive regulation of Ras protein signal transduction|Ras protein signal transduction	nucleus|protein phosphatase type 1 complex	protein phosphatase binding|protein phosphatase regulator activity			ovary(1)|skin(1)	2				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	112799758	112799758	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112799758delA								SHOC2 (26334 upstream) : ADRA2A (37032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113217882	113217891	+	IGR	DEL	GTGTGTGAGA	-	-	rs71841549		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113217882_113217891delGTGTGTGAGA								ADRA2A (377222 upstream) : GPAM (691731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113958683	113958684	+	IGR	INS	-	T	T	rs112285181		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113958683_113958684insT								GPAM (15158 upstream) : TECTB (84809 downstream)																																			---	---	---	---
GUCY2GP	390003	broad.mit.edu	37	10	114074927	114074927	+	Intron	DEL	A	-	-	rs5787953		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114074927delA	uc010qri.1	-							NR_028134				Homo sapiens guanylate cyclase 2G homolog (mouse) pseudogene (GUCY2G), non-coding RNA, 611.												0																OREG0020540	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114772253	114772254	+	Intron	INS	-	A	A	rs147501617	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114772253_114772254insA	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114777139	114777146	+	Intron	DEL	AGTGGTGG	-	-	rs71973726		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114777139_114777146delAGTGGTGG	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114791240	114791241	+	Intron	DEL	TT	-	-	rs67887012		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114791240_114791241delTT	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114885140	114885141	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114885140_114885141insT	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron|TCF7L2_uc010qru.1_Intron|TCF7L2_uc010qrv.1_5'Flank	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	115857397	115857398	+	IGR	INS	-	CA	CA	rs149172582	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115857397_115857398insCA								ADRB1 (50732 upstream) : C10orf118 (24576 downstream)																																			---	---	---	---
C10orf118	55088	broad.mit.edu	37	10	115912098	115912098	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115912098delA	uc001lbb.1	-						C10orf118_uc001lbc.1_Intron|C10orf118_uc009xye.1_Intron	NM_018017	NP_060487			CTCL tumor antigen L14-2											ovary(2)	2		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)														---	---	---	---
C10orf82	143379	broad.mit.edu	37	10	118429827	118429827	+	5'Flank	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118429827delG	uc001lcr.2	-						C10orf82_uc001lcs.1_5'Flank	NM_144661	NP_653262			hypothetical protein LOC143379												0				all cancers(201;0.0143)														---	---	---	---
HSPA12A	259217	broad.mit.edu	37	10	118449124	118449127	+	Intron	DEL	ACAG	-	-	rs150349688		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118449124_118449127delACAG	uc001lct.2	-						HSPA12A_uc001lcu.2_Intron	NM_025015	NP_079291			heat shock 70kDa protein 12A								ATP binding			ovary(1)	1				all cancers(201;0.0158)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	119333657	119333657	+	IGR	DEL	A	-	-	rs5788239		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119333657delA								EMX2 (24601 upstream) : RAB11FIP2 (430772 downstream)																																			---	---	---	---
C10orf84	63877	broad.mit.edu	37	10	120081236	120081237	+	Intron	INS	-	AA	AA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120081236_120081237insAA	uc001ldo.2	-						C10orf84_uc010qss.1_Intron	NM_022063	NP_071346			hypothetical protein LOC63877												0		Colorectal(252;0.101)		all cancers(201;0.0244)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	120264017	120264017	+	IGR	DEL	G	-	-	rs112827469		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120264017delG								C10orf84 (162178 upstream) : PRLHR (88899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	120859812	120859813	+	IGR	INS	-	C	C	rs139207965	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120859812_120859813insC								EIF3A (19478 upstream) : FAM45A (3798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	121246231	121246231	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121246231delT								GRK5 (31101 upstream) : RGS10 (13109 downstream)																																			---	---	---	---
INPP5F	22876	broad.mit.edu	37	10	121577116	121577116	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121577116delT	uc001leo.2	+						INPP5F_uc001lep.2_5'Flank	NM_014937	NP_055752			inositol polyphosphate-5-phosphatase F								phosphoric ester hydrolase activity			ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	122698966	122698967	+	IGR	INS	-	CTGCG	CTGCG	rs143508003	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122698966_122698967insCTGCG								WDR11 (29931 upstream) : FGFR2 (538878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	123139492	123139493	+	IGR	DEL	AT	-	-	rs72390948		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123139492_123139493delAT								WDR11 (470457 upstream) : FGFR2 (98352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	123215911	123215913	+	IGR	DEL	AAT	-	-	rs148256120		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123215911_123215913delAAT								WDR11 (546876 upstream) : FGFR2 (21932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	125014608	125014609	+	IGR	INS	-	CAC	CAC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125014608_125014609insCAC								BUB3 (89722 upstream) : GPR26 (411262 downstream)																																			---	---	---	---
CHST15	51363	broad.mit.edu	37	10	125781417	125781417	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125781417delA	uc001lhl.2	-						CHST15_uc001lhm.2_Intron|CHST15_uc001lhn.2_Intron|CHST15_uc010que.1_Intron|CHST15_uc001lho.2_Intron	NM_015892	NP_056976			B cell RAG associated protein						hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity			ovary(1)	1																		---	---	---	---
CHST15	51363	broad.mit.edu	37	10	125802544	125802544	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125802544delG	uc001lhl.2	-						CHST15_uc001lhm.2_Intron|CHST15_uc001lhn.2_Intron|CHST15_uc010que.1_Intron|CHST15_uc001lho.2_Intron	NM_015892	NP_056976			B cell RAG associated protein						hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	126576688	126576689	+	IGR	DEL	GA	-	-	rs72350326		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126576688_126576689delGA								FAM175B (51450 upstream) : ZRANB1 (52283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	127227822	127227822	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127227822delT								CTBP2 (378198 upstream) : LOC100169752 (35118 downstream)																																			---	---	---	---
FANK1	92565	broad.mit.edu	37	10	127596142	127596143	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127596142_127596143delTG	uc001ljh.3	+						FANK1_uc010quk.1_Intron|FANK1_uc009yan.2_Intron	NM_145235	NP_660278			fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	129254251	129254252	+	IGR	INS	-	CT	CT	rs145923352	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129254251_129254252insCT								DOCK1 (3470 upstream) : NPS (93361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130163719	130163720	+	IGR	INS	-	C	C	rs148406361	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130163719_130163720insC								MKI67 (239251 upstream) : None (None downstream)																																			---	---	---	---
GLRX3	10539	broad.mit.edu	37	10	131933678	131933681	+	5'Flank	DEL	CTGT	-	-	rs76444431		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131933678_131933681delCTGT	uc001lkm.1	+						GLRX3_uc001lkn.1_5'Flank|GLRX3_uc001lko.2_5'Flank	NM_006541	NP_006532			glutaredoxin 3						cell redox homeostasis|negative regulation of cardiac muscle hypertrophy|regulation of the force of heart contraction	cell cortex	electron carrier activity|iron-sulfur cluster binding|metal ion binding|protein disulfide oxidoreductase activity				0		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	132039638	132039638	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132039638delA								GLRX3 (56854 upstream) : TCERG1L (851018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132191111	132191111	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132191111delT								GLRX3 (208327 upstream) : TCERG1L (699545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132879310	132879311	+	IGR	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132879310_132879311delCA								GLRX3 (896526 upstream) : TCERG1L (11345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	133281962	133281965	+	IGR	DEL	GATG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133281962_133281965delGATG								TCERG1L (171978 upstream) : PPP2R2D (465995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	133298705	133298706	+	IGR	INS	-	C	C	rs148845595	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133298705_133298706insC								TCERG1L (188721 upstream) : PPP2R2D (449254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	133577175	133577190	+	IGR	DEL	ATGGGAGGACGGGAGG	-	-	rs113113405		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133577175_133577190delATGGGAGGACGGGAGG								TCERG1L (467191 upstream) : PPP2R2D (170770 downstream)																																			---	---	---	---
JAKMIP3	282973	broad.mit.edu	37	10	133952553	133952554	+	Intron	INS	-	GT	GT	rs145371011	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133952553_133952554insGT	uc001lkx.3	+							NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)														---	---	---	---
JAKMIP3	282973	broad.mit.edu	37	10	133991025	133991026	+	Intron	INS	-	GT	GT	rs4009680		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133991025_133991026insGT	uc001lkx.3	+						JAKMIP3_uc001lky.1_Intron	NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)														---	---	---	---
STK32C	282974	broad.mit.edu	37	10	134081648	134081649	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134081648_134081649delTG	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)														---	---	---	---
INPP5A	3632	broad.mit.edu	37	10	134353790	134353792	+	Intron	DEL	TGA	-	-	rs75473158		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134353790_134353792delTGA	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	134718662	134718665	+	Intron	DEL	TTCT	-	-	rs10580367		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134718662_134718665delTTCT	uc010qux.1	-						uc009ybf.2_Intron	NM_017609	NP_060079			Homo sapiens cDNA, FLJ17989.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	135457159	135457160	+	IGR	INS	-	AA	AA	rs140350571		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135457159_135457160insAA								FRG2B (16860 upstream) : LOC653544 (33119 downstream)																																			---	---	---	---
SCGB1C1	147199	broad.mit.edu	37	11	191862	191862	+	5'Flank	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:191862delC	uc001loa.1	+							NM_145651	NP_663626			secretoglobin, family 1C, member 1 precursor							extracellular region	binding			skin(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)														---	---	---	---
PTDSS2	81490	broad.mit.edu	37	11	456341	456342	+	Intron	INS	-	T	T	rs34526529		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:456341_456342insT	uc001lpj.2	+						PTDSS2_uc009ybv.1_Intron	NM_030783	NP_110410			phosphatidylserine synthase 2							integral to membrane					0		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	571779	571780	+	IGR	INS	-	G	G	rs140443936	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:571779_571780insG								MIR210 (3581 upstream) : LOC143666 (2029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	1361770	1361772	+	IGR	DEL	ATG	-	-	rs138030605		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1361770_1361772delATG								TOLLIP (30931 upstream) : BRSK2 (49357 downstream)																																			---	---	---	---
KCNQ1	3784	broad.mit.edu	37	11	2555611	2555611	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2555611delA	uc001lwn.2	+						KCNQ1_uc009ydp.1_Intron|KCNQ1_uc001lwo.2_Intron	NM_000218	NP_000209			potassium voltage-gated channel, KQT-like						blood circulation|membrane depolarization|muscle contraction|sensory perception of sound		delayed rectifier potassium channel activity|protein binding			ovary(1)	1		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	3590656	3590657	+	IGR	INS	-	C	C	rs142804195	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3590656_3590657insC								LOC650368 (160278 upstream) : TRPC2 (47805 downstream)																																			---	---	---	---
STIM1	6786	broad.mit.edu	37	11	3936961	3936963	+	Intron	DEL	TTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3936961_3936963delTTG	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	4539135	4539136	+	IGR	INS	-	T	T	rs146196856	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4539135_4539136insT								OR52K1 (28060 upstream) : OR52M1 (27285 downstream)																																			---	---	---	---
HBE1	3046	broad.mit.edu	37	11	5311351	5311354	+	Intron	DEL	TCTA	-	-	rs35055889		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5311351_5311354delTCTA	uc001mam.1	-						HBG2_uc001mak.1_Intron	NM_005330	NP_005321			epsilon globin						blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity				0		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.34e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
OR56A4	120793	broad.mit.edu	37	11	6024933	6024933	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6024933delT	uc010qzv.1	-							NM_001005179	NP_001005179			olfactory receptor, family 56, subfamily A,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|skin(1)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	6109665	6109666	+	IGR	INS	-	T	T	rs139600320	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6109665_6109666insT								OR56A1 (60731 upstream) : OR56B4 (19343 downstream)																																			---	---	---	---
TPP1	1200	broad.mit.edu	37	11	6642010	6642011	+	5'Flank	INS	-	T	T	rs72353957		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6642010_6642011insT	uc001mel.1	-						TPP1_uc001mek.1_5'Flank|TPP1_uc010rar.1_5'Flank	NM_000391	NP_000382			tripeptidyl-peptidase I preproprotein						bone resorption|cell death|lipid metabolic process|lysosome organization|nervous system development|neuromuscular process controlling balance|peptide catabolic process|protein catabolic process|proteolysis	lysosome|melanosome|soluble fraction	metal ion binding|peptide binding|protein binding|serine-type endopeptidase activity|tripeptidyl-peptidase activity				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;3.45e-09)|BRCA - Breast invasive adenocarcinoma(625;0.131)														---	---	---	---
DCHS1	8642	broad.mit.edu	37	11	6670345	6670346	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6670345_6670346delCA	uc001mem.1	-							NM_003737	NP_003728			dachsous 1 precursor						calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	6826148	6826149	+	IGR	INS	-	A	A	rs74727312		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6826148_6826149insA								OR6A2 (9009 upstream) : OR10A5 (40765 downstream)																																			---	---	---	---
ZNF214	7761	broad.mit.edu	37	11	7038970	7038970	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7038970delA	uc001mfa.2	-						NLRP14_uc001mfb.1_5'Flank|ZNF214_uc010ray.1_Intron|ZNF214_uc009yfh.1_Intron	NM_013249	NP_037381			zinc finger protein 214						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	7213467	7213467	+	IGR	DEL	A	-	-	rs5789500		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7213467delA								RBMXL2 (101088 upstream) : MIR302E (42530 downstream)																																			---	---	---	---
SYT9	143425	broad.mit.edu	37	11	7276562	7276563	+	Intron	DEL	GT	-	-	rs10588341		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7276562_7276563delGT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	8198772	8198772	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8198772delG								RIC3 (8182 upstream) : LMO1 (47085 downstream)																																			---	---	---	---
TMEM9B	56674	broad.mit.edu	37	11	8971914	8971914	+	Intron	DEL	A	-	-	rs74477141		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8971914delA	uc001mhe.1	-						TMEM9B_uc001mhf.1_Intron|TMEM9B_uc010rbt.1_Intron	NM_020644	NP_065695			TMEM9 domain family, member B precursor						positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	signal transducer activity				0				Epithelial(150;4.39e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0237)														---	---	---	---
SCUBE2	57758	broad.mit.edu	37	11	9050606	9050607	+	Intron	INS	-	G	G	rs138840899	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9050606_9050607insG	uc001mhh.1	-						SCUBE2_uc001mhi.1_Intron|SCUBE2_uc001mhj.1_Intron	NM_020974	NP_066025			CEGP1 protein precursor							extracellular region	calcium ion binding			ovary(1)|skin(1)	2				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	9352995	9352998	+	IGR	DEL	TTTC	-	-	rs66923823		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9352995_9352998delTTTC								TMEM41B (16699 upstream) : IPO7 (53171 downstream)																																			---	---	---	---
IPO7	10527	broad.mit.edu	37	11	9456826	9456827	+	Intron	DEL	AT	-	-	rs142659173		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9456826_9456827delAT	uc001mho.2	+							NM_006391	NP_006382			importin 7						interspecies interaction between organisms|signal transduction	Golgi apparatus|nuclear pore|soluble fraction	protein transporter activity|Ran GTPase binding|small GTPase regulator activity			lung(1)|breast(1)	2				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)														---	---	---	---
ZNF143	7702	broad.mit.edu	37	11	9485630	9485633	+	Intron	DEL	TGTT	-	-	rs144180501	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9485630_9485633delTGTT	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	9965526	9965526	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9965526delG	uc001mib.2	-						SBF2_uc001mif.3_Intron	NM_030962	NP_112224			SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	10061135	10061135	+	Intron	DEL	C	-	-	rs16907424	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10061135delC	uc001mib.2	-						SBF2_uc001mif.3_Intron|SBF2_uc001mij.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	10097446	10097447	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10097446_10097447insT	uc001mib.2	-						SBF2_uc001mif.3_Intron	NM_030962	NP_112224			SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	10205097	10205102	+	Intron	DEL	TTTACA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10205097_10205102delTTTACA	uc001mib.2	-						SBF2_uc001mif.3_Intron	NM_030962	NP_112224			SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
RNF141	50862	broad.mit.edu	37	11	10549193	10549193	+	Intron	DEL	G	-	-	rs77440828		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10549193delG	uc001mis.1	-						RNF141_uc009yga.1_Intron|RNF141_uc001mit.1_Intron	NM_016422	NP_057506			ring finger protein 141								zinc ion binding				0				all cancers(16;4.63e-08)|Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.064)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	11117847	11117848	+	IGR	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11117847_11117848delAG								ZBED5 (238227 upstream) : GALNTL4 (174573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	11228760	11228760	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11228760delA								ZBED5 (349140 upstream) : GALNTL4 (63661 downstream)																																			---	---	---	---
MICAL2	9645	broad.mit.edu	37	11	12197133	12197134	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12197133_12197134delTG	uc001mjz.2	+						MICAL2_uc010rch.1_Intron|MICAL2_uc001mjy.2_Intron|MICAL2_uc001mka.2_Intron|MICAL2_uc010rci.1_Intron|MICAL2_uc001mkb.2_Intron|MICAL2_uc001mkc.2_Intron	NM_014632	NP_055447			microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding			upper_aerodigestive_tract(2)	2				Epithelial(150;0.00552)														---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12710560	12710561	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12710560_12710561insT	uc001mkj.3	+							NM_021961	NP_068780			TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12950710	12950711	+	Intron	INS	-	GTGTGTGTGT	GTGTGTGTGT	rs60060462		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12950710_12950711insGTGTGTGTGT	uc001mkj.3	+						TEAD1_uc001mkk.3_Intron|TEAD1_uc009ygl.2_Intron	NM_021961	NP_068780			TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	13242787	13242788	+	IGR	DEL	AT	-	-	rs12792589		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13242787_13242788delAT								RASSF10 (210140 upstream) : ARNTL (56537 downstream)																																			---	---	---	---
ARNTL	406	broad.mit.edu	37	11	13407913	13407914	+	Intron	INS	-	TG	TG	rs143415137	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13407913_13407914insTG	uc001mkr.2	+						ARNTL_uc001mko.2_Intron|ARNTL_uc001mkp.2_Intron|ARNTL_uc001mkq.2_Intron|ARNTL_uc001mks.2_Intron|ARNTL_uc001mkt.2_Intron|ARNTL_uc001mku.2_Intron|ARNTL_uc001mkw.2_Intron|ARNTL_uc001mkx.2_Intron|ARNTL_uc001mky.2_Intron	NM_001178	NP_001169			aryl hydrocarbon receptor nuclear						circadian rhythm|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	aryl hydrocarbon receptor binding|DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0				Epithelial(150;0.0243)														---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16382548	16382549	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16382548_16382549insA	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron|SOX6_uc001mmh.1_Intron|SOX6_uc009ygs.2_Intron|SOX6_uc001mmi.3_Intron|SOX6_uc001mmj.2_Intron	NM_001145819	NP_001139291			SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16558157	16558157	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16558157delT	uc001mmi.3	-						SOX6_uc001mmh.1_Intron|SOX6_uc001mmj.2_Intron					Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	17047803	17047804	+	IGR	INS	-	T	T	rs139917092	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17047803_17047804insT								PLEKHA7 (11840 upstream) : RPS13 (48136 downstream)																																			---	---	---	---
SERGEF	26297	broad.mit.edu	37	11	18016287	18016287	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18016287delC	uc001mnm.2	-						SERGEF_uc009yhd.2_Intron|SERGEF_uc001mnn.2_Intron|SERGEF_uc010rcz.1_Intron|SERGEF_uc001mno.1_Intron	NM_012139	NP_036271			deafness locus associated putative guanine						negative regulation of protein secretion|signal transduction	cytoplasm|nucleus	protein binding|Ran guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	18162351	18162352	+	IGR	INS	-	TT	TT	rs113724281		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18162351_18162352insTT								MRGPRX3 (2326 upstream) : MRGPRX4 (32032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	18201956	18201956	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18201956delA								MRGPRX4 (6129 upstream) : LOC494141 (28729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	19002899	19002900	+	IGR	DEL	AT	-	-	rs138264725		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19002899_19002900delAT								MRGPRX1 (46350 upstream) : MRGPRX2 (73105 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	19364156	19364157	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19364156_19364157delTG								E2F8 (100989 upstream) : NAV2 (8114 downstream)																																			---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19637850	19637851	+	Intron	INS	-	TG	TG	rs146490839	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19637850_19637851insTG	uc001mpp.2	+							NM_001111018	NP_001104488			neuron navigator 2 isoform 3							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19737624	19737625	+	Intron	INS	-	T	T	rs144078228	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19737624_19737625insT	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron|LOC100126784_uc010rdl.1_5'Flank	NM_145117	NP_660093			neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19856101	19856102	+	Intron	INS	-	T	T	rs113526447		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19856101_19856102insT	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	22487184	22487185	+	IGR	INS	-	TT	TT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22487184_22487185insTT								SLC17A6 (86140 upstream) : FANCF (156894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	22938166	22938166	+	Intron	DEL	G	-	-	rs79479417		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22938166delG	uc001mqq.1	+											full-length cDNA clone CS0DJ011YO21 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	23315010	23315017	+	IGR	DEL	ACACACAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23315010_23315017delACACACAC								SVIP (463628 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	25256614	25256615	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25256614_25256615delGT								LUZP2 (152432 upstream) : ANO3 (954214 downstream)																																			---	---	---	---
ANO3	63982	broad.mit.edu	37	11	26460582	26460584	+	Intron	DEL	ATT	-	-	rs34077039		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26460582_26460584delATT	uc001mqt.3	+						ANO3_uc010rdr.1_Intron	NM_031418	NP_113606			transmembrane protein 16C							chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
BDNFOS	497258	broad.mit.edu	37	11	27585667	27585668	+	Intron	DEL	TT	-	-	rs11030050		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27585667_27585668delTT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	27794764	27794764	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27794764delA								BDNF (51159 upstream) : KIF18A (247399 downstream)																																			---	---	---	---
MPPED2	744	broad.mit.edu	37	11	30510406	30510407	+	Intron	INS	-	AC	AC	rs149428709	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30510406_30510407insAC	uc001msr.2	-						MPPED2_uc001msq.3_Intron|MPPED2_uc009yji.2_Intron	NM_001584	NP_001575			metallophosphoesterase domain containing 2						nervous system development		hydrolase activity|metal ion binding			skin(1)	1																		---	---	---	---
DCDC1	341019	broad.mit.edu	37	11	31164036	31164037	+	Intron	DEL	TG	-	-	rs72265047		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31164036_31164037delTG	uc001msu.1	-											SubName: Full=Putative uncharacterized protein ENSP00000343496;						intracellular signal transduction					skin(1)	1	Lung SC(675;0.225)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	32570501	32570501	+	IGR	DEL	A	-	-	rs75218137		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32570501delA								WIT1 (102240 upstream) : EIF3M (34890 downstream)																																			---	---	---	---
CCDC73	493860	broad.mit.edu	37	11	32817025	32817026	+	5'Flank	DEL	AG	-	-	rs112013876		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32817025_32817026delAG	uc001mtv.2	-						CCDC73_uc001mtw.1_5'Flank|CCDC73_uc009yjt.2_5'Flank	NM_001008391	NP_001008392			sarcoma antigen NY-SAR-79											ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)																	---	---	---	---
TCP11L1	55346	broad.mit.edu	37	11	33068057	33068060	+	Intron	DEL	TTTG	-	-	rs71999343		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33068057_33068060delTTTG	uc001mud.2	+						TCP11L1_uc009yju.2_Intron|TCP11L1_uc010rei.1_Intron|TCP11L1_uc001mue.2_Intron	NM_018393	NP_060863			t-complex 11 (mouse) like 1												0																		---	---	---	---
C11orf41	25758	broad.mit.edu	37	11	33615859	33615859	+	Intron	DEL	T	-	-	rs75754160		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33615859delT	uc001mup.3	+						C11orf41_uc001mun.1_Intron	NM_012194	NP_036326			hypothetical protein LOC25758							integral to membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	33854489	33854490	+	IGR	INS	-	A	A	rs141564858	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33854489_33854490insA								FBXO3 (58418 upstream) : LMO2 (25635 downstream)																																			---	---	---	---
LMO2	4005	broad.mit.edu	37	11	33899712	33899713	+	Intron	INS	-	CCATGCTT	CCATGCTT	rs140797388	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33899712_33899713insCCATGCTT	uc010rem.1	-							NM_005574	NP_005565			LIM domain only 2 isoform 1						multicellular organismal development	nucleus	protein binding|zinc ion binding			lung(1)	1								T	TRD@	T-ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	11	33996214	33996215	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33996214_33996215delAC								LMO2 (82378 upstream) : CAPRIN1 (77015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	34446254	34446254	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34446254delA								ABTB2 (67452 upstream) : CAT (14224 downstream)																																			---	---	---	---
APIP	51074	broad.mit.edu	37	11	34899169	34899170	+	Intron	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34899169_34899170delAG	uc010reo.1	-											RecName: Full=APAF1-interacting protein;						apoptosis|L-methionine salvage	cytoplasm	identical protein binding|metal ion binding|methylthioribulose 1-phosphate dehydratase activity				0	all_epithelial(35;0.161)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.000425)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	35021680	35021680	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35021680delT								PDHX (4006 upstream) : CD44 (138737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	35110647	35110647	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35110647delA								PDHX (92973 upstream) : CD44 (49770 downstream)																																			---	---	---	---
SLC1A2	6506	broad.mit.edu	37	11	35274452	35274453	+	3'UTR	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35274452_35274453delCT	uc001mwd.2	-	11					SLC1A2_uc001mwe.2_3'UTR	NM_004171	NP_004162			excitatory amino acid transporter 2						D-aspartate import|L-glutamate import|synaptic transmission	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|central_nervous_system(1)	3	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)		L-Glutamic Acid(DB00142)													---	---	---	---
SLC1A2	6506	broad.mit.edu	37	11	35374590	35374591	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35374590_35374591insT	uc001mwd.2	-						SLC1A2_uc001mwe.2_Intron|SLC1A2_uc010rev.1_Intron	NM_004171	NP_004162			excitatory amino acid transporter 2						D-aspartate import|L-glutamate import|synaptic transmission	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|central_nervous_system(1)	3	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)		L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	35673152	35673153	+	IGR	INS	-	AG	AG	rs137905156	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35673152_35673153insAG								FJX1 (30733 upstream) : TRIM44 (11200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	37618574	37618589	+	IGR	DEL	TTCTTTCCTTCTTTCT	-	-	rs74222933	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37618574_37618589delTTCTTTCCTTCTTTCT								C11orf74 (922184 upstream) : None (None downstream)																																			---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40269205	40269206	+	Intron	INS	-	T	T	rs112867742	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40269205_40269206insT	uc001mxa.1	-						LRRC4C_uc001mxc.1_Intron|LRRC4C_uc001mxd.1_Intron|LRRC4C_uc001mxb.1_Intron	NM_020929	NP_065980			netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)																---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40879496	40879497	+	Intron	INS	-	GAAAGG	GAAAGG			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40879496_40879497insGAAAGG	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	40879567	40879571	+	Intron	DEL	GGAAG	-	-	rs143092598		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40879567_40879571delGGAAG	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	41408755	41408755	+	Intron	DEL	T	-	-	rs11355712		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41408755delT	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	42000233	42000234	+	IGR	INS	-	G	G	rs150080392	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42000233_42000234insG								LRRC4C (518910 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43106665	43106667	+	IGR	DEL	ACA	-	-	rs34500654		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43106665_43106667delACA								None (None upstream) : API5 (226838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43202826	43202827	+	IGR	INS	-	C	C	rs138455769	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43202826_43202827insC								None (None upstream) : API5 (130678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43240165	43240166	+	IGR	DEL	CT	-	-	rs71997787		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43240165_43240166delCT								None (None upstream) : API5 (93339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44347762	44347763	+	IGR	DEL	TG	-	-	rs112884773		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44347762_44347763delTG								ALX4 (16046 upstream) : CD82 (239378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44437178	44437179	+	IGR	INS	-	AA	AA	rs140569731	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44437178_44437179insAA								ALX4 (105462 upstream) : CD82 (149962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44487494	44487495	+	IGR	INS	-	TTCT	TTCT	rs112708954		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44487494_44487495insTTCT								ALX4 (155778 upstream) : CD82 (99646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44837636	44837637	+	IGR	INS	-	A	A	rs147978388	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44837636_44837637insA								CD82 (196323 upstream) : TSPAN18 (44242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45622032	45622032	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45622032delT								SYT13 (314148 upstream) : CHST1 (48395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45851175	45851175	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45851175delA								SLC35C1 (16609 upstream) : CRY2 (17494 downstream)																																			---	---	---	---
PHF21A	51317	broad.mit.edu	37	11	46005057	46005057	+	Intron	DEL	T	-	-	rs2946006	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46005057delT	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																		---	---	---	---
CREB3L1	90993	broad.mit.edu	37	11	46309527	46309527	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46309527delA	uc001ncf.2	+							NM_052854	NP_443086			cAMP responsive element binding protein 3-like						response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		FUS/CREB3L1(6)	soft_tissue(6)|ovary(2)	8				GBM - Glioblastoma multiforme(35;0.0285)				T	FUS	myxofibrosarcoma								---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46506495	46506495	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46506495delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	48747212	48747221	+	IGR	DEL	GAAGGTTTCT	-	-	rs147837463		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48747212_48747221delGAAGGTTTCT								OR4A47 (235940 upstream) : FOLH1 (420967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	50720273	50720273	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50720273delA								LOC646813 (340470 upstream) : OR4A5 (691175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	50764186	50764187	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50764186_50764187insA								LOC646813 (384383 upstream) : OR4A5 (647261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	51577360	51577363	+	IGR	DEL	TGTT	-	-	rs150165028		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51577360_51577363delTGTT								OR4C46 (61151 upstream) : None (None downstream)																																			---	---	---	---
SERPING1	710	broad.mit.edu	37	11	57378409	57378409	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57378409delT	uc001nkp.1	+						SERPING1_uc001nkq.1_Intron|SERPING1_uc010rju.1_Intron|SERPING1_uc010rjv.1_Intron|SERPING1_uc001nkr.1_Intron|SERPING1_uc009ymi.1_Intron|SERPING1_uc009ymj.1_Intron|SERPING1_uc001nks.1_Intron	NM_000062	NP_000053			serpin peptidase inhibitor, clade G, member 1						blood circulation|blood coagulation, intrinsic pathway|complement activation, classical pathway|innate immune response|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation	extracellular space|platelet alpha granule lumen	protein binding|serine-type endopeptidase inhibitor activity			central_nervous_system(1)	1														Hereditary_Angioedema				---	---	---	---
Unknown	0	broad.mit.edu	37	11	57608240	57608240	+	IGR	DEL	T	-	-	rs34435754		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57608240delT								CTNND1 (21589 upstream) : OR9Q1 (183113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	57636477	57636477	+	IGR	DEL	T	-	-	rs112814042		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57636477delT								CTNND1 (49826 upstream) : OR9Q1 (154876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	58592610	58592610	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58592610delT								GLYAT (93163 upstream) : GLYATL2 (8932 downstream)																																			---	---	---	---
MPEG1	219972	broad.mit.edu	37	11	58977224	58977225	+	3'UTR	DEL	GT	-	-	rs66826259		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58977224_58977225delGT	uc001nnu.3	-	1						NM_001039396	NP_001034485			macrophage expressed gene 1 precursor							integral to membrane				ovary(1)|skin(1)	2		all_epithelial(135;0.125)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	59089344	59089345	+	IGR	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59089344_59089345delTC								MPEG1 (108850 upstream) : OR5AN1 (42587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59733948	59733948	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59733948delT	uc001nok.1	+											Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit01-13-09-F.																														---	---	---	---
MS4A6A	64231	broad.mit.edu	37	11	59946963	59946964	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59946963_59946964insT	uc001nor.2	-						MS4A6A_uc001noq.2_Intron|MS4A6A_uc001nos.3_Intron|MS4A6A_uc009ymv.2_Intron|MS4A6A_uc001not.2_Intron|MS4A6A_uc010rla.1_Intron|MS4A6A_uc010rlb.1_Intron	NM_152852	NP_690591			membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	60120446	60120446	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60120446delT								MS4A6E (12006 upstream) : MS4A7 (25512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	60128357	60128358	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60128357_60128358delGT								MS4A6E (19917 upstream) : MS4A7 (17600 downstream)																																			---	---	---	---
C11orf64	283197	broad.mit.edu	37	11	60415530	60415533	+	Intron	DEL	CAGT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60415530_60415533delCAGT	uc001npt.2	+						C11orf64_uc001npu.2_Intron	NR_026946				Homo sapiens cDNA FLJ25394 fis, clone TST02552.												0																		---	---	---	---
CD5	921	broad.mit.edu	37	11	60867003	60867004	+	5'Flank	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60867003_60867004delTT	uc009ynk.2	+							NM_014207	NP_055022			CD5 molecule precursor						cell proliferation|cell recognition	integral to plasma membrane	scavenger receptor activity			ovary(1)	1		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	62049731	62049732	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62049731_62049732insA								SCGB2A2 (9104 upstream) : SCGB1D4 (14022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	62200736	62200736	+	IGR	DEL	A	-	-	rs34530452		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62200736delA								SCGB1A1 (10070 upstream) : AHNAK (280 downstream)																																			---	---	---	---
WDR74	54663	broad.mit.edu	37	11	62606232	62606233	+	Intron	INS	-	A	A	rs112966057		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62606232_62606233insA	uc001nvm.1	-						WDR74_uc001nvk.1_Intron|WDR74_uc001nvl.1_Intron|WDR74_uc001nvn.1_Intron|WDR74_uc009yoi.1_Intron|WDR74_uc010rmk.1_Intron	NM_018093	NP_060563			WD repeat domain 74							nucleolus				ovary(1)	1																		---	---	---	---
SLC22A8	9376	broad.mit.edu	37	11	62773602	62773603	+	Intron	DEL	TT	-	-	rs140436504		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62773602_62773603delTT	uc001nwo.2	-						SLC22A8_uc001nwp.2_Intron|SLC22A8_uc009yom.2_Intron|SLC22A8_uc010rmm.1_Intron|SLC22A8_uc009yon.2_Intron	NM_004254	NP_004245			solute carrier family 22 member 8						response to toxin	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|organic anion transmembrane transporter activity			skin(2)|ovary(1)	3																		---	---	---	---
MACROD1	28992	broad.mit.edu	37	11	63887474	63887474	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63887474delC	uc001nyh.2	-							NM_014067	NP_054786			MACRO domain containing 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	64147481	64147482	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64147481_64147482delGT								RPS6KA4 (7795 upstream) : SLC22A11 (175616 downstream)																																			---	---	---	---
NRXN2	9379	broad.mit.edu	37	11	64477381	64477381	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64477381delT	uc001oar.2	-						NRXN2_uc001oas.2_Intron	NM_015080	NP_055895			neurexin 2 isoform alpha-1 precursor						cell adhesion	integral to membrane				upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)|ovary(2)|kidney(1)|pancreas(1)	10																		---	---	---	---
CDC42EP2	10435	broad.mit.edu	37	11	65079800	65079801	+	5'Flank	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65079800_65079801insT	uc001odl.2	+							NM_006779	NP_006770			Cdc42 effector protein 2						actin filament organization|positive regulation of actin filament polymerization|positive regulation of pseudopodium assembly|regulation of cell shape	cytoplasm|cytoskeleton|endomembrane system|plasma membrane	GTP-Rho binding|Rho GTPase activator activity				0																		---	---	---	---
PACS1	55690	broad.mit.edu	37	11	65925318	65925319	+	Intron	INS	-	A	A	rs35418819		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65925318_65925319insA	uc001oha.1	+						PACS1_uc001ogz.1_Intron	NM_018026	NP_060496			phosphofurin acidic cluster sorting protein 1						interspecies interaction between organisms|regulation of defense response to virus by virus|viral reproduction	cytosol	protein binding			ovary(6)	6																		---	---	---	---
C11orf80	79703	broad.mit.edu	37	11	66522592	66522593	+	Intron	INS	-	T	T	rs7951710	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66522592_66522593insT	uc001ojf.2	+						C11orf80_uc001ojg.2_Intron|C11orf80_uc001ojh.2_Intron|C11orf80_uc010rpk.1_Intron	NM_024650	NP_078926			hypothetical protein LOC79703												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	67295288	67295289	+	IGR	DEL	GT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67295288_67295289delGT								CABP2 (4389 upstream) : GSTP1 (55777 downstream)																																			---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70482682	70482683	+	Intron	DEL	GA	-	-	rs72248779	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70482682_70482683delGA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	71281749	71281750	+	IGR	INS	-	TG	TG	rs146397927	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71281749_71281750insTG								KRTAP5-10 (4083 upstream) : KRTAP5-11 (11153 downstream)																																			---	---	---	---
FCHSD2	9873	broad.mit.edu	37	11	72786842	72786842	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72786842delA	uc009ytl.2	-						FCHSD2_uc010rrg.1_Intron|FCHSD2_uc001oth.3_Intron|FCHSD2_uc001oti.2_Intron	NM_014824	NP_055639			FCH and double SH3 domains 2								protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)															---	---	---	---
P4HA3	283208	broad.mit.edu	37	11	73983265	73983266	+	Intron	DEL	AC	-	-	rs34186062		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73983265_73983266delAC	uc001ouz.2	-						P4HA3_uc001ouy.3_Intron|P4HA3_uc010rrj.1_Intron	NM_182904	NP_878907			prolyl 4-hydroxylase, alpha III subunit							endoplasmic reticulum lumen	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			skin(1)	1	Breast(11;2.31e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	76015736	76015737	+	IGR	INS	-	CA	CA	rs138572698	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76015736_76015737insCA								WNT11 (93933 upstream) : PRKRIR (45267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	76275761	76275761	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76275761delA								C11orf30 (13173 upstream) : LRRC32 (92808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	76488195	76488196	+	IGR	INS	-	TC	TC	rs145863513	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76488195_76488196insTC								GUCY2E (55362 upstream) : TSKU (6089 downstream)																																			---	---	---	---
NARS2	79731	broad.mit.edu	37	11	78226359	78226359	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78226359delC	uc001ozi.2	-						NARS2_uc010rsq.1_Intron	NM_024678	NP_078954			asparaginyl-tRNA synthetase 2, mitochondrial						asparaginyl-tRNA aminoacylation	mitochondrial matrix	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding			ovary(2)	2	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)													---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	79034927	79034928	+	Intron	INS	-	AC	AC	rs146773899	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79034927_79034928insAC	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	79404693	79404694	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79404693_79404694delTG								ODZ4 (252998 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	79485287	79485288	+	IGR	INS	-	G	G	rs72325902		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79485287_79485288insG								ODZ4 (333592 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	79865013	79865013	+	IGR	DEL	C	-	-	rs35793154		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79865013delC								ODZ4 (713318 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80919608	80919608	+	IGR	DEL	T	-	-	rs35085616		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80919608delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	82134617	82134618	+	IGR	INS	-	A	A	rs71981078		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82134617_82134618insA								None (None upstream) : FAM181B (308435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	82393553	82393554	+	IGR	DEL	AG	-	-	rs56009328		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82393553_82393554delAG								None (None upstream) : FAM181B (49499 downstream)																																			---	---	---	---
PRCP	5547	broad.mit.edu	37	11	82559490	82559491	+	Intron	INS	-	AG	AG	rs150506139	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82559490_82559491insAG	uc001ozs.2	-						PRCP_uc001ozr.2_Intron	NM_005040	NP_005031			prolylcarboxypeptidase isoform 1 preproprotein						blood coagulation, intrinsic pathway|proteolysis	lysosome|plasma membrane	protein binding|serine-type carboxypeptidase activity			skin(1)	1																		---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83463780	83463781	+	Intron	INS	-	A	A	rs149559610	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83463780_83463781insA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83732397	83732397	+	Intron	DEL	A	-	-	rs35146858		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83732397delA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	85912620	85912620	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85912620delA								PICALM (131720 upstream) : EED (43195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	86430302	86430303	+	IGR	INS	-	TCTGTCTGTCTG	TCTGTCTGTCTG	rs2512993	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86430302_86430303insTCTGTCTGTCTG								ME3 (46624 upstream) : PRSS23 (81188 downstream)																																			---	---	---	---
TMEM135	65084	broad.mit.edu	37	11	87018423	87018423	+	Intron	DEL	A	-	-	rs67468091		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87018423delA	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	87109993	87109994	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87109993_87109994insA								TMEM135 (75425 upstream) : RAB38 (736437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	89926421	89926422	+	IGR	INS	-	AGTT	AGTT	rs144354625	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89926421_89926422insAGTT								NAALAD2 (651 upstream) : CHORDC1 (7175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90673971	90673978	+	IGR	DEL	AAAAAGAA	-	-	rs141485156	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90673971_90673978delAAAAAGAA								MIR1261 (71601 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91249930	91249937	+	IGR	DEL	CACACACA	-	-	rs10544165		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91249930_91249937delCACACACA								MIR1261 (647560 upstream) : FAT3 (835325 downstream)																																			---	---	---	---
CCDC67	159989	broad.mit.edu	37	11	93067761	93067762	+	Intron	INS	-	G	G	rs148044114	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93067761_93067762insG	uc001pdq.2	+						CCDC67_uc001pdo.1_Intron|CCDC67_uc001pdp.2_Intron	NM_181645	NP_857596			coiled-coil domain containing 67											ovary(1)	1		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	93291857	93291858	+	IGR	INS	-	A	A	rs5793643		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93291857_93291858insA								C11orf75 (15311 upstream) : KIAA1731 (102958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	93600403	93600404	+	IGR	INS	-	G	G	rs145290532	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93600403_93600404insG								C11orf90 (16735 upstream) : HEPHL1 (153974 downstream)																																			---	---	---	---
HEPHL1	341208	broad.mit.edu	37	11	93807628	93807629	+	Intron	DEL	TG	-	-	rs35911978		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93807628_93807629delTG	uc001pep.2	+						uc001pen.1_Intron	NM_001098672	NP_001092142			hephaestin-like 1 precursor						copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	95227665	95227666	+	IGR	INS	-	TG	TG	rs140175021	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95227665_95227666insTG								SESN3 (261960 upstream) : FAM76B (274440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	96674523	96674523	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96674523delA								JRKL (547796 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	96699451	96699452	+	IGR	INS	-	T	T	rs147995571	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96699451_96699452insT								JRKL (572724 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	97045654	97045655	+	IGR	INS	-	A	A	rs149651070	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97045654_97045655insA								JRKL (918927 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	97422759	97422759	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97422759delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	97840904	97840904	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97840904delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	97993981	97993982	+	IGR	INS	-	T	T	rs36115164		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97993981_97993982insT								None (None upstream) : CNTN5 (897889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98279083	98279083	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98279083delA								None (None upstream) : CNTN5 (612788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98702764	98702765	+	IGR	INS	-	TA	TA	rs141966977	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98702764_98702765insTA								None (None upstream) : CNTN5 (189106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98720760	98720761	+	IGR	INS	-	AA	AA	rs144932565	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98720760_98720761insAA								None (None upstream) : CNTN5 (171110 downstream)																																			---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	98955780	98955780	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98955780delT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99081021	99081021	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99081021delT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99685308	99685309	+	Intron	INS	-	A	A	rs148166621	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99685308_99685309insA	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	100826913	100826915	+	Intron	DEL	CAT	-	-	rs145079973		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100826913_100826915delCAT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	100870268	100870268	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100870268delT								TMEM133 (5603 upstream) : PGR (30087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	101127166	101127169	+	IGR	DEL	TCTC	-	-	rs34657185		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101127166_101127169delTCTC								PGR (126622 upstream) : TRPC6 (195127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	101222590	101222590	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101222590delA								PGR (222046 upstream) : TRPC6 (99706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	102690601	102690601	+	Intron	DEL	C	-	-	rs113006933		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102690601delC	uc001phh.1	+											Homo sapiens cDNA FLJ40486 fis, clone TESTI2043866.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	103426782	103426783	+	IGR	DEL	TA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103426782_103426783delTA								DYNC2H1 (76191 upstream) : PDGFD (351132 downstream)																																			---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	103912693	103912693	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103912693delA	uc001phq.2	-						PDGFD_uc001php.2_Intron	NM_025208	NP_079484			platelet derived growth factor D isoform 1						positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	104042526	104042527	+	IGR	DEL	GT	-	-	rs150648273		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104042526_104042527delGT								PDGFD (7499 upstream) : CASP12 (713915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	106482149	106482152	+	IGR	DEL	AGAG	-	-	rs148273299		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106482149_106482152delAGAG								AASDHPPT (512730 upstream) : GUCY1A2 (75758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	107576557	107576558	+	IGR	DEL	AC	-	-	rs66465468		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107576557_107576558delAC								ELMOD1 (39053 upstream) : SLN (1551 downstream)																																			---	---	---	---
EXPH5	23086	broad.mit.edu	37	11	108379665	108379666	+	3'UTR	INS	-	T	T	rs145028998	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108379665_108379666insT	uc001pkk.2	-	6					EXPH5_uc010rvy.1_3'UTR|EXPH5_uc010rvz.1_3'UTR|EXPH5_uc010rwa.1_3'UTR	NM_015065	NP_055880			exophilin 5 isoform a						intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	109213034	109213035	+	IGR	DEL	GT	-	-	rs113161768		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109213034_109213035delGT								DDX10 (401388 upstream) : C11orf87 (79840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109803288	109803289	+	IGR	DEL	GA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109803288_109803289delGA								C11orf87 (503450 upstream) : ZC3H12C (160637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	111280545	111280546	+	Intron	INS	-	A	A	rs144955754	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111280545_111280546insA	uc001plh.1	-											Homo sapiens, clone IMAGE:4694422, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	111297000	111297001	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111297000_111297001insA	uc001plh.1	-											Homo sapiens, clone IMAGE:4694422, mRNA.																														---	---	---	---
SIK2	23235	broad.mit.edu	37	11	111493828	111493828	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111493828delT	uc001plt.2	+							NM_015191	NP_056006			SNF1-like kinase 2						intracellular protein kinase cascade|regulation of insulin receptor signaling pathway	Golgi apparatus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|skin(1)	3																		---	---	---	---
C11orf52	91894	broad.mit.edu	37	11	111794645	111794645	+	Intron	DEL	A	-	-	rs149626679		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111794645delA	uc001pmh.2	+						C11orf52_uc001pmi.2_Intron	NM_080659	NP_542390			hypothetical protein LOC91894											ovary(1)	1		all_cancers(61;8.8e-15)|all_epithelial(67;6.27e-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;3.63e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.7e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)														---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	113058285	113058286	+	Intron	INS	-	TG	TG	rs145196029	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113058285_113058286insTG	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)														---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	113066178	113066179	+	Intron	DEL	CA	-	-	rs34523359		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113066178_113066179delCA	uc009yyq.1	+						NCAM1_uc001pno.2_Intron	NM_001076682	NP_001070150			neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	113761341	113761341	+	IGR	DEL	A	-	-	rs3133377		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113761341delA								USP28 (15085 upstream) : HTR3B (14248 downstream)																																			---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	113993184	113993184	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113993184delT	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	114523474	114523475	+	IGR	DEL	CT	-	-	rs147217045		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114523474_114523475delCT								FAM55D (56990 upstream) : FAM55B (25725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	115007983	115007983	+	IGR	DEL	A	-	-	rs5794955		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115007983delA								FAM55B (430331 upstream) : CADM1 (31970 downstream)																																			---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115191377	115191377	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115191377delT	uc001ppi.3	-						CADM1_uc001ppf.3_Intron|CADM1_uc001ppk.3_Intron|CADM1_uc001ppj.3_Intron|CADM1_uc001ppl.2_Intron	NM_014333	NP_055148			immunoglobulin superfamily, member 4D isoform 1						adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	115580382	115580383	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115580382_115580383delTT								CADM1 (205141 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116043554	116043555	+	IGR	INS	-	A	A	rs145754777	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116043554_116043555insA								CADM1 (668313 upstream) : BUD13 (575333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116359168	116359170	+	IGR	DEL	GAG	-	-	rs150647122		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116359168_116359170delGAG								CADM1 (983927 upstream) : BUD13 (259718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116434121	116434121	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116434121delT								None (None upstream) : BUD13 (184767 downstream)																																			---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116840829	116840829	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116840829delA	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440			serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12																		---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116943766	116943766	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116943766delA	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron|uc001pqc.2_5'Flank	NM_025164	NP_079440			serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12																		---	---	---	---
MLL	4297	broad.mit.edu	37	11	118372188	118372188	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118372188delA	uc001pta.2	+						MLL_uc001ptb.2_Intron	NM_005933	NP_005924			myeloid/lymphoid or mixed-lineage leukemia						apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)				T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	11	118913149	118913149	+	IGR	DEL	A	-	-	rs75998693		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118913149delA								SLC37A4 (11533 upstream) : HYOU1 (1747 downstream)																																			---	---	---	---
CCDC153	283152	broad.mit.edu	37	11	119065487	119065488	+	Intron	INS	-	T	T	rs60630529		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119065487_119065488insT	uc010rze.1	-							NM_001145018	NP_001138490			coiled-coil domain containing 153												0																		---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120206636	120206636	+	5'Flank	DEL	G	-	-	rs3840762		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120206636delG	uc001pxl.1	+						ARHGEF12_uc009zat.2_5'Flank	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	120643350	120643351	+	Intron	DEL	GC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120643350_120643351delGC	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	120700897	120700897	+	Intron	DEL	A	-	-	rs10892627	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120700897delA	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	120779132	120779133	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120779132_120779133delAC	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
TECTA	7007	broad.mit.edu	37	11	121060085	121060085	+	Intron	DEL	T	-	-	rs35723886		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121060085delT	uc010rzo.1	+							NM_005422	NP_005413			tectorin alpha precursor						cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	121542663	121542664	+	IGR	INS	-	T	T	rs72382708		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121542663_121542664insT								SORL1 (38192 upstream) : LOC399959 (417147 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	122327581	122327581	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122327581delA								LOC399959 (89114 upstream) : UBASH3B (198817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	122381240	122381241	+	IGR	DEL	AG	-	-	rs73602085		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122381240_122381241delAG								LOC399959 (142773 upstream) : UBASH3B (145157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	122395102	122395103	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122395102_122395103insA								LOC399959 (156635 upstream) : UBASH3B (131295 downstream)																																			---	---	---	---
UBASH3B	84959	broad.mit.edu	37	11	122570234	122570239	+	Intron	DEL	TCTTTC	-	-	rs67145831	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122570234_122570239delTCTTTC	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)														---	---	---	---
CRTAM	56253	broad.mit.edu	37	11	122708413	122708416	+	5'Flank	DEL	ATGG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122708413_122708416delATGG	uc001pyj.2	+							NM_019604	NP_062550			class-I MHC-restricted T cell associated						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	123314666	123314667	+	IGR	INS	-	T	T	rs147486255	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123314666_123314667insT								ASAM (248659 upstream) : GRAMD1B (81861 downstream)																																			---	---	---	---
OR8D4	338662	broad.mit.edu	37	11	123776391	123776391	+	5'Flank	DEL	T	-	-	rs34426662		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123776391delT	uc010saa.1	+							NM_001005197	NP_001005197			olfactory receptor, family 8, subfamily D,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(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;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	125313731	125313731	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125313731delG								PKNOX2 (10448 upstream) : FEZ1 (1919 downstream)																																			---	---	---	---
FEZ1	9638	broad.mit.edu	37	11	125332901	125332902	+	Intron	INS	-	A	A	rs112179481		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125332901_125332902insA	uc001qbx.2	-						FEZ1_uc010sbc.1_Intron	NM_005103	NP_005094			zygin 1 isoform 1						axon guidance|cell adhesion|transport	microtubule|plasma membrane				central_nervous_system(3)|ovary(1)	4	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;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0934)														---	---	---	---
DDX25	29118	broad.mit.edu	37	11	125790815	125790816	+	Intron	DEL	AC	-	-	rs34938153		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125790815_125790816delAC	uc001qcz.3	+						DDX25_uc010sbk.1_Intron	NM_013264	NP_037396			DEAD (Asp-Glu-Ala-Asp) box polypeptide 25						mRNA export from nucleus|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|nucleus	ATP binding|ATP-dependent RNA helicase activity|RNA binding			ovary(1)	1	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	126066658	126066659	+	IGR	INS	-	A	A	rs11393401		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126066658_126066659insA								CDON (133471 upstream) : RPUSD4 (5331 downstream)																																			---	---	---	---
DCPS	28960	broad.mit.edu	37	11	126200096	126200097	+	Intron	INS	-	T	T	rs141410099	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126200096_126200097insT	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)														---	---	---	---
KIRREL3	84623	broad.mit.edu	37	11	126546948	126546948	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126546948delT	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron|uc009zcf.1_Intron	NM_032531	NP_115920			kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	127455113	127455124	+	IGR	DEL	ATTCATTCATTT	-	-	rs149322973		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127455113_127455124delATTCATTCATTT								KIRREL3 (581758 upstream) : ETS1 (873532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	127804124	127804135	+	IGR	DEL	TCCTTCCTTCCC	-	-	rs149704644	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127804124_127804135delTCCTTCCTTCCC								KIRREL3 (930769 upstream) : ETS1 (524521 downstream)																																			---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	128843573	128843573	+	Intron	DEL	A	-	-	rs10893942	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128843573delA	uc009zcp.2	-						ARHGAP32_uc009zcq.1_3'UTR|ARHGAP32_uc009zco.2_5'UTR|ARHGAP32_uc001qez.2_Intron	NM_001142685	NP_001136157			Rho GTPase-activating protein isoform 1						cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	129130588	129130588	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129130588delA								ARHGAP32 (68495 upstream) : BARX2 (115293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	130353894	130353894	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130353894delC								ADAMTS15 (10179 upstream) : SNX19 (391873 downstream)																																			---	---	---	---
NTM	50863	broad.mit.edu	37	11	131395740	131395741	+	Intron	DEL	TG	-	-	rs113346408		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131395740_131395741delTG	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530			neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
NTM	50863	broad.mit.edu	37	11	131893647	131893648	+	Intron	INS	-	TTG	TTG			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131893647_131893648insTTG	uc001qgp.2	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_Intron|NTM_uc001qgq.2_Intron	NM_016522	NP_057606			neurotrimin isoform 1						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
GLB1L3	112937	broad.mit.edu	37	11	134178014	134178016	+	Intron	DEL	CAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134178014_134178016delCAT	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	134339365	134339366	+	Intron	INS	-	TA	TA	rs138862104	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134339365_134339366insTA	uc001qhs.2	+											Homo sapiens cDNA FLJ37762 fis, clone BRHIP2024347, weakly similar to GALECTIN-3.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	134689791	134689792	+	IGR	DEL	GA	-	-	rs66721383		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134689791_134689792delGA								B3GAT1 (407979 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	134822715	134822718	+	IGR	DEL	ACAC	-	-	rs147493077		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134822715_134822718delACAC								B3GAT1 (540903 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	852438	852439	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:852438_852439insA								NINJ2 (79683 upstream) : WNK1 (9786 downstream)																																			---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1340311	1340312	+	Intron	INS	-	T	T	rs79094176		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1340311_1340312insT	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	1385740	1385741	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1385740_1385741insT	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)															---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2272605	2272606	+	Intron	INS	-	T	T	rs111785756		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2272605_2272606insT	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	2418644	2418645	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2418644_2418645delCA	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	2487990	2487991	+	Intron	INS	-	TCTT	TCTT	rs147464208	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2487990_2487991insTCTT	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630			calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	2829188	2829189	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2829188_2829189delAC								CACNA1C (22073 upstream) : FKBP4 (74919 downstream)																																			---	---	---	---
PRMT8	56341	broad.mit.edu	37	12	3589817	3589818	+	Intron	INS	-	C	C	rs140905732	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3589817_3589818insC	uc009zed.2	+						uc001qmc.1_5'Flank|uc010sem.1_5'Flank	NM_019854	NP_062828			HMT1 hnRNP methyltransferase-like 4						regulation of protein binding	cytoplasm|plasma membrane	histone-arginine N-methyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity			ovary(3)|central_nervous_system(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	5367838	5367838	+	IGR	DEL	T	-	-	rs75733680		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5367838delT								KCNA5 (211890 upstream) : NTF3 (173442 downstream)																																			---	---	---	---
ANO2	57101	broad.mit.edu	37	12	5882376	5882376	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5882376delA	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	6190498	6190499	+	Intron	INS	-	T	T	rs150420125	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6190498_6190499insT	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543			von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	6298084	6298085	+	IGR	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6298084_6298085delAG								VWF (64248 upstream) : CD9 (10788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	6592004	6592005	+	IGR	INS	-	AGG	AGG	rs149276116	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6592004_6592005insAGG								VAMP1 (12161 upstream) : MRPL51 (9311 downstream)																																			---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6718833	6718833	+	5'Flank	DEL	A	-	-	rs71450160		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6718833delA	uc001qpo.2	-						CHD4_uc001qpp.2_5'Flank	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																		---	---	---	---
CLSTN3	9746	broad.mit.edu	37	12	7290352	7290353	+	Intron	INS	-	TGTG	TGTG	rs35489298		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7290352_7290353insTGTG	uc001qsr.2	+						CLSTN3_uc001qss.2_Intron	NM_014718	NP_055533			calsyntenin 3 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	8143741	8143741	+	IGR	DEL	A	-	-	rs151331623		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8143741delA								SLC2A3 (54849 upstream) : FOXJ2 (41618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	9188189	9188189	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9188189delA								KLRG1 (24851 upstream) : LOC144571 (29584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	10392131	10392132	+	IGR	DEL	TT	-	-	rs71049072		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10392131_10392132delTT								GABARAPL1 (16409 upstream) : KLRD1 (64918 downstream)																																			---	---	---	---
PRB4	5545	broad.mit.edu	37	12	11317919	11317920	+	Intron	DEL	CT	-	-	rs71803797		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11317919_11317920delCT	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	12	13416202	13416202	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13416202delA								EMP1 (46495 upstream) : C12orf36 (107821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	13574088	13574093	+	IGR	DEL	GTGTGT	-	-	rs71448869		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13574088_13574093delGTGTGT								C12orf36 (44443 upstream) : GRIN2B (140317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	14187145	14187145	+	IGR	DEL	G	-	-	rs149120726		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14187145delG								GRIN2B (54123 upstream) : ATF7IP (331466 downstream)																																			---	---	---	---
PLBD1	79887	broad.mit.edu	37	12	14658041	14658047	+	Intron	DEL	TTTTTTT	-	-	rs63168360		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14658041_14658047delTTTTTTT	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	15080434	15080436	+	Intron	DEL	TGT	-	-	rs34068450		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15080434_15080436delTGT	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	15175686	15175686	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15175686delT								PDE6H (40889 upstream) : RERG (85032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	16580216	16580217	+	IGR	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16580216_16580217delAG								MGST1 (56874 upstream) : LMO3 (121090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	17878326	17878326	+	IGR	DEL	T	-	-	rs67676820		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17878326delT								None (None upstream) : RERGL (355478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	18166041	18166042	+	IGR	DEL	TG	-	-	rs139337724		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18166041_18166042delTG								None (None upstream) : RERGL (67762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	18406786	18406786	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18406786delT								RERGL (163672 upstream) : PIK3C2G (7688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	18917508	18917509	+	IGR	INS	-	ACGA	ACGA	rs143057600	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18917508_18917509insACGA								CAPZA3 (25387 upstream) : PLEKHA5 (365139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	19715720	19715722	+	IGR	DEL	TTA	-	-	rs35036271		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19715720_19715722delTTA								AEBP2 (40547 upstream) : PDE3A (806475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	19791732	19791736	+	IGR	DEL	AAACA	-	-	rs72013839		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19791732_19791736delAAACA								AEBP2 (116559 upstream) : PDE3A (730461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	20006505	20006505	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20006505delT								AEBP2 (331332 upstream) : PDE3A (515692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	20152643	20152644	+	IGR	INS	-	AGAGAGAGAGGAAAG	AGAGAGAGAGGAAAG	rs146360760	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20152643_20152644insAGAGAGAGAGGAAAG								AEBP2 (477470 upstream) : PDE3A (369553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	20171973	20171974	+	IGR	INS	-	AAACAAAC	AAACAAAC	rs140217661	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20171973_20171974insAAACAAAC								AEBP2 (496800 upstream) : PDE3A (350223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	20363883	20363883	+	IGR	DEL	A	-	-	rs112731444		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20363883delA								AEBP2 (688710 upstream) : PDE3A (158314 downstream)																																			---	---	---	---
PDE3A	5139	broad.mit.edu	37	12	20521540	20521540	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20521540delT	uc001reh.1	+							NM_000921	NP_000912			phosphodiesterase 3A						lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)	4	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)													---	---	---	---
PDE3A	5139	broad.mit.edu	37	12	20761009	20761010	+	Intron	INS	-	A	A	rs138084082	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20761009_20761010insA	uc001reh.1	+							NM_000921	NP_000912			phosphodiesterase 3A						lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)	4	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)													---	---	---	---
SLCO1B3	28234	broad.mit.edu	37	12	20979164	20979165	+	Intron	INS	-	T	T	rs141660731	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20979164_20979165insT	uc001rek.2	+						SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron	NM_019844	NP_062818			solute carrier organic anion transporter family,						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	25627675	25627676	+	IGR	INS	-	AGTT	AGTT	rs147735932	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25627675_25627676insAGTT								KRAS (223812 upstream) : IFLTD1 (1340 downstream)																																			---	---	---	---
RASSF8	11228	broad.mit.edu	37	12	26158994	26158995	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26158994_26158995delAC	uc001rgx.2	+						RASSF8_uc001rgy.2_Intron|RASSF8_uc001rgz.2_Intron|RASSF8_uc009zjd.1_Intron|RASSF8_uc001rgw.1_Intron	NM_007211	NP_009142			Ras association (RalGDS/AF-6) domain family						signal transduction						0	Colorectal(261;0.0847)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	27364679	27364679	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27364679delA								C12orf71 (129224 upstream) : STK38L (32399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	28082450	28082450	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28082450delC								KLHDC5 (126478 upstream) : PTHLH (28568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	28208615	28208616	+	IGR	INS	-	ACACACACCT	ACACACACCT	rs139609237		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28208615_28208616insACACACACCT								PTHLH (83699 upstream) : CCDC91 (123594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	28297881	28297882	+	IGR	INS	-	T	T	rs147450915	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28297881_28297882insT								PTHLH (172965 upstream) : CCDC91 (34328 downstream)																																			---	---	---	---
OVCH1	341350	broad.mit.edu	37	12	29601725	29601725	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29601725delT	uc001rix.1	-							NM_183378	NP_899234			ovochymase 1 precursor						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)																	---	---	---	---
OVCH1	341350	broad.mit.edu	37	12	29624284	29624284	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29624284delC	uc001rix.1	-							NM_183378	NP_899234			ovochymase 1 precursor						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)																	---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31565865	31565865	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31565865delT	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	31940819	31940819	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31940819delT								AMN1 (58711 upstream) : H3F3C (3302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38092606	38092607	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38092606_38092607insT								None (None upstream) : ALG10B (617950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38669183	38669184	+	IGR	INS	-	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38669183_38669184insC								None (None upstream) : ALG10B (41373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	39373001	39373001	+	IGR	DEL	A	-	-	rs35797525		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39373001delA								CPNE8 (73581 upstream) : KIF21A (314030 downstream)																																			---	---	---	---
C12orf40	283461	broad.mit.edu	37	12	40069120	40069121	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40069120_40069121insT	uc001rmc.2	+						C12orf40_uc009zjv.1_Intron	NM_001031748	NP_001026918			hypothetical protein LOC283461											ovary(6)	6																		---	---	---	---
SLC2A13	114134	broad.mit.edu	37	12	40335931	40335931	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40335931delA	uc010skm.1	-							NM_052885	NP_443117			solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)													HNSCC(50;0.14)			---	---	---	---
LRRK2	120892	broad.mit.edu	37	12	40636959	40636959	+	Intron	DEL	A	-	-	rs75585436		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40636959delA	uc001rmg.3	+							NM_198578	NP_940980			leucine-rich repeat kinase 2						activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	40910269	40910269	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40910269delG								LRRK2 (147185 upstream) : CNTN1 (176089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	40923632	40923633	+	Intron	INS	-	CT	CT	rs144994467	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40923632_40923633insCT	uc001rmj.1	+											Homo sapiens mRNA; cDNA DKFZp686N11246 (from clone DKFZp686N11246).																														---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41725607	41725607	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41725607delA	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)																---	---	---	---
PRICKLE1	144165	broad.mit.edu	37	12	42880513	42880513	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42880513delT	uc001rnm.2	-						PRICKLE1_uc001rnl.2_5'Flank|PRICKLE1_uc010skw.1_5'Flank|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	43092567	43092568	+	IGR	INS	-	C	C	rs11181642		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43092567_43092568insC								PRICKLE1 (108995 upstream) : ADAMTS20 (655445 downstream)																																			---	---	---	---
PUS7L	83448	broad.mit.edu	37	12	44130669	44130669	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44130669delA	uc001rnq.3	-						PUS7L_uc001rnr.3_Intron|PUS7L_uc001rns.3_Intron|PUS7L_uc009zkb.2_Intron	NM_001098615	NP_001092085			pseudouridylate synthase 7 homolog (S.						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			pancreas(1)	1	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)														---	---	---	---
TMEM117	84216	broad.mit.edu	37	12	44229284	44229285	+	5'Flank	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44229284_44229285delTG	uc001rod.2	+						TMEM117_uc001roe.2_5'Flank|TMEM117_uc009zkc.2_5'Flank	NM_032256	NP_115632			transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	44837709	44837709	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44837709delG								TMEM117 (54169 upstream) : NELL2 (64349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	45868474	45868474	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45868474delG								ANO6 (34287 upstream) : LOC400027 (251336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	49035058	49035061	+	IGR	DEL	TTCT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49035058_49035061delTTCT								LALBA (71229 upstream) : C12orf41 (11934 downstream)																																			---	---	---	---
RACGAP1	29127	broad.mit.edu	37	12	50404102	50404103	+	Intron	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50404102_50404103delTT	uc001rvt.2	-						RACGAP1_uc009zlm.1_Intron|RACGAP1_uc001rvs.2_Intron|RACGAP1_uc001rvu.2_Intron	NM_013277	NP_037409			Rac GTPase activating protein 1						blood coagulation|cytokinesis, actomyosin contractile ring assembly|cytokinesis, initiation of separation|embryo development|microtubule-based movement|neuroblast proliferation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|spermatogenesis|sulfate transport	acrosomal vesicle|cytosol|microtubule|midbody|nucleus|spindle	alpha-tubulin binding|beta-tubulin binding|gamma-tubulin binding|GTPase activator activity|metal ion binding			kidney(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	50564396	50564397	+	IGR	DEL	AC	-	-	rs140305164		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50564396_50564397delAC								LASS5 (3299 upstream) : LIMA1 (5168 downstream)																																			---	---	---	---
FAM186A	121006	broad.mit.edu	37	12	50779685	50779685	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50779685delA	uc001rwl.2	-							NM_001145475	NP_001138947			family with sequence similarity 186, member A												0																		---	---	---	---
BIN2	51411	broad.mit.edu	37	12	51699254	51699254	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51699254delA	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																		---	---	---	---
KRT83	3889	broad.mit.edu	37	12	52710027	52710027	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52710027delT	uc001saf.2	-							NM_002282	NP_002273			keratin 83						epidermis development	keratin filament	structural molecule activity			skin(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
KRT84	3890	broad.mit.edu	37	12	52778044	52778045	+	Intron	INS	-	GAG	GAG	rs149199933		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52778044_52778045insGAG	uc001sah.1	-							NM_033045	NP_149034			keratin, hair, basic, 4							keratin filament	structural constituent of epidermis			skin(1)	1	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
ATP5G2	517	broad.mit.edu	37	12	54067128	54067135	+	Intron	DEL	AAACAAAA	-	-	rs71068164	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54067128_54067135delAAACAAAA	uc009znc.2	-						ATP5G2_uc001sec.2_Intron|ATP5G2_uc001sed.2_Intron	NM_001002031	NP_001002031			ATP synthase, H+ transporting, mitochondrial F0						ATP hydrolysis coupled proton transport|ATP synthesis coupled proton transport	integral to membrane|mitochondrial proton-transporting ATP synthase complex|proton-transporting ATP synthase complex, coupling factor F(o)	hydrogen ion transmembrane transporter activity|lipid binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	54168726	54168727	+	IGR	INS	-	T	T	rs145371667	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54168726_54168727insT								CALCOCO1 (47419 upstream) : HOXC13 (163849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	54201224	54201226	+	IGR	DEL	GTC	-	-	rs34983064		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54201224_54201226delGTC								CALCOCO1 (79917 upstream) : HOXC13 (131350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55283687	55283688	+	IGR	DEL	CA	-	-	rs72404518		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55283687_55283688delCA								MUCL1 (31515 upstream) : KIAA0748 (60177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55404310	55404311	+	IGR	DEL	TC	-	-	rs71710073		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55404310_55404311delTC								KIAA0748 (25854 upstream) : NEUROD4 (9418 downstream)																																			---	---	---	---
RPS26	6231	broad.mit.edu	37	12	56437596	56437596	+	Intron	DEL	A	-	-	rs72234051		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56437596delA	uc001sjf.2	+							NM_001029	NP_001020			ribosomal protein S26						endocrine pancreas development|negative regulation of RNA splicing|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	mRNA binding|protein binding|structural constituent of ribosome			breast(1)	1			OV - Ovarian serous cystadenocarcinoma(18;0.123)															---	---	---	---
STAT2	6773	broad.mit.edu	37	12	56736369	56736369	+	3'UTR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56736369delG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	58406598	58406598	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58406598delA								XRCC6BP1 (55547 upstream) : LRIG3 (859340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	59982967	59982967	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59982967delA								LRIG3 (668705 upstream) : SLC16A7 (6881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	60204954	60204954	+	IGR	DEL	A	-	-	rs34514585		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60204954delA								SLC16A7 (29547 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	63671643	63671646	+	IGR	DEL	TCTG	-	-	rs72072473		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63671643_63671646delTCTG								AVPR1A (125053 upstream) : DPY19L2 (281047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	63756499	63756500	+	IGR	INS	-	TGTG	TGTG	rs149572427	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63756499_63756500insTGTG								AVPR1A (209909 upstream) : DPY19L2 (196193 downstream)																																			---	---	---	---
TBK1	29110	broad.mit.edu	37	12	64877791	64877802	+	Intron	DEL	ACACACACACAC	-	-	rs72209165		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64877791_64877802delACACACACACAC	uc001ssc.1	+							NM_013254	NP_037386			TANK-binding kinase 1						I-kappaB kinase/NF-kappaB cascade|innate immune response|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription from RNA polymerase II promoter|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|large_intestine(1)|breast(1)	5				GBM - Glioblastoma multiforme(28;0.0386)														---	---	---	---
GNS	2799	broad.mit.edu	37	12	65127903	65127903	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65127903delG	uc001ssg.3	-						GNS_uc001ssf.2_Intron|GNS_uc010ssq.1_Intron|GNS_uc010ssr.1_Intron	NM_002076	NP_002067			glucosamine (N-acetyl)-6-sulfatase precursor							lysosome	metal ion binding|N-acetylglucosamine-6-sulfatase activity|protein binding			central_nervous_system(1)	1	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	65377262	65377273	+	IGR	DEL	CCTTCCTTCCTT	-	-	rs10552557		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65377262_65377273delCCTTCCTTCCTT								GNS (224036 upstream) : WIF1 (67134 downstream)																																			---	---	---	---
WIF1	11197	broad.mit.edu	37	12	65512657	65512658	+	Intron	INS	-	GAGA	GAGA	rs142653496	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65512657_65512658insGAGA	uc001ssk.2	-							NM_007191	NP_009122			WNT inhibitory factor 1 precursor						multicellular organismal development|Wnt receptor signaling pathway	extracellular region	protein tyrosine kinase activity			ovary(2)|lung(1)|skin(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)				T	HMGA2	pleomorphic salivary gland adenoma								---	---	---	---
Unknown	0	broad.mit.edu	37	12	68035729	68035729	+	IGR	DEL	C	-	-	rs71088274		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68035729delC								CAND1 (327341 upstream) : DYRK2 (6783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68376827	68376828	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68376827_68376828insT								DYRK2 (320384 upstream) : IFNG (171722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68589617	68589618	+	IGR	INS	-	TTTA	TTTA	rs142024217	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68589617_68589618insTTTA								IFNG (36096 upstream) : IL26 (5511 downstream)																																			---	---	---	---
IL26	55801	broad.mit.edu	37	12	68607555	68607556	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68607555_68607556insT	uc001stx.1	-							NM_018402	NP_060872			interleukin 26 precursor						cell-cell signaling|negative regulation of epithelial cell proliferation|positive regulation of cytokine secretion|positive regulation of ERK1 and ERK2 cascade|positive regulation of JAK-STAT cascade|positive regulation of protein kinase B signaling cascade|positive regulation of stress-activated MAPK cascade|positive regulation of transcription from RNA polymerase II promoter	cytosol|extracellular space|soluble fraction	cytokine activity				0			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000515)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	68755260	68755261	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68755260_68755261delAC								MDM1 (29099 upstream) : RAP1B (249391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	69464040	69464041	+	IGR	INS	-	T	T	rs150822359	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69464040_69464041insT								CPM (107020 upstream) : CPSF6 (169276 downstream)																																			---	---	---	---
YEATS4	8089	broad.mit.edu	37	12	69772702	69772703	+	Intron	INS	-	CT	CT	rs145982196	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69772702_69772703insCT	uc001sux.2	+							NM_006530	NP_006521			glioma-amplified sequence-41						histone H2A acetylation|histone H4 acetylation|mitosis|positive regulation of transcription, DNA-dependent|regulation of growth	NuA4 histone acetyltransferase complex|nuclear matrix	DNA binding|protein C-terminus binding|sequence-specific DNA binding transcription factor activity|structural constituent of cytoskeleton				0	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)															---	---	---	---
FRS2	10818	broad.mit.edu	37	12	69915971	69915984	+	Intron	DEL	TGTGTGTGTGTGTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69915971_69915984delTGTGTGTGTGTGTG	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	70392217	70392217	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70392217delA								RAB3IP (175235 upstream) : CNOT2 (244560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	70430783	70430786	+	IGR	DEL	ACAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70430783_70430786delACAC								RAB3IP (213801 upstream) : CNOT2 (205991 downstream)																																			---	---	---	---
CNOT2	4848	broad.mit.edu	37	12	70654787	70654788	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70654787_70654788insT	uc001svv.2	+						CNOT2_uc009zro.2_Intron|CNOT2_uc009zrp.2_Intron|CNOT2_uc009zrq.2_Intron	NM_014515	NP_055330			CCR4-NOT transcription complex, subunit 2						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	protein binding|RNA polymerase II transcription cofactor activity				0	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)															---	---	---	---
KCNMB4	27345	broad.mit.edu	37	12	70817256	70817257	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70817256_70817257insT	uc001svx.2	+							NM_014505	NP_055320			calcium-activated potassium channel beta 4						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of neurotransmitter secretion|regulation of vasoconstriction|synaptic transmission	voltage-gated potassium channel complex	calcium-activated potassium channel activity|protein binding				0	Renal(347;0.236)		Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	70879132	70879132	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70879132delT	uc001svz.2	+											Homo sapiens cDNA clone IMAGE:4823238.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	71459236	71459237	+	IGR	DEL	AT	-	-	rs35371180		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71459236_71459237delAT								PTPRR (144652 upstream) : TSPAN8 (59640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	71507507	71507508	+	IGR	INS	-	A	A	rs149275779	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71507507_71507508insA								PTPRR (192923 upstream) : TSPAN8 (11369 downstream)																																			---	---	---	---
TBC1D15	64786	broad.mit.edu	37	12	72290306	72290307	+	Intron	INS	-	A	A	rs148885326	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72290306_72290307insA	uc001swu.2	+						TBC1D15_uc009zrv.2_Intron|TBC1D15_uc010stt.1_Intron|TBC1D15_uc001swv.2_Intron|TBC1D15_uc001sww.2_Intron	NM_022771	NP_073608			TBC1 domain family, member 15 isoform 1								protein binding|Rab GTPase activator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	74122939	74122939	+	IGR	DEL	T	-	-	rs5799149		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74122939delT								None (None upstream) : ATXN7L3B (808612 downstream)																																			---	---	---	---
KCNC2	3747	broad.mit.edu	37	12	75564855	75564856	+	Intron	INS	-	A	A	rs150541036	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75564855_75564856insA	uc001sxg.1	-						KCNC2_uc009zry.2_Intron|KCNC2_uc001sxe.2_Intron|KCNC2_uc001sxf.2_Intron|KCNC2_uc010stw.1_Intron	NM_139137	NP_631875			Shaw-related voltage-gated potassium channel						energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6																		---	---	---	---
OSBPL8	114882	broad.mit.edu	37	12	76889949	76889950	+	Intron	INS	-	T	T	rs113018378		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76889949_76889950insT	uc001sye.1	-						OSBPL8_uc001syf.1_Intron|OSBPL8_uc001syg.1_Intron	NM_020841	NP_065892			oxysterol-binding protein-like protein 8 isoform						lipid transport		lipid binding			ovary(1)	1																		---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78605521	78605522	+	3'UTR	INS	-	TT	TT	rs139201184	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78605521_78605522insTT	uc001syp.2	+	40					NAV3_uc001syo.2_3'UTR|NAV3_uc010sub.1_3'UTR|NAV3_uc009zsf.2_3'UTR	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	78620293	78620293	+	IGR	DEL	A	-	-	rs34500281		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78620293delA								NAV3 (13505 upstream) : SYT1 (637480 downstream)																																			---	---	---	---
SYT1	6857	broad.mit.edu	37	12	79325186	79325189	+	Intron	DEL	AGGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79325186_79325189delAGGA	uc001sys.2	+						SYT1_uc001syt.2_Intron|SYT1_uc001syu.2_Intron	NM_001135805	NP_001129277			synaptotagmin I						detection of calcium ion|glutamate secretion|neurotransmitter secretion|protein homooligomerization	cell junction|chromaffin granule membrane|clathrin sculpted acetylcholine transport vesicle membrane|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|clathrin sculpted glutamate transport vesicle membrane|clathrin sculpted monoamine transport vesicle membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	1-phosphatidylinositol binding|low-density lipoprotein particle receptor binding|metal ion binding|syntaxin-1 binding|transporter activity			skin(3)|pancreas(2)|ovary(1)	6																		---	---	---	---
SYT1	6857	broad.mit.edu	37	12	79669920	79669923	+	Intron	DEL	AAAC	-	-	rs113391398		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79669920_79669923delAAAC	uc001sys.2	+						SYT1_uc001syt.2_Intron|SYT1_uc001syu.2_Intron|SYT1_uc001syv.2_Intron	NM_001135805	NP_001129277			synaptotagmin I						detection of calcium ion|glutamate secretion|neurotransmitter secretion|protein homooligomerization	cell junction|chromaffin granule membrane|clathrin sculpted acetylcholine transport vesicle membrane|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|clathrin sculpted glutamate transport vesicle membrane|clathrin sculpted monoamine transport vesicle membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	1-phosphatidylinositol binding|low-density lipoprotein particle receptor binding|metal ion binding|syntaxin-1 binding|transporter activity			skin(3)|pancreas(2)|ovary(1)	6																		---	---	---	---
PAWR	5074	broad.mit.edu	37	12	80015314	80015314	+	Intron	DEL	T	-	-	rs8176868		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80015314delT	uc001syx.2	-							NM_002583	NP_002574			PRKC, apoptosis, WT1, regulator						actin filament bundle assembly|apoptosis|induction of apoptosis|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	actin binding|enzyme binding|leucine zipper domain binding|transcription corepressor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	80666123	80666134	+	IGR	DEL	TGTGTGTGTGTG	-	-	rs72157969		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80666123_80666134delTGTGTGTGTGTG								PPP1R12A (336888 upstream) : PTPRQ (171992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	80676314	80676314	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80676314delT								PPP1R12A (347079 upstream) : PTPRQ (161812 downstream)																																			---	---	---	---
ACSS3	79611	broad.mit.edu	37	12	81530916	81530916	+	Intron	DEL	T	-	-	rs146736352		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81530916delT	uc001szl.1	+						ACSS3_uc001szm.1_Intron	NM_024560	NP_078836			acyl-CoA synthetase short-chain family member 3							mitochondrion	acetate-CoA ligase activity|ATP binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	84049092	84049093	+	IGR	INS	-	ACAC	ACAC	rs141231787	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84049092_84049093insACAC								TMTC2 (521029 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	84049513	84049513	+	IGR	DEL	A	-	-	rs140451812		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84049513delA								TMTC2 (521450 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85755124	85755124	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85755124delA								ALX1 (59565 upstream) : RASSF9 (443207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89352672	89352672	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89352672delA								KITLG (378434 upstream) : DUSP6 (389167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	92342331	92342332	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92342331_92342332insA								DCN (765525 upstream) : BTG1 (36534 downstream)																																			---	---	---	---
EEA1	8411	broad.mit.edu	37	12	93321938	93321939	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93321938_93321939insA	uc001tck.2	-							NM_003566	NP_003557			early endosome antigen 1, 162kD						early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
CRADD	8738	broad.mit.edu	37	12	94148742	94148742	+	Intron	DEL	A	-	-	rs79005051		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94148742delA	uc001tda.2	+						CRADD_uc010sur.1_Intron|CRADD_uc010sus.1_Intron	NM_003805	NP_003796			CASP2 and RIPK1 domain containing adaptor with						apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1																		---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94773867	94773867	+	Intron	DEL	C	-	-	rs79266886		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94773867delC	uc001tdd.2	-						CCDC41_uc001tde.2_Intron|CCDC41_uc009zsw.1_Intron|CCDC41_uc001tdf.2_Intron	NM_016122	NP_057206			NY-REN-58 antigen												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	95307243	95307246	+	IGR	DEL	ATTC	-	-	rs144025636		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95307243_95307246delATTC								MIR492 (78954 upstream) : NDUFA12 (57866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	95834831	95834831	+	IGR	DEL	T	-	-	rs112913429		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95834831delT								MIR331 (132542 upstream) : METAP2 (32991 downstream)																																			---	---	---	---
USP44	84101	broad.mit.edu	37	12	95947398	95947399	+	5'Flank	INS	-	AATGGA	AATGGA	rs141279132	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95947398_95947399insAATGGA	uc001teh.2	-							NM_032147	NP_115523			ubiquitin thiolesterase 44						anaphase|cell division|mitosis|negative regulation of mitotic anaphase-promoting complex activity|protein deubiquitination|regulation of spindle checkpoint|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)|breast(1)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	95980731	95980732	+	IGR	INS	-	AA	AA	rs35206663		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95980731_95980732insAA								USP44 (35468 upstream) : NTN4 (70852 downstream)																																			---	---	---	---
CDK17	5128	broad.mit.edu	37	12	96683804	96683804	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96683804delA	uc001tep.1	-						CDK17_uc009ztk.2_Intron|CDK17_uc010svb.1_Intron	NM_002595	NP_002586			PCTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity			ovary(3)|lung(2)|kidney(1)|central_nervous_system(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	97012403	97012404	+	Intron	INS	-	A	A	rs147243525	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97012403_97012404insA	uc001ter.1	+											Homo sapiens cDNA FLJ31514 fis, clone NT2RI1000164.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	97576781	97576785	+	IGR	DEL	AAAAG	-	-	rs72338894		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97576781_97576785delAAAAG								NEDD1 (229320 upstream) : RMST (282014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98545881	98545884	+	IGR	DEL	ATGG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98545881_98545884delATGG								RMST (587088 upstream) : LOC100128191 (360869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98576007	98576008	+	IGR	INS	-	A	A	rs139821708	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98576007_98576008insA								RMST (617214 upstream) : LOC100128191 (330745 downstream)																																			---	---	---	---
UHRF1BP1L	23074	broad.mit.edu	37	12	100480162	100480162	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100480162delA	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron|UHRF1BP1L_uc001tgp.2_Intron	NM_015054	NP_055869			UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2																		---	---	---	---
UHRF1BP1L	23074	broad.mit.edu	37	12	100530291	100530292	+	Intron	DEL	AT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100530291_100530292delAT	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron	NM_015054	NP_055869			UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	100543206	100543206	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100543206delT								UHRF1BP1L (6564 upstream) : GOLGA2B (6989 downstream)																																			---	---	---	---
DEPDC4	120863	broad.mit.edu	37	12	100643546	100643549	+	Intron	DEL	TGAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100643546_100643549delTGAG	uc001thh.1	-							NM_152317				DEP domain containing 4						intracellular signal transduction						0																		---	---	---	---
ANO4	121601	broad.mit.edu	37	12	101476739	101476739	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101476739delT	uc010svm.1	+						ANO4_uc001thw.2_Intron|ANO4_uc001thx.2_Intron|ANO4_uc001thy.2_Intron	NM_178826	NP_849148			anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6															HNSCC(74;0.22)			---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101736966	101736967	+	Intron	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101736966_101736967insG	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	101858224	101858224	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101858224delG								ARL1 (56652 upstream) : SPIC (10975 downstream)																																			---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102044242	102044243	+	Intron	INS	-	ACAT	ACAT	rs146182270	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102044242_102044243insACAT	uc001tii.2	+						MYBPC1_uc001tif.1_Intron|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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	103354501	103354502	+	IGR	DEL	TA	-	-	rs71303529		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103354501_103354502delTA								ASCL1 (214 upstream) : C12orf42 (276868 downstream)																																			---	---	---	---
C12orf42	374470	broad.mit.edu	37	12	103854062	103854062	+	Intron	DEL	G	-	-	rs34042722		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103854062delG	uc001tjt.2	-						C12orf42_uc001tjs.2_Intron|C12orf42_uc009zuf.1_Intron|C12orf42_uc001tju.2_Intron	NM_198521	NP_940923			hypothetical protein LOC374470											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	106003920	106003921	+	IGR	INS	-	CA	CA	rs140532310	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106003920_106003921insCA								C12orf75 (238625 upstream) : NUAK1 (453204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106594130	106594131	+	IGR	INS	-	C	C	rs57104622		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106594130_106594131insC								NUAK1 (60319 upstream) : CKAP4 (37529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	108647167	108647168	+	IGR	DEL	TC	-	-	rs151129717		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108647167_108647168delTC								WSCD2 (2856 upstream) : CMKLR1 (34654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	108891817	108891817	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108891817delA								CMKLR1 (158723 upstream) : FICD (17234 downstream)																																			---	---	---	---
USP30	84749	broad.mit.edu	37	12	109493981	109493983	+	Intron	DEL	TTG	-	-	rs139998701		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109493981_109493983delTTG	uc010sxi.1	+						USP30_uc001tnu.3_Intron	NM_032663	NP_116052			ubiquitin specific peptidase 30						ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial outer membrane	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(1)	1																		---	---	---	---
ACACB	32	broad.mit.edu	37	12	109557705	109557705	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109557705delA	uc001tob.2	+							NM_001093	NP_001084			acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
MYO1H	283446	broad.mit.edu	37	12	109866611	109866611	+	Intron	DEL	T	-	-	rs56809636		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109866611delT	uc010sxn.1	+							NM_001101421	NP_001094891			myosin 1H							myosin complex	motor activity				0																OREG0022104	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C12orf76	400073	broad.mit.edu	37	12	110504501	110504502	+	Intron	INS	-	A	A	rs147005035	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110504501_110504502insA	uc001tqd.1	-						C12orf76_uc001tqe.1_Intron|C12orf76_uc010sxx.1_5'Flank|uc001tqf.1_Intron	NM_207435	NP_997318			hypothetical protein LOC400073											large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	110517862	110517863	+	IGR	DEL	GA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110517862_110517863delGA								C12orf76 (6423 upstream) : IFT81 (44277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	110687292	110687292	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110687292delT								IFT81 (30693 upstream) : ATP2A2 (31740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	111431542	111431542	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111431542delA								MYL2 (73138 upstream) : CUX2 (40287 downstream)																																			---	---	---	---
FAM109A	144717	broad.mit.edu	37	12	111808743	111808743	+	5'Flank	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111808743delA	uc001tsd.3	-						FAM109A_uc009zvu.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																		---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	111939698	111939699	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111939698_111939699insT	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron	NM_002973	NP_002964			ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2																		---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	111978501	111978501	+	Intron	DEL	T	-	-	rs34545475		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111978501delT	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																		---	---	---	---
RPH3A	22895	broad.mit.edu	37	12	113052326	113052326	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113052326delA	uc010syl.1	+							NM_001143854	NP_001137326			rabphilin 3A homolog isoform 1						intracellular protein transport	cell junction|synaptic vesicle	Rab GTPase binding|transporter activity|zinc ion binding			ovary(3)|central_nervous_system(2)|skin(2)	7				BRCA - Breast invasive adenocarcinoma(302;0.00453)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	114046261	114046262	+	IGR	INS	-	T	T	rs11451839		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114046261_114046262insT								LHX5 (136384 upstream) : RBM19 (208281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114869631	114869632	+	IGR	INS	-	TG	TG	rs149179901	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114869631_114869632insTG								TBX5 (23384 upstream) : TBX3 (238427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114887980	114887982	+	IGR	DEL	ATG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114887980_114887982delATG								TBX5 (41733 upstream) : TBX3 (220077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115591843	115591843	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115591843delT								TBX3 (469874 upstream) : MED13L (804540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115787081	115787082	+	IGR	DEL	CT	-	-	rs147799369		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115787081_115787082delCT								TBX3 (665112 upstream) : MED13L (609301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	116181644	116181647	+	IGR	DEL	TGGA	-	-	rs112198645		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116181644_116181647delTGGA								None (None upstream) : MED13L (214736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	117070679	117070679	+	IGR	DEL	A	-	-	rs113957591		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117070679delA								MAP1LC3B2 (56254 upstream) : C12orf49 (82917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	117146438	117146439	+	IGR	DEL	CT	-	-	rs71442994		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117146438_117146439delCT								MAP1LC3B2 (132013 upstream) : C12orf49 (7157 downstream)																																			---	---	---	---
RNFT2	84900	broad.mit.edu	37	12	117273105	117273106	+	Intron	INS	-	CTC	CTC	rs10651412		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117273105_117273106insCTC	uc009zwn.2	+						RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron|RNFT2_uc001twc.3_Intron	NM_001109903	NP_001103373			transmembrane protein 118 isoform 1							integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)														---	---	---	---
FBXO21	23014	broad.mit.edu	37	12	117595441	117595443	+	Intron	DEL	ACT	-	-	rs11068378		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117595441_117595443delACT	uc001twk.2	-						FBXO21_uc001twj.2_Intron|FBXO21_uc009zwq.2_Intron|FBXO21_uc001twl.1_Intron	NM_033624	NP_296373			F-box only protein 21 isoform 1						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			kidney(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)														---	---	---	---
KSR2	283455	broad.mit.edu	37	12	117965106	117965107	+	Intron	DEL	AG	-	-	rs68177299		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117965106_117965107delAG	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	118770781	118770782	+	Intron	DEL	AC	-	-	rs72406347		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118770781_118770782delAC	uc001twx.2	-						TAOK3_uc001twy.3_Intron	NM_016281	NP_057365			TAO kinase 3						MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	119057492	119057493	+	IGR	INS	-	C	C	rs148290435		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119057492_119057493insC								SUDS3 (201653 upstream) : SRRM4 (361903 downstream)																																			---	---	---	---
CCDC60	160777	broad.mit.edu	37	12	119957682	119957683	+	Intron	DEL	TA	-	-	rs71900111	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119957682_119957683delTA	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)														---	---	---	---
CCDC64	92558	broad.mit.edu	37	12	120449588	120449589	+	Intron	INS	-	AT	AT	rs140344654	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120449588_120449589insAT	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)																	---	---	---	---
CABP1	9478	broad.mit.edu	37	12	121090166	121090167	+	Intron	INS	-	T	T	rs34224330		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121090166_121090167insT	uc001tyu.2	+						CABP1_uc001tyv.2_Intron|CABP1_uc001tyw.2_Intron	NM_001033677	NP_001028849			calcium binding protein 1 isoform 3							cell cortex|cell junction|Golgi apparatus|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|calcium-dependent protein binding|enzyme inhibitor activity|protein binding			central_nervous_system(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
CAMKK2	10645	broad.mit.edu	37	12	121690305	121690306	+	Intron	INS	-	CTGGTGATCCGC	CTGGTGATCCGC	rs146470009	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121690305_121690306insCTGGTGATCCGC	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_Intron|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)																	---	---	---	---
HPD	3242	broad.mit.edu	37	12	122302762	122302764	+	Intron	DEL	AAC	-	-	rs71453583		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122302762_122302764delAAC	uc001ubk.2	-							NM_002150	NP_002141			4-hydroxyphenylpyruvate dioxygenase						L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	4-hydroxyphenylpyruvate dioxygenase activity|metal ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)													---	---	---	---
BCL7A	605	broad.mit.edu	37	12	122465180	122465183	+	Intron	DEL	TTGT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122465180_122465183delTTGT	uc001ubp.2	+						BCL7A_uc001ubo.2_Intron	NM_001024808	NP_001019979			B-cell CLL/lymphoma 7A isoform b						negative regulation of transcription, DNA-dependent					ovary(1)|lung(1)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)				T	MYC	BNHL								---	---	---	---
PITPNM2	57605	broad.mit.edu	37	12	123614118	123614118	+	Intron	DEL	A	-	-	rs112969907		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123614118delA	uc001uek.1	-							NM_020845	NP_065896			phosphatidylinositol transfer protein,						metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124318321	124318322	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124318321_124318322insT	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	125168749	125168750	+	IGR	INS	-	T	T	rs112342078		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125168749_125168750insT								NCOR2 (116739 upstream) : SCARB1 (93425 downstream)																																			---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	125810215	125810218	+	5'Flank	DEL	CTGT	-	-	rs72371051		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125810215_125810218delCTGT	uc001uhe.1	+							NM_052907	NP_443139			transmembrane protein 132B							integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)														---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	125999793	125999796	+	Intron	DEL	CACA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125999793_125999796delCACA	uc001uhe.1	+							NM_052907	NP_443139			transmembrane protein 132B							integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	127566835	127566835	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127566835delT								LOC100128554 (609505 upstream) : None (None downstream)																																			---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	130208068	130208068	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130208068delT	uc009zyl.1	-							NM_133448	NP_597705			transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)														---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	130967413	130967414	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130967413_130967414delTG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	131744688	131744689	+	IGR	INS	-	GAGT	GAGT	rs143103988	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131744688_131744689insGAGT								LOC116437 (47213 upstream) : SFRS8 (450946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	131874396	131874397	+	IGR	INS	-	A	A	rs143800184	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131874396_131874397insA								LOC116437 (176921 upstream) : SFRS8 (321238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	131880275	131880280	+	IGR	DEL	TGATGG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131880275_131880280delTGATGG								LOC116437 (182800 upstream) : SFRS8 (315355 downstream)																																			---	---	---	---
SFRS8	6433	broad.mit.edu	37	12	132250360	132250361	+	Intron	INS	-	CTC	CTC	rs72528827	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132250360_132250361insCTC	uc001uja.1	+						SFRS8_uc010tbn.1_Intron|SFRS8_uc001ujb.1_Intron	NM_004592	NP_004583			splicing factor, arginine/serine-rich 8						mRNA splice site selection|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|RNA binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.44e-07)|Epithelial(86;2.94e-06)|all cancers(50;4.82e-05)														---	---	---	---
GALNT9	50614	broad.mit.edu	37	12	132815822	132815823	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132815822_132815823insT	uc001ukc.3	-						GALNT9_uc009zyr.2_Intron|GALNT9_uc001ukb.2_Intron	NM_001122636	NP_001116108			UDP-N-acetyl-alpha-D-galactosamine:polypeptide						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	133047340	133047345	+	IGR	DEL	ATGCAT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133047340_133047345delATGCAT								GALNT9 (141435 upstream) : FBRSL1 (19812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	133416543	133416544	+	IGR	INS	-	C	C	rs149468729	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133416543_133416544insC								GOLGA3 (11093 upstream) : CHFR (394 downstream)																																			---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19641870	19641871	+	Intron	INS	-	AC	AC	rs140275803	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19641870_19641871insAC	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19646950	19646950	+	Intron	DEL	T	-	-	rs36089073		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19646950delT	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19650308	19650308	+	Intron	DEL	G	-	-	rs77342385		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19650308delG	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20551636	20551637	+	Intron	INS	-	T	T	rs35672590		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20551636_20551637insT	uc001umr.2	+						ZMYM2_uc001umq.2_Intron|ZMYM2_uc001ums.2_Intron|ZMYM2_uc001umt.2_Intron|ZMYM2_uc009zzn.1_Intron|uc001umu.2_5'Flank	NM_003453	NP_003444			zinc finger protein 198						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)														---	---	---	---
IFT88	8100	broad.mit.edu	37	13	21232390	21232391	+	Intron	INS	-	A	A	rs138378465	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21232390_21232391insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	22049001	22049001	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22049001delT								ZDHHC20 (15578 upstream) : EFHA1 (17839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22347470	22347470	+	IGR	DEL	T	-	-	rs34759479		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22347470delT								FGF9 (68830 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22642835	22642835	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22642835delC	uc001uoi.2	+											Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	22876240	22876240	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22876240delA								FGF9 (597600 upstream) : SGCG (878820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23448271	23448272	+	IGR	INS	-	AA	AA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23448271_23448272insAA								None (None upstream) : SGCG (306788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23519545	23519546	+	IGR	INS	-	TA	TA	rs146669493	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23519545_23519546insTA								None (None upstream) : SGCG (235514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	25109369	25109370	+	IGR	INS	-	T	T	rs148887951	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25109369_25109370insT								PARP4 (22421 upstream) : LOC374491 (31641 downstream)																																			---	---	---	---
RNF17	56163	broad.mit.edu	37	13	25376818	25376820	+	Intron	DEL	GAA	-	-	rs5802306		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25376818_25376820delGAA	uc001upr.2	+						RNF17_uc010tdd.1_Intron|RNF17_uc010aab.2_Intron|RNF17_uc010tde.1_Intron|RNF17_uc001ups.2_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	25693622	25693625	+	IGR	DEL	TGTG	-	-	rs139047379		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25693622_25693625delTGTG								PABPC3 (20920 upstream) : FAM123A (49048 downstream)																																			---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26206021	26206021	+	Intron	DEL	A	-	-	rs68089743		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26206021delA	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	26276494	26276495	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26276494_26276495insT	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	26389172	26389172	+	Intron	DEL	A	-	-	rs77882497		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26389172delA	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron|ATP8A2_uc010aaj.1_Intron	NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	26695380	26695380	+	IGR	DEL	T	-	-	rs9581542	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26695380delT								SHISA2 (70182 upstream) : RNF6 (10873 downstream)																																			---	---	---	---
RNF6	6049	broad.mit.edu	37	13	26781367	26781368	+	Intron	INS	-	A	A	rs35773834		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26781367_26781368insA	uc001uqn.1	-											SubName: Full=RNF6 protein;						negative regulation of axon extension|positive regulation of transcription, DNA-dependent|protein K27-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|regulation of androgen receptor signaling pathway|ubiquitin-dependent protein catabolic process	axon|cytoplasm|PML body	androgen receptor binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	27609380	27609381	+	IGR	DEL	CA	-	-	rs71702032		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27609380_27609381delCA								GPR12 (274458 upstream) : USP12 (33057 downstream)																																			---	---	---	---
PAN3	255967	broad.mit.edu	37	13	28714074	28714076	+	Intron	DEL	TGT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28714074_28714076delTGT	uc010tdo.1	+							NM_175854	NP_787050			PABP1-dependent poly A-specific ribonuclease						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	29179147	29179147	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29179147delT								FLT1 (109882 upstream) : POMP (54094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	30553620	30553621	+	IGR	INS	-	T	T	rs139133865	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30553620_30553621insT								UBL3 (128800 upstream) : KATNAL1 (223147 downstream)																																			---	---	---	---
HSPH1	10808	broad.mit.edu	37	13	31733253	31733254	+	Intron	DEL	CA	-	-	rs144964137		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31733253_31733254delCA	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)														---	---	---	---
BRCA2	675	broad.mit.edu	37	13	32895956	32895956	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32895956delT	uc001uub.1	+						BRCA2_uc001uua.1_Intron	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	13	33362118	33362118	+	IGR	DEL	C	-	-	rs111932955		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33362118delC								PDS5B (9963 upstream) : KL (228083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	33401358	33401359	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33401358_33401359delTG								PDS5B (49203 upstream) : KL (188842 downstream)																																			---	---	---	---
STARD13	90627	broad.mit.edu	37	13	33792451	33792451	+	Intron	DEL	T	-	-	rs149113346		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33792451delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	34598466	34598467	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34598466_34598467delAC								RFC3 (57772 upstream) : NBEA (917989 downstream)																																			---	---	---	---
DCLK1	9201	broad.mit.edu	37	13	36386464	36386465	+	Intron	INS	-	A	A	rs147992911	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36386464_36386465insA	uc001uvf.2	-						DCLK1_uc001uve.3_Intron|DCLK1_uc010teh.1_Intron|DCLK1_uc010abk.2_Intron	NM_004734	NP_004725			doublecortin-like kinase 1						cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	37292925	37292926	+	IGR	INS	-	CACA	CACA	rs150493997	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37292925_37292926insCACA								C13orf36 (20952 upstream) : RFXAP (100413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37691251	37691251	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37691251delT								CSNK1A1L (11450 upstream) : POSTN (445469 downstream)																																			---	---	---	---
TRPC4	7223	broad.mit.edu	37	13	38410155	38410159	+	Intron	DEL	TGCTG	-	-	rs72268939		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38410155_38410159delTGCTG	uc001uws.2	-						TRPC4_uc001uwt.2_Intron|TRPC4_uc010tey.1_Intron|TRPC4_uc010abw.2_Intron|TRPC4_uc010abx.2_Intron|TRPC4_uc010aby.2_Intron	NM_016179	NP_057263			transient receptor potential cation channel,						axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	38737686	38737687	+	IGR	INS	-	GT	GT	rs151230957	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38737686_38737687insGT								TRPC4 (293747 upstream) : UFM1 (186255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	39235279	39235280	+	IGR	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39235279_39235280delCA								UFM1 (298137 upstream) : FREM2 (25893 downstream)																																			---	---	---	---
LHFP	10186	broad.mit.edu	37	13	40143286	40143289	+	Intron	DEL	GGAC	-	-	rs68124900	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40143286_40143289delGGAC	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								---	---	---	---
MTRF1	9617	broad.mit.edu	37	13	41810200	41810201	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41810200_41810201delCA	uc001uxx.2	-						MTRF1_uc001uxy.2_Intron|MTRF1_uc001uxz.2_Intron|MTRF1_uc010tff.1_Intron|MTRF1_uc001uyc.1_Intron|uc001uxv.1_RNA	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	42974145	42974146	+	IGR	DEL	TG	-	-	rs35031740		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42974145_42974146delTG								AKAP11 (76743 upstream) : TNFSF11 (162726 downstream)																																			---	---	---	---
DNAJC15	29103	broad.mit.edu	37	13	43681780	43681780	+	3'UTR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	44648030	44648031	+	IGR	INS	-	G	G	rs111249960		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44648030_44648031insG								LOC121838 (43432 upstream) : SERP2 (299947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	45295831	45295832	+	IGR	INS	-	G	G	rs144246416	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45295831_45295832insG								TSC22D1 (145130 upstream) : NUFIP1 (217552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	45376075	45376076	+	IGR	DEL	AG	-	-	rs147445661		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45376075_45376076delAG								TSC22D1 (225374 upstream) : NUFIP1 (137308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	45683550	45683551	+	IGR	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45683550_45683551delAG								KIAA1704 (75808 upstream) : GTF2F2 (11080 downstream)																																			---	---	---	---
C13orf18	80183	broad.mit.edu	37	13	47001168	47001169	+	Intron	INS	-	T	T	rs111701363		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47001168_47001169insT	uc001vbi.3	-							NM_025113	NP_079389			hypothetical protein LOC80183												0		Lung NSC(96;2.31e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;2.19e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	47536235	47536236	+	IGR	DEL	AA	-	-	rs72422303		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47536235_47536236delAA								HTR2A (65185 upstream) : SUCLA2 (980556 downstream)																																			---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	50908217	50908221	+	Intron	DEL	AACAA	-	-	rs142062058		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50908217_50908221delAACAA	uc010adl.1	+						DLEU1_uc001vee.1_Intron|DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron|uc001vek.1_Intron|uc001vel.1_Intron|uc001vem.1_Intron|uc001ven.1_Intron|uc001veo.1_Intron|uc001vep.1_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	51254635	51254640	+	IGR	DEL	CTCTCA	-	-	rs71807192		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51254635_51254640delCTCTCA								DLEU1 (151965 upstream) : DLEU7 (32119 downstream)																																			---	---	---	---
GUCY1B2	2974	broad.mit.edu	37	13	51593511	51593511	+	Intron	DEL	A	-	-	rs68148618		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51593511delA	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	52074221	52074222	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52074221_52074222delTT								INTS6 (46946 upstream) : WDFY2 (84262 downstream)																																			---	---	---	---
THSD1P1	374500	broad.mit.edu	37	13	52744597	52744598	+	Intron	INS	-	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52744597_52744598insC	uc001vgk.2	-						THSD1P1_uc001vgm.1_Intron|THSD1P1_uc010adx.1_Intron|THSD1P1_uc010ady.1_Intron|THSD1P1_uc001vgl.1_Intron					Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0																		---	---	---	---
LECT1	11061	broad.mit.edu	37	13	53315445	53315446	+	5'Flank	INS	-	T	T	rs142932209	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53315445_53315446insT	uc001vhf.2	-						LECT1_uc001vhg.2_5'Flank|LECT1_uc001vhh.2_5'Flank	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	53467585	53467586	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53467585_53467586insT								PCDH8 (44811 upstream) : OLFM4 (135386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	53720283	53720284	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53720283_53720284insA								OLFM4 (94097 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54236591	54236592	+	IGR	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54236591_54236592delCT								OLFM4 (610405 upstream) : MIR1297 (649515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54881539	54881542	+	IGR	DEL	AGAC	-	-	rs140121502		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54881539_54881542delAGAC								None (None upstream) : MIR1297 (4565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55512056	55512056	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55512056delG								MIR1297 (625873 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55678843	55678843	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55678843delG								MIR1297 (792660 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55818158	55818159	+	IGR	DEL	TA	-	-	rs150443861		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55818158_55818159delTA								MIR1297 (931975 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56282778	56282778	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56282778delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56528014	56528014	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56528014delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57501497	57501497	+	IGR	DEL	T	-	-	rs35849963		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57501497delT								None (None upstream) : PRR20C (213555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	58784441	58784441	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58784441delG								PCDH17 (481376 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	60117797	60117808	+	IGR	DEL	TAGGTAGGAAGC	-	-	rs143716183	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60117797_60117808delTAGGTAGGAAGC								None (None upstream) : DIAPH3 (121917 downstream)																																			---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60240492	60240492	+	3'UTR	DEL	A	-	-	rs68106632		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60240492delA	uc001vht.2	-	28					DIAPH3_uc001vhs.2_RNA	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	60515988	60515989	+	Intron	INS	-	A	A	rs143362125	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60515988_60515989insA	uc001vht.2	-						DIAPH3_uc001vhu.2_Intron|DIAPH3_uc001vhv.2_Intron	NM_001042517	NP_001035982			diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	60767403	60767404	+	IGR	INS	-	T	T	rs140491977		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60767403_60767404insT								DIAPH3 (29284 upstream) : TDRD3 (203187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	61200738	61200738	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61200738delT								TDRD3 (52726 upstream) : PCDH20 (783083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	62993420	62993420	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62993420delA								PCDH20 (991341 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63632524	63632527	+	IGR	DEL	TTTG	-	-	rs71734546		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63632524_63632527delTTTG								None (None upstream) : OR7E156P (679041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63635866	63635866	+	IGR	DEL	A	-	-	rs67882631		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63635866delA								None (None upstream) : OR7E156P (675702 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65282693	65282693	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65282693delT								OR7E156P (965992 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68648210	68648210	+	IGR	DEL	T	-	-	rs34493786		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68648210delT								PCDH9 (843742 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68684495	68684495	+	IGR	DEL	A	-	-	rs111445559		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68684495delA								PCDH9 (880027 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69467412	69467413	+	IGR	INS	-	TCTC	TCTC	rs148488114	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69467412_69467413insTCTC								None (None upstream) : KLHL1 (807313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69528083	69528084	+	IGR	INS	-	C	C	rs150058516	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69528083_69528084insC								None (None upstream) : KLHL1 (746642 downstream)																																			---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72291637	72291642	+	Intron	DEL	CACACA	-	-	rs138732310		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72291637_72291642delCACACA	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	72577228	72577231	+	IGR	DEL	TCTT	-	-	rs71710639		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72577228_72577231delTCTT								DACH1 (135898 upstream) : C13orf37 (705264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73736210	73736210	+	IGR	DEL	A	-	-	rs71990631		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73736210delA								KLF5 (84535 upstream) : KLF12 (523940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73842327	73842328	+	IGR	DEL	GT	-	-	rs111628699		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73842327_73842328delGT								KLF5 (190652 upstream) : KLF12 (417822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73966804	73966805	+	IGR	INS	-	G	G	rs76510242	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73966804_73966805insG								KLF5 (315129 upstream) : KLF12 (293345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73972702	73972702	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73972702delA								KLF5 (321027 upstream) : KLF12 (287448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75838112	75838113	+	IGR	DEL	TG	-	-	rs35457439		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75838112_75838113delTG								LOC647288 (23595 upstream) : TBC1D4 (20696 downstream)																																			---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76192418	76192418	+	5'Flank	DEL	G	-	-	rs34112227		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76192418delG	uc010thv.1	+							NM_005358	NP_005349			LIM domain only 7 isoform 1							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76221203	76221204	+	Intron	DEL	GT	-	-	rs35529765		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76221203_76221204delGT	uc010thv.1	+						LMO7_uc001vjt.1_Intron	NM_005358	NP_005349			LIM domain only 7 isoform 1							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	76445401	76445404	+	Intron	DEL	TCTC	-	-	rs71201200		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76445401_76445404delTCTC	uc001vjy.1	+											Homo sapiens cDNA FLJ35379 fis, clone SKMUS2006481.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	76609198	76609200	+	IGR	DEL	TCT	-	-	rs10543750		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76609198_76609200delTCT								LMO7 (175194 upstream) : KCTD12 (845104 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	76904079	76904082	+	IGR	DEL	ACAC	-	-	rs71773316		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76904079_76904082delACAC								LMO7 (470075 upstream) : KCTD12 (550222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77054627	77054628	+	IGR	DEL	AT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77054627_77054628delAT								LMO7 (620623 upstream) : KCTD12 (399676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77182457	77182458	+	IGR	DEL	TG	-	-	rs3037355		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77182457_77182458delTG								LMO7 (748453 upstream) : KCTD12 (271846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77554890	77554890	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77554890delA								BTF3L1 (51667 upstream) : CLN5 (11169 downstream)																																	OREG0022450	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	78515533	78515534	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78515533_78515534insA	uc001vkq.1	-						uc001vks.2_Intron	NM_000115	NP_000106			endothelin receptor type B isoform 1 precursor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction	integral to plasma membrane	endothelin-B receptor activity|peptide hormone binding				0		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)													---	---	---	---
EDNRB	1910	broad.mit.edu	37	13	78522498	78522498	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78522498delT	uc001vkq.1	-						uc001vks.2_Intron	NM_000115	NP_000106			endothelin receptor type B isoform 1 precursor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction	integral to plasma membrane	endothelin-B receptor activity|peptide hormone binding				0		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	78735849	78735851	+	Intron	DEL	CTC	-	-	rs75443520		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78735849_78735851delCTC	uc001vks.2	+						uc001vku.1_Intron					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	79243355	79243356	+	IGR	INS	-	A	A	rs145428988	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79243355_79243356insA								RNF219 (8655 upstream) : RBM26 (650744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79454567	79454568	+	IGR	DEL	GT	-	-	rs35196276		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79454567_79454568delGT								RNF219 (219867 upstream) : RBM26 (439532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80851975	80851975	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80851975delG								NDFIP2 (721770 upstream) : SPRY2 (58139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81857411	81857411	+	IGR	DEL	T	-	-	rs144244446		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81857411delT								SPRY2 (942325 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82175253	82175253	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82175253delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82193066	82193067	+	IGR	INS	-	CTCT	CTCT	rs139874101	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82193066_82193067insCTCT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82451554	82451555	+	IGR	INS	-	TG	TG	rs144615274	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82451554_82451555insTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83479535	83479535	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83479535delT								None (None upstream) : SLITRK1 (971809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83489340	83489341	+	IGR	INS	-	A	A	rs138008507	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83489340_83489341insA								None (None upstream) : SLITRK1 (962003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	84434513	84434520	+	IGR	DEL	TCTCTCTC	-	-	rs145404015	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84434513_84434520delTCTCTCTC								None (None upstream) : SLITRK1 (16824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	84839353	84839354	+	IGR	DEL	GT	-	-	rs72514320		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84839353_84839354delGT								SLITRK1 (382825 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85140495	85140496	+	IGR	DEL	GT	-	-	rs74102958		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85140495_85140496delGT								SLITRK1 (683967 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86093855	86093855	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86093855delA								None (None upstream) : SLITRK6 (273067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87616207	87616207	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87616207delC								None (None upstream) : SLITRK5 (708663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87767044	87767044	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87767044delT								None (None upstream) : SLITRK5 (557826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90780255	90780255	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90780255delT								None (None upstream) : MIR622 (103181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91447291	91447292	+	IGR	INS	-	TCTT	TCTT	rs142907748	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91447291_91447292insTCTT								MIR622 (563760 upstream) : LOC144776 (95916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91465554	91465554	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91465554delT								MIR622 (582023 upstream) : LOC144776 (77654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91536434	91536435	+	IGR	DEL	CA	-	-	rs151205100		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91536434_91536435delCA								MIR622 (652903 upstream) : LOC144776 (6773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91763440	91763440	+	IGR	DEL	A	-	-	rs11322457		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91763440delA								LOC144776 (184589 upstream) : MIR17HG (236634 downstream)																																			---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92154626	92154627	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92154626_92154627insT	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	92373221	92373222	+	Intron	INS	-	A	A	rs143670938	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92373221_92373222insA	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	92672739	92672740	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92672739_92672740insT	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	93330693	93330694	+	Intron	DEL	TC	-	-	rs75678180		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93330693_93330694delTC	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	93784896	93784896	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93784896delA								GPC5 (265411 upstream) : GPC6 (94182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	95163616	95163616	+	IGR	DEL	C	-	-	rs59066355		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95163616delC								DCT (31680 upstream) : TGDS (62693 downstream)																																			---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	97052567	97052568	+	Intron	INS	-	CG	CG			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97052567_97052568insCG	uc001vmw.2	+							NM_153456	NP_703157			heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)																	---	---	---	---
MBNL2	10150	broad.mit.edu	37	13	97977339	97977340	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97977339_97977340delCA	uc010aft.2	+						MBNL2_uc001vmz.2_Intron|MBNL2_uc001vna.2_Intron|MBNL2_uc001vnb.2_Intron|MBNL2_uc010tij.1_Intron	NM_144778	NP_659002			muscleblind-like 2 isoform 1						mRNA processing|regulation of RNA splicing|RNA splicing	cytoplasm|nucleus	RNA binding|zinc ion binding				0	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)															---	---	---	---
MBNL2	10150	broad.mit.edu	37	13	97986050	97986052	+	Intron	DEL	CTT	-	-	rs79934162		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97986050_97986052delCTT	uc010aft.2	+						MBNL2_uc001vmz.2_Intron|MBNL2_uc001vna.2_Intron|MBNL2_uc001vnb.2_Intron|MBNL2_uc010tij.1_Intron	NM_144778	NP_659002			muscleblind-like 2 isoform 1						mRNA processing|regulation of RNA splicing|RNA splicing	cytoplasm|nucleus	RNA binding|zinc ion binding				0	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	98058521	98058522	+	IGR	INS	-	A	A	rs9516924	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98058521_98058522insA								MBNL2 (12149 upstream) : RAP2A (27953 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98505045	98505047	+	IGR	DEL	GAT	-	-	rs34544811		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98505045_98505047delGAT								RAP2A (384794 upstream) : IPO5 (100882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	99273946	99273946	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99273946delT								STK24 (44550 upstream) : SLC15A1 (62111 downstream)																																			---	---	---	---
PCCA	5095	broad.mit.edu	37	13	101045360	101045360	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101045360delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	101467662	101467663	+	IGR	INS	-	A	A	rs35311830		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101467662_101467663insA								TMTC4 (140559 upstream) : NALCN (238467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	103649502	103649502	+	IGR	DEL	T	-	-	rs66892796		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103649502delT								LOC121952 (101119 upstream) : SLC10A2 (46848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107097081	107097081	+	IGR	DEL	T	-	-	rs75978886	byFrequency;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107097081delT								DAOA (953699 upstream) : EFNB2 (45017 downstream)																																			---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	108347146	108347146	+	Intron	DEL	T	-	-	rs113861895		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108347146delT	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	108638471	108638472	+	IGR	INS	-	G	G	rs72523059		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108638471_108638472insG								FAM155A (119011 upstream) : LIG4 (221322 downstream)																																			---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109287287	109287289	+	Intron	DEL	AAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109287287_109287289delAAC	uc001vqt.1	+						MYO16_uc010agk.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	112537752	112537753	+	IGR	DEL	AA	-	-	rs34780298		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112537752_112537753delAA								C13orf16 (541159 upstream) : SOX1 (184160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112918010	112918010	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112918010delA								SOX1 (191990 upstream) : C13orf28 (112659 downstream)																																			---	---	---	---
TUBGCP3	10426	broad.mit.edu	37	13	113231638	113231638	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113231638delT	uc001vse.1	-						TUBGCP3_uc010tjq.1_Intron|TUBGCP3_uc001vsf.2_Intron|TUBGCP3_uc001vsg.1_Intron	NM_006322	NP_006313			tubulin, gamma complex associated protein 3						G2/M transition of mitotic cell cycle|microtubule nucleation|single fertilization	centriole|cytosol|polar microtubule	gamma-tubulin binding|structural constituent of cytoskeleton			central_nervous_system(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)																	---	---	---	---
TUBGCP3	10426	broad.mit.edu	37	13	113233471	113233472	+	Intron	INS	-	AC	AC	rs148691239	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113233471_113233472insAC	uc001vse.1	-						TUBGCP3_uc010tjq.1_Intron|TUBGCP3_uc001vsf.2_Intron|TUBGCP3_uc001vsg.1_Intron	NM_006322	NP_006313			tubulin, gamma complex associated protein 3						G2/M transition of mitotic cell cycle|microtubule nucleation|single fertilization	centriole|cytosol|polar microtubule	gamma-tubulin binding|structural constituent of cytoskeleton			central_nervous_system(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)																	---	---	---	---
C13orf35	400165	broad.mit.edu	37	13	113324890	113324890	+	Intron	DEL	T	-	-	rs72336281		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113324890delT	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)															---	---	---	---
MCF2L	23263	broad.mit.edu	37	13	113706778	113706778	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113706778delG	uc001vsu.2	+						MCF2L_uc001vsq.2_Intron|MCF2L_uc010tjr.1_Intron|MCF2L_uc001vsr.2_Intron|MCF2L_uc001vss.3_Intron|MCF2L_uc010tjs.1_Intron|MCF2L_uc001vst.1_Intron	NM_001112732	NP_001106203			MCF.2 cell line derived transforming						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)																---	---	---	---
Unknown	0	broad.mit.edu	37	13	114025755	114025755	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114025755delC								GRTP1 (7292 upstream) : ADPRHL1 (50505 downstream)																																			---	---	---	---
TFDP1	7027	broad.mit.edu	37	13	114256247	114256280	+	Intron	DEL	CTGAGAGGAGGACAGAGCTACTCCCTCTGTAGCC	-	-	rs146831541	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114256247_114256280delCTGAGAGGAGGACAGAGCTACTCCCTCTGTAGCC	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)			---	---	---	---
FAM70B	348013	broad.mit.edu	37	13	114460419	114460420	+	5'Flank	INS	-	TA	TA	rs35232490		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114460419_114460420insTA	uc001vuh.2	+						FAM70B_uc010tkh.1_5'Flank	NM_182614	NP_872420			family with sequence similarity 70, member B							integral to membrane					0	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.123)|all_epithelial(44;0.133)	all cancers(43;0.181)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	19746140	19746141	+	IGR	INS	-	G	G	rs145273571	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19746140_19746141insG								POTEG (161198 upstream) : P704P (237813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	20122482	20122482	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20122482delA								P704P (102210 upstream) : OR4Q3 (93105 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	21047061	21047061	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21047061delA								RNASE9 (17971 upstream) : RNASE11 (3993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	21324484	21324484	+	IGR	DEL	T	-	-	rs71416985		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21324484delT								RNASE1 (53448 upstream) : RNASE3 (35078 downstream)																																			---	---	---	---
HNRNPC	3183	broad.mit.edu	37	14	21687889	21687889	+	Intron	DEL	T	-	-	rs79242792		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21687889delT	uc001vzy.2	-						HNRNPC_uc001vzw.2_Intron|HNRNPC_uc001wad.2_Intron|HNRNPC_uc001vzx.2_Intron|HNRNPC_uc001vzz.2_Intron|HNRNPC_uc001waa.2_Intron|HNRNPC_uc010ail.2_Intron|HNRNPC_uc010tlq.1_Intron|HNRNPC_uc001wab.2_Intron|HNRNPC_uc001wac.2_Intron|HNRNPC_uc010tlr.1_Intron|HNRNPC_uc001waf.2_Intron|HNRNPC_uc001wae.2_Intron	NM_031314	NP_112604			heterogeneous nuclear ribonucleoprotein C							catalytic step 2 spliceosome|nucleoplasm	identical protein binding|nucleotide binding|RNA binding				0	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22443706	22443706	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22443706delT	uc001wbw.2	+						uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22519261	22519261	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22519261delG	uc001wbw.2	+						uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
RBM23	55147	broad.mit.edu	37	14	23385468	23385469	+	Intron	INS	-	T	T	rs143433642		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23385468_23385469insT	uc001whg.2	-						RBM23_uc001whh.2_Intron|RBM23_uc001whi.2_Intron|RBM23_uc010tne.1_Intron|RBM23_uc001whj.2_Intron|RBM23_uc001whk.1_Intron	NM_001077351	NP_001070819			RNA binding motif protein 23 isoform 1						mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	24862224	24862225	+	IGR	INS	-	TT	TT	rs138569002	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24862224_24862225insTT								NFATC4 (13416 upstream) : NYNRIN (5767 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	25254061	25254062	+	IGR	INS	-	GGTAGATACCTTACTTA	GGTAGATACCTTACTTA	rs142662007	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25254061_25254062insGGTAGATACCTTACTTA								GZMB (150629 upstream) : STXBP6 (27246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26120938	26120939	+	IGR	INS	-	AT	AT	rs149951184	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26120938_26120939insAT								STXBP6 (601767 upstream) : NOVA1 (794151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26149199	26149199	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26149199delT								STXBP6 (630028 upstream) : NOVA1 (765891 downstream)																																			---	---	---	---
NOVA1	4857	broad.mit.edu	37	14	27047562	27047562	+	Intron	DEL	T	-	-	rs76526958		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27047562delT	uc001wpy.2	-						NOVA1_uc001wpz.2_Intron|NOVA1_uc001wqa.2_Intron|NOVA1_uc001wqb.2_Intron	NM_002515	NP_002506			neuro-oncological ventral antigen 1 isoform 1						locomotory behavior|RNA splicing|synaptic transmission	nucleus	RNA binding			skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1)	5				GBM - Glioblastoma multiforme(265;0.0135)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	28313957	28313958	+	IGR	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28313957_28313958insG								None (None upstream) : FOXG1 (922329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28316686	28316687	+	IGR	DEL	TA	-	-	rs141366767	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28316686_28316687delTA								None (None upstream) : FOXG1 (919600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28587760	28587760	+	IGR	DEL	T	-	-	rs151200452		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28587760delT								None (None upstream) : FOXG1 (648527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	29563870	29563871	+	IGR	DEL	GT	-	-	rs56760137		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29563870_29563871delGT								C14orf23 (299871 upstream) : PRKD1 (481818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	30459655	30459656	+	IGR	INS	-	TA	TA	rs147514720	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30459655_30459656insTA								PRKD1 (62756 upstream) : G2E3 (568673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	30579651	30579652	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30579651_30579652insA								PRKD1 (182752 upstream) : G2E3 (448677 downstream)																																			---	---	---	---
G2E3	55632	broad.mit.edu	37	14	31074079	31074082	+	Intron	DEL	TTCA	-	-	rs5807591		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31074079_31074082delTTCA	uc001wqk.2	+						G2E3_uc010tpe.1_Intron|G2E3_uc010tpf.1_Intron	NM_017769	NP_060239			G2/M-phase specific E3 ubiquitin ligase						apoptosis|multicellular organismal development|protein modification process	Golgi apparatus|nucleolus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	31282679	31282680	+	IGR	INS	-	G	G	rs148418021	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31282679_31282680insG								SCFD1 (77661 upstream) : COCH (61061 downstream)																																			---	---	---	---
AP4S1	11154	broad.mit.edu	37	14	31512431	31512432	+	Intron	INS	-	AA	AA	rs114924988	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31512431_31512432insAA	uc001wqy.3	+						AP4S1_uc001wqw.3_Intron|AP4S1_uc001wqx.3_Intron|AP4S1_uc010amh.2_Intron|AP4S1_uc001wqz.3_Intron	NM_001128126	NP_001121598			adaptor-related protein complex 4, sigma 1							coated pit|Golgi apparatus	protein transporter activity				0	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.221)	GBM - Glioblastoma multiforme(265;0.00553)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	32402296	32402297	+	IGR	INS	-	TAAA	TAAA	rs138895246	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32402296_32402297insTAAA								NUBPL (71879 upstream) : C14orf128 (142329 downstream)																																			---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	34145188	34145188	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34145188delA	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	34256252	34256252	+	Intron	DEL	C	-	-	rs36008876		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34256252delC	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	34718210	34718210	+	IGR	DEL	T	-	-	rs66513841		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34718210delT								EGLN3 (297923 upstream) : C14orf147 (183935 downstream)																																			---	---	---	---
BAZ1A	11177	broad.mit.edu	37	14	35261712	35261712	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35261712delT	uc001wsk.2	-						BAZ1A_uc001wsl.2_Intron	NM_013448	NP_038476			bromodomain adjacent to zinc finger domain, 1A						chromatin remodeling|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ACF complex	zinc ion binding			lung(2)|central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	7	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	36388643	36388644	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36388643_36388644delAC								BRMS1L (47475 upstream) : MBIP (379120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	36522106	36522107	+	IGR	DEL	TG	-	-	rs66704646		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36522106_36522107delTG								BRMS1L (180938 upstream) : MBIP (245657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	38316600	38316600	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38316600delT	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38655555	38655555	+	IGR	DEL	A	-	-	rs75001309		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38655555delA								FOXA1 (591066 upstream) : SSTR1 (21649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	38699963	38699963	+	IGR	DEL	A	-	-	rs33938897		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38699963delA								SSTR1 (17695 upstream) : CLEC14A (23356 downstream)																																			---	---	---	---
CTAGE5	4253	broad.mit.edu	37	14	39756070	39756073	+	Intron	DEL	TGTG	-	-	rs71435636		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39756070_39756073delTGTG	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	39941174	39941175	+	IGR	INS	-	A	A	rs144372462	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39941174_39941175insA								FBXO33 (39470 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44018101	44018102	+	IGR	DEL	AG	-	-	rs72381444		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44018101_44018102delAG								None (None upstream) : FSCB (955253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44506098	44506098	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44506098delC								None (None upstream) : FSCB (467257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	45156918	45156918	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45156918delA								FSCB (180419 upstream) : C14orf28 (209589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	45969234	45969234	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45969234delT								C14orf106 (246629 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46757346	46757346	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46757346delT								None (None upstream) : RPL10L (362876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46985752	46985772	+	IGR	DEL	AAAGTTTTAGGATACAAAATA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46985752_46985772delAAAGTTTTAGGATACAAAATA								None (None upstream) : RPL10L (134450 downstream)																																			---	---	---	---
MDGA2	161357	broad.mit.edu	37	14	48032930	48032930	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48032930delT	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	48326611	48326612	+	IGR	INS	-	T	T	rs35859220		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48326611_48326612insT								MDGA2 (182623 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	49739470	49739471	+	IGR	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49739470_49739471delTC								None (None upstream) : SDCCAG1 (293556 downstream)																																			---	---	---	---
TRIM9	114088	broad.mit.edu	37	14	51472729	51472730	+	Intron	INS	-	CAA	CAA	rs140362042	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51472729_51472730insCAA	uc001wyx.3	-						TRIM9_uc001wyy.2_Intron|TRIM9_uc001wyz.3_Intron	NM_015163	NP_055978			tripartite motif protein 9 isoform 1						proteasomal ubiquitin-dependent protein catabolic process	cell junction|cytoskeleton|dendrite|synaptic vesicle	protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			skin(2)|lung(1)	3	all_epithelial(31;0.00418)|Breast(41;0.148)																	---	---	---	---
TRIM9	114088	broad.mit.edu	37	14	51539710	51539711	+	Intron	INS	-	T	T	rs148057036	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51539710_51539711insT	uc001wyx.3	-						TRIM9_uc001wyy.2_Intron|TRIM9_uc001wyz.3_Intron	NM_015163	NP_055978			tripartite motif protein 9 isoform 1						proteasomal ubiquitin-dependent protein catabolic process	cell junction|cytoskeleton|dendrite|synaptic vesicle	protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			skin(2)|lung(1)	3	all_epithelial(31;0.00418)|Breast(41;0.148)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	51635570	51635571	+	IGR	INS	-	C	C	rs143209327	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51635570_51635571insC								TRIM9 (73148 upstream) : TMX1 (71315 downstream)																																			---	---	---	---
GNG2	54331	broad.mit.edu	37	14	52311232	52311233	+	5'Flank	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52311232_52311233delTG	uc001wzh.2	+											Homo sapiens guanine nucleotide binding protein gamma 2 (GNG2) mRNA, complete cds.						cellular response to glucagon stimulus|energy reserve metabolic process|platelet activation|synaptic transmission	heterotrimeric G-protein complex	protein binding|signal transducer activity				0	all_epithelial(31;0.0659)|Breast(41;0.0684)				Halothane(DB01159)													---	---	---	---
GNG2	54331	broad.mit.edu	37	14	52426452	52426453	+	Intron	INS	-	TTGC	TTGC	rs75585414		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52426452_52426453insTTGC	uc001wzi.2	+						GNG2_uc001wzh.2_Intron|GNG2_uc010aoc.1_Intron|GNG2_uc001wzj.2_Intron|GNG2_uc001wzk.2_Intron	NM_053064	NP_444292			guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|platelet activation|synaptic transmission	heterotrimeric G-protein complex	protein binding|signal transducer activity				0	all_epithelial(31;0.0659)|Breast(41;0.0684)				Halothane(DB01159)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	52704324	52704324	+	IGR	DEL	C	-	-	rs71291811		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52704324delC								NID2 (168378 upstream) : PTGDR (30107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	52714008	52714009	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52714008_52714009insA								NID2 (178062 upstream) : PTGDR (20422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	53726031	53726031	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53726031delT								DDHD1 (105985 upstream) : BMP4 (690426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54362888	54362888	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54362888delT								DDHD1 (742842 upstream) : BMP4 (53569 downstream)																																			---	---	---	---
SAMD4A	23034	broad.mit.edu	37	14	55175997	55176000	+	Intron	DEL	AAAC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55175997_55176000delAAAC	uc001xbb.2	+						SAMD4A_uc001xbc.2_Intron|SAMD4A_uc001xbf.1_Intron	NM_015589	NP_056404			sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	56017469	56017470	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56017469_56017470delAC								TBPL2 (110206 upstream) : C14orf33 (7220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56329938	56329939	+	IGR	INS	-	TTT	TTT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56329938_56329939insTTT								C14orf34 (66546 upstream) : PELI2 (255154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	57892108	57892109	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57892108_57892109insT								NAA30 (12641 upstream) : C14orf105 (44486 downstream)																																			---	---	---	---
KIAA0586	9786	broad.mit.edu	37	14	58903071	58903071	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58903071delA	uc001xdv.3	+						KIAA0586_uc010trr.1_Intron|KIAA0586_uc001xdt.3_Intron|KIAA0586_uc001xdu.3_Intron|KIAA0586_uc010trs.1_Intron	NM_014749	NP_055564			talpid3 protein											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	59605427	59605428	+	IGR	INS	-	A	A	rs144411593	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59605427_59605428insA								DACT1 (490391 upstream) : DAAM1 (49971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	60770696	60770697	+	IGR	INS	-	TG	TG	rs149055727	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60770696_60770697insTG								PPM1A (4893 upstream) : C14orf39 (131978 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	62044966	62044971	+	Intron	DEL	CATCAT	-	-	rs68036425		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62044966_62044971delCATCAT	uc001xfp.2	+											Homo sapiens cDNA: FLJ22447 fis, clone HRC09479.																														---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63955695	63955695	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63955695delA	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron|PPP2R5E_uc001xgg.3_Intron	NM_006246	NP_006237			epsilon isoform of regulatory subunit B56,						signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64448080	64448081	+	Intron	INS	-	TA	TA	rs149771149	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64448080_64448081insTA	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	64623179	64623179	+	Intron	DEL	T	-	-	rs35788698		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64623179delT	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron|SYNE2_uc010apy.2_Intron|SYNE2_uc001xgn.2_Intron|SYNE2_uc001xgo.2_Intron|SYNE2_uc001xgp.2_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	64830317	64830318	+	IGR	INS	-	AAG	AAG	rs144833378	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64830317_64830318insAAG								ESR2 (25049 upstream) : MTHFD1 (24441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	65349877	65349877	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65349877delA								SPTB (3276 upstream) : CHURC1 (31263 downstream)																																			---	---	---	---
FUT8	2530	broad.mit.edu	37	14	66106976	66106977	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66106976_66106977insA	uc001xin.2	+						FUT8_uc001xio.2_Intron|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Intron|FUT8_uc001xiq.2_Intron	NM_178155	NP_835368			fucosyltransferase 8 isoform a						in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	66896638	66896638	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66896638delT								FUT8 (686677 upstream) : C14orf53 (56471 downstream)																																			---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68921775	68921776	+	Intron	INS	-	AC	AC	rs148675602	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68921775_68921776insAC	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193			RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)				T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
Unknown	0	broad.mit.edu	37	14	69315417	69315418	+	IGR	INS	-	CT	CT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69315417_69315418insCT								C14orf181 (52227 upstream) : ACTN1 (25423 downstream)																																			---	---	---	---
MAP3K9	4293	broad.mit.edu	37	14	71267150	71267150	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71267150delA	uc001xmm.2	-						MAP3K9_uc001xml.2_Intron	NM_033141	NP_149132			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			stomach(2)|lung(1)|central_nervous_system(1)|skin(1)	5				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	71289173	71289199	+	IGR	DEL	CCCTCTCCTCCCGCTCTCTCTCGCTCT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71289173_71289199delCCCTCTCCTCCCGCTCTCTCTCGCTCT								MAP3K9 (13285 upstream) : PCNX (84923 downstream)																																			---	---	---	---
DPF3	8110	broad.mit.edu	37	14	73251666	73251666	+	Intron	DEL	A	-	-	rs79145311		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73251666delA	uc001xnc.2	-						DPF3_uc001xnf.2_Intron|DPF3_uc010ari.1_Intron|DPF3_uc010ttq.1_Intron	NM_012074	NP_036206			D4, zinc and double PHD fingers, family 3						chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)														---	---	---	---
MLH3	27030	broad.mit.edu	37	14	75494724	75494724	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75494724delA	uc001xrd.1	-						MLH3_uc001xre.1_Intron|MLH3_uc010tuy.1_Intron	NM_001040108	NP_001035197			mutL homolog 3 isoform 1						mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00688)									MMR					---	---	---	---
Unknown	0	broad.mit.edu	37	14	75978994	75978994	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75978994delT								JDP2 (39592 upstream) : BATF (9790 downstream)																																			---	---	---	---
BATF	10538	broad.mit.edu	37	14	75989564	75989565	+	Intron	INS	-	AG	AG	rs112858666		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75989564_75989565insAG	uc001xrr.2	+							NM_006399	NP_006390			basic leucine zipper transcription factor,							nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.028)														---	---	---	---
FLVCR2	55640	broad.mit.edu	37	14	76091577	76091578	+	Intron	DEL	AT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76091577_76091578delAT	uc001xrs.2	+						FLVCR2_uc010tvd.1_Intron	NM_017791	NP_060261			feline leukemia virus subgroup C cellular						transmembrane transport	integral to membrane|plasma membrane	heme binding|heme transporter activity				0				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
ESRRB	2103	broad.mit.edu	37	14	76905310	76905310	+	Intron	DEL	T	-	-	rs112501536		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76905310delT	uc001xsq.1	+						ESRRB_uc001xsr.2_Intron|ESRRB_uc001xso.2_Intron	NM_004452	NP_004443			estrogen-related receptor beta							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.0213)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	77060490	77060491	+	IGR	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77060490_77060491delTC								ESRRB (92312 upstream) : VASH1 (167744 downstream)																																			---	---	---	---
ADCK1	57143	broad.mit.edu	37	14	78306681	78306681	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78306681delT	uc001xui.2	+						ADCK1_uc010tvo.1_Intron|ADCK1_uc001xuj.2_Intron	NM_020421	NP_065154			aarF domain containing kinase 1 isoform a							extracellular region	ATP binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79303835	79303836	+	Intron	INS	-	T	T	rs112707584	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79303835_79303836insT	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)														---	---	---	---
STON2	85439	broad.mit.edu	37	14	81821334	81821334	+	Intron	DEL	A	-	-	rs59397507	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81821334delA	uc010tvu.1	-						STON2_uc001xvk.1_Intron	NM_033104	NP_149095			stonin 2						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			skin(3)|pancreas(2)	5				BRCA - Breast invasive adenocarcinoma(234;0.0348)														---	---	---	---
STON2	85439	broad.mit.edu	37	14	81851197	81851197	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81851197delT	uc010tvu.1	-						STON2_uc001xvk.1_Intron	NM_033104	NP_149095			stonin 2						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			skin(3)|pancreas(2)	5				BRCA - Breast invasive adenocarcinoma(234;0.0348)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	81907496	81907497	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81907496_81907497delAC								STON2 (13748 upstream) : SEL1L (31743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83415886	83415886	+	IGR	DEL	T	-	-	rs35122263		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83415886delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84980213	84980213	+	IGR	DEL	A	-	-	rs75084799		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84980213delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85316227	85316228	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85316227_85316228insT								None (None upstream) : FLRT2 (680260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86447367	86447368	+	IGR	INS	-	AC	AC	rs148368770	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86447367_86447368insAC								FLRT2 (353098 upstream) : None (None downstream)																																			---	---	---	---
FOXN3	1112	broad.mit.edu	37	14	89736141	89736142	+	Intron	DEL	TA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89736141_89736142delTA	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940			checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3																		---	---	---	---
FOXN3	1112	broad.mit.edu	37	14	89991639	89991639	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89991639delG	uc001xxo.3	-						FOXN3_uc010atk.2_Intron|FOXN3_uc001xxp.2_Intron	NM_001085471	NP_001078940			checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3																		---	---	---	---
PSMC1	5700	broad.mit.edu	37	14	90731688	90731689	+	Intron	DEL	AA	-	-	rs34260220		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90731688_90731689delAA	uc001xyf.2	+						PSMC1_uc001xyg.2_Intron|PSMC1_uc001xyh.2_Intron|PSMC1_uc010twh.1_Intron	NM_002802	NP_002793			proteasome 26S ATPase subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding				0		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)														---	---	---	---
CALM1	801	broad.mit.edu	37	14	90866907	90866907	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90866907delG	uc001xyl.1	+						CALM1_uc010atq.1_Intron|CALM1_uc010atr.1_Intron|CALM1_uc001xym.1_Intron	NM_006888	NP_008819			calmodulin 1 isoform 1						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			central_nervous_system(1)	1		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.208)	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)													---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92503090	92503091	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92503090_92503091insA	uc001xzy.2	-						TRIP11_uc001xzz.3_Intron	NM_004239	NP_004230			thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)				T	PDGFRB	AML								---	---	---	---
RIN3	79890	broad.mit.edu	37	14	93128068	93128069	+	Intron	INS	-	CACA	CACA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93128068_93128069insCACA	uc001yap.2	+						RIN3_uc010auk.2_Intron|RIN3_uc001yaq.2_Intron|RIN3_uc001yas.1_Intron	NM_024832	NP_079108			Ras and Rab interactor 3						endocytosis|signal transduction	cytoplasmic membrane-bounded vesicle|early endosome	GTPase activator activity|Ras GTPase binding			lung(2)|ovary(1)	3		all_cancers(154;0.0701)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	93162170	93162170	+	IGR	DEL	T	-	-	rs72464736		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93162170delT								RIN3 (6838 upstream) : LGMN (7987 downstream)																																			---	---	---	---
PRIMA1	145270	broad.mit.edu	37	14	94214269	94214270	+	Intron	INS	-	A	A	rs142888025		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94214269_94214270insA	uc001ybw.1	-						PRIMA1_uc001ybx.1_Intron	NM_178013	NP_821092			proline rich membrane anchor 1 precursor						neurotransmitter catabolic process	cell junction|integral to membrane|synapse				large_intestine(1)|skin(1)	2		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)														---	---	---	---
C14orf48	256369	broad.mit.edu	37	14	94476535	94476536	+	Intron	INS	-	TGTT	TGTT	rs144478472	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94476535_94476536insTGTT	uc010twp.1	+							NR_024183				Homo sapiens cDNA FLJ40422 fis, clone TESTI2038858.												0				Epithelial(152;0.114)|all cancers(159;0.191)|COAD - Colon adenocarcinoma(157;0.208)														---	---	---	---
SERPINA12	145264	broad.mit.edu	37	14	94983291	94983292	+	Intron	DEL	CA	-	-	rs34263790		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94983291_94983292delCA	uc001ydj.2	-							NM_173850	NP_776249			serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			central_nervous_system(2)|ovary(1)|lung(1)	4				COAD - Colon adenocarcinoma(157;0.235)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	95284737	95284738	+	IGR	INS	-	AAA	AAA	rs149629103	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95284737_95284738insAAA								GSC (48238 upstream) : DICER1 (267827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	95958111	95958111	+	IGR	DEL	A	-	-	rs34866057		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95958111delA								C14orf49 (15938 upstream) : SNHG10 (41142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	96659235	96659236	+	IGR	INS	-	G	G	rs145775716	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96659235_96659236insG								C14orf132 (99102 upstream) : BDKRB2 (11899 downstream)																																			---	---	---	---
AK7	122481	broad.mit.edu	37	14	96865314	96865314	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96865314delT	uc001yfn.2	+						AK7_uc001yfm.1_3'UTR	NM_152327	NP_689540			adenylate kinase 7						cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	97436545	97436546	+	IGR	INS	-	CA	CA	rs141929238	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97436545_97436546insCA								VRK1 (88595 upstream) : C14orf64 (955401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	97638367	97638367	+	IGR	DEL	T	-	-	rs67517374		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97638367delT								VRK1 (290417 upstream) : C14orf64 (753580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98071520	98071521	+	IGR	INS	-	A	A	rs139803246		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98071520_98071521insA								VRK1 (723570 upstream) : C14orf64 (320426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98588775	98588776	+	IGR	INS	-	C	C	rs148064216	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98588775_98588776insC								C14orf64 (144314 upstream) : C14orf177 (589174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99370179	99370180	+	IGR	DEL	AC	-	-	rs150976480		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99370179_99370180delAC								C14orf177 (186082 upstream) : BCL11B (265447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99856634	99856635	+	IGR	DEL	AT	-	-	rs138490637		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99856634_99856635delAT								BCL11B (118812 upstream) : SETD3 (7449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	100092602	100092603	+	IGR	INS	-	GT	GT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100092602_100092603insGT								CCDC85C (21875 upstream) : HHIPL1 (18877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	100434243	100434243	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100434243delA								EML1 (25850 upstream) : EVL (3908 downstream)																																			---	---	---	---
WDR25	79446	broad.mit.edu	37	14	100950801	100950802	+	Intron	DEL	GT	-	-	rs72256910		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100950801_100950802delGT	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	100982330	100982331	+	Intron	INS	-	T	T	rs143630748		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100982330_100982331insT	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)																---	---	---	---
DYNC1H1	1778	broad.mit.edu	37	14	102451773	102451773	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102451773delT	uc001yks.2	+							NM_001376	NP_001367			cytoplasmic dynein 1 heavy chain 1						cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10																		---	---	---	---
MARK3	4140	broad.mit.edu	37	14	103887238	103887239	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103887238_103887239insT	uc001ymz.3	+						MARK3_uc001ymx.3_Intron|MARK3_uc001ymw.3_Intron|MARK3_uc001yna.3_Intron|MARK3_uc001ymy.3_Intron|MARK3_uc010awp.2_Intron	NM_001128918	NP_001122390			MAP/microtubule affinity-regulating kinase 3								ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	104826157	104826157	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104826157delG								KIF26A (178923 upstream) : C14orf180 (219899 downstream)																																			---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106252850	106252850	+	Intron	DEL	A	-	-	rs35328557		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106252850delA	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106726434	106726437	+	Intron	DEL	TATC	-	-	rs72146561		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106726434_106726437delTATC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106741371	106741371	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106741371delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107017875	107017876	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107017875_107017876insT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107161217	107161218	+	Intron	INS	-	T	T	rs111686343		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107161217_107161218insT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	20438899	20438900	+	IGR	DEL	TT	-	-	rs113721779		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20438899_20438900delTT								None (None upstream) : GOLGA6L6 (298194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20527129	20527130	+	IGR	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20527129_20527130delCT								None (None upstream) : GOLGA6L6 (209964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22535656	22535656	+	IGR	DEL	A	-	-	rs112331509		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22535656delA								MIR1268 (22376 upstream) : GOLGA8DP (166629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	23758263	23758264	+	IGR	DEL	GC	-	-	rs139524188		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23758263_23758264delGC								GOLGA8E (309840 upstream) : MKRN3 (52190 downstream)																																			---	---	---	---
PWRN2	791115	broad.mit.edu	37	15	24411003	24411004	+	RNA	DEL	AA	-	-	rs148691390		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-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																		---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25138847	25138847	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25138847delA	uc001ywp.1	+						SNRPN_uc001ywq.1_Intron|SNRPN_uc001ywr.1_Intron|SNRPN_uc001yws.1_Intron|SNRPN_uc001ywt.1_Intron	NM_022807	NP_073718			small nuclear ribonucleoprotein polypeptide N						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)										Prader-Willi_syndrome				---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	26810315	26810316	+	Intron	INS	-	TGA	TGA	rs149411177	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26810315_26810316insTGA	uc001zaz.2	-						GABRB3_uc010uae.1_Intron|GABRB3_uc001zba.2_Intron|GABRB3_uc001zbb.2_Intron	NM_000814	NP_000805			gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	26956058	26956059	+	Intron	DEL	TC	-	-	rs113429228		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26956058_26956059delTC	uc001zaz.2	-						GABRB3_uc001zba.2_Intron|GABRB3_uc001zbb.2_Intron	NM_000814	NP_000805			gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27485488	27485488	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27485488delG	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	27509097	27509101	+	Intron	DEL	AAAAG	-	-	rs149474765		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27509097_27509101delAAAAG	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	28700320	28700320	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28700320delG								GOLGA8G (63149 upstream) : WHAMML2 (282409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	28759400	28759401	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28759400_28759401delTT								GOLGA8G (122229 upstream) : WHAMML2 (223328 downstream)																																			---	---	---	---
APBA2	321	broad.mit.edu	37	15	29388288	29388288	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29388288delT	uc001zck.2	+						APBA2_uc010azj.2_Intron|APBA2_uc010uat.1_Intron|APBA2_uc001zcl.2_Intron|APBA2_uc001zcm.1_Intron	NM_005503	NP_005494			amyloid beta A4 precursor protein-binding,						nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)														---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29677738	29677738	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29677738delC	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	30127853	30127854	+	IGR	INS	-	A	A	rs150099460	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30127853_30127854insA								TJP1 (13147 upstream) : FAM7A3 (268081 downstream)																																			---	---	---	---
DKFZP434L187	26082	broad.mit.edu	37	15	30618413	30618414	+	Intron	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30618413_30618414delCT	uc001zds.2	+											Homo sapiens cDNA FLJ43588 fis, clone SKNSH2009991.												0																		---	---	---	---
MTMR15	22909	broad.mit.edu	37	15	31218673	31218675	+	Intron	DEL	ATG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31218673_31218675delATG	uc001zff.2	+						MTMR15_uc001zfe.2_Intron	NM_014967	NP_055782			myotubularin related protein 15 isoform a						double-strand break repair via homologous recombination|nucleotide-excision repair, DNA incision	nucleus	5'-3' exonuclease activity|5'-flap endonuclease activity|DNA binding|magnesium ion binding|phosphodiesterase I activity|ubiquitin binding				0		all_lung(180;2.23e-09)		all cancers(64;4.72e-15)|Epithelial(43;5.4e-11)|GBM - Glioblastoma multiforme(186;0.000136)|BRCA - Breast invasive adenocarcinoma(123;0.00402)|Lung(196;0.168)									Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
Unknown	0	broad.mit.edu	37	15	31427208	31427208	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31427208delA								TRPM1 (33284 upstream) : KLF13 (191875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	32201956	32201956	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32201956delT								OTUD7A (38964 upstream) : CHRNA7 (120770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	32235391	32235392	+	IGR	INS	-	A	A	rs147411963	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32235391_32235392insA								OTUD7A (72399 upstream) : CHRNA7 (87334 downstream)																																			---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33208872	33208872	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33208872delA	uc001zhf.3	-							NM_001103184	NP_001096654			formin 1						actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33674394	33674395	+	Intron	INS	-	A	A	rs148503658	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33674394_33674395insA	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	34215937	34215937	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34215937delA	uc001zhj.2	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	35424688	35424689	+	IGR	DEL	AC	-	-	rs34188660		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35424688_35424689delAC								ZNF770 (144234 upstream) : LOC723972 (104838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	35632455	35632464	+	IGR	DEL	TTTGAGCCTA	-	-	rs111947134		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35632455_35632464delTTTGAGCCTA								LOC723972 (102193 upstream) : ATPBD4 (30707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	36505021	36505021	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36505021delA								ATPBD4 (666617 upstream) : C15orf41 (366791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	36864258	36864258	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36864258delG								None (None upstream) : C15orf41 (7554 downstream)																																			---	---	---	---
MEIS2	4212	broad.mit.edu	37	15	37197235	37197236	+	Intron	INS	-	TG	TG	rs149657801	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37197235_37197236insTG	uc001zjr.2	-						MEIS2_uc001zjl.2_Intron|MEIS2_uc010ucj.1_Intron|MEIS2_uc001zjm.2_Intron|MEIS2_uc001zjn.2_Intron|MEIS2_uc001zjo.2_Intron|MEIS2_uc001zjp.2_Intron|MEIS2_uc001zjs.2_Intron|MEIS2_uc001zju.2_Intron|MEIS2_uc001zjt.2_Intron	NM_170675	NP_733775			Meis homeobox 2 isoform c						negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)	2		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	37668579	37668580	+	IGR	DEL	AT	-	-	rs147690701		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37668579_37668580delAT								MEIS2 (275079 upstream) : TMCO5A (558247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	37835436	37835439	+	IGR	DEL	GAAA	-	-	rs140319787		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37835436_37835439delGAAA								MEIS2 (441936 upstream) : TMCO5A (391388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	37907400	37907400	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37907400delA								MEIS2 (513900 upstream) : TMCO5A (319427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38348904	38348905	+	IGR	INS	-	CA	CA	rs148725375	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38348904_38348905insCA								TMCO5A (88979 upstream) : SPRED1 (196147 downstream)																																			---	---	---	---
RASGRP1	10125	broad.mit.edu	37	15	38834417	38834417	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38834417delA	uc001zke.3	-						RASGRP1_uc001zkd.3_Intron	NM_005739	NP_005730			RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	38865322	38865323	+	IGR	DEL	TG	-	-	rs35134214		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38865322_38865323delTG								RASGRP1 (8315 upstream) : C15orf53 (123476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39028345	39028348	+	IGR	DEL	CTCC	-	-	rs149222451	byFrequency	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39028345_39028348delCTCC								C15orf53 (36106 upstream) : C15orf54 (514537 downstream)																																			---	---	---	---
GPR176	11245	broad.mit.edu	37	15	40156665	40156666	+	Intron	DEL	CT	-	-	rs143217463		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40156665_40156666delCT	uc001zkj.1	-						GPR176_uc001zkk.1_Intron	NM_007223	NP_009154			G protein-coupled receptor 176						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	40605563	40605564	+	IGR	INS	-	T	T	rs35027211		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40605563_40605564insT								PLCB2 (5389 upstream) : C15orf52 (18090 downstream)																																			---	---	---	---
CASC5	57082	broad.mit.edu	37	15	40931970	40931970	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40931970delA	uc010bbs.1	+						CASC5_uc010bbt.1_Intron	NM_170589	NP_733468			cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)														---	---	---	---
RTF1	23168	broad.mit.edu	37	15	41736918	41736918	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41736918delT	uc001zny.2	+							NM_015138	NP_055953			Paf1/RNA polymerase II complex component						histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	42424462	42424462	+	IGR	DEL	C	-	-	rs34083840		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42424462delC								PLA2G4D (37710 upstream) : PLA2G4F (8937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	43000878	43000878	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43000878delT	uc010udj.1	+						uc010bcw.2_Intron					Homo sapiens mRNA for KIAA1300 protein, partial cds.																														---	---	---	---
TTBK2	146057	broad.mit.edu	37	15	43078331	43078332	+	Intron	INS	-	A	A	rs148720042		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43078331_43078332insA	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771			tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)														---	---	---	---
TP53BP1	7158	broad.mit.edu	37	15	43759725	43759726	+	Intron	INS	-	T	T	rs149317825	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43759725_43759726insT	uc001zrs.2	-						TP53BP1_uc010udp.1_Intron|TP53BP1_uc001zrq.3_Intron|TP53BP1_uc001zrr.3_Intron|TP53BP1_uc010udq.1_Intron	NM_005657	NP_005648			tumor protein p53 binding protein 1 isoform 3						double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)									Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					---	---	---	---
TP53BP1	7158	broad.mit.edu	37	15	43760859	43760860	+	Intron	INS	-	TATT	TATT	rs146000996	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43760859_43760860insTATT	uc001zrs.2	-						TP53BP1_uc010udp.1_Intron|TP53BP1_uc001zrq.3_Intron|TP53BP1_uc001zrr.3_Intron|TP53BP1_uc010udq.1_Intron	NM_005657	NP_005648			tumor protein p53 binding protein 1 isoform 3						double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)									Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					---	---	---	---
CASC4	113201	broad.mit.edu	37	15	44688707	44688707	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44688707delG	uc001zto.1	+						CASC4_uc001ztp.2_Intron|CASC4_uc001ztq.2_Intron	NM_138423	NP_612432			cancer susceptibility candidate 4 isoform a							integral to membrane				ovary(1)	1		all_cancers(109;1.69e-13)|all_epithelial(112;3.94e-11)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.027)		all cancers(107;2.91e-20)|GBM - Glioblastoma multiforme(94;1.57e-06)|COAD - Colon adenocarcinoma(120;0.217)|Colorectal(105;0.237)														---	---	---	---
CTDSPL2	51496	broad.mit.edu	37	15	44800543	44800543	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44800543delA	uc001ztr.2	+						CTDSPL2_uc001zts.2_Intron|CTDSPL2_uc001ztt.2_Intron|CTDSPL2_uc010bdv.2_Intron	NM_016396	NP_057480			CTD (carboxy-terminal domain, RNA polymerase II,								phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)														---	---	---	---
EIF3J	8669	broad.mit.edu	37	15	44835921	44835921	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44835921delT	uc001ztv.2	+						EIF3J_uc010ueg.1_Intron|EIF3J_uc001ztw.2_Intron	NM_003758	NP_003749			eukaryotic translation initiation factor 3,							cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity				0		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	46305115	46305116	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46305115_46305116insT								SQRDL (321637 upstream) : None (None downstream)																																			---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	47518946	47518947	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47518946_47518947insA	uc001zvw.2	+							NM_020858	NP_065909			semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)														---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	47781855	47781855	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47781855delT	uc001zvw.2	+							NM_020858	NP_065909			semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)														---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	47935197	47935198	+	Intron	DEL	GA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47935197_47935198delGA	uc001zvw.2	+							NM_020858	NP_065909			semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	49397399	49397399	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49397399delA								SECISBP2L (58769 upstream) : COPS2 (20074 downstream)																																			---	---	---	---
USP50	373509	broad.mit.edu	37	15	50797990	50797990	+	Intron	DEL	T	-	-	rs138285017	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50797990delT	uc001zyq.3	-							NM_203494	NP_987090			ubiquitin specific protease 50						ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			lung(1)|breast(1)	2				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)														---	---	---	---
TRPM7	54822	broad.mit.edu	37	15	50948502	50948503	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50948502_50948503insT	uc001zyt.3	-						TRPM7_uc010bew.1_Intron	NM_017672	NP_060142			transient receptor potential cation channel,						cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity			ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1)	10				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)														---	---	---	---
TNFAIP8L3	388121	broad.mit.edu	37	15	51376380	51376381	+	Intron	INS	-	GT	GT	rs149474014	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51376380_51376381insGT	uc001zyy.2	-							NM_207381	NP_997264			tumor necrosis factor, alpha-induced protein												0				all cancers(107;0.000389)|GBM - Glioblastoma multiforme(94;0.00338)														---	---	---	---
MYO5C	55930	broad.mit.edu	37	15	52533944	52533945	+	Intron	INS	-	GA	GA	rs143153658	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52533944_52533945insGA	uc010bff.2	-						MYO5C_uc010uga.1_Intron|MYO5C_uc010ugb.1_Intron	NM_018728	NP_061198			myosin VC							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)														---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54367059	54367059	+	Intron	DEL	T	-	-	rs35476938		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54367059delT	uc002ack.2	+							NM_001080534	NP_001074003			unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	54973305	54973305	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54973305delT								UNC13C (52500 upstream) : RSL24D1 (500216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	56055548	56055548	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56055548delA								PRTG (20371 upstream) : NEDD4 (63583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	56095735	56095736	+	IGR	INS	-	TC	TC	rs143405112	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56095735_56095736insTC								PRTG (60558 upstream) : NEDD4 (23395 downstream)																																			---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57329632	57329633	+	Intron	INS	-	AAAC	AAAC	rs149616566	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57329632_57329633insAAAC	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron	NM_207038	NP_996921			transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)				T	TEC	extraskeletal myxoid chondrosarcoma								---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57538219	57538220	+	Intron	INS	-	A	A	rs146116134	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57538219_57538220insA	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_5'Flank|TCF12_uc010ugq.1_5'Flank	NM_207038	NP_996921			transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)				T	TEC	extraskeletal myxoid chondrosarcoma								---	---	---	---
Unknown	0	broad.mit.edu	37	15	57874769	57874769	+	IGR	DEL	G	-	-	rs34160979		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57874769delG								CGNL1 (31849 upstream) : GCOM1 (9345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	58038101	58038107	+	IGR	DEL	GCATCAG	-	-	rs67714812		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58038101_58038107delGCATCAG								GCOM1 (28349 upstream) : ALDH1A2 (207521 downstream)																																			---	---	---	---
ADAM10	102	broad.mit.edu	37	15	58916181	58916182	+	Intron	INS	-	A	A	rs34638861		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58916181_58916182insA	uc002afd.1	-						ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron|ADAM10_uc002aff.1_5'Flank	NM_001110	NP_001101			ADAM metallopeptidase domain 10 precursor						cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)														---	---	---	---
ADAM10	102	broad.mit.edu	37	15	59007614	59007614	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59007614delA	uc002afd.1	-						ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron|ADAM10_uc002afg.2_Intron	NM_001110	NP_001101			ADAM metallopeptidase domain 10 precursor						cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	59685000	59685000	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59685000delA								MYO1E (19929 upstream) : FAM81A (45372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	60050674	60050674	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60050674delT								BNIP2 (69032 upstream) : FOXB1 (245747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	60329917	60329918	+	IGR	INS	-	AC	AC	rs56736736		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60329917_60329918insAC								FOXB1 (1509 upstream) : ANXA2 (309433 downstream)																																			---	---	---	---
RORA	6095	broad.mit.edu	37	15	60998905	60998905	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60998905delT	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	61300403	61300406	+	Intron	DEL	TGTG	-	-	rs12900169		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61300403_61300406delTGTG	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	61310671	61310671	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61310671delA	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	61402245	61402246	+	Intron	DEL	CA	-	-	rs146215616		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61402245_61402246delCA	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	62413825	62413826	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62413825_62413826insT								C2CD4A (50716 upstream) : C2CD4B (41911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	63252863	63252863	+	IGR	DEL	C	-	-	rs34644444		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63252863delC								TLN2 (116036 upstream) : TPM1 (81975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	63776633	63776641	+	IGR	DEL	ATGCCTGTA	-	-	rs145029213		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63776633_63776641delATGCCTGTA								CA12 (102558 upstream) : USP3 (20169 downstream)																																			---	---	---	---
HERC1	8925	broad.mit.edu	37	15	64127624	64127626	+	5'Flank	DEL	AAC	-	-	rs10571496		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64127624_64127626delAAC	uc002amp.2	-						HERC1_uc010uil.1_5'Flank|HERC1_uc010bgt.1_5'Flank|HERC1_uc002amq.1_5'Flank	NM_003922	NP_003913			hect domain and RCC1-like domain 1						protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	65171261	65171261	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65171261delG								PLEKHO2 (11062 upstream) : ANKDD1A (32840 downstream)																																			---	---	---	---
ANKDD1A	348094	broad.mit.edu	37	15	65246090	65246091	+	Intron	INS	-	TTCTTC	TTCTTC	rs149246295	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65246090_65246091insTTCTTC	uc002aoa.2	+						ANKDD1A_uc002aoc.2_Intron|ANKDD1A_uc010bha.2_Intron	NM_182703	NP_874362			ankyrin repeat and death domain containing 1A						signal transduction					ovary(1)	1																		---	---	---	---
ANKDD1A	348094	broad.mit.edu	37	15	65247184	65247185	+	Intron	INS	-	CTT	CTT	rs141456893	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65247184_65247185insCTT	uc002aoa.2	+						ANKDD1A_uc002aoc.2_Intron|ANKDD1A_uc010bha.2_Intron	NM_182703	NP_874362			ankyrin repeat and death domain containing 1A						signal transduction					ovary(1)	1																		---	---	---	---
MEGF11	84465	broad.mit.edu	37	15	66273477	66273478	+	Intron	INS	-	AA	AA	rs143332772	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66273477_66273478insAA	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821			multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1																OREG0023199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MEGF11	84465	broad.mit.edu	37	15	66482187	66482188	+	Intron	INS	-	T	T	rs72570661		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66482187_66482188insT	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821			multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1																		---	---	---	---
MAP2K5	5607	broad.mit.edu	37	15	67844647	67844647	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67844647delC	uc002aqu.2	+						MAP2K5_uc002aqt.1_Intron|MAP2K5_uc002aqv.2_Intron|MAP2K5_uc010ujw.1_Intron	NM_145160	NP_660143			mitogen-activated protein kinase kinase 5						nerve growth factor receptor signaling pathway		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	68255671	68255674	+	IGR	DEL	TTTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68255671_68255674delTTTC								LBXCOR1 (129497 upstream) : PIAS1 (90898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	68845689	68845690	+	IGR	INS	-	T	T	rs72531966		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68845689_68845690insT								ITGA11 (121197 upstream) : CORO2B (25883 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70490624	70490625	+	IGR	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70490624_70490625delCA								TLE3 (100368 upstream) : UACA (456270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70594996	70594999	+	IGR	DEL	ATGG	-	-	rs112069030		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70594996_70594999delATGG								TLE3 (204740 upstream) : UACA (351896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70595691	70595709	+	IGR	DEL	TGGATGGGTGGATATGAGA	-	-	rs78894967		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70595691_70595709delTGGATGGGTGGATATGAGA								TLE3 (205435 upstream) : UACA (351186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70741560	70741567	+	IGR	DEL	GGAGAGAT	-	-	rs146732507	by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70741560_70741567delGGAGAGAT								TLE3 (351304 upstream) : UACA (205328 downstream)																																			---	---	---	---
LRRC49	54839	broad.mit.edu	37	15	71314956	71314956	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71314956delA	uc002asw.2	+						LRRC49_uc002asu.2_Intron|LRRC49_uc002asx.2_Intron|LRRC49_uc010ukf.1_Intron|LRRC49_uc002asy.2_Intron|LRRC49_uc002asz.2_Intron	NM_017691	NP_060161			leucine rich repeat containing 49							cytoplasm|microtubule				ovary(1)	1																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71824420	71824423	+	Intron	DEL	AGTA	-	-	rs75078467		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71824420_71824423delAGTA	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
PARP6	56965	broad.mit.edu	37	15	72553348	72553349	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72553348_72553349insA	uc002auc.2	-						PARP6_uc002aua.2_Intron|PARP6_uc002aub.2_Intron|PARP6_uc002aud.3_Intron|PARP6_uc002auf.1_Intron	NM_020214	NP_064599			poly (ADP-ribose) polymerase family, member 6								NAD+ ADP-ribosyltransferase activity				0																		---	---	---	---
BBS4	585	broad.mit.edu	37	15	73000901	73000902	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73000901_73000902insA	uc002avb.2	+						BBS4_uc010ukv.1_Intron|BBS4_uc002avc.2_Intron|BBS4_uc002avd.2_Intron	NM_033028	NP_149017			Bardet-Biedl syndrome 4						adult behavior|brain morphogenesis|cell cycle cytokinesis|centrosome organization|cerebral cortex development|convergent extension involved in gastrulation|dendrite development|fat cell differentiation|heart looping|hippocampus development|intracellular transport|maintenance of protein location in nucleus|melanosome transport|microtubule anchoring at centrosome|neural tube closure|nonmotile primary cilium assembly|photoreceptor cell maintenance|pigment granule aggregation in cell center|positive regulation of flagellum assembly|regulation of cilium beat frequency involved in ciliary motility|regulation of cytokinesis|regulation of lipid metabolic process|retina homeostasis|retinal rod cell development|sensory perception of smell|sensory processing|spermatid development|striatum development	BBSome|centriolar satellite|centriole|cilium membrane|microtubule basal body|motile cilium|nonmotile primary cilium|nucleus|pericentriolar material	alpha-tubulin binding|beta-tubulin binding|dynactin binding|microtubule motor activity				0														Bardet-Biedl_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	15	73092499	73092500	+	IGR	DEL	TG	-	-	rs149303720		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73092499_73092500delTG								ADPGK (15832 upstream) : NEO1 (252375 downstream)																																			---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73450257	73450257	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73450257delA	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	73504109	73504109	+	Intron	DEL	A	-	-	rs148286130		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73504109delA	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																		---	---	---	---
NPTN	27020	broad.mit.edu	37	15	73898067	73898068	+	Intron	INS	-	A	A	rs144893768		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73898067_73898068insA	uc002avs.2	-						NPTN_uc010bjc.2_Intron|NPTN_uc002avt.2_Intron|NPTN_uc002avr.2_Intron|NPTN_uc010ula.1_Intron	NM_012428	NP_036560			neuroplastin isoform b precursor						elevation of cytosolic calcium ion concentration|homophilic cell adhesion|long-term synaptic potentiation|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of long-term neuronal synaptic plasticity|positive regulation of neuron projection development|positive regulation of protein phosphorylation	integral to membrane|plasma membrane|presynaptic membrane	cell adhesion molecule binding|type 1 fibroblast growth factor receptor binding				0																		---	---	---	---
CD276	80381	broad.mit.edu	37	15	73999304	73999305	+	Intron	INS	-	T	T	rs138988783	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73999304_73999305insT	uc002avv.1	+						CD276_uc010bjd.1_Intron|CD276_uc002avu.1_Intron|CD276_uc002avw.1_Intron|CD276_uc010ulb.1_Intron|CD276_uc002avx.2_Intron	NM_001024736	NP_001019907			CD276 antigen isoform a						cell proliferation|immune response|positive regulation of interferon-gamma biosynthetic process|positive regulation of T cell proliferation|regulation of immune response|T cell activation	external side of plasma membrane|integral to membrane	receptor binding			skin(1)	1																		---	---	---	---
GOLGA6A	342096	broad.mit.edu	37	15	74377791	74377791	+	5'Flank	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74377791delA	uc002axa.1	-							NM_001038640	NP_001033729			golgi autoantigen, golgin subfamily a, 6												0																		---	---	---	---
DNM1P35	100128285	broad.mit.edu	37	15	76024223	76024224	+	Intron	DEL	CT	-	-	rs35247110		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76024223_76024224delCT	uc002bay.1	-											Homo sapiens cDNA FLJ33925 fis, clone CTONG2017292.												0																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76852404	76852404	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76852404delT	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	77199950	77199951	+	5'Flank	INS	-	AA	AA	rs34445565		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77199950_77199951insAA	uc002bbz.1	-						SCAPER_uc002bca.1_5'Flank|SCAPER_uc002bcb.1_5'Flank|SCAPER_uc002bcc.1_5'Flank	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																		---	---	---	---
DNAJA4	55466	broad.mit.edu	37	15	78571323	78571324	+	Intron	INS	-	A	A	rs144577472	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78571323_78571324insA	uc002bdj.1	+						DNAJA4_uc002bdi.2_Intron|DNAJA4_uc002bdk.2_Intron|DNAJA4_uc002bdm.1_Intron	NM_001130182	NP_001123654			DnaJ (Hsp40) homolog, subfamily A, member 4						protein folding|response to heat	membrane	ATP binding|heat shock protein binding|metal ion binding|unfolded protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	79477728	79477731	+	IGR	DEL	CTTG	-	-	rs146430112		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79477728_79477731delCTTG								RASGRF1 (94513 upstream) : MIR184 (24399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	79910525	79910525	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79910525delT								KIAA1024 (145883 upstream) : MTHFS (226795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80559653	80559676	+	Intron	DEL	TGGGTCAGGACGGGTGCCTCTGCC	-	-	rs113616682		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80559653_80559676delTGGGTCAGGACGGGTGCCTCTGCC	uc002bfo.2	-											Homo sapiens cDNA FLJ40463 fis, clone TESTI2042149.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	80570418	80570419	+	Intron	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80570418_80570419delAG	uc002bfo.2	-											Homo sapiens cDNA FLJ40463 fis, clone TESTI2042149.																														---	---	---	---
ARNT2	9915	broad.mit.edu	37	15	80709896	80709897	+	Intron	INS	-	TT	TT	rs139540445	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80709896_80709897insTT	uc002bfr.2	+						ARNT2_uc002bfq.2_Intron	NM_014862	NP_055677			aryl hydrocarbon receptor nuclear translocator						central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	84063020	84063021	+	IGR	INS	-	AGGG	AGGG	rs59433795	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84063020_84063021insAGGG								BNC1 (109552 upstream) : SH3GL3 (53070 downstream)																																			---	---	---	---
UBE2Q2P1	388165	broad.mit.edu	37	15	85077360	85077360	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85077360delA	uc002bkn.1	-							NR_003661				Homo sapiens cDNA FLJ43276 fis, clone KIDNE2011532, moderately similar to Homo sapiens melanoma-associated chondroitin sulfate proteoglycan 4.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	85795076	85795077	+	IGR	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85795076_85795077delTG								PDE8A (112706 upstream) : AKAP13 (128794 downstream)																																			---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	85988303	85988303	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85988303delA	uc002blv.1	+						AKAP13_uc002bls.2_Intron|AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron	NM_007200	NP_009131			A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	86589547	86589548	+	IGR	INS	-	GAA	GAA	rs145729348	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86589547_86589548insGAA								KLHL25 (251358 upstream) : AGBL1 (95694 downstream)																																			---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	87361789	87361789	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87361789delG	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	87461021	87461021	+	Intron	DEL	G	-	-	rs11322762		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87461021delG	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	88407792	88407792	+	5'Flank	DEL	A	-	-	rs35064447		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88407792delA	uc002bmd.2	-											Homo sapiens cDNA FLJ37610 fis, clone BRCOC2011398.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	88916764	88916764	+	IGR	DEL	T	-	-	rs34425412		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88916764delT								NTRK3 (117103 upstream) : MRPL46 (85944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	89127721	89127721	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89127721delA								DET1 (37809 upstream) : MIR1179 (23617 downstream)																																			---	---	---	---
HAPLN3	145864	broad.mit.edu	37	15	89439936	89439937	+	5'Flank	INS	-	GTGT	GTGT	rs138542989	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89439936_89439937insGTGT	uc002bnc.2	-						HAPLN3_uc002bne.2_5'Flank|HAPLN3_uc002bnd.2_5'Flank	NM_178232	NP_839946			hyaluronan and proteoglycan link protein 3						cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding				0	Lung NSC(78;0.0392)|all_lung(78;0.077)																	---	---	---	---
Unknown	0	broad.mit.edu	37	15	90001772	90001773	+	IGR	INS	-	A	A	rs144090323	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90001772_90001773insA								LOC254559 (60054 upstream) : RHCG (12865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	92860451	92860451	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92860451delC								SLCO3A1 (144786 upstream) : ST8SIA2 (76689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	93363439	93363439	+	IGR	DEL	C	-	-	rs8182061	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93363439delC								FAM174B (86135 upstream) : CHD2 (65994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	94122109	94122109	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94122109delT								RGMA (489676 upstream) : MCTP2 (652692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95400195	95400196	+	IGR	INS	-	AAAA	AAAA	rs144881114		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95400195_95400196insAAAA								MCTP2 (373015 upstream) : LOC145820 (576126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97910740	97910741	+	IGR	INS	-	AAG	AAG	rs141971488	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97910740_97910741insAAG								SPATA8 (581896 upstream) : LOC91948 (375105 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97947963	97947964	+	IGR	INS	-	CTAT	CTAT	rs146651245	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97947963_97947964insCTAT								SPATA8 (619119 upstream) : LOC91948 (337882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98906457	98906460	+	IGR	DEL	AGAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98906457_98906460delAGAA								ARRDC4 (389390 upstream) : FAM169B (73931 downstream)																																			---	---	---	---
FAM169B	283777	broad.mit.edu	37	15	98980907	98980920	+	3'UTR	DEL	GGATGACGGATGGA	-	-	rs58790202		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98980907_98980920delGGATGACGGATGGA	uc002buk.1	-	7						NM_182562	NP_872368			hypothetical protein LOC283777												0																		---	---	---	---
MEF2A	4205	broad.mit.edu	37	15	100147680	100147680	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100147680delT	uc002bve.2	+						MEF2A_uc010urv.1_Intron|MEF2A_uc010bos.2_Intron|MEF2A_uc002bvf.2_Intron|MEF2A_uc002bvg.2_Intron|MEF2A_uc002bvi.2_Intron	NM_001130926	NP_001124398			myocyte enhancer factor 2A isoform 2						apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development	nuclear chromatin|nucleoplasm	activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding			ovary(1)	1	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)															---	---	---	---
RAB11FIP3	9727	broad.mit.edu	37	16	507512	507512	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:507512delT	uc002chf.2	+							NM_014700	NP_055515			rab11-family interacting protein 3 isoform 1						cell cycle|cytokinesis|endocytic recycling|protein transport	centrosome|cleavage furrow|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		Hepatocellular(16;0.0218)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	896911	896912	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:896911_896912insA								PRR25 (33051 upstream) : LMF1 (6723 downstream)																																			---	---	---	---
LMF1	64788	broad.mit.edu	37	16	909247	909247	+	Intron	DEL	C	-	-	rs67965864		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:909247delC	uc002ckj.2	-						LMF1_uc010brg.2_Intron|LMF1_uc010brh.2_Intron|LMF1_uc010bri.2_Intron|LMF1_uc002ckk.2_Intron	NM_022773	NP_073610			lipase maturation factor 1							endoplasmic reticulum membrane|integral to membrane					0		Hepatocellular(780;0.00308)																---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1265667	1265668	+	Intron	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1265667_1265668delCT	uc002cks.2	+						CACNA1H_uc002ckt.2_Intron|CACNA1H_uc002cku.2_Intron|CACNA1H_uc010brj.2_Intron|CACNA1H_uc002ckv.2_Intron	NM_021098	NP_066921			calcium channel, voltage-dependent, T type,						aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)													---	---	---	---
ABCA3	21	broad.mit.edu	37	16	2346237	2346237	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2346237delT	uc002cpy.1	-						ABCA3_uc010bsk.1_Intron|ABCA3_uc010bsl.1_Intron	NM_001089	NP_001080			ATP-binding cassette, sub-family A member 3						response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	2922839	2922840	+	IGR	INS	-	A	A	rs151051086		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2922839_2922840insA								PRSS22 (14668 upstream) : FLYWCH2 (10356 downstream)																																			---	---	---	---
TRAP1	10131	broad.mit.edu	37	16	3737879	3737879	+	Intron	DEL	C	-	-	rs113513981		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3737879delC	uc002cvt.3	-						TRAP1_uc010uxf.1_Intron	NM_016292	NP_057376			TNF receptor-associated protein 1 precursor						cellular response to oxidative stress|protein folding	mitochondrion	ATP binding|tumor necrosis factor receptor binding|unfolded protein binding			central_nervous_system(1)	1		Ovarian(90;0.0261)																---	---	---	---
ADCY9	115	broad.mit.edu	37	16	4082512	4082513	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4082512_4082513insT	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																		---	---	---	---
C16orf5	29965	broad.mit.edu	37	16	4584692	4584692	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4584692delT	uc002cwv.2	-						C16orf5_uc002cww.2_Intron|C16orf5_uc010uxl.1_Intron|C16orf5_uc010uxm.1_Intron|C16orf5_uc010btu.2_Intron	NM_013399	NP_037531			cell death inducing protein						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|tumor necrosis factor-mediated signaling pathway	nucleus				ovary(1)	1		Ovarian(90;0.17)																---	---	---	---
GLYR1	84656	broad.mit.edu	37	16	4867127	4867127	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4867127delT	uc002cxx.3	-						GLYR1_uc002cxy.2_Intron|GLYR1_uc002cxz.1_Intron|GLYR1_uc002cya.2_Intron|GLYR1_uc010uxv.1_Intron	NM_032569	NP_115958			cytokine-like nuclear factor n-pac						pentose-phosphate shunt	nucleus	coenzyme binding|DNA binding|methylated histone residue binding|phosphogluconate dehydrogenase (decarboxylating) activity				0																		---	---	---	---
PPL	5493	broad.mit.edu	37	16	4939233	4939233	+	Intron	DEL	G	-	-	rs71139659		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4939233delG	uc002cyd.1	-							NM_002705	NP_002696			periplakin						keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	5185674	5185674	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5185674delG								FAM86A (37885 upstream) : A2BP1 (883458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	5316549	5316550	+	Intron	INS	-	T	T	rs3035524		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5316549_5316550insT	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	5629926	5629926	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5629926delA	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6550359	6550360	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6550359_6550360delAC	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	6757479	6757480	+	Intron	INS	-	TT	TT	rs61418784		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6757479_6757480insTT	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	7713846	7713846	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7713846delT	uc002cys.2	+						A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.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	7993430	7993430	+	IGR	DEL	T	-	-	rs5815445		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7993430delT								A2BP1 (230090 upstream) : TMEM114 (626073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8009922	8009923	+	IGR	INS	-	TCT	TCT	rs140824448	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8009922_8009923insTCT								A2BP1 (246582 upstream) : TMEM114 (609580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8112519	8112522	+	IGR	DEL	GTGA	-	-	rs59260197		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8112519_8112522delGTGA								A2BP1 (349179 upstream) : TMEM114 (506981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8184655	8184655	+	IGR	DEL	A	-	-	rs10459833	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8184655delA								A2BP1 (421315 upstream) : TMEM114 (434848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8405408	8405409	+	IGR	DEL	GT	-	-	rs71396260		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8405408_8405409delGT								A2BP1 (642068 upstream) : TMEM114 (214094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9089560	9089560	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9089560delA								USP7 (32219 upstream) : C16orf72 (95977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9285317	9285318	+	IGR	INS	-	GAC	GAC	rs143609137	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9285317_9285318insGAC								C16orf72 (71772 upstream) : GRIN2A (561949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9499634	9499635	+	IGR	INS	-	ATAC	ATAC	rs140181290	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9499634_9499635insATAC								C16orf72 (286089 upstream) : GRIN2A (347632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9518085	9518086	+	IGR	INS	-	TT	TT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9518085_9518086insTT								C16orf72 (304540 upstream) : GRIN2A (329181 downstream)																																			---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	10235246	10235246	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10235246delA	uc002czo.3	-						GRIN2A_uc010uym.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	10412167	10412168	+	IGR	INS	-	A	A	rs139211864	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10412167_10412168insA								GRIN2A (135556 upstream) : ATF7IP2 (67744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	10415844	10415844	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10415844delC								GRIN2A (139233 upstream) : ATF7IP2 (64068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	10708726	10708741	+	IGR	DEL	TTCCTTCTTTCCTTCT	-	-	rs35214438		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10708726_10708741delTTCCTTCTTTCCTTCT								EMP2 (34187 upstream) : TEKT5 (12620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	11318701	11318701	+	IGR	DEL	A	-	-	rs75188452		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11318701delA								CLEC16A (42657 upstream) : C16orf75 (24805 downstream)																																			---	---	---	---
TXNDC11	51061	broad.mit.edu	37	16	11812345	11812346	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11812345_11812346insT	uc010buu.1	-						TXNDC11_uc002dbg.1_Intron	NM_015914	NP_056998			thioredoxin domain containing 11						cell redox homeostasis	endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12236858	12236858	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12236858delT	uc002dby.3	+						SNX29_uc010uyx.1_Intron	NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12275741	12275741	+	Intron	DEL	T	-	-	rs5815670		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12275741delT	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	12986407	12986408	+	IGR	INS	-	TT	TT	rs150578842		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12986407_12986408insTT								CPPED1 (88663 upstream) : SHISA9 (9069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13529085	13529085	+	IGR	DEL	T	-	-	rs150465685		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13529085delT								SHISA9 (194813 upstream) : ERCC4 (484929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13530628	13530629	+	IGR	INS	-	C	C	rs143680017	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13530628_13530629insC								SHISA9 (196356 upstream) : ERCC4 (483385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13837306	13837306	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13837306delC								SHISA9 (503034 upstream) : ERCC4 (176708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	14495013	14495014	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14495013_14495014insA								MIR365-1 (91785 upstream) : PARN (34545 downstream)																																			---	---	---	---
NPIP	9284	broad.mit.edu	37	16	15037002	15037003	+	Intron	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15037002_15037003delTT	uc002dcy.3	+						NPIP_uc002dcx.3_Intron	NM_006985	NP_008916			nuclear pore complex interacting protein						mRNA transport|protein transport|transmembrane transport	nuclear membrane|nuclear pore					0																		---	---	---	---
C16orf45	89927	broad.mit.edu	37	16	15590401	15590401	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15590401delT	uc002ddo.2	+							NM_033201	NP_149978			hypothetical protein LOC89927 isoform 1											ovary(1)	1																		---	---	---	---
NDE1	54820	broad.mit.edu	37	16	15785984	15785984	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15785984delT	uc002ddt.1	+						NDE1_uc010uzy.1_Intron|NDE1_uc002dds.2_Intron|NDE1_uc002ddu.1_Intron	NM_017668	NP_060138			nuclear distribution gene E homolog 1						cell differentiation|cell division|centrosome duplication|establishment of chromosome localization|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|mitotic prometaphase|nervous system development	cleavage furrow|condensed chromosome kinetochore|cytosol|microtubule|spindle pole centrosome	microtubule binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	15985656	15985659	+	IGR	DEL	TTTC	-	-	rs35632908		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15985656_15985659delTTTC								C16orf63 (3209 upstream) : ABCC1 (57775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	16988794	16988794	+	IGR	DEL	A	-	-	rs67200903		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16988794delA								LOC339047 (544357 upstream) : XYLT1 (207389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	17069110	17069110	+	IGR	DEL	A	-	-	rs148522925		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17069110delA								LOC339047 (624673 upstream) : XYLT1 (127073 downstream)																																			---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17255532	17255533	+	Intron	INS	-	CT	CT	rs111901583		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17255532_17255533insCT	uc002dfa.2	-							NM_022166	NP_071449			xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4																		---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17528728	17528729	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17528728_17528729insA	uc002dfa.2	-							NM_022166	NP_071449			xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	18271859	18271860	+	IGR	INS	-	AC	AC	rs141481701	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18271859_18271860insAC								XYLT1 (707121 upstream) : NOMO2 (239323 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18991357	18991357	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18991357delT								SMG1 (53631 upstream) : TMC7 (3899 downstream)																																			---	---	---	---
TMC5	79838	broad.mit.edu	37	16	19430050	19430050	+	Intron	DEL	T	-	-	rs148960287		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19430050delT	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	19446907	19446908	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19446907_19446908delAC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	20039534	20039534	+	IGR	DEL	A	-	-	rs5816078		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20039534delA								GPRC5B (142702 upstream) : GPR139 (3509 downstream)																																			---	---	---	---
PDILT	204474	broad.mit.edu	37	16	20400235	20400235	+	Intron	DEL	A	-	-	rs113078364		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20400235delA	uc002dhc.1	-							NM_174924	NP_777584			protein disulfide isomerase-like, testis						cell differentiation|cell redox homeostasis|multicellular organismal development|spermatogenesis	endoplasmic reticulum	isomerase activity			large_intestine(1)	1																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21022384	21022384	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21022384delG	uc010vbe.1	-							NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21545062	21545063	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21545062_21545063insT	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
OTOA	146183	broad.mit.edu	37	16	21740364	21740364	+	Intron	DEL	T	-	-	rs34039836		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21740364delT	uc002djh.2	+						uc002diq.3_Intron|OTOA_uc010vbj.1_Intron|OTOA_uc002dji.2_Intron|OTOA_uc010vbk.1_Intron	NM_144672	NP_653273			otoancorin isoform 1						sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(48;0.0414)														---	---	---	---
LOC653786	653786	broad.mit.edu	37	16	22562583	22562583	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22562583delA	uc002dlh.3	+							NR_003676				RecName: Full=Otoancorin; Flags: Precursor;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	22704733	22704734	+	IGR	INS	-	T	T	rs5816184		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22704733_22704734insT								LOC653786 (116547 upstream) : HS3ST2 (121126 downstream)																																			---	---	---	---
HS3ST2	9956	broad.mit.edu	37	16	22859464	22859464	+	Intron	DEL	A	-	-	rs72288819		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22859464delA	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)														---	---	---	---
GGA2	23062	broad.mit.edu	37	16	23492806	23492806	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23492806delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	24584780	24584781	+	IGR	INS	-	T	T	rs145865989	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24584780_24584781insT								RBBP6 (599 upstream) : TNRC6A (156268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	24718672	24718673	+	IGR	DEL	CA	-	-	rs71688203		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24718672_24718673delCA								RBBP6 (134491 upstream) : TNRC6A (22376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25352916	25352916	+	IGR	DEL	A	-	-	rs112459195		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25352916delA								ZKSCAN2 (84061 upstream) : HS3ST4 (350431 downstream)																																			---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	25869220	25869221	+	Intron	INS	-	CTTC	CTTC	rs72453395		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25869220_25869221insCTTC	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	26396713	26396714	+	IGR	DEL	AC	-	-	rs147506259		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26396713_26396714delAC								HS3ST4 (247705 upstream) : C16orf82 (681505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27180782	27180786	+	IGR	DEL	AAGGG	-	-	rs149006021	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27180782_27180786delAAGGG								C16orf82 (100296 upstream) : JMJD5 (34021 downstream)																																			---	---	---	---
IL21R	50615	broad.mit.edu	37	16	27434161	27434161	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27434161delT	uc002doq.1	+						IL21R_uc002dor.1_Intron	NM_181078	NP_851564			interleukin 21 receptor precursor						natural killer cell activation	integral to membrane	interleukin-21 receptor activity			ovary(2)|lung(1)|breast(1)	4								T	BCL6	NHL								---	---	---	---
GSG1L	146395	broad.mit.edu	37	16	28015796	28015796	+	Intron	DEL	A	-	-	rs71389519		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28015796delA	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233			GSG1-like isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	28228927	28228927	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28228927delT								XPO6 (5737 upstream) : SBK1 (74913 downstream)																																			---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	29859759	29859761	+	Intron	DEL	CTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29859759_29859761delCTC	uc010bzb.1	-						uc002dtf.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																OREG0023723	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TBC1D10B	26000	broad.mit.edu	37	16	30373856	30373857	+	Intron	INS	-	G	G	rs139662564	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30373856_30373857insG	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)															---	---	---	---
SRCAP	10847	broad.mit.edu	37	16	30747236	30747237	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30747236_30747237insT	uc002dze.1	+						SRCAP_uc002dzf.2_Intron|SRCAP_uc002dzg.1_Intron	NM_006662	NP_006653			Snf2-related CBP activator protein						interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)															---	---	---	---
Unknown	0	broad.mit.edu	37	16	31205616	31205616	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31205616delT								FUS (2519 upstream) : PYCARD (7193 downstream)																																			---	---	---	---
ITGAM	3684	broad.mit.edu	37	16	31273563	31273566	+	Intron	DEL	CCTT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31273563_31273566delCCTT	uc002ebq.2	+						ITGAM_uc002ebr.2_Intron	NM_000632	NP_000623			integrin alpha M isoform 2 precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	32495050	32495051	+	IGR	INS	-	TT	TT	rs142716802	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32495050_32495051insTT								HERC2P4 (331176 upstream) : TP53TG3B (189790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32522545	32522545	+	IGR	DEL	C	-	-	rs76051919		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32522545delC								HERC2P4 (358671 upstream) : TP53TG3B (162296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32558547	32558547	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32558547delT								HERC2P4 (394673 upstream) : TP53TG3B (126294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32839154	32839155	+	IGR	INS	-	C	C	rs148065916		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32839154_32839155insC								TP53TG3B (150276 upstream) : SLC6A10P (49642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32841066	32841066	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32841066delC								TP53TG3B (152188 upstream) : SLC6A10P (47731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33041000	33041001	+	IGR	DEL	AT	-	-	rs79665710		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33041000_33041001delAT								SLC6A10P (144537 upstream) : MIR1826 (924507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33543042	33543046	+	IGR	DEL	CACAC	-	-	rs80034619	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33543042_33543046delCACAC								SLC6A10P (646579 upstream) : MIR1826 (422462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33942533	33942536	+	IGR	DEL	ACAG	-	-	rs67338600	by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33942533_33942536delACAG								None (None upstream) : MIR1826 (22972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34008364	34008364	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34008364delC								MIR1826 (42772 upstream) : UBE2MP1 (395438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34247904	34247904	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34247904delA								MIR1826 (282312 upstream) : UBE2MP1 (155898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34899076	34899076	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34899076delA								LOC146481 (184109 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	35194539	35194539	+	IGR	DEL	C	-	-	rs79268238		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35194539delC								LOC146481 (479572 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	35244735	35244736	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35244735_35244736insA								LOC146481 (529768 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	35269833	35269834	+	IGR	INS	-	T	T	rs145409973	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35269833_35269834insT								LOC146481 (554866 upstream) : None (None downstream)																																			---	---	---	---
C16orf87	388272	broad.mit.edu	37	16	46863841	46863841	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46863841delA	uc002eek.1	-							NM_001001436	NP_001001436			hypothetical protein LOC388272												0																		---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47204343	47204344	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47204343_47204344insT	uc002eet.2	-						ITFG1_uc010vgg.1_Intron|ITFG1_uc010vgh.1_Intron	NM_030790	NP_110417			integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	48106829	48106830	+	IGR	INS	-	GT	GT	rs35920256		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48106829_48106830insGT								PHKB (371396 upstream) : ABCC12 (10054 downstream)																																			---	---	---	---
ABCC12	94160	broad.mit.edu	37	16	48184998	48184998	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48184998delA	uc002efe.1	-						ABCC12_uc002efd.1_Intron|ABCC12_uc010vgj.1_Intron	NM_033226	NP_150229			ATP-binding cassette protein C12							integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)																---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49548096	49548097	+	Intron	INS	-	AC	AC	rs138050694	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49548096_49548097insAC	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	49654047	+	Intron	DEL	ACAC	-	-	rs68006357		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49654044_49654047delACAC	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)																---	---	---	---
HEATR3	55027	broad.mit.edu	37	16	50119019	50119019	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50119019delA	uc002efw.2	+						HEATR3_uc002efx.2_Intron	NM_182922	NP_891552			HEAT repeat containing 3								binding			ovary(1)|skin(1)	2																		---	---	---	---
ADCY7	113	broad.mit.edu	37	16	50320931	50320931	+	5'Flank	DEL	T	-	-	rs111250106		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50320931delT	uc002egd.1	+						ADCY7_uc002egb.1_Intron|ADCY7_uc002egc.1_Intron	NM_001114	NP_001105			adenylate cyclase 7						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to ethanol|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of cAMP biosynthetic process|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			skin(1)	1		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)	Bromocriptine(DB01200)													---	---	---	---
NOD2	64127	broad.mit.edu	37	16	50757050	50757051	+	Intron	INS	-	A	A	rs11423748		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50757050_50757051insA	uc002egm.1	+						NOD2_uc010cbl.1_Intron|NOD2_uc010cbm.1_Intron|NOD2_uc010cbn.1_Intron|NOD2_uc010cbo.1_Intron|NOD2_uc010cbp.1_Intron|NOD2_uc010cbq.1_Intron|NOD2_uc010cbr.1_Intron|NOD2_uc010vgq.1_Intron	NM_022162	NP_071445			nucleotide-binding oligomerization domain						activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)|skin(1)	4		all_cancers(37;0.0156)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	51327493	51327497	+	IGR	DEL	TTTCT	-	-	rs71382346		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51327493_51327497delTTTCT								SALL1 (142310 upstream) : None (None downstream)																																			---	---	---	---
TOX3	27324	broad.mit.edu	37	16	52478411	52478412	+	Intron	INS	-	CACACA	CACACA	rs139630584	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52478411_52478412insCACACA	uc002egw.2	-						TOX3_uc010vgt.1_Intron|TOX3_uc010vgu.1_Intron	NM_001080430	NP_001073899			TOX high mobility group box family member 3						apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity				0																		---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53093247	53093247	+	Intron	DEL	G	-	-	rs35148824		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53093247delG	uc002egy.2	+							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	53280417	53280418	+	Intron	INS	-	TTG	TTG	rs151082897	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53280417_53280418insTTG	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002eha.1_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc002ehd.2_Intron|CHD9_uc002ehe.1_Intron	NM_025134	NP_079410			chromodomain helicase DNA binding protein 9						cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	53392856	53392856	+	IGR	DEL	A	-	-	rs35275448		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53392856delA								CHD9 (31443 upstream) : RBL2 (75495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	53615400	53615400	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53615400delA								AKTIP (78230 upstream) : RPGRIP1L (18423 downstream)																																			---	---	---	---
RPGRIP1L	23322	broad.mit.edu	37	16	53691152	53691153	+	Intron	INS	-	A	A	rs77569762		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53691152_53691153insA	uc002ehp.2	-						RPGRIP1L_uc002eho.3_Intron|RPGRIP1L_uc010vgy.1_Intron|RPGRIP1L_uc010cbx.2_Intron|RPGRIP1L_uc010vgz.1_Intron	NM_015272	NP_056087			RPGRIP1-like isoform a						negative regulation of G-protein coupled receptor protein signaling pathway	cell-cell junction|centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	54521205	54521206	+	IGR	DEL	TT	-	-	rs71800747		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54521205_54521206delTT								IRX3 (200827 upstream) : IRX5 (443905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54584285	54584286	+	IGR	INS	-	T	T	rs66995749		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54584285_54584286insT								IRX3 (263907 upstream) : IRX5 (380825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54810538	54810539	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54810538_54810539delAC								IRX3 (490160 upstream) : IRX5 (154572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55329383	55329384	+	IGR	INS	-	TCTCTGTCTCTCTG	TCTCTGTCTCTCTG	rs141338131	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55329383_55329384insTCTCTGTCTCTCTG								IRX5 (360990 upstream) : IRX6 (29087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	56046286	56046287	+	IGR	INS	-	CA	CA	rs141675016	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56046286_56046287insCA								CES7 (86914 upstream) : LOC283856 (80612 downstream)																																			---	---	---	---
LOC283856	283856	broad.mit.edu	37	16	56212560	56212561	+	Intron	INS	-	CC	CC	rs149729684	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56212560_56212561insCC	uc002eis.1	-							NR_027078				Homo sapiens hypothetical protein LOC283856, mRNA (cDNA clone IMAGE:5263025).												0																		---	---	---	---
GNAO1	2775	broad.mit.edu	37	16	56320567	56320568	+	Intron	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56320567_56320568delTC	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)																---	---	---	---
NUDT21	11051	broad.mit.edu	37	16	56475812	56475812	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56475812delT	uc002eja.2	-						NUDT21_uc002eiz.2_Intron	NM_007006	NP_008937			cleavage and polyadenylation specific factor 5						mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription	centrosome|mRNA cleavage factor complex|paraspeckles	AU-rich element binding|histone deacetylase binding|hydrolase activity|mRNA binding|protein homodimerization activity				0																		---	---	---	---
CETP	1071	broad.mit.edu	37	16	57015336	57015347	+	Intron	DEL	CTGCCAGGAAGA	-	-	rs67188110		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57015336_57015347delCTGCCAGGAAGA	uc002eki.2	+						CETP_uc002ekj.2_Intron	NM_000078	NP_000069			cholesteryl ester transfer protein, plasma						cholesterol homeostasis|cholesterol metabolic process|high-density lipoprotein particle remodeling|lipoprotein metabolic process|low-density lipoprotein particle remodeling|phosphatidylcholine metabolic process|phospholipid homeostasis|receptor-mediated endocytosis|regulation of cholesterol efflux|triglyceride homeostasis|triglyceride metabolic process|very-low-density lipoprotein particle remodeling	high-density lipoprotein particle|vesicle	cholesterol binding|cholesterol transporter activity|phosphatidylcholine binding|phospholipid transporter activity|triglyceride binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
CPNE2	221184	broad.mit.edu	37	16	57130611	57130611	+	Intron	DEL	A	-	-	rs72381078		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57130611delA	uc002eks.1	+						CPNE2_uc010cct.1_Intron	NM_152727	NP_689940			copine II											central_nervous_system(1)|skin(1)	2		all_neural(199;0.224)																---	---	---	---
RSPRY1	89970	broad.mit.edu	37	16	57245625	57245626	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57245625_57245626insT	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																		---	---	---	---
DOK4	55715	broad.mit.edu	37	16	57508356	57508357	+	Intron	INS	-	A	A	rs148579026	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57508356_57508357insA	uc010cdb.2	-						DOK4_uc002elu.1_Intron|DOK4_uc002elv.3_Intron	NM_018110	NP_060580			docking protein 4								insulin receptor binding			skin(1)	1																		---	---	---	---
GPR114	221188	broad.mit.edu	37	16	57583895	57583895	+	Intron	DEL	T	-	-	rs140337365		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57583895delT	uc002elx.3	+						GPR114_uc010vhr.1_Intron|GPR114_uc002ely.2_Intron	NM_153837	NP_722579			G protein-coupled receptor 114 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)	1																		---	---	---	---
GPR114	221188	broad.mit.edu	37	16	57603920	57603921	+	Intron	INS	-	CACCACCTCCTC	CACCACCTCCTC	rs141672193	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57603920_57603921insCACCACCTCCTC	uc002elx.3	+						GPR114_uc010vhr.1_Intron|GPR114_uc002ely.2_Intron	NM_153837	NP_722579			G protein-coupled receptor 114 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)	1																		---	---	---	---
KIFC3	3801	broad.mit.edu	37	16	57884886	57884887	+	Intron	INS	-	T	T	rs142877655		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57884886_57884887insT	uc002emr.1	-							NM_001130099	NP_001123571			kinesin family member C3 isoform 3						epithelial cell-cell adhesion|microtubule-based movement|visual perception|zonula adherens maintenance	centrosome|cytoplasmic vesicle membrane|kinesin complex|microtubule|zonula adherens	ATP binding|microtubule motor activity			central_nervous_system(2)|ovary(1)	3		all_neural(199;0.224)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	58175156	58175156	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58175156delA								C16orf80 (11860 upstream) : CSNK2A2 (16660 downstream)																																			---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58565410	58565411	+	Intron	DEL	GA	-	-	rs147078253		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58565410_58565411delGA	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc002ent.2_Intron|CNOT1_uc010vik.1_Intron	NM_016284	NP_057368			CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	58886326	58886326	+	IGR	DEL	A	-	-	rs35791085		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58886326delA								GOT2 (118080 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	58900514	58900515	+	IGR	INS	-	TAAC	TAAC	rs140898873	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58900514_58900515insTAAC								GOT2 (132268 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59212037	59212037	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59212037delG								GOT2 (443791 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59632063	59632072	+	IGR	DEL	TTTCTTTCTT	-	-	rs71388610		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59632063_59632072delTTTCTTTCTT								GOT2 (863817 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61653044	61653045	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61653044_61653045delAC								None (None upstream) : CDH8 (34190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63135969	63135970	+	IGR	INS	-	TCTC	TCTC	rs139469712	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63135969_63135970insTCTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63516087	63516087	+	IGR	DEL	T	-	-	rs34313725		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63516087delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63723996	63723997	+	IGR	INS	-	A	A	rs79989233		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63723996_63723997insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64356772	64356773	+	IGR	INS	-	TG	TG	rs145744040	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64356772_64356773insTG								None (None upstream) : CDH11 (623912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64420458	64420459	+	IGR	INS	-	T	T	rs140226705	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64420458_64420459insT								None (None upstream) : CDH11 (560226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65275606	65275606	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65275606delT								CDH11 (119687 upstream) : LOC283867 (42796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65799889	65799889	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65799889delT								LOC283867 (189686 upstream) : CDH5 (600636 downstream)																																			---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	68948862	68948873	+	Intron	DEL	ACACACACACAC	-	-	rs71966143		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68948862_68948873delACACACACACAC	uc002ewi.3	+							NM_024562	NP_078838			transmembrane and coiled-coil domains 7							integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)														---	---	---	---
NFAT5	10725	broad.mit.edu	37	16	69646603	69646604	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69646603_69646604delAC	uc002exm.1	+						NFAT5_uc002exh.1_Intron|NFAT5_uc002exi.2_Intron|NFAT5_uc002exj.1_Intron|NFAT5_uc002exk.1_Intron|NFAT5_uc002exl.1_Intron|NFAT5_uc002exn.1_Intron	NM_006599	NP_006590			nuclear factor of activated T-cells 5 isoform c						excretion|signal transduction|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	70615304	70615304	+	IGR	DEL	T	-	-	rs71797250		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70615304delT								SF3B3 (3734 upstream) : IL34 (65164 downstream)																																			---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	71087770	71087771	+	Intron	INS	-	T	T	rs146595001	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71087770_71087771insT	uc002ezr.2	-						HYDIN_uc010cfz.1_Intron|HYDIN_uc002ezv.2_Intron|HYDIN_uc010vmc.1_Intron|HYDIN_uc010vmd.1_Intron	NM_032821	NP_116210			hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72902749	72902750	+	Intron	INS	-	A	A	rs142772318	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72902749_72902750insA	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	73710306	73710307	+	IGR	INS	-	T	T	rs145945005	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73710306_73710307insT								HTA (582636 upstream) : PSMD7 (620374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74216994	74216994	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74216994delT								None (None upstream) : PSMD7 (113687 downstream)																																			---	---	---	---
MLKL	197259	broad.mit.edu	37	16	74719861	74719861	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74719861delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	75225506	75225506	+	IGR	DEL	C	-	-	rs80350992		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75225506delC								ZFP1 (19375 upstream) : CTRB2 (12489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	75246934	75246934	+	IGR	DEL	G	-	-	rs66550721		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75246934delG								CTRB2 (5862 upstream) : CTRB1 (5950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	75854989	75854989	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75854989delC								TERF2IP (163661 upstream) : CNTNAP4 (456187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	76037199	76037200	+	IGR	INS	-	A	A	rs141282289	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76037199_76037200insA								TERF2IP (345871 upstream) : CNTNAP4 (273976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	77030574	77030574	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77030574delC								CNTNAP4 (437439 upstream) : MON1B (194262 downstream)																																			---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77320455	77320455	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77320455delA	uc002ffc.3	-							NM_199355	NP_955387			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	77722266	77722267	+	IGR	DEL	TT	-	-	rs67633997		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77722266_77722267delTT								ADAMTS18 (253255 upstream) : NUDT7 (34144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	77814886	77814887	+	IGR	INS	-	GGGAGG	GGGAGG	rs149079000	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77814886_77814887insGGGAGG								NUDT7 (38733 upstream) : VAT1L (7596 downstream)																																			---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78540591	78540610	+	Intron	DEL	TGTTTTTTTTTTTTTTTTTT	-	-	rs72430732		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78540591_78540610delTGTTTTTTTTTTTTTTTTTT	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	78541888	78541891	+	Intron	DEL	TGCG	-	-	rs144400727	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78541888_78541891delTGCG	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	78947557	78947558	+	Intron	INS	-	T	T	rs112963247		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78947557_78947558insT	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	78999466	78999466	+	Intron	DEL	A	-	-	rs113152925		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78999466delA	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	79094145	79094145	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79094145delA	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	79727970	79727971	+	IGR	INS	-	T	T	rs144566657	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79727970_79727971insT								MAF (93348 upstream) : DYNLRB2 (846883 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	79914886	79914886	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79914886delA								MAF (280264 upstream) : DYNLRB2 (659968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	79997539	79997540	+	IGR	INS	-	AAC	AAC	rs140538211	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79997539_79997540insAAC								MAF (362917 upstream) : DYNLRB2 (577314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80612695	80612695	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80612695delT								DYNLRB2 (28156 upstream) : CDYL2 (24983 downstream)																																			---	---	---	---
C16orf61	56942	broad.mit.edu	37	16	81035447	81035448	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81035447_81035448delAC	uc002ffu.2	-						C16orf61_uc002ffv.2_Intron	NM_020188	NP_064573			hypothetical protein LOC56942												0																		---	---	---	---
PKD1L2	114780	broad.mit.edu	37	16	81183625	81183626	+	Intron	DEL	TT	-	-	rs35446881		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81183625_81183626delTT	uc002fgh.1	-						PKD1L2_uc002fgg.1_Intron	NM_052892	NP_443124			polycystin 1-like 2 isoform a						neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81498101	81498104	+	Intron	DEL	TCAT	-	-	rs66489725		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81498101_81498104delTCAT	uc002fgp.2	+							NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81533877	81533878	+	Intron	INS	-	TCCT	TCCT	rs143054986	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81533877_81533878insTCCT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	81806414	81806415	+	IGR	INS	-	A	A	rs145165527	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81806414_81806415insA								CMIP (61049 upstream) : PLCG2 (6515 downstream)																																			---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82905259	82905260	+	Intron	DEL	AC	-	-	rs146892438		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82905259_82905260delAC	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	83217694	83217695	+	Intron	INS	-	AC	AC	rs141565714	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83217694_83217695insAC	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	83640180	83640180	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83640180delA	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)														---	---	---	---
ATP2C2	9914	broad.mit.edu	37	16	84446059	84446060	+	Intron	DEL	TG	-	-	rs151017915		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84446059_84446060delTG	uc002fhx.2	+						ATP2C2_uc010chj.2_Intron|ATP2C2_uc002fhy.2_Intron|ATP2C2_uc002fhz.2_Intron	NM_014861	NP_055676			ATPase, Ca++ transporting, type 2C, member 2						ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2																		---	---	---	---
COTL1	23406	broad.mit.edu	37	16	84652554	84652554	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84652554delT	uc002fid.2	-						COTL1_uc002fie.2_5'Flank|COTL1_uc010chk.2_5'Flank	NM_021149	NP_066972			coactosin-like 1							cytoplasm|cytoskeleton	actin binding|enzyme binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	84709180	84709181	+	IGR	DEL	GC	-	-	rs60737451		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84709180_84709181delGC								KLHL36 (13265 upstream) : USP10 (24374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86124097	86124097	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86124097delT								IRF8 (167888 upstream) : LOC732275 (241359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86256380	86256380	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86256380delA								IRF8 (300171 upstream) : LOC732275 (109076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86751604	86751606	+	IGR	DEL	GAG	-	-	rs144157809		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86751604_86751606delGAG								FOXL1 (136301 upstream) : FBXO31 (611338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86879096	86879097	+	IGR	INS	-	G	G	rs142813352	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86879096_86879097insG								FOXL1 (263793 upstream) : FBXO31 (483847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	87282361	87282362	+	Intron	DEL	AC	-	-	rs72502971		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87282361_87282362delAC	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																														---	---	---	---
JPH3	57338	broad.mit.edu	37	16	87673933	87673934	+	Intron	INS	-	A	A	rs146492007	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87673933_87673934insA	uc002fkd.2	+						JPH3_uc010vou.1_Intron	NM_020655	NP_065706			junctophilin 3						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)														---	---	---	---
ZC3H18	124245	broad.mit.edu	37	16	88657380	88657380	+	Intron	DEL	T	-	-	rs149132675		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88657380delT	uc002fky.2	+						ZC3H18_uc010voy.1_Intron|ZC3H18_uc010voz.1_Intron	NM_144604	NP_653205			zinc finger CCCH-type containing 18							nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	88936505	88936506	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88936505_88936506insT								PABPN1L (3491 upstream) : CBFA2T3 (4761 downstream)																																			---	---	---	---
RPH3AL	9501	broad.mit.edu	37	17	159304	159308	+	Intron	DEL	GCCCT	-	-	rs71947005		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:159304_159308delGCCCT	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	226186	226187	+	IGR	INS	-	TT	TT	rs5818747		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:226186_226187insTT								RPH3AL (23610 upstream) : C17orf97 (33931 downstream)																																			---	---	---	---
NXN	64359	broad.mit.edu	37	17	738548	738548	+	Intron	DEL	A	-	-	rs79364284		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:738548delA	uc002fsa.2	-						NXN_uc002fsb.1_Intron|NXN_uc002frz.2_Intron|NXN_uc010vqe.1_Intron	NM_022463	NP_071908			nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)														---	---	---	---
ABR	29	broad.mit.edu	37	17	1040220	1040221	+	Intron	INS	-	TT	TT	rs149585678	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1040220_1040221insTT	uc002fsd.2	-						ABR_uc002fse.2_Intron	NM_021962	NP_068781			active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)														---	---	---	---
TUSC5	286753	broad.mit.edu	37	17	1185429	1185430	+	Intron	INS	-	GT	GT	rs143150460	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1185429_1185430insGT	uc002fsi.1	+							NM_172367	NP_758955			LOST1						response to biotic stimulus	integral to membrane				skin(2)	2				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)														---	---	---	---
RTN4RL1	146760	broad.mit.edu	37	17	1847227	1847228	+	Intron	INS	-	T	T	rs146291379	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1847227_1847228insT	uc002ftp.2	-							NM_178568	NP_848663			reticulon 4 receptor-like 1 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	3105177	3105177	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3105177delA								OR1A2 (3435 upstream) : OR1A1 (13738 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	3876025	3876025	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3876025delT								ATP2A3 (8289 upstream) : ZZEF1 (31715 downstream)																																			---	---	---	---
ANKFY1	51479	broad.mit.edu	37	17	4147227	4147228	+	Intron	INS	-	T	T	rs113664000		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4147227_4147228insT	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																		---	---	---	---
PFN1	5216	broad.mit.edu	37	17	4848972	4848973	+	3'UTR	INS	-	A	A	rs77750855		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4848972_4848973insA	uc002gaa.2	-	3					PFN1_uc002fzz.2_3'UTR	NM_005022	NP_005013			profilin 1						actin cytoskeleton organization|platelet activation|platelet degranulation	actin cytoskeleton|cytoplasm	actin binding|proline-rich region binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	5103405	5103406	+	Intron	INS	-	A	A	rs9893898	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5103405_5103406insA	uc002gbf.1	+						uc002gbg.1_Intron					Homo sapiens cDNA FLJ11816 fis, clone HEMBA1006416.																														---	---	---	---
XAF1	54739	broad.mit.edu	37	17	6672359	6672360	+	Intron	INS	-	T	T	rs150097321	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6672359_6672360insT	uc002gdn.2	+						XAF1_uc002gdm.1_Intron|XAF1_uc002gdo.2_Intron|XAF1_uc002gdp.2_Intron|XAF1_uc002gdq.2_Intron|XAF1_uc002gdr.2_Intron	NM_017523	NP_059993			XIAP associated factor 1 isoform 1						apoptosis|type I interferon-mediated signaling pathway	mitochondrion|nucleus	zinc ion binding				0																		---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7714181	7714188	+	Intron	DEL	AGAGGCTC	-	-	rs140112761		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7714181_7714188delAGAGGCTC	uc002giu.1	+						DNAH2_uc010cnm.1_Intron	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	7718955	7718956	+	Intron	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7718955_7718956delCA	uc002giu.1	+						DNAH2_uc010cnm.1_Intron	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)																---	---	---	---
STX8	9482	broad.mit.edu	37	17	9193104	9193105	+	Intron	INS	-	AAAAA	AAAAA	rs148674859	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9193104_9193105insAAAAA	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	9723979	9723979	+	IGR	DEL	T	-	-	rs66692549		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9723979delT								DHRS7C (29378 upstream) : GLP2R (5402 downstream)																																			---	---	---	---
GAS7	8522	broad.mit.edu	37	17	9979525	9979530	+	Intron	DEL	GGGAGG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9979525_9979530delGGGAGG	uc002gmg.1	-						GAS7_uc010coh.1_Intron	NM_201433	NP_958839			growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2								T	MLL	AML*								---	---	---	---
GAS7	8522	broad.mit.edu	37	17	10087162	10087162	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10087162delA	uc002gmg.1	-							NM_201433	NP_958839			growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2								T	MLL	AML*								---	---	---	---
Unknown	0	broad.mit.edu	37	17	10332950	10332951	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10332950_10332951insT	uc002gml.1	+											Homo sapiens cDNA FLJ40181 fis, clone TESTI2018178.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	10907171	10907171	+	IGR	DEL	T	-	-	rs113860538		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10907171delT								PIRT (165753 upstream) : SHISA6 (237569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	11121439	11121439	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11121439delA								PIRT (380021 upstream) : SHISA6 (23301 downstream)																																			---	---	---	---
SHISA6	388336	broad.mit.edu	37	17	11286047	11286047	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11286047delT	uc002gna.3	+						SHISA6_uc002gnb.3_Intron|SHISA6_uc010com.2_Intron	NM_207386	NP_997269			shisa homolog 6							integral to membrane				breast(1)	1																		---	---	---	---
RICH2	9912	broad.mit.edu	37	17	12796111	12796111	+	Intron	DEL	T	-	-	rs142814685		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12796111delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	13333628	13333628	+	IGR	DEL	A	-	-	rs113295124		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13333628delA								ELAC2 (412269 upstream) : HS3ST3A1 (65378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	13718235	13718235	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13718235delA								HS3ST3A1 (212991 upstream) : CDRT15P (209580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	13919895	13919895	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13919895delT								HS3ST3A1 (414651 upstream) : CDRT15P (7920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14507115	14507115	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14507115delA								HS3ST3B1 (257623 upstream) : PMP22 (625982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	15708330	15708331	+	IGR	INS	-	TTCC	TTCC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15708330_15708331insTTCC								MEIS3P1 (15313 upstream) : ADORA2B (139900 downstream)																																			---	---	---	---
NCOR1	9611	broad.mit.edu	37	17	15994864	15994865	+	Intron	INS	-	CTCA	CTCA	rs148981996	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15994864_15994865insCTCA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpp.1_Intron|NCOR1_uc002gpq.1_Intron	NM_006311	NP_006302			nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)														---	---	---	---
CENPV	201161	broad.mit.edu	37	17	16248848	16248848	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16248848delA	uc002gpw.2	-							NM_181716	NP_859067			proline rich 6						cell division|centromeric heterochromatin formation|mitosis|positive regulation of cytokinesis|regulation of chromosome organization	condensed chromosome kinetochore|cytoplasm|nucleus|spindle midzone	carbon-sulfur lyase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	16485023	16485024	+	IGR	DEL	TG	-	-	rs112289802		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16485023_16485024delTG								ZNF287 (12503 upstream) : ZNF624 (39024 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	16590062	16590065	+	IGR	DEL	ACAC	-	-	rs62073711		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16590062_16590065delACAC								ZNF624 (32904 upstream) : CCDC144A (3574 downstream)																																			---	---	---	---
PEMT	10400	broad.mit.edu	37	17	17494546	17494548	+	Intron	DEL	ACA	-	-	rs145214572		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17494546_17494548delACA	uc002grl.2	-						PEMT_uc010vwx.1_Intron	NM_148172	NP_680477			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	19334347	19334347	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19334347delT								RNF112 (13760 upstream) : SLC47A1 (102820 downstream)																																			---	---	---	---
CCDC144NL	339184	broad.mit.edu	37	17	20772478	20772478	+	Intron	DEL	G	-	-	rs36064579		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20772478delG	uc002gyf.2	-						uc002gyg.1_Intron|uc002gyh.1_Intron	NM_001004306	NP_001004306			coiled-coil domain containing 144 family,												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	20871340	20871341	+	Intron	DEL	TG	-	-	rs35001087		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20871340_20871341delTG	uc002gyk.1	+											Homo sapiens hypothetical protein LOC339260, mRNA (cDNA clone IMAGE:5168338), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	21247082	21247083	+	IGR	INS	-	G	G	rs113371593		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21247082_21247083insG								MAP2K3 (28533 upstream) : KCNJ12 (32616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21507129	21507129	+	IGR	DEL	A	-	-	rs113637029		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-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	21530529	21530531	+	IGR	DEL	CTG	-	-	rs113355264		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21530529_21530531delCTG								C17orf51 (52798 upstream) : FAM27L (294839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21542115	21542116	+	IGR	INS	-	TT	TT	rs140996132		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21542115_21542116insTT								C17orf51 (64384 upstream) : FAM27L (283254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21556610	21556610	+	IGR	DEL	T	-	-	rs62051562		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21556610delT								C17orf51 (78879 upstream) : FAM27L (268760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25281690	25281691	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25281690_25281691insA								None (None upstream) : WSB1 (339415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25289230	25289233	+	IGR	DEL	TCTA	-	-	rs138697975		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25289230_25289233delTCTA								None (None upstream) : WSB1 (331873 downstream)																																			---	---	---	---
NLK	51701	broad.mit.edu	37	17	26438952	26438952	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26438952delT	uc010crj.2	+						NLK_uc010cri.1_Intron	NM_016231	NP_057315			nemo like kinase						intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
SSH2	85464	broad.mit.edu	37	17	28240642	28240642	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28240642delA	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																		---	---	---	---
LRRC37B2	147172	broad.mit.edu	37	17	28957604	28957605	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28957604_28957605insT	uc002hfl.3	+						LRRC37B2_uc010csj.1_Intron|LRRC37B2_uc010wbq.1_Intron|LRRC37B2_uc010csi.2_Intron					RecName: Full=Putative LRRC37B-like protein 2;												0																		---	---	---	---
ATAD5	79915	broad.mit.edu	37	17	29194634	29194634	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29194634delT	uc002hfs.1	+						ATAD5_uc002hft.1_Intron	NM_024857	NP_079133			ATPase family, AAA domain containing 5						response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)																---	---	---	---
NF1	4763	broad.mit.edu	37	17	29419180	29419180	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29419180delT	uc002hgg.2	+						NF1_uc002hge.1_5'Flank|NF1_uc002hgf.1_5'Flank|NF1_uc002hgh.2_5'Flank	NM_001042492	NP_001035957			neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	29924148	29924148	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29924148delC								MIR365-2 (21608 upstream) : C17orf79 (254737 downstream)																																			---	---	---	---
UTP6	55813	broad.mit.edu	37	17	30211761	30211762	+	Intron	INS	-	AT	AT	rs149908172	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30211761_30211762insAT	uc002hgr.2	-						UTP6_uc002hgq.2_Intron|UTP6_uc010cst.2_Intron|UTP6_uc010wbw.1_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	31227604	31227605	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31227604_31227605insT								MYO1D (23702 upstream) : TMEM98 (27323 downstream)																																			---	---	---	---
CCL3	6348	broad.mit.edu	37	17	34419250	34419251	+	5'Flank	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34419250_34419251delTC	uc002hkv.2	-							NM_002983	NP_002974			chemokine (C-C motif) ligand 3						cell-cell signaling|cellular calcium ion homeostasis|cellular component movement|cytoskeleton organization|exocytosis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response|regulation of viral genome replication	extracellular space|soluble fraction	chemoattractant activity|chemokine activity|signal transducer activity				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	36420162	36420162	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36420162delT	uc002hpx.2	-											Homo sapiens cDNA FLJ43844 fis, clone TESTI4006308, highly  similar to Puromycin-sensitive aminopeptidase (EC 3.4.11.-).																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	36770300	36770301	+	IGR	DEL	CA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36770300_36770301delCA								SRCIN1 (8117 upstream) : C17orf96 (57660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	37363293	37363294	+	IGR	INS	-	A	A	rs36033558		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37363293_37363294insA								RPL19 (2313 upstream) : STAC2 (3496 downstream)																																			---	---	---	---
FBXL20	84961	broad.mit.edu	37	17	37555453	37555453	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37555453delC	uc010wed.1	-						FBXL20_uc002hrt.2_Intron|FBXL20_uc010cvu.2_Intron	NM_032875	NP_116264			F-box and leucine-rich repeat protein 20							cytoplasm				ovary(1)	1			LUAD - Lung adenocarcinoma(14;0.146)															---	---	---	---
IKZF3	22806	broad.mit.edu	37	17	37924305	37924305	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37924305delA	uc002hsu.2	-						IKZF3_uc002htd.2_Intron|IKZF3_uc010cwd.2_Intron|IKZF3_uc002hsv.2_Intron|IKZF3_uc010cwe.2_Intron|IKZF3_uc010cwf.2_Intron|IKZF3_uc010cwg.2_Intron|IKZF3_uc002hsw.2_Intron|IKZF3_uc002hsx.2_Intron|IKZF3_uc002hsy.2_Intron|IKZF3_uc002hsz.2_Intron|IKZF3_uc002hta.2_Intron|IKZF3_uc002htb.2_Intron|IKZF3_uc010cwh.2_Intron|IKZF3_uc002htc.2_Intron|IKZF3_uc010wel.1_Intron	NM_012481	NP_036613			aiolos isoform 1						B cell activation|mesoderm development|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)|kidney(2)|skin(2)	6	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
GSDMA	284110	broad.mit.edu	37	17	38121558	38121561	+	Intron	DEL	AAAT	-	-	rs10524484		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38121558_38121561delAAAT	uc002htl.1	+						GSDMA_uc002htm.1_5'Flank	NM_178171	NP_835465			gasdermin 1						apoptosis|induction of apoptosis	perinuclear region of cytoplasm					0																		---	---	---	---
PSMD3	5709	broad.mit.edu	37	17	38150570	38150570	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38150570delG	uc002htn.1	+						PSMD3_uc010wen.1_Intron|PSMD3_uc010weo.1_Intron	NM_002809	NP_002800			proteasome 26S non-ATPase subunit 3						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	enzyme regulator activity|protein binding			ovary(1)|pancreas(1)	2	Colorectal(19;0.000442)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	38261016	38261019	+	IGR	DEL	TGTG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38261016_38261019delTGTG								NR1D1 (4043 upstream) : MSL1 (17771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	38781832	38781833	+	IGR	INS	-	AT	AT	rs72538196		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38781832_38781833insAT								CCR7 (60108 upstream) : SMARCE1 (2143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	39331026	39331026	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39331026delG								KRTAP4-3 (6602 upstream) : KRTAP4-2 (2674 downstream)																																			---	---	---	---
RAB5C	5878	broad.mit.edu	37	17	40302869	40302869	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40302869delA	uc002hyz.2	-						RAB5C_uc002hza.2_Intron|RAB5C_uc010cxx.2_Intron|RAB5C_uc010cxy.2_Intron	NM_201434	NP_958842			RAB5C, member RAS oncogene family isoform a						protein transport|small GTPase mediated signal transduction	early endosome membrane|melanosome|plasma membrane	GTP binding|GTPase activity|protein binding			large_intestine(1)|skin(1)	2		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)														---	---	---	---
STAT3	6774	broad.mit.edu	37	17	40482140	40482141	+	Intron	INS	-	T	T	rs11392125		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40482140_40482141insT	uc002hzl.1	-						STAT3_uc002hzk.1_Intron|STAT3_uc002hzm.1_Intron|STAT3_uc010wgh.1_Intron|STAT3_uc002hzn.1_Intron	NM_139276	NP_644805			signal transducer and activator of transcription						cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)										Hyperimmunoglobulin_E_Recurrent_Infection_Syndrome				---	---	---	---
PTRF	284119	broad.mit.edu	37	17	40566913	40566913	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40566913delC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	41524031	41524032	+	IGR	INS	-	G	G	rs147960894	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41524031_41524032insG								MIR2117 (1778 upstream) : DHX8 (37302 downstream)																																			---	---	---	---
ETV4	2118	broad.mit.edu	37	17	41609865	41609865	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41609865delA	uc002idw.2	-						ETV4_uc002idv.2_5'Flank|ETV4_uc010wih.1_Intron|ETV4_uc010czh.2_Intron|ETV4_uc010wii.1_Intron|ETV4_uc002idx.2_Intron|ETV4_uc010wij.1_Intron	NM_001986	NP_001977			ets variant gene 4 (E1A enhancer binding						positive regulation of transcription, DNA-dependent	nucleolus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/ETV4(6)	bone(4)|soft_tissue(2)|ovary(1)	7		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)				T	EWSR1|TMPRSS2|DDX5|KLK2|CANT1	Ewing sarcoma|Prostate carcinoma								---	---	---	---
Unknown	0	broad.mit.edu	37	17	41780665	41780666	+	IGR	DEL	AG	-	-	rs138999628		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41780665_41780666delAG								MEOX1 (41403 upstream) : SOST (50433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	41943620	41943621	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41943620_41943621insT								CD300LG (2626 upstream) : MPP2 (9106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	41948940	41948941	+	IGR	INS	-	TG	TG	rs76270653		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41948940_41948941insTG								CD300LG (7946 upstream) : MPP2 (3786 downstream)																																			---	---	---	---
G6PC3	92579	broad.mit.edu	37	17	42150089	42150090	+	Intron	DEL	TT	-	-	rs143287187		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42150089_42150090delTT	uc002iex.2	+						G6PC3_uc002iey.2_Intron|G6PC3_uc010czo.2_Intron|G6PC3_uc002iez.2_Intron|G6PC3_uc002ifa.1_3'UTR|G6PC3_uc002ifb.2_5'Flank|G6PC3_uc002ifc.2_5'Flank	NM_138387	NP_612396			glucose-6-phosphatase catalytic subunit 3						gluconeogenesis|transmembrane transport	endoplasmic reticulum membrane|integral to membrane	glucose-6-phosphatase activity			skin(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.113)														---	---	---	---
DBF4B	80174	broad.mit.edu	37	17	42817437	42817438	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42817437_42817438insT	uc002ihf.2	+						DBF4B_uc010wjb.1_Intron|DBF4B_uc002ihe.2_Intron|DBF4B_uc010wjc.1_Intron	NM_145663	NP_663696			DBF4 homolog B isoform 1						cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)																---	---	---	---
LOC644172	644172	broad.mit.edu	37	17	43679861	43679864	+	5'Flank	DEL	TTTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43679861_43679864delTTTC	uc010wjw.1	-							NR_026901				Homo sapiens cDNA clone IMAGE:3941904, partial cds.												0																		---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44277432	44277433	+	Intron	INS	-	A	A	rs7207512		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44277432_44277433insA	uc010dav.2	-							NM_015443	NP_056258			hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	44448142	44448142	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44448142delA								ARL17A (8979 upstream) : LRRC37A2 (141934 downstream)																																			---	---	---	---
ITGB3	3690	broad.mit.edu	37	17	45366698	45366699	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45366698_45366699insT	uc002ilj.2	+						ITGB3_uc002ili.1_Intron|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)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	46900431	46900432	+	IGR	INS	-	T	T	rs71369221		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46900431_46900432insT								TTLL6 (5962 upstream) : CALCOCO2 (7940 downstream)																																			---	---	---	---
GIP	2695	broad.mit.edu	37	17	47041521	47041522	+	Intron	INS	-	A	A	rs149710802		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47041521_47041522insA	uc002iol.1	-							NM_004123	NP_004114			gastric inhibitory polypeptide preproprotein						energy reserve metabolic process|signal transduction	extracellular region|soluble fraction	hormone activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	48236102	48236103	+	IGR	INS	-	A	A	rs146135559	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48236102_48236103insA								PPP1R9B (8225 upstream) : SGCA (7263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	48407341	48407341	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48407341delG								TMEM92 (48497 upstream) : XYLT2 (16052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	48411983	48411984	+	IGR	INS	-	T	T	rs71353635		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48411983_48411984insT								TMEM92 (53139 upstream) : XYLT2 (11409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	48582423	48582424	+	IGR	INS	-	A	A	rs111463857		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48582423_48582424insA								RSAD1 (19087 upstream) : MYCBPAP (3321 downstream)																																			---	---	---	---
MBTD1	54799	broad.mit.edu	37	17	49330094	49330095	+	Intron	INS	-	A	A	rs149211789	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49330094_49330095insA	uc002itr.3	-						MBTD1_uc002itq.3_Intron	NM_017643	NP_060113			mbt domain containing 1						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	50295164	50295165	+	IGR	INS	-	ACAC	ACAC	rs141993952	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50295164_50295165insACAC								CA10 (57787 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51308962	51308963	+	IGR	DEL	CA	-	-	rs4563079		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51308962_51308963delCA								None (None upstream) : KIF2B (591276 downstream)																																			---	---	---	---
STXBP4	252983	broad.mit.edu	37	17	53139785	53139786	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53139785_53139786insT	uc002iuf.1	+						STXBP4_uc010dcd.1_Intron	NM_178509	NP_848604			syntaxin binding protein 4							cytoplasm	calcium ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	53466103	53466103	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53466103delT								HLF (63677 upstream) : MMD (3872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	54752348	54752350	+	IGR	DEL	CTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54752348_54752350delCTC								NOG (79397 upstream) : C17orf67 (116925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	54951203	54951203	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54951203delA								DGKE (5169 upstream) : MTVR2 (10260 downstream)																																			---	---	---	---
MSI2	124540	broad.mit.edu	37	17	55481290	55481291	+	Intron	INS	-	TG	TG	rs146179814	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55481290_55481291insTG	uc002iuz.1	+						MSI2_uc010wnm.1_Intron|MSI2_uc002iva.2_Intron	NM_138962	NP_620412			musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)				T	HOXA9	CML								---	---	---	---
CUEDC1	404093	broad.mit.edu	37	17	56012763	56012764	+	Intron	INS	-	AA	AA	rs147468295	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56012763_56012764insAA	uc002ive.1	-							NM_017949	NP_060419			CUE domain-containing 1											skin(2)	2																		---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56681249	56681262	+	Intron	DEL	TGTGTGTGTGTGTG	-	-	rs72057528		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56681249_56681262delTGTGTGTGTGTGTG	uc010dcz.1	-						TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron	NM_198393	NP_938207			testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56702491	56702491	+	Intron	DEL	T	-	-	rs11324185		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56702491delT	uc010dcz.1	-						TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron	NM_198393	NP_938207			testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56756797	56756798	+	Intron	INS	-	TCG	TCG	rs142746101	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56756797_56756798insTCG	uc010dcz.1	-						TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron|TEX14_uc010wnz.1_Intron	NM_198393	NP_938207			testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	58187432	58187432	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58187432delT								LOC653653 (7152 upstream) : CA4 (39870 downstream)																																			---	---	---	---
MED13	9969	broad.mit.edu	37	17	60043317	60043317	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60043317delT	uc002izo.2	-							NM_005121	NP_005112			mediator complex subunit 13						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	60426356	60426359	+	IGR	DEL	TGTC	-	-	rs113458042	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60426356_60426359delTGTC								TBC1D3P2 (73340 upstream) : EFCAB3 (21220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	61505538	61505539	+	IGR	INS	-	G	G	rs149469680	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61505538_61505539insG								TANC2 (472 upstream) : CYB561 (4127 downstream)																																			---	---	---	---
ICAM2	3384	broad.mit.edu	37	17	62092067	62092090	+	Intron	DEL	AAGGAAGGAAGGAAGGAAGAAAGA	-	-	rs68006305	by1000genomes;by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62092067_62092090delAAGGAAGGAAGGAAGGAAGAAAGA	uc002jdw.3	-						ICAM2_uc010ded.2_Intron|ICAM2_uc002jdx.3_Intron|ICAM2_uc002jdv.3_Intron|ICAM2_uc010wpx.1_Intron	NM_001099788	NP_001093258			intercellular adhesion molecule 2 precursor						cell-cell adhesion|regulation of immune response	integral to plasma membrane	integrin binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	63289313	63289313	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63289313delT								RGS9 (65494 upstream) : AXIN2 (235372 downstream)																																			---	---	---	---
AXIN2	8313	broad.mit.edu	37	17	63553625	63553626	+	Intron	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63553625_63553626delCT	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				---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	63967712	63967722	+	Intron	DEL	TGCATATTGTG	-	-	rs142038132		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63967712_63967722delTGCATATTGTG	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	64809106	64809113	+	IGR	DEL	TCTCTCTG	-	-	rs59166117	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64809106_64809113delTCTCTCTG								PRKCA (2244 upstream) : CACNG5 (22122 downstream)																																			---	---	---	---
NOL11	25926	broad.mit.edu	37	17	65734795	65734795	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65734795delA	uc002jgd.1	+						NOL11_uc010wql.1_Intron|NOL11_uc010deu.1_Intron|SNORA38B_uc010dev.2_5'Flank	NM_015462	NP_056277			nucleolar protein 11							nucleolus					0	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
BPTF	2186	broad.mit.edu	37	17	65929378	65929379	+	Intron	DEL	GA	-	-	rs111771831		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65929378_65929379delGA	uc002jgf.2	+						BPTF_uc002jge.2_Intron	NM_182641	NP_872579			bromodomain PHD finger transcription factor						brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
ARSG	22901	broad.mit.edu	37	17	66390008	66390009	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66390008_66390009insA	uc002jhc.2	+						ARSG_uc002jhb.1_Intron	NM_014960	NP_055775			Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
ARSG	22901	broad.mit.edu	37	17	66412931	66412932	+	Intron	INS	-	AGA	AGA	rs146791223	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66412931_66412932insAGA	uc002jhc.2	+						ARSG_uc002jhb.1_Intron|ARSG_uc010dex.1_Intron	NM_014960	NP_055775			Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	66771948	66771948	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66771948delT								FAM20A (174853 upstream) : ABCA8 (91485 downstream)																																			---	---	---	---
ABCA8	10351	broad.mit.edu	37	17	66892274	66892274	+	Intron	DEL	T	-	-	rs74715793		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66892274delT	uc002jhp.2	-						ABCA8_uc002jhq.2_Intron|ABCA8_uc010wqq.1_Intron|ABCA8_uc010wqr.1_Intron|ABCA8_uc002jhr.2_Intron	NM_007168	NP_009099			ATP-binding cassette, sub-family A member 8							integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	67407588	67407588	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67407588delA								ABCA5 (84265 upstream) : MAP2K6 (3250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68149770	68149771	+	IGR	DEL	TG	-	-	rs34935077		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68149770_68149771delTG								KCNJ16 (18026 upstream) : KCNJ2 (15043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70143303	70143304	+	IGR	INS	-	AGA	AGA	rs144636895	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70143303_70143304insAGA								SOX9 (20751 upstream) : SLC39A11 (498782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70239294	70239295	+	IGR	DEL	AA	-	-	rs113775184		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70239294_70239295delAA								SOX9 (116742 upstream) : SLC39A11 (402791 downstream)																																			---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	71048456	71048457	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71048456_71048457insA	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																		---	---	---	---
C17orf54	283982	broad.mit.edu	37	17	71745488	71745490	+	3'UTR	DEL	GAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71745488_71745490delGAA	uc010dfo.2	-	4						NR_027146				SubName: Full=C17orf54 protein; Flags: Fragment;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	72005443	72005444	+	IGR	DEL	AA	-	-	rs68157042		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72005443_72005444delAA								C17orf54 (180767 upstream) : RPL38 (194351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	72630415	72630416	+	IGR	DEL	AG	-	-	rs71157078		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72630415_72630416delAG								CD300E (10614 upstream) : RAB37 (36840 downstream)																																			---	---	---	---
MIF4GD	57409	broad.mit.edu	37	17	73265084	73265084	+	Intron	DEL	A	-	-	rs75797498		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73265084delA	uc002jnr.2	-						MIF4GD_uc002jno.2_Intron|MIF4GD_uc002jnp.2_Intron|MIF4GD_uc002jnq.2_Intron					RecName: Full=MIF4G domain-containing protein; AltName: Full=SLBP-interacting protein 1;          Short=hSLIP1;						regulation of translation|RNA metabolic process	cytoplasm|nucleus	protein C-terminus binding			ovary(1)	1	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)															---	---	---	---
KIAA0195	9772	broad.mit.edu	37	17	73460405	73460406	+	Intron	INS	-	A	A	rs112636101		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73460405_73460406insA	uc002jnz.3	+							NM_014738	NP_055553			hypothetical protein LOC9772						ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
QRICH2	84074	broad.mit.edu	37	17	74301246	74301247	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74301246_74301247insT	uc002jrd.1	-						QRICH2_uc010dgw.1_Intron	NM_032134	NP_115510			glutamine rich 2								protein binding			ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
MXRA7	439921	broad.mit.edu	37	17	74676150	74676152	+	Intron	DEL	TGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74676150_74676152delTGA	uc002jsk.1	-						MXRA7_uc002jsl.2_3'UTR|MXRA7_uc002jsm.2_3'UTR	NM_001008528	NP_001008528			transmembrane anchor protein 1 isoform 1							integral to membrane					0																		---	---	---	---
PGS1	9489	broad.mit.edu	37	17	76401503	76401503	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76401503delT	uc002jvm.2	+						PGS1_uc010wtt.1_Intron|PGS1_uc010dho.2_Intron|PGS1_uc002jvn.2_Intron|PGS1_uc002jvo.2_Intron|PGS1_uc002jvp.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)															---	---	---	---
USP36	57602	broad.mit.edu	37	17	76812241	76812241	+	Intron	DEL	T	-	-	rs79164046		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76812241delT	uc002jvz.1	-						USP36_uc002jwa.1_Intron|USP36_uc002jwb.1_5'Flank|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)															---	---	---	---
USP36	57602	broad.mit.edu	37	17	76832881	76832882	+	Intron	DEL	AC	-	-	rs72448173		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76832881_76832882delAC	uc002jvz.1	-						USP36_uc002jwa.1_Intron|USP36_uc002jwd.1_Intron	NM_025090	NP_079366			ubiquitin specific peptidase 36						ubiquitin-dependent protein catabolic process	nucleolus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|kidney(1)	5			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)															---	---	---	---
TIMP2	7077	broad.mit.edu	37	17	76853077	76853078	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76853077_76853078insT	uc002jwf.2	-						TIMP2_uc002jwe.2_Intron|TIMP2_uc010wty.1_Intron	NM_003255	NP_003246			TIMP metallopeptidase inhibitor 2 precursor								metal ion binding|metalloendopeptidase inhibitor activity			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)															---	---	---	---
CANT1	124583	broad.mit.edu	37	17	77001294	77001295	+	Intron	DEL	GA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77001294_77001295delGA	uc002jwn.2	-						CANT1_uc002jwk.2_Intron|CANT1_uc002jwj.2_Intron|CANT1_uc002jwl.2_Intron	NM_001159772	NP_001153244			calcium activated nucleotidase 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	endoplasmic reticulum membrane|Golgi cisterna membrane|integral to membrane	calcium ion binding|nucleoside-diphosphatase activity|signal transducer activity				0			BRCA - Breast invasive adenocarcinoma(99;0.0362)|OV - Ovarian serous cystadenocarcinoma(97;0.139)					T	ETV4	prostate								---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77240845	77240848	+	Intron	DEL	CTTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77240845_77240848delCTTC	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044			hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)															---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77310730	77310731	+	Intron	INS	-	T	T	rs140905387	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77310730_77310731insT	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)															---	---	---	---
P4HB	5034	broad.mit.edu	37	17	79812762	79812762	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79812762delA	uc002kbn.1	-						P4HB_uc002kbm.1_Intron	NM_000918	NP_000909			prolyl 4-hydroxylase, beta subunit precursor						cell redox homeostasis|glycerol ether metabolic process|lipid metabolic process|lipoprotein metabolic process|peptidyl-proline hydroxylation to 4-hydroxy-L-proline	cell surface|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|extracellular region|melanosome|plasma membrane	electron carrier activity|procollagen-proline 4-dioxygenase activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)															---	---	---	---
ASPSCR1	79058	broad.mit.edu	37	17	79955363	79955364	+	Intron	INS	-	T	T	rs7222954		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79955363_79955364insT	uc002kcx.2	+						ASPSCR1_uc002kcw.1_Intron|ASPSCR1_uc002kcy.2_Intron|ASPSCR1_uc002kcz.2_Intron|ASPSCR1_uc002kda.2_Intron|ASPSCR1_uc002kdb.1_Intron	NM_024083	NP_076988			alveolar soft part sarcoma chromosome region,								protein binding		ASPSCR1/TFE3(161)	soft_tissue(118)|kidney(43)|breast(1)	162	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)					T	TFE3	alveolar soft part sarcoma								---	---	---	---
RAB40B	10966	broad.mit.edu	37	17	80630219	80630222	+	Intron	DEL	CACT	-	-	rs10532447		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80630219_80630222delCACT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	274943	274944	+	IGR	DEL	TC	-	-	rs72383613		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:274943_274944delTC								THOC1 (6884 upstream) : COLEC12 (44412 downstream)																																			---	---	---	---
COLEC12	81035	broad.mit.edu	37	18	340073	340074	+	Intron	DEL	GC	-	-	rs60991743		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:340073_340074delGC	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	521979	521980	+	IGR	INS	-	TT	TT	rs72314743		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:521979_521980insTT								COLEC12 (21250 upstream) : CETN1 (58389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1484052	1484053	+	IGR	INS	-	ACAC	ACAC	rs146559549	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1484052_1484053insACAC								C18orf2 (76871 upstream) : None (None downstream)																																			---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2671545	2671545	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2671545delT	uc002klm.3	+							NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	3467710	3467710	+	IGR	DEL	A	-	-	rs11348622		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3467710delA								TGIF1 (9306 upstream) : DLGAP1 (31127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	4988203	4988203	+	IGR	DEL	C	-	-	rs74717522		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4988203delC								DLGAP1 (532937 upstream) : LOC642597 (155469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5081115	5081115	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5081115delG								DLGAP1 (625849 upstream) : LOC642597 (62557 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5204763	5204765	+	IGR	DEL	ACC	-	-	rs148412782		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5204763_5204765delACC								LOC642597 (7508 upstream) : C18orf18 (31959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	6495988	6495989	+	IGR	DEL	GT	-	-	rs71912949		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6495988_6495989delGT								L3MBTL4 (81078 upstream) : ARHGAP28 (292504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	7180823	7180824	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7180823_7180824insA								LAMA1 (63010 upstream) : LRRC30 (50313 downstream)																																			---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	7620149	7620149	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7620149delC	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)																---	---	---	---
KIAA0802	23255	broad.mit.edu	37	18	8793367	8793371	+	Intron	DEL	CTAAT	-	-	rs139117276		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8793367_8793371delCTAAT	uc002knr.2	+						KIAA0802_uc002knq.2_Intron|KIAA0802_uc002kns.2_Intron	NM_015210	NP_056025			hypothetical protein LOC23255												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	8843041	8843041	+	IGR	DEL	T	-	-	rs80315115		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8843041delT								KIAA0802 (10266 upstream) : NDUFV2 (259634 downstream)																																			---	---	---	---
TWSG1	57045	broad.mit.edu	37	18	9388097	9388097	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9388097delC	uc002knz.2	+						TWSG1_uc002koa.2_5'UTR	NM_020648	NP_065699			twisted gastrulation precursor											ovary(1)|pancreas(1)	2																		---	---	---	---
RAB31	11031	broad.mit.edu	37	18	9733899	9733900	+	Intron	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9733899_9733900insG	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																		---	---	---	---
VAPA	9218	broad.mit.edu	37	18	9942469	9942469	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9942469delC	uc002kok.2	+						VAPA_uc002koj.2_Intron	NM_194434	NP_919415			vesicle-associated membrane protein-associated						cell death|cellular membrane fusion|neuron projection development|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein localization in endoplasmic reticulum|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane|vesicle	protein heterodimerization activity|signal transducer activity|structural molecule activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	11061771	11061772	+	IGR	INS	-	AT	AT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11061771_11061772insAT								FAM38B (359792 upstream) : GNAL (627364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14469804	14469805	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14469804_14469805delTT								LOC284233 (127282 upstream) : CXADRP3 (8151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15069925	15069926	+	IGR	INS	-	A	A	rs137864979	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15069925_15069926insA								ANKRD30B (217188 upstream) : LOC644669 (243629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15362842	15362843	+	IGR	DEL	CC	-	-	rs149447457	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15362842_15362843delCC								LOC644669 (36924 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15409039	15409039	+	IGR	DEL	A	-	-	rs144372703		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15409039delA								LOC644669 (83121 upstream) : None (None downstream)																																			---	---	---	---
MIB1	57534	broad.mit.edu	37	18	19308454	19308455	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19308454_19308455insA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	19856787	19856788	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19856787_19856788insT								GATA6 (74560 upstream) : CTAGE1 (136776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	20292914	20292915	+	IGR	INS	-	AA	AA	rs34990450		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20292914_20292915insAA								CTAGE1 (295036 upstream) : RBBP8 (220380 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	22588989	22588989	+	IGR	DEL	C	-	-	rs34457519		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22588989delC								HRH4 (529069 upstream) : ZNF521 (52899 downstream)																																			---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22827938	22827939	+	Intron	INS	-	C	C	rs139273067	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22827938_22827939insC	uc002kvk.2	-						ZNF521_uc010xbe.1_Intron|ZNF521_uc010dly.2_Intron|ZNF521_uc002kvl.2_Intron	NM_015461	NP_056276			zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)							T	PAX5	ALL								---	---	---	---
KCTD1	284252	broad.mit.edu	37	18	24190794	24190795	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24190794_24190795insT	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)															---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25692668	25692669	+	Intron	INS	-	AAC	AAC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25692668_25692669insAAC	uc002kwg.2	-							NM_001792	NP_001783			cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4																		---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25752041	25752042	+	Intron	DEL	GT	-	-	rs72438915		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25752041_25752042delGT	uc002kwg.2	-							NM_001792	NP_001783			cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	27512161	27512161	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27512161delA								None (None upstream) : MIR302F (366715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28002545	28002545	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28002545delT								MIR302F (123619 upstream) : DSC3 (567508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28698907	28698907	+	IGR	DEL	T	-	-	rs35848131		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28698907delT								DSC2 (16519 upstream) : DSC1 (10309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28823076	28823076	+	IGR	DEL	T	-	-	rs34655401		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28823076delT								DSC1 (80257 upstream) : DSG1 (74976 downstream)																																			---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29509155	29509155	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29509155delA	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																		---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	29972166	29972167	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29972166_29972167insT	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	30055477	30055477	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30055477delA								FAM59A (5030 upstream) : WBP11P1 (36149 downstream)																																			---	---	---	---
C18orf34	374864	broad.mit.edu	37	18	30747056	30747056	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30747056delC	uc002kxn.2	-						C18orf34_uc010dme.1_Intron|C18orf34_uc010xbr.1_Intron|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Intron|C18orf34_uc002kxp.2_Intron	NM_001105528	NP_001098998			hypothetical protein LOC374864 isoform 1											ovary(1)	1																		---	---	---	---
NOL4	8715	broad.mit.edu	37	18	31705932	31705932	+	Intron	DEL	A	-	-	rs34689802		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31705932delA	uc010dmi.2	-						NOL4_uc002kxr.3_Intron|NOL4_uc010xbt.1_Intron|NOL4_uc010dmh.2_Intron|NOL4_uc010xbu.1_Intron|NOL4_uc002kxt.3_Intron|NOL4_uc010xbw.1_Intron	NM_003787	NP_003778			nucleolar protein 4							nucleolus	RNA binding			ovary(3)	3																		---	---	---	---
INO80C	125476	broad.mit.edu	37	18	33038185	33038185	+	Intron	DEL	T	-	-	rs34278502		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33038185delT	uc002kyw.1	-							NM_194281	NP_919257			Ies6-similar protein isoform 2						DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex|MLL1 complex					0																		---	---	---	---
C18orf21	83608	broad.mit.edu	37	18	33558574	33558575	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33558574_33558575insA	uc002kzc.2	+						C18orf21_uc002kzd.2_Intron	NM_031446	NP_113634			chromosome 18 open reading frame 21												0																		---	---	---	---
CELF4	56853	broad.mit.edu	37	18	35128620	35128620	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35128620delA	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	35234593	35234593	+	5'Flank	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35234593delG	hsa-mir-4318|MI0015847	+																																									---	---	---	---
Unknown	0	broad.mit.edu	37	18	35467608	35467608	+	IGR	DEL	T	-	-	rs34909114		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35467608delT								CELF4 (321608 upstream) : None (None downstream)																																			---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	37134242	37134243	+	Intron	INS	-	A	A	rs141137001	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37134242_37134243insA	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	37519309	37519310	+	IGR	INS	-	TC	TC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37519309_37519310insTC								LOC647946 (139027 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	37915789	37915790	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37915789_37915790insT								LOC647946 (535507 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38323686	38323689	+	IGR	DEL	GTGC	-	-	rs113793322		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38323686_38323689delGTGC								LOC647946 (943404 upstream) : KC6 (736549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38482239	38482240	+	IGR	INS	-	A	A	rs147932957	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38482239_38482240insA								None (None upstream) : KC6 (577998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38707214	38707214	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38707214delA								None (None upstream) : KC6 (353024 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38845177	38845178	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38845177_38845178delAC								None (None upstream) : KC6 (215060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39407155	39407155	+	IGR	DEL	A	-	-	rs5824376		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39407155delA								KC6 (306594 upstream) : PIK3C3 (128044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39752545	39752545	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39752545delC								PIK3C3 (91101 upstream) : RIT2 (570648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39861638	39861639	+	Intron	INS	-	T	T	rs142796758	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39861638_39861639insT	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	40234631	40234632	+	Intron	INS	-	TATT	TATT	rs138827387	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40234631_40234632insTATT	uc002lau.2	+											Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																														---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	42772580	42772585	+	Intron	DEL	TGTGTG	-	-	rs140643395		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42772580_42772585delTGTGTG	uc002lbb.2	+							NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	43562467	43562471	+	IGR	DEL	TTTTT	-	-	rs34280081		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43562467_43562471delTTTTT								KIAA1632 (15162 upstream) : PSTPIP2 (1032 downstream)																																			---	---	---	---
RNF165	494470	broad.mit.edu	37	18	43917769	43917769	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43917769delT	uc002lcb.1	+						RNF165_uc002lby.1_Intron|RNF165_uc010dnn.1_Intron	NM_152470	NP_689683			ring finger protein 165								zinc ion binding				0				READ - Rectum adenocarcinoma(1;0.0873)														---	---	---	---
RNF165	494470	broad.mit.edu	37	18	44016240	44016241	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44016240_44016241delTG	uc002lcb.1	+						RNF165_uc002lby.1_Intron|RNF165_uc010dnn.1_Intron	NM_152470	NP_689683			ring finger protein 165								zinc ion binding				0				READ - Rectum adenocarcinoma(1;0.0873)														---	---	---	---
KATNAL2	83473	broad.mit.edu	37	18	44501657	44501657	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44501657delA	uc010dnq.1	+						PIAS2_uc002lcn.1_5'Flank					SubName: Full=Putative uncharacterized protein DKFZp667C165; Flags: Fragment;							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
KATNAL2	83473	broad.mit.edu	37	18	44588236	44588236	+	Intron	DEL	T	-	-	rs77869357		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44588236delT	uc002lco.2	+						KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lcp.3_Intron	NM_031303	NP_112593			katanin p60 subunit A-like 2							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	44741365	44741366	+	5'Flank	INS	-	A	A	rs34384622		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44741365_44741366insA	uc002lcv.1	-											Homo sapiens CH18515 mRNA, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	44977358	44977359	+	Intron	DEL	CA	-	-	rs35034851		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44977358_44977359delCA	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	44984978	44984979	+	Intron	DEL	AA	-	-	rs10533435	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44984978_44984979delAA	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	45126926	45126928	+	IGR	DEL	ACA	-	-	rs73435757	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45126926_45126928delACA								IER3IP1 (424181 upstream) : SMAD2 (232539 downstream)																																			---	---	---	---
SMAD2	4087	broad.mit.edu	37	18	45382513	45382513	+	Intron	DEL	T	-	-	rs35798864		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45382513delT	uc002lcy.2	-						SMAD2_uc002lcz.2_Intron|SMAD2_uc010xdc.1_Intron|SMAD2_uc010xdd.1_Intron	NM_005901	NP_005892			Sma- and Mad-related protein 2 isoform 1						anterior/posterior pattern formation|cell fate commitment|common-partner SMAD protein phosphorylation|intracellular signal transduction|mesoderm formation|negative regulation of transcription, DNA-dependent|palate development|paraxial mesoderm morphogenesis|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|regulation of binding|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|zygotic specification of dorsal/ventral axis	activin responsive factor complex|cytosol	activating transcription factor binding|co-SMAD binding|double-stranded DNA binding|I-SMAD binding|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding			large_intestine(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45635981	45635982	+	Intron	INS	-	CA	CA	rs149483322	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45635981_45635982insCA	uc010dnv.2	-						ZBTB7C_uc002ldb.2_Intron|ZBTB7C_uc010dnu.2_Intron|ZBTB7C_uc010dnw.2_Intron|ZBTB7C_uc010dnx.1_Intron|ZBTB7C_uc010dny.1_Intron|ZBTB7C_uc010dnz.1_Intron|ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449			zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45657841	45657842	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45657841_45657842insT	uc010dnv.2	-						ZBTB7C_uc002ldb.2_Intron|ZBTB7C_uc010dnu.2_Intron|ZBTB7C_uc010dnw.2_Intron|ZBTB7C_uc010dnx.1_Intron|ZBTB7C_uc010dny.1_Intron|ZBTB7C_uc010dnz.1_Intron|ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449			zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46104528	46104528	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46104528delT	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron	NM_014772	NP_055587			hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46373031	46373034	+	Intron	DEL	TGGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46373031_46373034delTGGA	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron|KIAA0427_uc002lde.3_Intron	NM_014772	NP_055587			hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	47348488	47348489	+	IGR	INS	-	A	A	rs34878474		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47348488_47348489insA								SCARNA17 (7675 upstream) : MYO5B (667 downstream)																																			---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47580031	47580036	+	Intron	DEL	GTGCAC	-	-	rs5824819	byFrequency	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47580031_47580036delGTGCAC	uc002leb.2	-						MYO5B_uc002lec.1_Intron	NM_001080467	NP_001073936			myosin VB						protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	48300612	48300612	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48300612delA								MAPK4 (42417 upstream) : MRO (20879 downstream)																																			---	---	---	---
SMAD4	4089	broad.mit.edu	37	18	48530060	48530060	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48530060delA	uc010xdo.1	+											Homo sapiens D29 mRNA, complete cds.						BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity			pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)										Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				---	---	---	---
DCC	1630	broad.mit.edu	37	18	51023279	51023281	+	Intron	DEL	AGT	-	-	rs34970199		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51023279_51023281delAGT	uc002lfe.1	+						DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	51234906	51234907	+	IGR	DEL	AG	-	-	rs3062422		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51234906_51234907delAG								DCC (177124 upstream) : MBD2 (445668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	51826370	51826370	+	IGR	DEL	A	-	-	rs34407740		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51826370delA								POLI (1768 upstream) : STARD6 (24693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	52655276	52655277	+	IGR	DEL	GA	-	-	rs77341780		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52655276_52655277delGA								CCDC68 (28537 upstream) : TCF4 (234285 downstream)																																			---	---	---	---
TCF4	6925	broad.mit.edu	37	18	53290112	53290113	+	Intron	INS	-	TGTGTGTGTG	TGTGTGTGTG	rs138216350	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53290112_53290113insTGTGTGTGTG	uc002lga.2	-							NM_001083962	NP_001077431			transcription factor 4 isoform a						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	53492811	53492811	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53492811delT								TCF4 (189626 upstream) : TXNL1 (777244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	53836328	53836328	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53836328delT								TCF4 (533143 upstream) : TXNL1 (433727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55192010	55192016	+	IGR	DEL	AAGAAAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55192010_55192016delAAGAAAG								ONECUT2 (33481 upstream) : FECH (20058 downstream)																																			---	---	---	---
ATP8B1	5205	broad.mit.edu	37	18	55377229	55377230	+	Intron	INS	-	T	T	rs28546813		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55377229_55377230insT	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	55835154	55835154	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55835154delA	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	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																		---	---	---	---
MALT1	10892	broad.mit.edu	37	18	56336272	56336272	+	5'Flank	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56336272delT	uc002lhm.1	+						MALT1_uc002lhn.1_5'Flank	NM_006785	NP_006776			mucosa associated lymphoid tissue lymphoma						activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			ovary(2)|lung(1)|central_nervous_system(1)	4								T	BIRC3	MALT								---	---	---	---
CCBE1	147372	broad.mit.edu	37	18	57191985	57191986	+	Intron	INS	-	TG	TG	rs149804739	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57191985_57191986insTG	uc002lib.2	-							NM_133459	NP_597716			collagen and calcium binding EGF domains 1						lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)																---	---	---	---
CCBE1	147372	broad.mit.edu	37	18	57347930	57347931	+	Intron	INS	-	A	A	rs142799321	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57347930_57347931insA	uc002lib.2	-							NM_133459	NP_597716			collagen and calcium binding EGF domains 1						lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	58721703	58721704	+	IGR	INS	-	GT	GT	rs148677759	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58721703_58721704insGT								MC4R (681702 upstream) : CDH20 (279284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58985494	58985495	+	IGR	DEL	AC	-	-	rs72153427		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58985494_58985495delAC								MC4R (945493 upstream) : CDH20 (15493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	59335219	59335219	+	IGR	DEL	T	-	-	rs34219713		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59335219delT								CDH20 (112854 upstream) : RNF152 (147085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	60099569	60099570	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60099569_60099570insA								TNFRSF11A (46067 upstream) : ZCCHC2 (91088 downstream)																																			---	---	---	---
ZCCHC2	54877	broad.mit.edu	37	18	60188149	60188151	+	5'Flank	DEL	AAC	-	-	rs72351056		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60188149_60188151delAAC	uc002lip.3	+						ZCCHC2_uc002lio.2_5'Flank	NM_017742	NP_060212			zinc finger, CCHC domain containing 2						cell communication	cytoplasm	nucleic acid binding|phosphatidylinositol binding|zinc ion binding			lung(1)|prostate(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	60758188	60758188	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60758188delT								PHLPP1 (110523 upstream) : BCL2 (32391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	61128929	61128929	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61128929delT								VPS4B (39177 upstream) : SERPINB5 (15215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	61515441	61515442	+	IGR	DEL	AC	-	-	rs34169228		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61515441_61515442delAC								SERPINB7 (42838 upstream) : SERPINB2 (39497 downstream)																																			---	---	---	---
SERPINB10	5273	broad.mit.edu	37	18	61577995	61577996	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61577995_61577996delTG	uc010xev.1	+						SERPINB2_uc002ljp.1_Intron|SERPINB2_uc002ljq.1_Intron	NM_005024	NP_005015			serine (or cysteine) proteinase inhibitor, clade							cytoplasm|nucleus	serine-type endopeptidase inhibitor activity			lung(1)|kidney(1)|skin(1)	3		Esophageal squamous(42;0.131)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	62307235	62307236	+	IGR	DEL	TA	-	-	rs150694766		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62307235_62307236delTA								C18orf20 (490975 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	62400794	62400795	+	IGR	DEL	CC	-	-	rs9962864	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62400794_62400795delCC								C18orf20 (584534 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	62831904	62831906	+	IGR	DEL	AAC	-	-	rs72491411		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62831904_62831906delAAC								None (None upstream) : CDH7 (585582 downstream)																																			---	---	---	---
CDH7	1005	broad.mit.edu	37	18	63471935	63471936	+	Intron	INS	-	GTGT	GTGT	rs141411077	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63471935_63471936insGTGT	uc002ljz.2	+						CDH7_uc002lka.2_Intron|CDH7_uc002lkb.2_Intron	NM_033646	NP_387450			cadherin 7, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4		Esophageal squamous(42;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	64879090	64879091	+	IGR	INS	-	AG	AG	rs148999317	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64879090_64879091insAG								CDH19 (607874 upstream) : DSEL (294728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	64988653	64988653	+	IGR	DEL	G	-	-	rs11151355	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64988653delG								CDH19 (717437 upstream) : DSEL (185166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	65005429	65005432	+	IGR	DEL	TCCC	-	-	rs142545695	by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65005429_65005432delTCCC								CDH19 (734213 upstream) : DSEL (168387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	65848244	65848247	+	IGR	DEL	ACAC	-	-	rs35900844		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65848244_65848247delACAC								DSEL (664277 upstream) : TMX3 (492680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66155589	66155589	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66155589delA								DSEL (971622 upstream) : TMX3 (185338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66313888	66313889	+	IGR	INS	-	A	A	rs147934018	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66313888_66313889insA								None (None upstream) : TMX3 (27038 downstream)																																			---	---	---	---
CCDC102B	79839	broad.mit.edu	37	18	66582212	66582213	+	Intron	DEL	GA	-	-	rs34159363		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66582212_66582213delGA	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	68689839	68689840	+	IGR	INS	-	A	A	rs141717051	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68689839_68689840insA								SOCS6 (692405 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	68824615	68824615	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68824615delT								SOCS6 (827181 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	68930930	68930931	+	IGR	DEL	GA	-	-	rs10597215		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68930930_68930931delGA								SOCS6 (933496 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71182748	71182748	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71182748delA								NETO1 (647938 upstream) : FBXO15 (557840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71236874	71236874	+	IGR	DEL	C	-	-	rs34088192		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71236874delC								NETO1 (702064 upstream) : FBXO15 (503714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71293213	71293215	+	IGR	DEL	AAG	-	-	rs5826276		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71293213_71293215delAAG								NETO1 (758403 upstream) : FBXO15 (447373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71383212	71383212	+	IGR	DEL	A	-	-	rs113699000		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71383212delA								NETO1 (848402 upstream) : FBXO15 (357376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73106035	73106038	+	IGR	DEL	TCTC	-	-	rs112677576		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73106035_73106038delTCTC								TSHZ1 (104135 upstream) : C18orf62 (15789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76596645	76596645	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76596645delA								None (None upstream) : SALL3 (143630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76659946	76659946	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76659946delC								None (None upstream) : SALL3 (80329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	77343414	77343414	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77343414delT								NFATC1 (54092 upstream) : CTDP1 (96387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	77393848	77393850	+	IGR	DEL	GCA	-	-	rs144433300	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77393848_77393850delGCA								NFATC1 (104526 upstream) : CTDP1 (45951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	77543479	77543480	+	IGR	DEL	AC	-	-	rs71339918		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77543479_77543480delAC								CTDP1 (28972 upstream) : KCNG2 (80188 downstream)																																			---	---	---	---
PQLC1	80148	broad.mit.edu	37	18	77679932	77679932	+	Intron	DEL	A	-	-	rs68180537		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77679932delA	uc002lnl.2	-						PQLC1_uc010dre.2_Intron|PQLC1_uc002lnk.2_Intron|PQLC1_uc010xfm.1_Intron	NM_025078	NP_079354			PQ loop repeat containing 1 isoform 1							integral to membrane				large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0212)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;8.2e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0258)														---	---	---	---
PARD6G	84552	broad.mit.edu	37	18	77997328	77997328	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77997328delA	uc002lny.2	-						PARD6G_uc010xfp.1_Intron	NM_032510	NP_115899			PAR-6 gamma protein						cell cycle|cell division|tight junction assembly	cytosol|tight junction	protein binding				0		all_cancers(4;5.63e-22)|all_epithelial(4;5.86e-15)|all_lung(4;1.32e-05)|Ovarian(4;1.33e-05)|Lung NSC(4;2.77e-05)|Esophageal squamous(42;0.0157)|all_hematologic(56;0.13)|Melanoma(33;0.144)		Epithelial(2;1.48e-13)|all cancers(1;5.77e-13)|OV - Ovarian serous cystadenocarcinoma(15;2.74e-10)|BRCA - Breast invasive adenocarcinoma(31;0.00166)|STAD - Stomach adenocarcinoma(84;0.18)|Lung(128;0.23)														---	---	---	---
ARID3A	1820	broad.mit.edu	37	19	966459	966459	+	Intron	DEL	A	-	-	rs71335324		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:966459delA	uc002lql.2	+							NM_005224	NP_005215			AT rich interactive domain 3A (BRIGHT- like)							cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
CSNK1G2	1455	broad.mit.edu	37	19	1947212	1947213	+	Intron	INS	-	CAAGT	CAAGT	rs139325671	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1947212_1947213insCAAGT	uc002lul.3	+							NM_001319	NP_001310			casein kinase 1, gamma 2						sphingolipid metabolic process|Wnt receptor signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity			stomach(1)	1		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	2364190	2364191	+	IGR	INS	-	TGAA	TGAA	rs146229451	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2364190_2364191insTGAA								SPPL2B (9091 upstream) : TMPRSS9 (25593 downstream)																																			---	---	---	---
GNG7	2788	broad.mit.edu	37	19	2568096	2568097	+	Intron	DEL	CT	-	-	rs35977511	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2568096_2568097delCT	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)														---	---	---	---
CELF5	60680	broad.mit.edu	37	19	3230075	3230076	+	Intron	INS	-	TCAT	TCAT	rs141880703	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3230075_3230076insTCAT	uc002lxm.2	+						CELF5_uc002lxl.1_Intron|CELF5_uc010dtj.1_Intron|CELF5_uc010xhg.1_Intron	NM_021938	NP_068757			bruno-like 5, RNA binding protein						mRNA processing	cytoplasm|nucleus	nucleotide binding|RNA binding			ovary(2)	2																		---	---	---	---
NFIC	4782	broad.mit.edu	37	19	3370479	3370480	+	Intron	DEL	CT	-	-	rs67863049		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3370479_3370480delCT	uc010xhi.1	+						NFIC_uc002lxo.2_Intron|NFIC_uc010xhh.1_Intron|NFIC_uc002lxp.2_Intron|NFIC_uc010xhj.1_Intron	NM_205843	NP_995315			nuclear factor I/C isoform 2						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)														---	---	---	---
PIAS4	51588	broad.mit.edu	37	19	4035957	4035958	+	Intron	INS	-	CATC	CATC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4035957_4035958insCATC	uc002lzg.2	+							NM_015897	NP_056981			protein inhibitor of activated STAT, 4						positive regulation of protein sumoylation|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|PML body	DNA binding|SUMO ligase activity|ubiquitin protein ligase binding|zinc ion binding			pancreas(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	4808017	4808018	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4808017_4808018delTT								FEM1A (12448 upstream) : TICAM1 (7921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	5469505	5469505	+	IGR	DEL	A	-	-	rs33932503		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5469505delA								ZNRF4 (12639 upstream) : PLAC2 (88675 downstream)																																			---	---	---	---
INSR	3643	broad.mit.edu	37	19	7191901	7191902	+	Intron	INS	-	GA	GA	rs147258718	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7191901_7191902insGA	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199			insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
INSR	3643	broad.mit.edu	37	19	7289416	7289416	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7289416delC	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199			insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	7842924	7842924	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7842924delT								CLEC4M (8434 upstream) : CLEC4GP1 (9446 downstream)																																			---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8171614	8171617	+	Intron	DEL	TGGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8171614_8171617delTGGA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	8453308	8453308	+	Intron	DEL	T	-	-	rs77250095		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8453308delT	uc002mjt.3	-						RAB11B_uc010xkd.1_5'Flank|RAB11B_uc002mju.3_5'Flank					Homo sapiens, clone IMAGE:4863312, mRNA.																														---	---	---	---
HNRNPM	4670	broad.mit.edu	37	19	8541462	8541464	+	Intron	DEL	AAG	-	-	rs61477212		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8541462_8541464delAAG	uc010dwe.2	+						HNRNPM_uc010xke.1_Intron|HNRNPM_uc010dwd.2_Intron|HNRNPM_uc002mka.2_Intron	NM_005968	NP_005959			heterogeneous nuclear ribonucleoprotein M						alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	9173287	9173288	+	IGR	DEL	CC	-	-	rs10417127	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9173287_9173288delCC								MUC16 (81269 upstream) : OR1M1 (30633 downstream)																																			---	---	---	---
ZNF121	7675	broad.mit.edu	37	19	9683692	9683693	+	Intron	INS	-	AAC	AAC	rs150992104	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9683692_9683693insAAC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	9831816	9831816	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9831816delT								ZNF562 (46040 upstream) : ZNF846 (31000 downstream)																																			---	---	---	---
OLFM2	93145	broad.mit.edu	37	19	10012104	10012107	+	Intron	DEL	AAAC	-	-	rs113197528		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10012104_10012107delAAAC	uc002mmp.2	-							NM_058164	NP_477512			olfactomedin 2 precursor							extracellular region				large_intestine(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	10055747	10055748	+	IGR	DEL	AA	-	-	rs3075687	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10055747_10055748delAA								OLFM2 (8677 upstream) : COL5A3 (14489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	10187459	10187462	+	IGR	DEL	GGAA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10187459_10187462delGGAA								C3P1 (2648 upstream) : C19orf66 (9344 downstream)																																			---	---	---	---
CARM1	10498	broad.mit.edu	37	19	10995017	10995017	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10995017delC	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																		---	---	---	---
ELAVL3	1995	broad.mit.edu	37	19	11569767	11569767	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11569767delT	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																		---	---	---	---
ZNF443	10224	broad.mit.edu	37	19	12548230	12548231	+	Intron	INS	-	AAAAG	AAAAG	rs75498086		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12548230_12548231insAAAAG	uc002mtu.2	-							NM_005815	NP_005806			zinc finger protein 443						induction of apoptosis|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1																		---	---	---	---
WDR83	84292	broad.mit.edu	37	19	12785926	12785927	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12785926_12785927insA	uc002mue.3	+						WDR83_uc002muc.2_Intron|WDR83_uc010dyw.2_Intron	NM_001099737	NP_001093207			mitogen-activated protein kinase organizer 1						nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|cytoplasm				lung(1)|breast(1)	2																		---	---	---	---
GADD45GIP1	90480	broad.mit.edu	37	19	13067472	13067473	+	Intron	INS	-	AAAC	AAAC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13067472_13067473insAAAC	uc002mwb.2	-							NM_052850	NP_443082			growth arrest and DNA-damage-inducible, gamma						cell cycle|interspecies interaction between organisms	nucleus	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13318995	13319003	+	Intron	DEL	GGAGGAGGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13318995_13319003delGGAGGAGGA	uc010dze.2	-						CACNA1A_uc010xnd.1_Intron|CACNA1A_uc002mwx.3_Intron|CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc002mwv.3_Intron	NM_001127221	NP_001120693			calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13619413	13619414	+	5'Flank	INS	-	TG	TG	rs72530550		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13619413_13619414insTG	uc010dze.2	-						CACNA1A_uc002mwy.3_5'Flank	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)													---	---	---	---
CC2D1A	54862	broad.mit.edu	37	19	14025455	14025455	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14025455delT	uc002mxo.2	+						CC2D1A_uc002mxn.2_Intron|CC2D1A_uc002mxp.2_Intron|CC2D1A_uc010dzh.2_Intron	NM_017721	NP_060191			coiled-coil and C2 domain containing 1A						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|plasma membrane	DNA binding|signal transducer activity				0			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)															---	---	---	---
TECR	9524	broad.mit.edu	37	19	14665892	14665892	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14665892delT	uc002mza.2	+						TECR_uc002mzb.2_Intron|TECR_uc010xns.1_Intron|TECR_uc002mzc.2_Intron|TECR_uc002mzd.2_Intron	NM_138501	NP_612510			glycoprotein, synaptic 2						fatty acid elongation|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	integral to endoplasmic reticulum membrane	trans-2-enoyl-CoA reductase (NADPH) activity|very long-chain-acyl-CoA dehydrogenase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	14921185	14921185	+	IGR	DEL	T	-	-	rs71333316		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14921185delT								OR7C1 (10237 upstream) : OR7A5 (15955 downstream)																																			---	---	---	---
NOTCH3	4854	broad.mit.edu	37	19	15296715	15296717	+	Intron	DEL	TTC	-	-	rs10407433	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15296715_15296717delTTC	uc002nan.2	-						NOTCH3_uc002nao.1_Intron	NM_000435	NP_000426			Notch homolog 3 precursor						Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1)	21			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	15449750	15449750	+	IGR	DEL	A	-	-	rs74639657		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15449750delA								BRD4 (6408 upstream) : AKAP8 (14591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	15691076	15691077	+	IGR	INS	-	CAC	CAC	rs144280948	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15691076_15691077insCAC								CYP4F22 (27949 upstream) : CYP4F8 (34952 downstream)																																			---	---	---	---
CYP4F12	66002	broad.mit.edu	37	19	15788760	15788763	+	Intron	DEL	CCTC	-	-	rs62106475		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15788760_15788763delCCTC	uc002nbl.2	+						CYP4F12_uc010xoo.1_Intron|CYP4F12_uc010xop.1_Intron	NM_023944	NP_076433			cytochrome P450, family 4, subfamily F,											skin(3)|ovary(2)|central_nervous_system(2)	7	Acute lymphoblastic leukemia(2;0.0367)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	15968384	15968384	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15968384delA								UCA1 (22154 upstream) : CYP4F2 (20450 downstream)																																			---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17056983	17056984	+	Intron	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17056983_17056984insG	uc002nfb.2	-							NM_015692	NP_056507			C3 and PZP-like, alpha-2-macroglobulin domain							extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
MYO9B	4650	broad.mit.edu	37	19	17266006	17266006	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17266006delT	uc010eak.2	+						MYO9B_uc002nfi.2_Intron|MYO9B_uc002nfj.1_Intron	NM_004145	NP_004136			myosin IXB isoform 1						actin filament-based movement	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1																		---	---	---	---
GMIP	51291	broad.mit.edu	37	19	19742797	19742797	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19742797delA	uc002nnd.2	-						GMIP_uc010xrb.1_Intron|GMIP_uc010xrc.1_Intron	NM_016573	NP_057657			GEM interacting protein						negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	20863572	20863572	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20863572delT								ZNF626 (19170 upstream) : ZNF85 (242508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	22050291	22050294	+	IGR	DEL	TCTA	-	-	rs73013658	byFrequency;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22050291_22050294delTCTA								ZNF43 (15461 upstream) : ZNF208 (65466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	22956460	22956460	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22956460delT								ZNF99 (3676 upstream) : ZNF91 (564959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23666444	23666444	+	IGR	DEL	A	-	-	rs74373005		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23666444delA								ZNF91 (88175 upstream) : ZNF675 (169265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23904544	23904545	+	IGR	DEL	GA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23904544_23904545delGA								ZNF675 (34527 upstream) : ZNF681 (17454 downstream)																																			---	---	---	---
ZNF681	148213	broad.mit.edu	37	19	23928252	23928252	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23928252delT	uc002nrk.3	-						ZNF681_uc002nrl.3_Intron|ZNF681_uc002nrj.3_Intron	NM_138286	NP_612143			zinc finger protein 681						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	24062031	24062032	+	IGR	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24062031_24062032delAG								RPSAP58 (51114 upstream) : ZNF254 (154215 downstream)																																			---	---	---	---
ZNF254	9534	broad.mit.edu	37	19	24229842	24229842	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24229842delT	uc010xrk.1	+						uc002nrr.1_Intron|uc002nrs.1_Intron	NM_203282	NP_975011			zinc finger protein 254						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	24550625	24550626	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24550625_24550626insT								LOC100101266 (204376 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27879008	27879009	+	IGR	INS	-	AC	AC	rs145042475		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27879008_27879009insAC								None (None upstream) : LOC148189 (402393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28081135	28081135	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28081135delT								None (None upstream) : LOC148189 (200267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28395934	28395935	+	IGR	INS	-	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28395934_28395935insG								LOC148189 (111086 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28780591	28780591	+	IGR	DEL	T	-	-	rs34900295		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28780591delT								LOC148189 (495743 upstream) : LOC148145 (675449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29446396	29446396	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29446396delG								None (None upstream) : LOC148145 (9644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29833839	29833840	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29833839_29833840insA	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	30401907	30401922	+	IGR	DEL	TCTTTCTTTCTTTCTT	-	-	rs56128977	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30401907_30401922delTCTTTCTTTCTTTCTT								CCNE1 (86689 upstream) : C19orf2 (12629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31509858	31509858	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31509858delT								ZNF536 (460893 upstream) : DKFZp566F0947 (130925 downstream)																																			---	---	---	---
TSHZ3	57616	broad.mit.edu	37	19	31796224	31796225	+	Intron	INS	-	A	A	rs113824162		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31796224_31796225insA	uc002nsy.3	-							NM_020856	NP_065907			zinc finger protein 537						negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	32668522	32668523	+	IGR	INS	-	AAGGCAGG	AAGGCAGG			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32668522_32668523insAAGGCAGG								TSHZ3 (828332 upstream) : ZNF507 (167991 downstream)																																			---	---	---	---
ZNF507	22847	broad.mit.edu	37	19	32852807	32852808	+	Intron	INS	-	TCCT	TCCT	rs142244109	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32852807_32852808insTCCT	uc002nte.2	+						ZNF507_uc002ntd.2_Intron	NM_001136156	NP_001129628			zinc finger protein 507						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(110;0.162)																	---	---	---	---
TDRD12	91646	broad.mit.edu	37	19	33257528	33257528	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33257528delT	uc002ntq.2	+						TDRD12_uc002ntr.3_Intron					RecName: Full=Tudor domain-containing protein 12; AltName: Full=ES cell-associated transcript 8 protein;								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	Esophageal squamous(110;0.137)																	---	---	---	---
CCDC123	84902	broad.mit.edu	37	19	33392917	33392918	+	Intron	DEL	TG	-	-	rs71176164	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33392917_33392918delTG	uc002nty.2	-						CCDC123_uc002ntx.2_Intron|CCDC123_uc010edg.2_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	33509937	33509938	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33509937_33509938insA	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	34476676	34476677	+	IGR	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34476676_34476677delAG								KCTD15 (170011 upstream) : LSM14A (186675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34652912	34652912	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34652912delC								KCTD15 (346247 upstream) : LSM14A (10440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	35153409	35153410	+	Intron	INS	-	AC	AC	rs138247202	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35153409_35153410insAC	uc002nvo.1	-											Homo sapiens cDNA FLJ36176 fis, clone TESTI2026491.																														---	---	---	---
ZNF573	126231	broad.mit.edu	37	19	38296329	38296329	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38296329delT	uc010efs.2	-							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)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38657577	38657577	+	Intron	DEL	A	-	-	rs71912350		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38657577delA	uc002ohk.2	+							NM_015073	NP_055888			signal-induced proliferation-associated 1 like						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
MAP4K1	11184	broad.mit.edu	37	19	39081605	39081606	+	Intron	INS	-	CA	CA	rs80091989		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39081605_39081606insCA	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)															---	---	---	---
FBXO17	115290	broad.mit.edu	37	19	39467391	39467391	+	5'Flank	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39467391delC	uc002okg.1	-							NM_024907	NP_079183			F-box protein FBG4 isoform 2						protein catabolic process	SCF ubiquitin ligase complex	glycoprotein binding				0	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)													OREG0025456	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SELV	348303	broad.mit.edu	37	19	40007068	40007069	+	Intron	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40007068_40007069delTC	uc010xvc.1	+							NM_182704	NP_874363			selenoprotein V						cell redox homeostasis		selenium binding				0	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;8.61e-26)|all cancers(26;2.76e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	41157496	41157497	+	IGR	INS	-	GAAA	GAAA			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41157496_41157497insGAAA								LTBP4 (21771 upstream) : NUMBL (14317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	41324352	41324353	+	IGR	INS	-	A	A	rs144591646	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41324352_41324353insA								EGLN2 (10016 upstream) : CYP2A6 (25091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	41541994	41541994	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41541994delG								CYP2A7 (7826 upstream) : CYP2A13 (52374 downstream)																																			---	---	---	---
CYP2F1	1572	broad.mit.edu	37	19	41636701	41636701	+	Intron	DEL	T	-	-	rs112962283		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41636701delT	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																		---	---	---	---
CYP2F1	1572	broad.mit.edu	37	19	41640432	41640433	+	Intron	INS	-	AA	AA	rs143073423	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41640432_41640433insAA	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	42359508	42359510	+	IGR	DEL	TTC	-	-	rs113352144		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42359508_42359510delTTC								DMRTC2 (3113 upstream) : RPS19 (4478 downstream)																																			---	---	---	---
LIPE	3991	broad.mit.edu	37	19	42924507	42924507	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42924507delG	uc002otr.2	-						uc010eif.1_Intron|LIPE_uc002ots.1_Intron	NM_005357	NP_005348			hormone-sensitive lipase						cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	43080891	43080891	+	Intron	DEL	T	-	-	rs35986913		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43080891delT	uc010eif.1	+						uc010eig.1_Intron|uc010eih.1_Intron					Homo sapiens cDNA FLJ39530 fis, clone PUAEN2004400.																														---	---	---	---
TEX101	83639	broad.mit.edu	37	19	43897255	43897256	+	Intron	INS	-	GAAA	GAAA	rs7409161	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43897255_43897256insGAAA	uc002owk.2	+							NM_031451	NP_113639			testis expressed 101 isoform 1							anchored to membrane|plasma membrane				ovary(1)	1		Prostate(69;0.0199)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	44526342	44526342	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44526342delT								ZNF230 (8270 upstream) : ZNF284 (3152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	44593267	44593271	+	IGR	DEL	TTTTG	-	-	rs67645517		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44593267_44593271delTTTTG								ZNF284 (1644 upstream) : ZNF224 (5226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	45132698	45132698	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45132698delT	uc002ozk.2	+											SubName: Full=LOC147710 protein; Flags: Fragment;																														---	---	---	---
EXOC3L2	90332	broad.mit.edu	37	19	45718188	45718188	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45718188delC	uc002pay.1	-							NM_138568	NP_612635			exocyst complex component 3-like 2											ovary(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)														---	---	---	---
RUVBL2	10856	broad.mit.edu	37	19	49512743	49512744	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49512743_49512744insA	uc002plr.1	+						RUVBL2_uc002plq.1_Intron|RUVBL2_uc010yab.1_Intron|RUVBL2_uc002pls.1_Intron|RUVBL2_uc010emn.1_Intron|RUVBL2_uc010yac.1_Intron	NM_006666	NP_006657			RuvB-like 2						cellular response to UV|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|protein folding|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex|membrane|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|ATP-dependent DNA helicase activity|damaged DNA binding|identical protein binding|unfolded protein binding				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)														---	---	---	---
CGB7	94027	broad.mit.edu	37	19	49562908	49562909	+	Intron	DEL	GA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49562908_49562909delGA	uc010yah.1	-						CGB7_uc002pme.2_5'Flank|CGB7_uc010emq.1_5'Flank					SubName: Full=cDNA FLJ60732;						apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Choriogonadotropin alfa(DB00097)													---	---	---	---
TEAD2	8463	broad.mit.edu	37	19	49864057	49864057	+	Intron	DEL	G	-	-	rs66557222		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49864057delG	uc002pnj.2	-						TEAD2_uc002png.2_5'Flank|TEAD2_uc002pnh.2_Intron|TEAD2_uc002pni.2_Intron|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Intron|DKKL1_uc002pnk.2_5'Flank	NM_003598	NP_003589			TEA domain family member 2						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)														---	---	---	---
SLC17A7	57030	broad.mit.edu	37	19	49942434	49942435	+	Intron	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49942434_49942435delCT	uc002pnp.2	-						SLC17A7_uc002pnq.1_5'Flank	NM_020309	NP_064705			solute carrier family 17, member 7						glutamate secretion|neurotransmitter secretion	cell junction|clathrin sculpted glutamate transport vesicle membrane|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|sodium-dependent phosphate transmembrane transporter activity|sodium:inorganic phosphate symporter activity			ovary(1)|pancreas(1)|skin(1)	3		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(486;0.0245)														---	---	---	---
KLK6	5653	broad.mit.edu	37	19	51463582	51463599	+	Intron	DEL	GTTTCTGCCTGTGTCTCC	-	-	rs117202961		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51463582_51463599delGTTTCTGCCTGTGTCTCC	uc002pui.2	-						KLK6_uc010eoj.2_Intron|KLK6_uc002puh.2_Intron|KLK6_uc002puj.2_Intron|KLK6_uc010ycn.1_Intron|KLK6_uc002pul.2_Intron|KLK6_uc002pum.2_Intron	NM_001012964	NP_001012982			kallikrein-related peptidase 6 isoform A						amyloid precursor protein metabolic process|central nervous system development|collagen catabolic process|hormone metabolic process|myelination|positive regulation of G-protein coupled receptor protein signaling pathway|protein autoprocessing|proteolysis|regulation of cell differentiation|tissue regeneration	endoplasmic reticulum|extracellular region|microsome|mitochondrion|nucleolus	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)														---	---	---	---
ZNF808	388558	broad.mit.edu	37	19	53036949	53036950	+	Intron	DEL	AT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53036949_53036950delAT	uc010epq.1	+						ZNF808_uc002pzq.2_Intron	NM_001039886	NP_001034975			zinc finger protein 808						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	54490834	54490835	+	IGR	INS	-	T	T	rs150204106	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54490834_54490835insT								CACNG8 (4695 upstream) : CACNG6 (4707 downstream)																																			---	---	---	---
KIR3DX1	90011	broad.mit.edu	37	19	55053966	55053966	+	Intron	DEL	T	-	-	rs66488179		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55053966delT	uc010erm.2	+						KIR3DX1_uc010yfa.1_Intron|KIR3DX1_uc010yfb.1_Intron|KIR3DX1_uc010yfc.1_Intron|KIR3DX1_uc010yfd.1_Intron					Homo sapiens killer cell immunoglobulin-like receptor, three domains, X1, mRNA (cDNA clone IMAGE:4849085).											ovary(1)	1				GBM - Glioblastoma multiforme(193;0.099)														---	---	---	---
KIR2DL3	3804	broad.mit.edu	37	19	55268037	55268038	+	Intron	INS	-	G	G	rs59900172		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55268037_55268038insG	uc010erw.1	+						KIR2DS4_uc010yfj.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL3_uc002qha.1_Intron|KIR3DP1_uc010yfi.1_Intron	NM_015868	NP_056952			killer cell immunoglobulin-like receptor, two						immune response|regulation of immune response	integral to plasma membrane	antigen binding|protein binding|receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(193;0.0192)														---	---	---	---
KIR2DL3	3804	broad.mit.edu	37	19	55271765	55271766	+	Intron	DEL	GA	-	-	rs112795662		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55271765_55271766delGA	uc010erw.1	+						KIR2DS4_uc010yfj.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL3_uc002qha.1_Intron|KIR3DP1_uc010yfi.1_Intron	NM_015868	NP_056952			killer cell immunoglobulin-like receptor, two						immune response|regulation of immune response	integral to plasma membrane	antigen binding|protein binding|receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(193;0.0192)														---	---	---	---
HSPBP1	23640	broad.mit.edu	37	19	55777843	55777845	+	Intron	DEL	TCC	-	-	rs146055875		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55777843_55777845delTCC	uc002qjx.2	-						HSPBP1_uc002qjy.2_Intron|HSPBP1_uc002qkb.2_Intron|HSPBP1_uc002qka.2_Intron|HSPBP1_uc002qkd.2_Intron|HSPBP1_uc002qkc.2_Intron|uc002qke.2_5'Flank	NM_012267	NP_036399			hsp70-interacting protein						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein folding		enzyme inhibitor activity|protein binding				0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	56062590	56062591	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56062590_56062591insT								SBK2 (14929 upstream) : ZNF579 (26301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	57696781	57696781	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57696781delA								DUXA (17925 upstream) : ZNF264 (6088 downstream)																																			---	---	---	---
ZNF587	84914	broad.mit.edu	37	19	58375410	58375410	+	3'UTR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58375410delA	uc002qql.2	+	3					ZNF814_uc002qqk.2_Intron	NM_032828	NP_116217			zinc finger protein 587						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)														---	---	---	---
Unknown	0	broad.mit.edu	37	20	1478403	1478404	+	IGR	INS	-	T	T	rs140197528	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1478403_1478404insT								SIRPB2 (6170 upstream) : SIRPD (36495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	1656228	1656228	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1656228delG								SIRPG (17803 upstream) : SIRPA (218585 downstream)																																			---	---	---	---
TMC2	117532	broad.mit.edu	37	20	2602017	2602017	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2602017delA	uc002wgf.1	+						TMC2_uc002wgg.1_Intron	NM_080751	NP_542789			transmembrane cochlear-expressed protein 2							integral to membrane				ovary(3)	3																		---	---	---	---
TMC2	117532	broad.mit.edu	37	20	2606757	2606757	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2606757delT	uc002wgf.1	+						TMC2_uc002wgg.1_Intron	NM_080751	NP_542789			transmembrane cochlear-expressed protein 2							integral to membrane				ovary(3)	3																		---	---	---	---
TMC2	117532	broad.mit.edu	37	20	2617265	2617272	+	Intron	DEL	TTTGTTTG	-	-	rs113628494		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2617265_2617272delTTTGTTTG	uc002wgf.1	+						TMC2_uc002wgg.1_Intron	NM_080751	NP_542789			transmembrane cochlear-expressed protein 2							integral to membrane				ovary(3)	3																		---	---	---	---
FASTKD5	60493	broad.mit.edu	37	20	3138549	3138550	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3138549_3138550insT	uc002whz.2	-						UBOX5_uc002whw.2_Intron|UBOX5_uc002whx.2_Intron|UBOX5_uc002why.1_Intron	NM_021826	NP_068598			FAST kinase domains 5						apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity				0																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3551161	3551161	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3551161delT	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	3557342	3557343	+	Intron	INS	-	TCTGTCTGTCTG	TCTGTCTGTCTG	rs142073329	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3557342_3557343insTCTGTCTGTCTG	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																		---	---	---	---
HSPA12B	116835	broad.mit.edu	37	20	3715384	3715385	+	Intron	INS	-	T	T	rs35209985		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3715384_3715385insT	uc002wjd.2	+						HSPA12B_uc010zqi.1_Intron|HSPA12B_uc002wje.2_Intron|HSPA12B_uc010zqj.1_Intron	NM_052970	NP_443202			heat shock 70kD protein 12B								ATP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	3788005	3788006	+	5'Flank	INS	-	C	C	rs144822866	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3788005_3788006insC	uc002wjr.2	+											Homo sapiens, clone IMAGE:5932306, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	4259753	4259753	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4259753delT								ADRA1D (30094 upstream) : PRNP (407044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	4512524	4512524	+	IGR	DEL	C	-	-	rs113936900		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4512524delC								ADRA1D (282865 upstream) : PRNP (154273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	4758232	4758233	+	IGR	INS	-	CA	CA	rs139268822	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4758232_4758233insCA								PRNT (36918 upstream) : RASSF2 (2437 downstream)																																			---	---	---	---
SLC23A2	9962	broad.mit.edu	37	20	4975581	4975581	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4975581delA	uc002wlg.1	-						SLC23A2_uc010zqr.1_Intron|SLC23A2_uc002wlh.1_Intron|SLC23A2_uc002wli.2_Intron|SLC23A2_uc002wlj.1_Intron	NM_005116	NP_005107			solute carrier family 23 (nucleobase						L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	6763474	6763475	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6763474_6763475insA								BMP2 (2564 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7115407	7115407	+	IGR	DEL	C	-	-	rs35045267		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7115407delC								BMP2 (354497 upstream) : HAO1 (748224 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	8053042	8053043	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8053042_8053043insT								TMX4 (52649 upstream) : PLCB1 (42057 downstream)																																			---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8525532	8525532	+	Intron	DEL	T	-	-	rs34588603		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8525532delT	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9137868	9137868	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9137868delA	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																		---	---	---	---
PAK7	57144	broad.mit.edu	37	20	9755919	9755919	+	Intron	DEL	A	-	-	rs113581123		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9755919delA	uc002wnl.2	-						PAK7_uc002wnk.2_Intron|PAK7_uc002wnj.2_Intron|PAK7_uc010gby.1_Intron	NM_020341	NP_065074			p21-activated kinase 7								ATP binding|protein binding|protein serine/threonine kinase activity			lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1)	23			COAD - Colon adenocarcinoma(9;0.194)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	10306102	10306102	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10306102delT								SNAP25 (18037 upstream) : MKKS (79731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10670898	10670899	+	IGR	INS	-	TT	TT	rs35308833		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10670898_10670899insTT								JAG1 (16204 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10943774	10943799	+	IGR	DEL	TAGATGAACATGTGACCCACGCTCAC	-	-	rs36225954	by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10943774_10943799delTAGATGAACATGTGACCCACGCTCAC								JAG1 (289080 upstream) : BTBD3 (927678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11514559	11514559	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11514559delA								JAG1 (859865 upstream) : BTBD3 (356918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12073245	12073246	+	IGR	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12073245_12073246delCT								BTBD3 (166003 upstream) : SPTLC3 (916381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12665085	12665085	+	IGR	DEL	T	-	-	rs11479044		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12665085delT								BTBD3 (757843 upstream) : SPTLC3 (324542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12945356	12945359	+	IGR	DEL	AAAC	-	-	rs33968856		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12945356_12945359delAAAC								None (None upstream) : SPTLC3 (44268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	13191264	13191265	+	IGR	DEL	GT	-	-	rs72428034		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13191264_13191265delGT								SPTLC3 (43853 upstream) : ISM1 (11153 downstream)																																			---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	14112775	14112776	+	Intron	INS	-	AA	AA	rs10654042		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14112775_14112776insAA	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	14204152	14204152	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14204152delC	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	14428622	14428623	+	Intron	INS	-	TG	TG	rs140990904	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14428622_14428623insTG	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)																---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16446412	16446413	+	Intron	INS	-	A	A	rs11484109		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16446412_16446413insA	uc002wpg.1	-						KIF16B_uc010gch.1_Intron|KIF16B_uc010gci.1_Intron|KIF16B_uc010gcj.1_Intron	NM_024704	NP_078980			kinesin-like motor protein C20orf23						cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	19109633	19109636	+	IGR	DEL	TTAG	-	-	rs137868430		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19109633_19109636delTTAG								C20orf79 (314600 upstream) : SLC24A3 (83654 downstream)																																			---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19472627	19472628	+	Intron	INS	-	T	T	rs139706849	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19472627_19472628insT	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	19558908	19558909	+	Intron	DEL	GT	-	-	rs72371170		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19558908_19558909delGT	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	19638429	19638432	+	Intron	DEL	CTGT	-	-	rs139891119		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19638429_19638432delCTGT	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	19700153	19700153	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19700153delG	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	19873224	19873227	+	Intron	DEL	TCTT	-	-	rs11468067		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19873224_19873227delTCTT	uc002wro.1	+						RIN2_uc010gcu.1_Intron	NM_018993	NP_061866			Ras and Rab interactor 2						endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5																		---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20156163	20156164	+	Intron	INS	-	T	T	rs144677336	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20156163_20156164insT	uc002wru.2	+						C20orf26_uc010zse.1_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
PLK1S1	55857	broad.mit.edu	37	20	21166355	21166355	+	Intron	DEL	T	-	-	rs113144272		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21166355delT	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	22084641	22084641	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22084641delC								PAX1 (388021 upstream) : LOC284788 (296330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22766283	22766283	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22766283delT								FOXA2 (200182 upstream) : SSTR4 (249774 downstream)																																			---	---	---	---
CST2	1470	broad.mit.edu	37	20	23809926	23809927	+	5'Flank	INS	-	T	T	rs142555761	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23809926_23809927insT	uc002wtq.1	-							NM_001322	NP_001313			cystatin SA precursor							extracellular region	cysteine-type endopeptidase inhibitor activity				0																		---	---	---	---
GINS1	9837	broad.mit.edu	37	20	25387103	25387104	+	5'Flank	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25387103_25387104insA	uc002wuv.1	+						GINS1_uc010zte.1_5'Flank	NM_021067	NP_066545			GINS complex subunit 1						DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	cytoplasm|nucleoplasm				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
FAM182B	728882	broad.mit.edu	37	20	25758057	25758057	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25758057delG	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	25862045	25862045	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25862045delC								FAM182B (13259 upstream) : LOC100134868 (128390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25884965	25884965	+	IGR	DEL	C	-	-	rs112916433		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25884965delC								FAM182B (36179 upstream) : LOC100134868 (105470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25889453	25889454	+	IGR	INS	-	T	T	rs148292572	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25889453_25889454insT								FAM182B (40667 upstream) : LOC100134868 (100981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25904449	25904449	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25904449delG								FAM182B (55663 upstream) : LOC100134868 (85986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26202319	26202319	+	IGR	DEL	C	-	-	rs74486893		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26202319delC								MIR663 (13405 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29481292	29481292	+	IGR	DEL	A	-	-	rs112843353		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29481292delA								None (None upstream) : FRG1B (130587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29484520	29484521	+	IGR	DEL	TT	-	-	rs6119179		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29484520_29484521delTT								None (None upstream) : FRG1B (127358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29527652	29527653	+	IGR	INS	-	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29527652_29527653insC								None (None upstream) : FRG1B (84226 downstream)																																			---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29634956	29634956	+	Intron	DEL	C	-	-	rs35890078		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29634956delC	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	29814232	29814236	+	IGR	DEL	CACTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29814232_29814236delCACTC								FRG1B (160324 upstream) : DEFB115 (31231 downstream)																																			---	---	---	---
COMMD7	149951	broad.mit.edu	37	20	31317662	31317663	+	Intron	DEL	AA	-	-	rs111435161		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31317662_31317663delAA	uc002wya.3	-						COMMD7_uc010ged.2_Intron|COMMD7_uc002wyb.2_Intron	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																		---	---	---	---
COMMD7	149951	broad.mit.edu	37	20	31334245	31334246	+	5'Flank	INS	-	A	A	rs149284398	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31334245_31334246insA	uc002wya.3	-						COMMD7_uc010ged.2_5'Flank|COMMD7_uc002wyb.2_5'Flank	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	32479665	32479666	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32479665_32479666insT								CHMP4B (37496 upstream) : RALY (102066 downstream)																																			---	---	---	---
ITCH	83737	broad.mit.edu	37	20	33035660	33035660	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33035660delC	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																		---	---	---	---
TRPC4AP	26133	broad.mit.edu	37	20	33656763	33656764	+	Intron	INS	-	ACA	ACA	rs72350296		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33656763_33656764insACA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	33702584	33702584	+	IGR	DEL	G	-	-	rs66748954		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33702584delG								TRPC4AP (21966 upstream) : EDEM2 (576 downstream)																																			---	---	---	---
FAM83C	128876	broad.mit.edu	37	20	33880781	33880782	+	5'Flank	INS	-	TAAG	TAAG	rs141993781	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33880781_33880782insTAAG	uc010zux.1	-						FAM83C_uc002xcb.1_5'Flank	NM_178468	NP_848563			hypothetical protein LOC128876											ovary(2)	2			BRCA - Breast invasive adenocarcinoma(18;0.00252)															---	---	---	---
CPNE1	8904	broad.mit.edu	37	20	34217578	34217578	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34217578delT	uc002xdf.2	-						CPNE1_uc002xdc.2_Intron|CPNE1_uc010zvj.1_Intron|CPNE1_uc002xde.2_Intron|CPNE1_uc002xdg.2_Intron|CPNE1_uc010gfi.2_Intron|CPNE1_uc010gfj.2_Intron|CPNE1_uc002xdh.2_Intron|CPNE1_uc002xdi.2_Intron|CPNE1_uc002xdj.2_Intron|CPNE1_uc002xdk.2_Intron|CPNE1_uc002xdl.2_Intron|CPNE1_uc002xdm.2_Intron	NM_152931	NP_690908			copine I isoform a						lipid metabolic process|vesicle-mediated transport		calcium-dependent phospholipid binding|phosphatidylserine binding|transporter activity			upper_aerodigestive_tract(1)	1	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)															---	---	---	---
C20orf152	140894	broad.mit.edu	37	20	34579807	34579808	+	Intron	INS	-	T	T	rs6579270		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34579807_34579808insT	uc002xes.1	+						C20orf152_uc002xer.1_Intron|C20orf152_uc010gfp.1_Intron					SubName: Full=C20orf152 protein;												0	Breast(12;0.00631)																	---	---	---	---
DSN1	79980	broad.mit.edu	37	20	35398305	35398306	+	Intron	INS	-	AC	AC	rs141146657	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35398305_35398306insAC	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)																---	---	---	---
C20orf118	140711	broad.mit.edu	37	20	35518312	35518313	+	Intron	INS	-	TG	TG	rs145364344	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35518312_35518313insTG	uc002xgg.1	+							NM_080628	NP_542195			hypothetical protein LOC140711												0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	37028866	37028871	+	IGR	DEL	TGTGTG	-	-	rs72054532		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37028866_37028871delTGTGTG								LBP (23213 upstream) : LOC388796 (20368 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37268745	37268747	+	IGR	DEL	TCC	-	-	rs146443168	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37268745_37268747delTCC								ADIG (51641 upstream) : SLC32A1 (84358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37816108	37816109	+	IGR	INS	-	T	T	rs112465408		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37816108_37816109insT								DHX35 (147745 upstream) : LOC339568 (26315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38069124	38069124	+	IGR	DEL	T	-	-	rs11475751		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38069124delT								LOC339568 (215733 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38713423	38713423	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38713423delT								LOC339568 (860032 upstream) : MAFB (601096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38802304	38802305	+	IGR	INS	-	T	T	rs11086772		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38802304_38802305insT								LOC339568 (948913 upstream) : MAFB (512214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38906393	38906393	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38906393delA								None (None upstream) : MAFB (408126 downstream)																																			---	---	---	---
TOP1	7150	broad.mit.edu	37	20	39673434	39673435	+	Intron	DEL	GA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39673434_39673435delGA	uc002xjl.2	+						TOP1_uc010gge.1_Intron	NM_003286	NP_003277			DNA topoisomerase I						DNA topological change|interspecies interaction between organisms|phosphorylation|programmed cell death|response to drug	chromosome|nucleolus|nucleoplasm	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity|protein binding			breast(3)|ovary(2)|central_nervous_system(1)|kidney(1)	7		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Topotecan(DB01030)			T	NUP98	AML*								---	---	---	---
Unknown	0	broad.mit.edu	37	20	40501144	40501144	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40501144delT								CHD6 (254011 upstream) : PTPRT (200249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	40624908	40624909	+	IGR	DEL	TG	-	-	rs138123008		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40624908_40624909delTG								CHD6 (377775 upstream) : PTPRT (76484 downstream)																																			---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41063646	41063647	+	Intron	INS	-	G	G	rs150029156	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41063646_41063647insG	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	41253425	41253428	+	Intron	DEL	TATT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41253425_41253428delTATT	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	42043560	42043563	+	IGR	DEL	GAAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42043560_42043563delGAAG								PTPRT (225003 upstream) : SFRS6 (42941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	44225932	44225932	+	IGR	DEL	T	-	-	rs67874241		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44225932delT								WFDC8 (17967 upstream) : WFDC9 (10647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	44264271	44264272	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44264271_44264272delTT								WFDC9 (4364 upstream) : WFDC11 (12931 downstream)																																			---	---	---	---
SNX21	90203	broad.mit.edu	37	20	44464600	44464601	+	Intron	INS	-	A	A	rs150693611	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44464600_44464601insA	uc002xpv.1	+						SNX21_uc002xps.1_Intron|SNX21_uc002xpt.1_Intron|SNX21_uc002xpu.1_Intron|SNX21_uc002xpw.1_Intron|SNX21_uc002xpx.2_Intron|SNX21_uc010zxd.1_Intron|SNX21_uc002xpy.1_Intron	NM_033421	NP_219489			sorting nexin 21 isoform a						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding			breast(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
CDH22	64405	broad.mit.edu	37	20	44813723	44813724	+	Intron	INS	-	CAAACAAA	CAAACAAA	rs139877494	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44813723_44813724insCAAACAAA	uc002xrm.2	-						CDH22_uc010ghk.1_Intron	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)																---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45678223	45678249	+	Intron	DEL	GTCGTGTGACACCCCCTGCTCCATGTT	-	-	rs72084892		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45678223_45678249delGTCGTGTGACACCCCCTGCTCCATGTT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	46433930	46433932	+	IGR	DEL	AAG	-	-	rs59139327		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46433930_46433932delAAG								SULF2 (18570 upstream) : LOC284749 (554722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	47211082	47211083	+	IGR	INS	-	A	A	rs140450192	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47211082_47211083insA								LOC284749 (211701 upstream) : PREX1 (29710 downstream)																																			---	---	---	---
DDX27	55661	broad.mit.edu	37	20	47834766	47834767	+	5'Flank	INS	-	T	T	rs11086279		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47834766_47834767insT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	48236206	48236207	+	IGR	INS	-	GGAT	GGAT	rs141199932	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48236206_48236207insGGAT								PTGIS (51499 upstream) : B4GALT5 (13278 downstream)																																			---	---	---	---
BCAS4	55653	broad.mit.edu	37	20	49457964	49457965	+	Intron	INS	-	C	C	rs148159050	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49457964_49457965insC	uc002xvq.2	+						BCAS4_uc002xvr.2_Intron|BCAS4_uc002xvs.2_Intron	NM_017843	NP_060313			breast carcinoma amplified sequence 4 isoform a							cytoplasm					0																		---	---	---	---
ADNP	23394	broad.mit.edu	37	20	49544098	49544098	+	Intron	DEL	T	-	-	rs139362432		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49544098delT	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																		---	---	---	---
DPM1	8813	broad.mit.edu	37	20	49556624	49556625	+	Intron	DEL	TG	-	-	rs11469059		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49556624_49556625delTG	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	49586277	49586277	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49586277delT								MOCS3 (8457 upstream) : KCNG1 (33917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49604653	49604654	+	IGR	DEL	TT	-	-	rs72554570		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49604653_49604654delTT								MOCS3 (26833 upstream) : KCNG1 (15540 downstream)																																			---	---	---	---
NFATC2	4773	broad.mit.edu	37	20	50136975	50136976	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50136975_50136976insT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	50201852	50201852	+	IGR	DEL	T	-	-	rs73625466		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50201852delT								NFATC2 (22684 upstream) : ATP9A (11462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50688865	50688865	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50688865delT								SALL4 (269817 upstream) : ZFP64 (11686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50967491	50967491	+	IGR	DEL	T	-	-	rs71647383		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50967491delT								ZFP64 (158967 upstream) : TSHZ2 (621386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51553775	51553775	+	IGR	DEL	T	-	-	rs34069821		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51553775delT								ZFP64 (745251 upstream) : TSHZ2 (35102 downstream)																																			---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51588062	51588063	+	5'Flank	INS	-	GT	GT	rs138537476	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51588062_51588063insGT	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	51630300	51630300	+	Intron	DEL	C	-	-	rs34346315		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51630300delC	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	51693797	51693797	+	Intron	DEL	A	-	-	rs5841927		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51693797delA	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	51809728	51809728	+	Intron	DEL	A	-	-	rs111551519		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51809728delA	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	52370597	52370598	+	IGR	INS	-	TCTC	TCTC	rs72111562		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52370597_52370598insTCTC								ZNF217 (159796 upstream) : SUMO1P1 (120444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52387115	52387116	+	IGR	INS	-	T	T	rs11374506		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52387115_52387116insT								ZNF217 (176314 upstream) : SUMO1P1 (103926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52405097	52405098	+	IGR	INS	-	AATG	AATG			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52405097_52405098insAATG								ZNF217 (194296 upstream) : SUMO1P1 (85944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54035032	54035032	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54035032delA								DOK5 (767323 upstream) : CBLN4 (537465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54284402	54284403	+	IGR	DEL	AG	-	-	rs143050106		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54284402_54284403delAG								None (None upstream) : CBLN4 (288094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54568751	54568751	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54568751delA								None (None upstream) : CBLN4 (3746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55291293	55291294	+	IGR	INS	-	AGAA	AGAA	rs143243936	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55291293_55291294insAGAA								TFAP2C (76957 upstream) : BMP7 (452515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55552209	55552216	+	IGR	DEL	CTCCTGAA	-	-	rs61045000		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55552209_55552216delCTCCTGAA								TFAP2C (337873 upstream) : BMP7 (191593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55991175	55991176	+	IGR	DEL	GA	-	-	rs67976496		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55991175_55991176delGA								RBM38 (6791 upstream) : CTCFL (72704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	56352270	56352273	+	IGR	DEL	ACTT	-	-	rs10616992		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56352270_56352273delACTT								PMEPA1 (65729 upstream) : C20orf85 (373710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	56503645	56503645	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56503645delA								PMEPA1 (217104 upstream) : C20orf85 (222338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	57373613	57373614	+	IGR	INS	-	G	G	rs145177418	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57373613_57373614insG								NPEPL1 (82246 upstream) : MIR296 (19056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	57975084	57975085	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57975084_57975085delAC								EDN3 (74038 upstream) : PHACTR3 (177479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59339298	59339299	+	IGR	INS	-	ACACACAC	ACACACAC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59339298_59339299insACACACAC								MIR646 (455673 upstream) : CDH4 (488260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59391358	59391360	+	IGR	DEL	TTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59391358_59391360delTTC								MIR646 (507733 upstream) : CDH4 (436199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59634817	59634818	+	IGR	INS	-	T	T	rs11467998		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59634817_59634818insT								MIR646 (751192 upstream) : CDH4 (192741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59777332	59777333	+	IGR	INS	-	A	A	rs139777993	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59777332_59777333insA								MIR646 (893707 upstream) : CDH4 (50226 downstream)																																			---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60267294	60267303	+	Intron	DEL	TGTATGTGTG	-	-	rs3831187	by1000genomes;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60267294_60267303delTGTATGTGTG	uc002ybn.1	+						CDH4_uc002ybo.1_Intron|CDH4_uc002ybp.1_Intron	NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60308125	60308132	+	Intron	DEL	ATGGACAG	-	-	rs139772948		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60308125_60308132delATGGACAG	uc002ybn.1	+						CDH4_uc002ybo.1_Intron|CDH4_uc002ybp.1_Intron	NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	61182524	61182525	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61182524_61182525delAC								C20orf166 (14554 upstream) : SLCO4A1 (91272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	61190103	61190104	+	IGR	DEL	GC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61190103_61190104delGC								C20orf166 (22133 upstream) : SLCO4A1 (83693 downstream)																																			---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61519783	61519783	+	Intron	DEL	G	-	-	rs146228116	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61519783delG	uc002ydr.1	-						DIDO1_uc002yds.1_Intron|DIDO1_uc002ydt.1_3'UTR|DIDO1_uc002ydu.1_3'UTR	NM_033081	NP_149072			death inducer-obliterator 1 isoform c						apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
ZGPAT	84619	broad.mit.edu	37	20	62350417	62350418	+	Intron	INS	-	A	A	rs4063142		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62350417_62350418insA	uc002ygk.2	+						ZGPAT_uc002ygi.2_Intron|ZGPAT_uc002ygj.2_Intron|ZGPAT_uc010gkk.1_Intron|ZGPAT_uc010gkl.1_Intron|ZGPAT_uc002ygm.2_Intron|ZGPAT_uc002ygn.3_Intron	NM_032527	NP_115916			zinc finger, CCCH-type with G patch domain						negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)																	---	---	---	---
ZGPAT	84619	broad.mit.edu	37	20	62363021	62363022	+	Intron	DEL	TG	-	-	rs138381752		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62363021_62363022delTG	uc002ygk.2	+						ZGPAT_uc002ygi.2_Intron|ZGPAT_uc002ygj.2_Intron|ZGPAT_uc010gkk.1_Intron|ZGPAT_uc010gkl.1_Intron|ZGPAT_uc002ygm.2_Intron|ZGPAT_uc002ygn.3_Intron	NM_032527	NP_115916			zinc finger, CCCH-type with G patch domain						negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)																	---	---	---	---
TCEA2	6919	broad.mit.edu	37	20	62696882	62696885	+	Intron	DEL	GGGA	-	-	rs71333732		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62696882_62696885delGGGA	uc011abs.1	+						TCEA2_uc011abr.1_Intron|TCEA2_uc010gkq.2_Intron|TCEA2_uc010gks.2_Intron|TCEA2_uc010gkt.2_5'Flank|TCEA2_uc010gku.1_5'Flank	NM_003195	NP_003186			transcription elongation factor A protein 2						regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation, DNA-dependent	transcription elongation factor complex	DNA binding|protein binding|translation elongation factor activity|zinc ion binding				0	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	21	9676785	9676785	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9676785delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9856378	9856380	+	IGR	DEL	CTC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9856378_9856380delCTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10092863	10092864	+	IGR	INS	-	T	T	rs76360022		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10092863_10092864insT								None (None upstream) : TPTE (813879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10522306	10522307	+	Intron	DEL	TA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10522306_10522307delTA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10722995	10722996	+	IGR	DEL	AG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10722995_10722996delAG								None (None upstream) : TPTE (183747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10822834	10822835	+	IGR	INS	-	GAATG	GAATG	rs113733133		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10822834_10822835insGAATG								None (None upstream) : TPTE (83908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10842718	10842722	+	IGR	DEL	GAATG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10842718_10842722delGAATG								None (None upstream) : TPTE (64021 downstream)																																			---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11042864	11042867	+	Intron	DEL	AGTA	-	-	rs138861085		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11042864_11042867delAGTA	uc002yit.1	-							NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11069158	11069158	+	Intron	DEL	T	-	-	rs148402445		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11069158delT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
C21orf99	149992	broad.mit.edu	37	21	14414165	14414166	+	Intron	INS	-	TA	TA	rs142269777	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14414165_14414166insTA	uc002yiy.3	+						C21orf99_uc002yja.3_Intron					Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	14673999	14674000	+	IGR	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14673999_14674000delAC								C21orf99 (183430 upstream) : POTED (308498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	15405594	15405595	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15405594_15405595insA	uc002yjk.2	+						uc002yjl.2_Intron					Homo sapiens, clone IMAGE:4102980, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	15428695	15428734	+	Intron	DEL	CAGGGCCAGGGCCAGGACCAGGAAAGGGCAATGTCAGGAC	-	-	rs67423764		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15428695_15428734delCAGGGCCAGGGCCAGGACCAGGAAAGGGCAATGTCAGGAC	uc002yjk.2	+						uc002yjl.2_Intron					Homo sapiens, clone IMAGE:4102980, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	15806099	15806100	+	IGR	INS	-	A	A	rs144186151	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15806099_15806100insA								HSPA13 (50590 upstream) : SAMSN1 (51449 downstream)																																			---	---	---	---
C21orf34	388815	broad.mit.edu	37	21	17812810	17812811	+	Intron	INS	-	TTTTT	TTTTT	rs72254658		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17812810_17812811insTTTTT	uc002ykb.2	+						C21orf34_uc010glc.2_Intron|C21orf34_uc002ykc.2_Intron	NR_027790				Homo sapiens C21ORF34 (C21orf34) mRNA, partial cds, alternatively spliced.												0		Breast(209;0.152)		Epithelial(23;8.3e-05)|all cancers(11;0.000383)|Colorectal(24;0.00387)|COAD - Colon adenocarcinoma(22;0.0113)|OV - Ovarian serous cystadenocarcinoma(11;0.0127)|LUSC - Lung squamous cell carcinoma(23;0.153)														---	---	---	---
C21orf34	388815	broad.mit.edu	37	21	17956633	17956634	+	Intron	DEL	AC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17956633_17956634delAC	uc002ykb.2	+						C21orf34_uc010glc.2_Intron|C21orf34_uc002ykc.2_Intron	NR_027790				Homo sapiens C21ORF34 (C21orf34) mRNA, partial cds, alternatively spliced.												0		Breast(209;0.152)		Epithelial(23;8.3e-05)|all cancers(11;0.000383)|Colorectal(24;0.00387)|COAD - Colon adenocarcinoma(22;0.0113)|OV - Ovarian serous cystadenocarcinoma(11;0.0127)|LUSC - Lung squamous cell carcinoma(23;0.153)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	20572436	20572436	+	IGR	DEL	A	-	-	rs72042866		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20572436delA								TMPRSS15 (796466 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20699341	20699341	+	IGR	DEL	T	-	-	rs111363494		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20699341delT								TMPRSS15 (923371 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20749634	20749634	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20749634delA								TMPRSS15 (973664 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23609874	23609875	+	IGR	DEL	AC	-	-	rs144621983		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23609874_23609875delAC								NCAM2 (698660 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	25302989	25303067	+	IGR	DEL	AGGGAGGAAGGAAAAGGAAAGAGGGAAAAAGGGAAATGAAGGAGTGAAGGAAGAAAGGGCAGAAGAAAGGATAGAAGAG	-	-	rs71182215		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25302989_25303067delAGGGAGGAAGGAAAAGGAAAGAGGGAAAAAGGGAAATGAAGGAGTGAAGGAAGAAAGGGCAGAAGAAAGGATAGAAGAG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	25545894	25545895	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25545894_25545895insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26042151	26042152	+	IGR	INS	-	G	G	rs142839193	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26042151_26042152insG								None (None upstream) : NCRNA00158 (715982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26353670	26353671	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26353670_26353671insT								None (None upstream) : NCRNA00158 (404463 downstream)																																			---	---	---	---
MRPL39	54148	broad.mit.edu	37	21	26966562	26966563	+	Intron	DEL	TT	-	-	rs72426988		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26966562_26966563delTT	uc002ylo.2	-						MRPL39_uc002yln.2_Intron	NM_017446	NP_059142			mitochondrial ribosomal protein L39 isoform a							mitochondrial ribosome	nucleotide binding				0																		---	---	---	---
GABPA	2551	broad.mit.edu	37	21	27135847	27135847	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27135847delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	27216003	27216003	+	IGR	DEL	T	-	-	rs71704429		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27216003delT								GABPA (71233 upstream) : APP (36859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28572518	28572519	+	IGR	DEL	AA	-	-	rs68051590		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28572518_28572519delAA								ADAMTS5 (233079 upstream) : NCRNA00113 (522179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	29060971	29060972	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29060971_29060972insT								ADAMTS5 (721532 upstream) : NCRNA00113 (33726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	30118995	30118995	+	IGR	DEL	A	-	-	rs141286233		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30118995delA								NCRNA00161 (206319 upstream) : N6AMT1 (125518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	30548308	30548308	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30548308delA								C21orf7 (108 upstream) : NCRNA00189 (17493 downstream)																																			---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	30979114	30979118	+	Intron	DEL	TCTTG	-	-	rs72042869		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30979114_30979118delTCTTG	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron|uc002ynp.1_Intron	NM_000830	NP_000821			glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	31417540	31417541	+	IGR	INS	-	T	T	rs141526108		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31417540_31417541insT								GRIK1 (105258 upstream) : CLDN17 (120722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	32443854	32443855	+	IGR	INS	-	TCAA	TCAA	rs146305315	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32443854_32443855insTCAA								KRTAP19-8 (33059 upstream) : TIAM1 (46881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	33150281	33150281	+	IGR	DEL	A	-	-	rs113556721		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33150281delA								SFRS15 (45850 upstream) : HUNK (95347 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	33574607	33574608	+	IGR	INS	-	A	A	rs141138568	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33574607_33574608insA								NCRNA00159 (45791 upstream) : C21orf45 (65924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	33613681	33613681	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33613681delA								NCRNA00159 (84865 upstream) : C21orf45 (26851 downstream)																																			---	---	---	---
URB1	9875	broad.mit.edu	37	21	33749844	33749844	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33749844delA	uc002ypn.2	-						SNORA80_uc002ypo.2_5'Flank	NM_014825	NP_055640			URB1 ribosome biogenesis 1 homolog							nucleolus	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	34474026	34474027	+	IGR	DEL	AC	-	-	rs149260698		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34474026_34474027delAC								OLIG1 (29299 upstream) : C21orf54 (63750 downstream)																																			---	---	---	---
IFNAR1	3454	broad.mit.edu	37	21	34722229	34722229	+	Intron	DEL	A	-	-	rs113802899		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34722229delA	uc002yrn.2	+						IFNAR1_uc011adv.1_Intron	NM_000629	NP_000620			interferon-alpha receptor 1 precursor						JAK-STAT cascade|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	integral to plasma membrane	type I interferon receptor activity			central_nervous_system(1)|skin(1)	2					Interferon Alfa-2a, Recombinant(DB00034)|Interferon Alfa-2b, Recombinant(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	34754378	34754378	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34754378delC								IFNAR1 (22252 upstream) : IFNGR2 (20824 downstream)																																			---	---	---	---
SON	6651	broad.mit.edu	37	21	34945074	34945075	+	Intron	INS	-	T	T	rs11289167		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34945074_34945075insT	uc002yse.1	+						SON_uc002ysd.2_Intron|SON_uc002ysf.1_Intron|SON_uc002ysh.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																		---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35055493	35055494	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35055493_35055494insT	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Intron|ITSN1_uc002ysz.2_Intron|ITSN1_uc010gmg.2_Intron|ITSN1_uc010gmh.2_Intron|ITSN1_uc002ysw.2_Intron|ITSN1_uc010gmi.2_Intron|ITSN1_uc010gmj.2_Intron|ITSN1_uc002ysy.2_Intron|ITSN1_uc002ysx.2_Intron|ITSN1_uc002ytb.1_Intron	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35188497	35188498	+	Intron	INS	-	A	A	rs113561711		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35188497_35188498insA	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Intron|ITSN1_uc002ysz.2_Intron|ITSN1_uc010gmg.2_Intron|ITSN1_uc010gmh.2_Intron|ITSN1_uc002ysw.2_Intron|ITSN1_uc010gmi.2_Intron|ITSN1_uc010gmj.2_Intron|ITSN1_uc002ysy.2_Intron|ITSN1_uc002ysx.2_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytc.1_Intron|ITSN1_uc002ytd.2_Intron|ITSN1_uc010gmk.2_Intron|ITSN1_uc010gml.2_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron|ITSN1_uc002yte.2_Intron|ITSN1_uc002ytf.1_Intron|ITSN1_uc002ytg.1_5'Flank	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36172216	36172216	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36172216delT	uc002yuh.2	-						RUNX1_uc002yui.2_Intron|RUNX1_uc010gmu.2_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yul.1_Intron|RUNX1_uc002yum.1_Intron	NM_001001890	NP_001001890			runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
RUNX1	861	broad.mit.edu	37	21	37097476	37097476	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37097476delT	uc002yut.1	-											Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
Unknown	0	broad.mit.edu	37	21	37988244	37988245	+	IGR	INS	-	A	A	rs149028404		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37988244_37988245insA								CLDN14 (39377 upstream) : SIM2 (83746 downstream)																																			---	---	---	---
HLCS	3141	broad.mit.edu	37	21	38345363	38345364	+	Intron	INS	-	AC	AC	rs61340805		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38345363_38345364insAC	uc002yvs.2	-							NM_000411	NP_000402			holocarboxylase synthetase						cell proliferation|histone biotinylation|response to biotin	chromatin|cytosol|mitochondrion|nuclear lamina|nuclear matrix	ATP binding|biotin binding|biotin-[acetyl-CoA-carboxylase] ligase activity|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity|enzyme binding			ovary(2)|breast(1)|kidney(1)|liver(1)	5		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	38426815	38426816	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38426815_38426816delTT								DSCR6 (34859 upstream) : PIGP (10848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	38975394	38975394	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38975394delT								DYRK1A (87716 upstream) : KCNJ6 (21392 downstream)																																			---	---	---	---
KCNJ6	3763	broad.mit.edu	37	21	39060424	39060426	+	Intron	DEL	TTC	-	-	rs67288636		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39060424_39060426delTTC	uc011aej.1	-						KCNJ6_uc002ywo.2_Intron	NM_002240	NP_002231			potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)													---	---	---	---
KCNJ6	3763	broad.mit.edu	37	21	39085044	39085044	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39085044delC	uc011aej.1	-						KCNJ6_uc002ywo.2_Intron	NM_002240	NP_002231			potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	39362734	39362737	+	IGR	DEL	AGGA	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39362734_39362737delAGGA								KCNJ6 (74038 upstream) : DSCR4 (63577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	40350477	40350477	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40350477delT								ETS2 (153601 upstream) : PSMG1 (196913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	40379990	40379990	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40379990delA								ETS2 (183114 upstream) : PSMG1 (167400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	41344298	41344299	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41344298_41344299insT								PCP4 (42978 upstream) : DSCAM (40044 downstream)																																			---	---	---	---
FAM3B	54097	broad.mit.edu	37	21	42727483	42727484	+	Intron	INS	-	AAAC	AAAC	rs143882608	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42727483_42727484insAAAC	uc002yzb.1	+						FAM3B_uc002yza.2_Intron|FAM3B_uc002yzc.1_Intron|FAM3B_uc002yzd.1_Intron	NM_058186	NP_478066			family with sequence similarity 3, member B						apoptosis|insulin secretion	extracellular space	cytokine activity				0		Prostate(19;1.57e-07)|all_epithelial(19;0.0404)																---	---	---	---
MX1	4599	broad.mit.edu	37	21	42796154	42796161	+	Intron	DEL	GTGTGTGT	-	-	rs144397233		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42796154_42796161delGTGTGTGT	uc002yzh.2	+						MX1_uc002yzi.2_5'Flank|MX1_uc010goq.2_5'Flank	NM_001144925	NP_001138397			myxovirus resistance protein 1						induction of apoptosis|response to virus|type I interferon-mediated signaling pathway	cytosol	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)																---	---	---	---
PDXK	8566	broad.mit.edu	37	21	45170791	45170798	+	Intron	DEL	GCATGTGT	-	-	rs111339726		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45170791_45170798delGCATGTGT	uc002zdm.3	+						PDXK_uc010gpj.2_Intron|PDXK_uc002zdn.3_Intron|PDXK_uc002zdq.3_Intron	NM_003681	NP_003672			pyridoxal kinase						cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)													---	---	---	---
PFKL	5211	broad.mit.edu	37	21	45723126	45723127	+	Intron	INS	-	A	A	rs149775115	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45723126_45723127insA	uc002zel.2	+						PFKL_uc002zek.2_Intron|PFKL_uc011afd.1_Intron	NM_002626	NP_002617			liver phosphofructokinase						fructose 6-phosphate metabolic process|glycolysis|protein oligomerization	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|fructose-6-phosphate binding|identical protein binding|kinase binding|metal ion binding				0				Colorectal(79;0.0811)														---	---	---	---
TRPM2	7226	broad.mit.edu	37	21	45813641	45813641	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45813641delT	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron	NM_003307	NP_003298			transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
TRPM2	7226	broad.mit.edu	37	21	45839534	45839536	+	Intron	DEL	TGG	-	-	rs142846437		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45839534_45839536delTGG	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron|uc011afe.1_Intron	NM_003307	NP_003298			transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
PCNT	5116	broad.mit.edu	37	21	47778543	47778544	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47778543_47778544insT	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	16909234	16909235	+	IGR	INS	-	A	A	rs74380866		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16909234_16909235insA								OR11H1 (459430 upstream) : CCT8L2 (162413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17497779	17497780	+	IGR	INS	-	T	T	rs113361321		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17497779_17497780insT								GAB4 (8667 upstream) : CECR7 (19680 downstream)																																			---	---	---	---
IL17RA	23765	broad.mit.edu	37	22	17583493	17583493	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17583493delA	uc002zly.2	+						IL17RA_uc010gqt.2_Intron	NM_014339	NP_055154			interleukin 17A receptor precursor						fibroblast activation|positive regulation of interleukin-23 production	integral to plasma membrane	interleukin-17 receptor activity			skin(2)	2		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)														---	---	---	---
SLC25A18	83733	broad.mit.edu	37	22	18052551	18052551	+	Intron	DEL	A	-	-	rs111240928		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18052551delA	uc002zmp.1	+						SLC25A18_uc010gqx.2_Intron|SLC25A18_uc002zmq.1_Intron	NM_031481	NP_113669			solute carrier							integral to membrane|mitochondrial inner membrane	binding|symporter activity				0				Lung(27;0.124)	L-Glutamic Acid(DB00142)													---	---	---	---
BCL2L13	23786	broad.mit.edu	37	22	18125363	18125364	+	Intron	INS	-	T	T	rs140823227		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18125363_18125364insT	uc002zmw.2	+						BCL2L13_uc002zmu.2_Intron|BCL2L13_uc002zmv.2_Intron|BCL2L13_uc002zmx.2_Intron|BCL2L13_uc002zmy.2_Intron|BCL2L13_uc010gqy.2_Intron|BCL2L13_uc011agk.1_Intron	NM_015367	NP_056182			BCL2-like 13 (apoptosis facilitator)						induction of apoptosis	integral to membrane|mitochondrial membrane|nucleus	caspase activator activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4		all_epithelial(15;0.123)		Lung(27;0.199)														---	---	---	---
DGCR2	9993	broad.mit.edu	37	22	19104468	19104477	+	Intron	DEL	ATCACCTCCC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19104468_19104477delATCACCTCCC	uc002zoq.1	-						DGCR2_uc002zor.1_Intron|DGCR2_uc011agr.1_Intron	NM_005137	NP_005128			integral membrane protein DGCR2 precursor						cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding			large_intestine(1)	1	Colorectal(54;0.0993)																	---	---	---	---
GNB1L	54584	broad.mit.edu	37	22	19815242	19815242	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19815242delG	uc002zqe.1	-						GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqf.1_Intron	NM_053004	NP_443730			guanine nucleotide binding protein						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	internal side of plasma membrane|intracellular				breast(1)	1	Colorectal(54;0.0993)																	---	---	---	---
C22orf25	128989	broad.mit.edu	37	22	20012443	20012443	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20012443delC	uc010grw.1	+						C22orf25_uc002zrb.1_Intron|C22orf25_uc002zrc.1_Intron|C22orf25_uc002zrd.1_Intron|C22orf25_uc002zre.2_Intron|C22orf25_uc010grx.2_Intron|C22orf25_uc011ahe.1_Intron|C22orf25_uc011ahf.1_Intron|C22orf25_uc011ahg.1_Intron|C22orf25_uc002zrg.2_Intron|C22orf25_uc011ahh.1_Intron|C22orf25_uc002zrf.2_Intron|C22orf25_uc011ahi.1_Intron	NM_152906	NP_690870			hypothetical protein LOC128989												0	Colorectal(54;0.0533)																	---	---	---	---
PPIL2	23759	broad.mit.edu	37	22	22047215	22047215	+	Intron	DEL	A	-	-	rs113931448		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22047215delA	uc010gtj.1	+						PPIL2_uc002zvh.3_Intron|PPIL2_uc002zvi.3_Intron|PPIL2_uc002zvg.3_Intron|PPIL2_uc011aij.1_Intron|PPIL2_uc002zvk.3_Intron	NM_148175	NP_680480			peptidylprolyl isomerase-like 2 isoform a						blood coagulation|leukocyte migration|protein folding|protein polyubiquitination	Golgi lumen|nucleus|ubiquitin ligase complex	peptidyl-prolyl cis-trans isomerase activity|ubiquitin-ubiquitin ligase activity			ovary(2)	2	Colorectal(54;0.105)																	---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22511912	22511913	+	Intron	INS	-	TG	TG	rs148266841	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22511912_22511913insTG	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22761414	22761414	+	Intron	DEL	A	-	-	rs11293393		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22761414delA	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22821923	22821923	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22821923delA	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23247453	23247462	+	Intron	DEL	TCTGTCTCTC	-	-	rs138768797	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23247453_23247462delTCTGTCTCTC	uc011aim.1	+						uc002zws.2_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC91316	91316	broad.mit.edu	37	22	24025806	24025806	+	Intron	DEL	C	-	-	rs34936243		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24025806delC	uc002zxh.3	-						LOC91316_uc002zxi.3_Intron|LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron|LOC91316_uc002zxm.3_Intron					Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0																		---	---	---	---
DDT	1652	broad.mit.edu	37	22	24273326	24273326	+	Intron	DEL	G	-	-	rs34204106		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24273326delG	uc011ajf.1	-							NM_001355	NP_001346			D-dopachrome tautomerase						melanin biosynthetic process	cytoplasm	D-dopachrome decarboxylase activity|dopachrome isomerase activity|protein binding				0																		---	---	---	---
ADRBK2	157	broad.mit.edu	37	22	25967823	25967823	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25967823delT	uc003abx.3	+						ADRBK2_uc010gux.2_Intron|ADRBK2_uc003abw.2_Intron|ADRBK2_uc003aby.3_Intron	NM_005160	NP_005151			beta-adrenergic receptor kinase 2								ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)													---	---	---	---
ADRBK2	157	broad.mit.edu	37	22	25977102	25977103	+	Intron	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25977102_25977103insA	uc003abx.3	+						ADRBK2_uc010gux.2_Intron|ADRBK2_uc003abw.2_Intron|ADRBK2_uc003aby.3_Intron	NM_005160	NP_005151			beta-adrenergic receptor kinase 2								ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)													---	---	---	---
MIAT	440823	broad.mit.edu	37	22	27106633	27106633	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27106633delA	uc003adf.1	+											Homo sapiens cDNA: FLJ22849 fis, clone KAIA987.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	27504196	27504197	+	IGR	INS	-	GG	GG	rs149551488	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27504196_27504197insGG								MIAT (389247 upstream) : MN1 (640069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	28028169	28028172	+	IGR	DEL	GTGT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28028169_28028172delGTGT								MIAT (913220 upstream) : MN1 (116094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	28075245	28075245	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28075245delA								MIAT (960296 upstream) : MN1 (69021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	28121566	28121567	+	IGR	INS	-	CAC	CAC	rs111374872		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28121566_28121567insCAC								None (None upstream) : MN1 (22699 downstream)																																			---	---	---	---
CHEK2	11200	broad.mit.edu	37	22	29121896	29121897	+	Intron	INS	-	A	A	rs142082814		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29121896_29121897insA	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				---	---	---	---
KREMEN1	83999	broad.mit.edu	37	22	29486213	29486214	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29486213_29486214delTG	uc011akm.1	+						KREMEN1_uc003ael.2_Intron	NM_032045	NP_114434			kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5																		---	---	---	---
NIPSNAP1	8508	broad.mit.edu	37	22	29962814	29962814	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29962814delA	uc003afx.3	-						NIPSNAP1_uc011akp.1_Intron	NM_003634	NP_003625			nipsnap homolog 1									p.?(1)		skin(1)	1																		---	---	---	---
RNF185	91445	broad.mit.edu	37	22	31576898	31576905	+	Intron	DEL	TCTCTGTG	-	-	rs66499709		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31576898_31576905delTCTCTGTG	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																		---	---	---	---
LIMK2	3985	broad.mit.edu	37	22	31644035	31644035	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31644035delT	uc003akh.2	+						LIMK2_uc003akg.2_Intron|LIMK2_uc003aki.2_Intron|LIMK2_uc003akj.2_5'Flank|LIMK2_uc003akk.2_5'Flank|LIMK2_uc011aln.1_5'Flank	NM_005569	NP_005560			LIM domain kinase 2 isoform 2a							mitochondrion|nucleus	ATP binding|protein serine/threonine kinase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	32387706	32387707	+	IGR	DEL	TC	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32387706_32387707delTC								YWHAH (34117 upstream) : SLC5A1 (51330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	33476937	33476938	+	IGR	INS	-	TCCA	TCCA	rs113437956		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33476937_33476938insTCCA								SYN3 (22560 upstream) : LARGE (192125 downstream)																																			---	---	---	---
LARGE	9215	broad.mit.edu	37	22	34137310	34137310	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34137310delC	uc003and.3	-						LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|uc003ang.2_Intron|uc003anh.2_Intron	NM_004737	NP_004728			like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	34792684	34792685	+	IGR	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34792684_34792685delCT								LARGE (474100 upstream) : ISX (669444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	34910005	34910013	+	IGR	DEL	GAGAGTGAG	-	-	rs130721		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34910005_34910013delGAGAGTGAG								LARGE (591421 upstream) : ISX (552116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35025184	35025184	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35025184delC								LARGE (706600 upstream) : ISX (436945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35639517	35639517	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35639517delT								ISX (156139 upstream) : HMGXB4 (13928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35909501	35909502	+	IGR	DEL	GT	-	-	rs10597104		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35909501_35909502delGT								MCM5 (89007 upstream) : RASD2 (27850 downstream)																																			---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36319994	36319994	+	Intron	DEL	A	-	-	rs139980519		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36319994delA	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																		---	---	---	---
APOL2	23780	broad.mit.edu	37	22	36625428	36625428	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36625428delA	uc003aoz.2	-						APOL2_uc011amm.1_Intron|APOL2_uc003apa.2_Intron	NM_030882	NP_112092			apolipoprotein L2						acute-phase response|cholesterol metabolic process|lipid transport|lipoprotein metabolic process|maternal process involved in female pregnancy|multicellular organismal development	endoplasmic reticulum membrane|extracellular region	high-density lipoprotein particle binding|lipid binding|receptor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	37383376	37383376	+	IGR	DEL	T	-	-	rs35706626		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37383376delT								CSF2RB (46899 upstream) : C22orf33 (3785 downstream)																																			---	---	---	---
ELFN2	114794	broad.mit.edu	37	22	37809608	37809608	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37809608delA	uc003asq.3	-							NM_052906	NP_443138			leucine rich repeat containing 62							cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)																	---	---	---	---
MICALL1	85377	broad.mit.edu	37	22	38308681	38308681	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38308681delT	uc003aui.2	+							NM_033386	NP_203744			molecule interacting with Rab13							cytoplasm|cytoskeleton	protein binding|zinc ion binding			breast(1)	1	Melanoma(58;0.045)																	---	---	---	---
PICK1	9463	broad.mit.edu	37	22	38458691	38458693	+	Intron	DEL	TCC	-	-	rs10563532		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38458691_38458693delTCC	uc003auq.2	+						PICK1_uc003aur.2_Intron|PICK1_uc003aus.2_Intron|PICK1_uc003aut.2_Intron	NM_012407	NP_036539			protein interacting with C kinase 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|DNA methylation involved in embryo development|DNA methylation involved in gamete generation|monoamine transport|neuronal ion channel clustering|protein phosphorylation|receptor clustering|retrograde vesicle-mediated transport, Golgi to ER|synaptic transmission	cell junction|endocytic vesicle membrane|Golgi apparatus|perinuclear region of cytoplasm|presynaptic membrane	ATPase activity|metal ion binding|protein C-terminus binding|protein kinase C binding|receptor binding				0	Melanoma(58;0.045)																	---	---	---	---
TAB1	10454	broad.mit.edu	37	22	39782828	39782829	+	Intron	DEL	AA	-	-	rs141402106		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39782828_39782829delAA	uc003axr.2	+							NM_006116	NP_006107			mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|activation of MAPKKK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane	catalytic activity|protein binding			breast(1)	1																		---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40666318	40666318	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40666318delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	41128420	41128421	+	IGR	INS	-	A	A	rs148290638	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41128420_41128421insA								MCHR1 (49603 upstream) : SLC25A17 (37220 downstream)																																			---	---	---	---
NDUFA6	4700	broad.mit.edu	37	22	42488610	42488611	+	5'Flank	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42488610_42488611insA	uc003bcb.2	-						uc003bcc.1_Intron|uc003bcd.1_Intron	NM_002490	NP_002481			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|response to oxidative stress|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0					NADH(DB00157)													---	---	---	---
NDUFA6	4700	broad.mit.edu	37	22	42489839	42489839	+	5'Flank	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42489839delA	uc003bcb.2	-						uc003bcc.1_Intron|uc003bcd.1_Intron	NM_002490	NP_002481			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|response to oxidative stress|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	22	42678905	42678906	+	IGR	INS	-	GCG	GCG	rs144380040	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42678905_42678906insGCG								TCF20 (67460 upstream) : NFAM1 (97509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	43062563	43062563	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43062563delA								CYB5R3 (17158 upstream) : A4GALT (25565 downstream)																																			---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44468286	44468287	+	Intron	DEL	AC	-	-	rs71785821		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44468286_44468287delAC	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	44728014	44728014	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44728014delT								KIAA1644 (19283 upstream) : LDOC1L (160436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	44741694	44741694	+	IGR	DEL	G	-	-	rs147422869	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44741694delG								KIAA1644 (32963 upstream) : LDOC1L (146756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	46050315	46050316	+	IGR	INS	-	T	T	rs60395059		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46050315_46050316insT								FBLN1 (51618 upstream) : ATXN10 (17371 downstream)																																			---	---	---	---
PPARA	5465	broad.mit.edu	37	22	46604815	46604816	+	Intron	DEL	GT	-	-	rs35637220		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46604815_46604816delGT	uc003bgw.1	+						PPARA_uc003bgx.1_Intron|PPARA_uc010hab.1_Intron|PPARA_uc003bha.2_Intron|PPARA_uc003bhb.1_Intron|PPARA_uc010hac.1_Intron	NM_005036	NP_005027			peroxisome proliferative activated receptor,						fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)													---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46920439	46920442	+	Intron	DEL	GTGT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46920439_46920442delGTGT	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)														---	---	---	---
TBC1D22A	25771	broad.mit.edu	37	22	47269689	47269689	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47269689delT	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	47684064	47684065	+	IGR	INS	-	ATCCATCC	ATCCATCC	rs12166451		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47684064_47684065insATCCATCC								TBC1D22A (114342 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	47820820	47820821	+	IGR	DEL	GC	-	-	rs67662121		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47820820_47820821delGC								TBC1D22A (251098 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48542882	48542885	+	IGR	DEL	ACAC	-	-	rs148439461		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48542882_48542885delACAC								TBC1D22A (973160 upstream) : FAM19A5 (342403 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48839407	48839414	+	IGR	DEL	GGAAGGAA	-	-	rs61518508	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48839407_48839414delGGAAGGAA								None (None upstream) : FAM19A5 (45874 downstream)																																			---	---	---	---
FAM19A5	25817	broad.mit.edu	37	22	49097941	49097942	+	Intron	DEL	GT	-	-	rs144871856		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49097941_49097942delGT	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436			family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)														---	---	---	---
FAM19A5	25817	broad.mit.edu	37	22	49131686	49131686	+	Intron	DEL	G	-	-	rs10716843		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49131686delG	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436			family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	49712770	49712771	+	IGR	INS	-	G	G	rs148650307	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49712770_49712771insG								FAM19A5 (565028 upstream) : C22orf34 (95405 downstream)																																			---	---	---	---
C22orf34	348645	broad.mit.edu	37	22	49834119	49834121	+	Intron	DEL	TTG	-	-	rs34580885		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49834119_49834121delTTG	uc003biq.2	-											Homo sapiens cDNA FLJ42972 fis, clone BRSTN2019129.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	51063094	51063094	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51063094delG								MAPK8IP2 (13116 upstream) : ARSA (356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	442174	442174	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:442174delG								PPP2R3B (94547 upstream) : SHOX (142905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	731530	731531	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:731530_731531insT								SHOX (111385 upstream) : CRLF2 (583356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	732617	732618	+	IGR	DEL	CT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:732617_732618delCT								SHOX (112472 upstream) : CRLF2 (582269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	1346803	1346806	+	IGR	DEL	GATG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1346803_1346806delGATG								CRLF2 (15273 upstream) : CSF2RA (40887 downstream)																																			---	---	---	---
SLC25A6	293	broad.mit.edu	37	X	1512743	1512744	+	5'Flank	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1512743_1512744insT	uc004cpt.2	-						SLC25A6_uc004cpu.2_5'Flank	NM_001636	NP_001627			adenine nucleotide translocator 3						active induction of host immune response by virus|apoptosis|energy reserve metabolic process|regulation of insulin secretion|viral infectious cycle	integral to membrane|mitochondrial inner membrane presequence translocase complex	ATP:ADP antiporter activity|protein 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)			Clodronate(DB00720)													---	---	---	---
P2RY8	286530	broad.mit.edu	37	X	1643783	1643784	+	Intron	INS	-	ATCC	ATCC			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1643783_1643784insATCC	uc004cpz.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	1898833	1898837	+	IGR	DEL	TAGAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1898833_1898837delTAGAG								ASMT (136860 upstream) : DHRSX (238720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	4183910	4183910	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:4183910delT								PRKX (552249 upstream) : None (None downstream)																																			---	---	---	---
TBL1X	6907	broad.mit.edu	37	X	9557600	9557600	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9557600delT	uc010ndq.2	+						TBL1X_uc004csq.3_Intron|TBL1X_uc010ndr.2_Intron|TBL1X_uc004csr.2_Intron	NM_001139466	NP_001132938			transducin beta-like 1X isoform a						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|sensory perception of sound|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein C-terminus binding|protein domain specific binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Hepatocellular(5;0.000888)																---	---	---	---
BMX	660	broad.mit.edu	37	X	15554697	15554697	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15554697delA	uc004cww.2	+						BMX_uc004cwx.3_Intron|BMX_uc004cwy.3_Intron	NM_203281	NP_975010			BMX non-receptor tyrosine kinase						cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)																	---	---	---	---
PCYT1B	9468	broad.mit.edu	37	X	24583677	24583677	+	Intron	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24583677delC	uc004dbi.2	-						PCYT1B_uc004dbk.3_Intron|PCYT1B_uc004dbj.2_Intron	NM_004845	NP_004836			choline phosphate cytidylyltransferase 1 beta							endoplasmic reticulum	choline-phosphate cytidylyltransferase activity				0					Choline(DB00122)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	26374384	26374384	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26374384delC								MAGEB6 (160622 upstream) : VENTXP1 (202070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	35068315	35068315	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35068315delA								FAM47B (105281 upstream) : MAGEB16 (748144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42608944	42608944	+	IGR	DEL	A	-	-	rs141189366		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42608944delA								CASK (826657 upstream) : PPP1R2P9 (27675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42611716	42611716	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42611716delA								CASK (829429 upstream) : PPP1R2P9 (24903 downstream)																																			---	---	---	---
SSX3	10214	broad.mit.edu	37	X	48217952	48217953	+	5'Flank	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48217952_48217953insA	uc004djd.1	-						SSX3_uc004dje.2_5'Flank|SSX3_uc010nic.2_5'Flank	NM_021014	NP_066294			synovial sarcoma, X breakpoint 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	48704979	48704979	+	IGR	DEL	C	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48704979delC								PCSK1N (11019 upstream) : TIMM17B (45753 downstream)																																			---	---	---	---
GAGE12J	729396	broad.mit.edu	37	X	49228012	49228013	+	Intron	INS	-	GT	GT			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49228012_49228013insGT	uc004dnl.3	+						GAGE13_uc004dnn.3_Intron|GAGE8_uc011mne.1_Intron|GAGE8_uc011mnf.1_Intron|GAGE8_uc011mng.1_Intron|GAGE2A_uc004dnr.3_Intron|GAGE8_uc004dnq.3_Intron|GAGE2A_uc004dnv.3_Intron|GAGE4_uc011mnk.1_Intron|GAGE2A_uc004dny.3_Intron|GAGE8_uc011mnl.1_Intron|GAGE8_uc004dnz.3_Intron|GAGE12D_uc011mnm.1_Intron|GAGE8_uc011mnh.1_Intron|GAGE2B_uc011mnj.1_Intron|GAGE2C_uc004doa.2_Intron|GAGE2D_uc004dob.3_Intron	NM_001098406	NP_001465			G antigen 12J												0	Ovarian(276;0.236)																	---	---	---	---
PAGE2	203569	broad.mit.edu	37	X	55117232	55117232	+	Intron	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55117232delG	uc004duf.1	+							NM_207339	NP_997222			P antigen family, member 2											ovary(2)	2																		---	---	---	---
EDA	1896	broad.mit.edu	37	X	69051739	69051740	+	Intron	INS	-	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69051739_69051740insC	uc004dxs.2	+						EDA_uc004dxr.2_Intron|EDA_uc011mpj.1_Intron|EDA_uc004dxn.1_Intron|EDA_uc004dxm.1_Intron|EDA_uc004dxp.1_Intron|EDA_uc004dxq.1_Intron	NM_001399	NP_001390			ectodysplasin A isoform EDA-A1						cell differentiation|ectoderm development|immune response|positive regulation of NF-kappaB transcription factor activity|signal transduction	collagen|cytoskeleton|membrane fraction	tumor necrosis factor receptor binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	94682115	94682115	+	IGR	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:94682115delA								MIR548M (363890 upstream) : LOC643486 (909971 downstream)																																			---	---	---	---
TMEM164	84187	broad.mit.edu	37	X	109348404	109348407	+	Intron	DEL	CCAT	-	-	rs66721177		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109348404_109348407delCCAT	uc004eom.2	+						TMEM164_uc004eol.2_Intron|TMEM164_uc010npq.2_Intron	NM_032227	NP_115603			transmembrane protein 164 isoform b							integral to membrane				large_intestine(1)|lung(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	125426856	125426858	+	IGR	DEL	AAG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125426856_125426858delAAG								DCAF12L2 (126922 upstream) : DCAF12L1 (256510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	132586842	132586842	+	IGR	DEL	A	-	-	rs111994410		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132586842delA								GPC4 (37637 upstream) : GPC3 (82934 downstream)																																			---	---	---	---
SPANXN4	441525	broad.mit.edu	37	X	142114125	142114125	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142114125delT	uc004fbv.3	+							NM_001009613	NP_001009613			SPANX family, member N4											ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
AFF2	2334	broad.mit.edu	37	X	147621595	147621595	+	Intron	DEL	A	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147621595delA	uc004fcp.2	+						AFF2_uc004fco.2_Intron|AFF2_uc004fcq.2_Intron|AFF2_uc004fcr.2_Intron|AFF2_uc011mxb.1_Intron|AFF2_uc004fcs.2_Intron	NM_002025	NP_002016			fragile X mental retardation 2						brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
AFF2	2334	broad.mit.edu	37	X	147924771	147924772	+	Intron	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147924771_147924772insT	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)																	---	---	---	---
PNMA5	114824	broad.mit.edu	37	X	152179038	152179038	+	Intron	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152179038delT	uc004fha.3	-							NM_052926	NP_443158			paraneoplastic antigen like 5						apoptosis					ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
GDI1	2664	broad.mit.edu	37	X	153668023	153668023	+	Intron	DEL	A	-	-	rs71922846		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153668023delA	uc004fli.3	+						GDI1_uc011mzo.1_Intron|GDI1_uc004flj.2_5'Flank	NM_001493	NP_001484			GDP dissociation inhibitor 1						protein transport|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|midbody	GTPase activator activity|protein binding				0	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	154472891	154472892	+	IGR	DEL	TG	-	-	rs111387940		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154472891_154472892delTG								VBP1 (4795 upstream) : RAB39B (14635 downstream)																																			---	---	---	---
IL9R	3581	broad.mit.edu	37	X	155238667	155238668	+	Intron	DEL	TG	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155238667_155238668delTG	uc004fnv.1	+						IL9R_uc004fnu.1_Intron	NM_002186	NP_002177			interleukin 9 receptor precursor						cell proliferation	extracellular space|integral to plasma membrane	interleukin-9 receptor activity				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)																	---	---	---	---
Unknown	0	broad.mit.edu	37	Y	10024484	10024485	+	IGR	DEL	TT	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10024484_10024485delTT								TTTY22 (373630 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13273657	13273657	+	IGR	DEL	G	-	-	rs112787450		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13273657delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13422376	13422377	+	IGR	INS	-	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13422376_13422377insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13531497	13531497	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13531497delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13706007	13706007	+	IGR	DEL	T	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13706007delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	21082468	21082468	+	IGR	DEL	G	-	-			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:21082468delG								NCRNA00185 (42354 upstream) : TTTY14 (12119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	58834308	58834312	+	IGR	DEL	CATAG	-	-	rs139115545		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58834308_58834312delCATAG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59002251	59002252	+	IGR	DEL	AA	-	-	rs146446459		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59002251_59002252delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59008746	59008747	+	IGR	INS	-	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59008746_59008747insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59030837	59030837	+	IGR	DEL	T	-	-	rs147048784		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59030837delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59032254	59032255	+	IGR	INS	-	TT	TT	rs56224050		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59032254_59032255insTT								None (None upstream) : None (None downstream)																																			---	---	---	---
SLC2A7	155184	broad.mit.edu	37	1	9073627	9073627	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9073627G>A	uc009vmo.1	-	8	971	c.971C>T	c.(970-972)ACG>ATG	p.T324M		NM_207420	NP_997303	Q6PXP3	GTR7_HUMAN	intestinal facilitative glucose transporter 7	324	Helical; (Potential).					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)														---	---	---	---
PDPN	10630	broad.mit.edu	37	1	13936891	13936891	+	Missense_Mutation	SNP	A	C	C	rs150037960		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13936891A>C	uc001avd.2	+	3	488	c.439A>C	c.(439-441)AGT>CGT	p.S147R	PDPN_uc001avc.2_Missense_Mutation_p.S147R|PDPN_uc009vob.2_Missense_Mutation_p.S29R|PDPN_uc009voc.2_Missense_Mutation_p.S29R|PDPN_uc001ave.2_Missense_Mutation_p.S29R|PDPN_uc001avf.2_Missense_Mutation_p.S29R	NM_006474	NP_006465	Q86YL7	PDPN_HUMAN	lung type-I cell membrane-associated	71	Extracellular (Potential).				cell morphogenesis|lymphangiogenesis|regulation of cell shape	filopodium membrane|integral to plasma membrane|lamellipodium membrane|microvillus membrane|ruffle membrane				ovary(2)	2	Ovarian(185;0.249)	all_lung(284;2.29e-05)|Lung NSC(185;4.37e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00969)|Colorectal(212;4.48e-06)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000347)|Kidney(185;0.00087)|KIRC - Kidney renal clear cell carcinoma(229;0.0027)|STAD - Stomach adenocarcinoma(313;0.00802)|READ - Rectum adenocarcinoma(331;0.0678)														---	---	---	---
PUM1	9698	broad.mit.edu	37	1	31426699	31426699	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31426699C>A	uc001bsi.1	-	15	2566	c.2453G>T	c.(2452-2454)CGA>CTA	p.R818L	PUM1_uc001bsf.1_Missense_Mutation_p.R484L|PUM1_uc001bsg.1_Missense_Mutation_p.R552L|PUM1_uc001bsh.1_Missense_Mutation_p.R818L|PUM1_uc001bsj.1_Missense_Mutation_p.R792L|PUM1_uc010oga.1_Missense_Mutation_p.R674L|PUM1_uc001bsk.1_Missense_Mutation_p.R854L|PUM1_uc010ogb.1_Missense_Mutation_p.R759L	NM_014676	NP_055491	Q14671	PUM1_HUMAN	pumilio 1 isoform 2	818					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)														---	---	---	---
ZMYM4	9202	broad.mit.edu	37	1	35865160	35865160	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35865160C>T	uc001byt.2	+	23	3591	c.3511C>T	c.(3511-3513)CCC>TCC	p.P1171S	ZMYM4_uc009vuu.2_Missense_Mutation_p.P1139S|ZMYM4_uc001byu.2_Missense_Mutation_p.P847S|ZMYM4_uc009vuv.2_Missense_Mutation_p.P910S	NM_005095	NP_005086	Q5VZL5	ZMYM4_HUMAN	zinc finger protein 262	1171					multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
TIE1	7075	broad.mit.edu	37	1	43783580	43783580	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43783580C>T	uc001ciu.2	+	17	2838	c.2759C>T	c.(2758-2760)GCC>GTC	p.A920V	TIE1_uc010oke.1_Missense_Mutation_p.A875V|TIE1_uc009vwq.2_Missense_Mutation_p.A876V|TIE1_uc010okg.1_Missense_Mutation_p.A565V	NM_005424	NP_005415	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and	920	Cytoplasmic (Potential).|Protein kinase.				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)																---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44201955	44201955	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44201955C>T	uc001ckc.2	+	2	199	c.22C>T	c.(22-24)CGC>TGC	p.R8C	ST3GAL3_uc009vwu.1_RNA|ST3GAL3_uc010okj.1_RNA|ST3GAL3_uc001cjz.2_Missense_Mutation_p.R8C|ST3GAL3_uc001cka.2_Missense_Mutation_p.R8C|ST3GAL3_uc001ckb.2_Missense_Mutation_p.R8C|ST3GAL3_uc001ckd.2_Missense_Mutation_p.R8C|ST3GAL3_uc001cke.2_Missense_Mutation_p.R8C|ST3GAL3_uc001ckf.2_Missense_Mutation_p.R8C|ST3GAL3_uc001ckg.2_Missense_Mutation_p.R8C|ST3GAL3_uc001ckh.2_Missense_Mutation_p.R8C|ST3GAL3_uc001cki.2_Missense_Mutation_p.R8C|ST3GAL3_uc009vwv.2_Missense_Mutation_p.R8C|ST3GAL3_uc001ckj.2_RNA|ST3GAL3_uc009vww.2_RNA|ST3GAL3_uc001ckk.2_Missense_Mutation_p.R8C|ST3GAL3_uc009vwy.2_5'UTR|ST3GAL3_uc009vwx.2_RNA|ST3GAL3_uc001ckm.2_Missense_Mutation_p.R8C|ST3GAL3_uc001ckl.2_Missense_Mutation_p.R8C|ST3GAL3_uc009vwz.2_5'UTR|ST3GAL3_uc001ckn.2_RNA|ST3GAL3_uc001ckp.2_Missense_Mutation_p.R8C|ST3GAL3_uc001cko.2_Missense_Mutation_p.R8C|ST3GAL3_uc009vxa.2_5'UTR|ST3GAL3_uc001ckq.2_Missense_Mutation_p.R8C|ST3GAL3_uc001ckr.2_Missense_Mutation_p.R8C|ST3GAL3_uc009vxb.2_Missense_Mutation_p.R8C	NM_006279	NP_006270	Q11203	SIAT6_HUMAN	sialyltransferase 6 isoform j	8	Cytoplasmic (Potential).				protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)																---	---	---	---
PRPF38A	84950	broad.mit.edu	37	1	52878197	52878197	+	Silent	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52878197A>G	uc001ctv.3	+	5	713	c.510A>G	c.(508-510)GTA>GTG	p.V170V	PRPF38A_uc001ctw.3_5'UTR	NM_032864	NP_116253	Q8NAV1	PR38A_HUMAN	PRP38 pre-mRNA processing factor 38 (yeast)	170	Potential.				mRNA processing|RNA splicing	spliceosomal complex					0																		---	---	---	---
C1orf173	127254	broad.mit.edu	37	1	75037620	75037620	+	Silent	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75037620A>C	uc001dgg.2	-	14	3993	c.3774T>G	c.(3772-3774)GCT>GCG	p.A1258A		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	1258	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5																		---	---	---	---
ELTD1	64123	broad.mit.edu	37	1	79383714	79383714	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79383714C>T	uc001diq.3	-	11	1639	c.1483G>A	c.(1483-1485)GGA>AGA	p.G495R		NM_022159	NP_071442	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain	495	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(1)|skin(1)	2				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)														---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	82408791	82408791	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82408791G>A	uc001dit.3	+	6	717	c.536G>A	c.(535-537)CGT>CAT	p.R179H	LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Missense_Mutation_p.R179H|LPHN2_uc001div.2_Missense_Mutation_p.R179H|LPHN2_uc009wcd.2_Missense_Mutation_p.R179H	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor	179	Extracellular (Potential).|Olfactomedin-like.				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
TTLL7	79739	broad.mit.edu	37	1	84383341	84383341	+	Silent	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84383341A>G	uc001djc.2	-	14	1929	c.1533T>C	c.(1531-1533)TGT>TGC	p.C511C	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	511					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)														---	---	---	---
PALMD	54873	broad.mit.edu	37	1	100154368	100154368	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100154368G>A	uc001dsg.2	+	7	995	c.552G>A	c.(550-552)TTG>TTA	p.L184L	PALMD_uc001dsf.2_Silent_p.L184L	NM_017734	NP_060204	Q9NP74	PALMD_HUMAN	palmdelphin	184					regulation of cell shape	cytoplasm|membrane				ovary(2)|pancreas(1)	3		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)														---	---	---	---
AGL	178	broad.mit.edu	37	1	100342129	100342129	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100342129C>T	uc001dsi.1	+	11	1799	c.1399C>T	c.(1399-1401)CCT>TCT	p.P467S	AGL_uc001dsj.1_Missense_Mutation_p.P467S|AGL_uc001dsk.1_Missense_Mutation_p.P467S|AGL_uc001dsl.1_Missense_Mutation_p.P467S|AGL_uc001dsm.1_Missense_Mutation_p.P451S|AGL_uc001dsn.1_Missense_Mutation_p.P450S	NM_000642	NP_000633	P35573	GDE_HUMAN	amylo-1,6-glucosidase,	467	4-alpha-glucanotransferase.				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)														---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103468314	103468314	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103468314T>C	uc001dul.2	-	22	2350	c.2032A>G	c.(2032-2034)AAA>GAA	p.K678E	COL11A1_uc001duk.2_5'UTR|COL11A1_uc001dum.2_Missense_Mutation_p.K690E|COL11A1_uc001dun.2_Missense_Mutation_p.K639E|COL11A1_uc009weh.2_Missense_Mutation_p.K562E	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	678	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)														---	---	---	---
AMY1A	276	broad.mit.edu	37	1	104203067	104203067	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104203067G>A	uc001duu.2	+	7	1178	c.964G>A	c.(964-966)GCT>ACT	p.A322T	AMY1A_uc001duv.2_Missense_Mutation_p.A322T	NM_001008221	NP_001008222	P04745	AMY1_HUMAN	salivary amylase alpha 1A precursor	322					carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding|protein binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)														---	---	---	---
HIPK1	204851	broad.mit.edu	37	1	114500812	114500812	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114500812T>C	uc001eem.2	+	8	2041	c.1880T>C	c.(1879-1881)GTT>GCT	p.V627A	HIPK1_uc001eel.2_Missense_Mutation_p.V627A|HIPK1_uc001een.2_Missense_Mutation_p.V627A|HIPK1_uc001eeo.2_Missense_Mutation_p.V253A|HIPK1_uc001eep.2_Missense_Mutation_p.V233A	NM_198268	NP_938009	Q86Z02	HIPK1_HUMAN	homeodomain-interacting protein kinase 1 isoform	627					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(4)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
CD2	914	broad.mit.edu	37	1	117297488	117297488	+	Silent	SNP	C	A	A	rs41275574		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117297488C>A	uc001egu.3	+	2	326	c.297C>A	c.(295-297)ACC>ACA	p.T99T	CD2_uc010owz.1_Silent_p.T99T|CD2_uc010oxa.1_Silent_p.T99T	NM_001767	NP_001758	P06729	CD2_HUMAN	CD2 molecule precursor	99	Extracellular (Potential).|Ig-like V-type.				blood coagulation|cell surface receptor linked signaling pathway|cell-cell adhesion|induction of apoptosis|leukocyte migration|membrane raft polarization|natural killer cell activation|positive regulation of myeloid dendritic cell activation|regulation of T cell differentiation|T cell activation	integral to plasma membrane	receptor activity			breast(1)	1	Lung SC(450;0.225)	all_cancers(81;3.15e-06)|Acute lymphoblastic leukemia(138;1.7e-08)|all_epithelial(167;8.38e-07)|all_lung(203;3.37e-06)|Lung NSC(69;2.31e-05)		Epithelial(280;6.71e-26)|OV - Ovarian serous cystadenocarcinoma(397;4.74e-24)|all cancers(265;1.93e-22)|Lung(183;0.0543)|Kidney(133;0.0813)|Colorectal(144;0.174)|KIRC - Kidney renal clear cell carcinoma(1967;0.176)|LUSC - Lung squamous cell carcinoma(189;0.189)|BRCA - Breast invasive adenocarcinoma(282;0.201)	Alefacept(DB00092)													---	---	---	---
ITGA10	8515	broad.mit.edu	37	1	145534222	145534222	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145534222G>A	uc001eoa.2	+	14	1803	c.1727G>A	c.(1726-1728)GGG>GAG	p.G576E	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Missense_Mutation_p.G445E|ITGA10_uc009wiw.2_Missense_Mutation_p.G433E|ITGA10_uc010oyw.1_Missense_Mutation_p.G521E	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	576	Extracellular (Potential).|FG-GAP 6.				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)																	---	---	---	---
PIAS3	10401	broad.mit.edu	37	1	145579308	145579308	+	Silent	SNP	C	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145579308C>G	uc001eoc.1	+	5	736	c.645C>G	c.(643-645)GTC>GTG	p.V215V	NBPF10_uc001emp.3_Intron|PIAS3_uc010oyy.1_Silent_p.V206V|PIAS3_uc001eod.1_5'Flank	NM_006099	NP_006090	Q9Y6X2	PIAS3_HUMAN	protein inhibitor of activated STAT, 3	215	PINIT.				positive regulation of protein sumoylation|protein sumoylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	enzyme binding|nucleic acid binding|protein C-terminus binding|zinc ion binding			ovary(1)	1	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)																	---	---	---	---
ANXA9	8416	broad.mit.edu	37	1	150955602	150955602	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150955602G>C	uc001ewa.2	+	3	491	c.21G>C	c.(19-21)AAG>AAC	p.K7N		NM_003568	NP_003559	O76027	ANXA9_HUMAN	annexin A9	7					cell-cell adhesion	cell surface|cytosol	acetylcholine receptor activity|calcium ion binding|calcium-dependent phospholipid binding|phosphatidylserine binding|protein homodimerization activity				0	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
HRNR	388697	broad.mit.edu	37	1	152190844	152190844	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152190844C>T	uc001ezt.1	-	3	3337	c.3261G>A	c.(3259-3261)TCG>TCA	p.S1087S		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	1087	12.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
FLG	2312	broad.mit.edu	37	1	152280800	152280800	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152280800T>G	uc001ezu.1	-	3	6598	c.6562A>C	c.(6562-6564)AGT>CGT	p.S2188R		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2188	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											Ichthyosis				---	---	---	---
FLG2	388698	broad.mit.edu	37	1	152324600	152324600	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152324600C>T	uc001ezw.3	-	3	5735	c.5662G>A	c.(5662-5664)GTG>ATG	p.V1888M	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1888							calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
AQP10	89872	broad.mit.edu	37	1	154296165	154296165	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154296165T>C	uc001feu.2	+	5	630	c.590T>C	c.(589-591)CTG>CCG	p.L197P	AQP10_uc001fev.2_Missense_Mutation_p.L197P|ATP8B2_uc001few.2_5'Flank	NM_080429	NP_536354	Q96PS8	AQP10_HUMAN	aquaporin 10	197	Helical; (Potential).				response to toxin|transmembrane transport|water transport	integral to membrane|plasma membrane	transporter activity			central_nervous_system(1)	1	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
FDPS	2224	broad.mit.edu	37	1	155289653	155289653	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155289653C>G	uc001fkc.2	+	10	1212	c.993C>G	c.(991-993)AAC>AAG	p.N331K	RAG1AP1_uc010pey.1_Intron|FDPS_uc001fkd.2_Missense_Mutation_p.N265K|FDPS_uc001fke.2_Missense_Mutation_p.N331K|FDPS_uc001fkf.2_Missense_Mutation_p.N265K|C1orf104_uc001fkh.1_RNA|RUSC1_uc001fkj.2_5'Flank|RUSC1_uc001fkk.2_5'Flank|RUSC1_uc009wqn.1_5'Flank	NM_002004	NP_001995	P14324	FPPS_HUMAN	farnesyl diphosphate synthase isoform a	331					cholesterol biosynthetic process|interspecies interaction between organisms|isoprenoid biosynthetic process	cytosol|nucleus	dimethylallyltranstransferase activity|geranyltranstransferase activity|metal ion binding				0	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)													---	---	---	---
IFI16	3428	broad.mit.edu	37	1	158988058	158988058	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158988058A>T	uc001ftf.1	+	6	1196	c.589A>T	c.(589-591)AGA>TGA	p.R197*	IFI16_uc001ftg.2_Nonsense_Mutation_p.R197*|IFI16_uc010pis.1_Nonsense_Mutation_p.R141*	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	197	HIN-200 1.				cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)																	---	---	---	---
DDR2	4921	broad.mit.edu	37	1	162745434	162745434	+	Intron	SNP	C	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162745434C>G	uc001gcf.2	+						DDR2_uc001gcg.2_Intron	NM_001014796	NP_001014796			discoidin domain receptor family, member 2						cell adhesion	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)															---	---	---	---
KLHL20	27252	broad.mit.edu	37	1	173702971	173702971	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173702971A>G	uc001gjc.2	+	3	322	c.143A>G	c.(142-144)GAC>GGC	p.D48G	KLHL20_uc010pmr.1_Intron|KLHL20_uc009wwf.2_Missense_Mutation_p.D30G|KLHL20_uc001gjd.2_Missense_Mutation_p.D48G	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN	kelch-like 20	48					cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
C1orf125	126859	broad.mit.edu	37	1	179437659	179437659	+	Missense_Mutation	SNP	C	T	T	rs41267592	byFrequency;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179437659C>T	uc001gmo.2	+	17	2007	c.1880C>T	c.(1879-1881)ACG>ATG	p.T627M	C1orf125_uc009wxg.2_RNA|C1orf125_uc001gmn.1_3'UTR|C1orf125_uc010pnl.1_RNA|C1orf125_uc001gmp.2_Missense_Mutation_p.T627M	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1	627											0																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186094842	186094842	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186094842G>A	uc001grq.1	+	82	12835	c.12606G>A	c.(12604-12606)TGG>TGA	p.W4202*	HMCN1_uc001grs.1_5'Flank	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4202	Ig-like C2-type 41.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197403867	197403867	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197403867C>T	uc001gtz.2	+	9	3009	c.2874C>T	c.(2872-2874)AGC>AGT	p.S958S	CRB1_uc010poz.1_Silent_p.S934S|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Silent_p.S846S|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Silent_p.S439S|CRB1_uc001gub.1_Silent_p.S607S	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	958	Extracellular (Potential).|EGF-like 14.|Laminin G-like 3.				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9																		---	---	---	---
C1orf157	284573	broad.mit.edu	37	1	204006598	204006598	+	RNA	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204006598C>T	uc001haj.2	-	3		c.422G>A			C1orf157_uc001hak.2_RNA|C1orf157_uc010pqo.1_RNA	NR_027902				Homo sapiens cDNA FLJ40343 fis, clone TESTI2032774.												0	all_cancers(21;0.083)|Breast(84;0.193)|all_epithelial(62;0.21)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0754)|Kidney(21;0.0934)|Epithelial(59;0.233)															---	---	---	---
ATF3	467	broad.mit.edu	37	1	212791561	212791561	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212791561G>A	uc001hjf.2	+	3	466	c.333G>A	c.(331-333)ACG>ACA	p.T111T	ATF3_uc001hjj.2_Silent_p.T111T|ATF3_uc009xdg.1_Intron|ATF3_uc001hjh.2_Silent_p.T111T|ATF3_uc001hji.2_Silent_p.T111T|ATF3_uc010ptg.1_RNA	NM_001030287	NP_001025458	P18847	ATF3_HUMAN	activating transcription factor 3 isoform 1	111						nucleolus	identical protein binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)														---	---	---	---
ACTA1	58	broad.mit.edu	37	1	229567552	229567552	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229567552C>T	uc001htm.2	-	6	1011	c.906G>A	c.(904-906)TCG>TCA	p.S302S		NM_001100	NP_001091	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	302					muscle filament sliding|skeletal muscle fiber development|skeletal muscle thin filament assembly	actin filament|cytosol|stress fiber|striated muscle thin filament	ADP binding|ATP binding|myosin binding|structural constituent of cytoskeleton				0	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)			Dornase Alfa(DB00003)													---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237580427	237580427	+	Intron	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237580427A>C	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)															---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1843040	1843040	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1843040G>A	uc002qxe.2	-	21	3788	c.2961C>T	c.(2959-2961)GAC>GAT	p.D987D	MYT1L_uc002qxd.2_Silent_p.D985D|MYT1L_uc010ewk.2_Translation_Start_Site	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	987				D -> E (in Ref. 1; AAF14051).	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)														---	---	---	---
RNF144A	9781	broad.mit.edu	37	2	7164586	7164586	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7164586C>T	uc002qys.2	+	7	1038	c.596C>T	c.(595-597)GCG>GTG	p.A199V	RNF144A_uc002qyt.2_Missense_Mutation_p.A48V	NM_014746	NP_055561	P50876	R144A_HUMAN	ring finger protein 144	199	RING-type 2; degenerate.					Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)														---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15506800	15506800	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15506800G>A	uc002rcc.1	-	32	3747	c.3721C>T	c.(3721-3723)CGG>TGG	p.R1241W	NBAS_uc010exl.1_Missense_Mutation_p.R313W|NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	1241										ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
XPO1	7514	broad.mit.edu	37	2	61711133	61711133	+	Silent	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61711133T>C	uc002sbj.2	-	21	3344	c.2616A>G	c.(2614-2616)AAA>AAG	p.K872K	XPO1_uc010fcl.2_Silent_p.K868K|XPO1_uc010ypn.1_Silent_p.K868K|XPO1_uc002sbk.2_Silent_p.K433K|XPO1_uc002sbg.2_Silent_p.K69K|XPO1_uc002sbh.2_Silent_p.K519K	NM_003400	NP_003391	O14980	XPO1_HUMAN	exportin 1	872					intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)															---	---	---	---
FAM161A	84140	broad.mit.edu	37	2	62066813	62066813	+	Silent	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62066813G>T	uc010ypo.1	-	3	1428	c.1326C>A	c.(1324-1326)CTC>CTA	p.L442L	FAM161A_uc002sbm.3_Silent_p.L442L|FAM161A_uc002sbn.3_Silent_p.L252L|FAM161A_uc010fcm.1_RNA|FAM161A_uc010fcn.1_Silent_p.L333L	NM_032180	NP_115556	Q3B820	F161A_HUMAN	hypothetical protein LOC84140	442					response to stimulus|visual perception	centrosome				large_intestine(2)|ovary(1)	3																		---	---	---	---
POTEE	445582	broad.mit.edu	37	2	131976471	131976471	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131976471G>C	uc002tsn.2	+	1	548	c.496G>C	c.(496-498)GTG>CTG	p.V166L	PLEKHB2_uc002tsh.2_Intron|POTEE_uc002tsk.2_5'UTR|POTEE_uc002tsl.2_5'UTR	NM_001083538	NP_001077007	Q6S8J3	POTEE_HUMAN	protein expressed in prostate, ovary, testis,	166							ATP binding				0																		---	---	---	---
LYPD6B	130576	broad.mit.edu	37	2	150071107	150071107	+	Silent	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150071107C>A	uc002twv.1	+	7	908	c.507C>A	c.(505-507)CCC>CCA	p.P169P	LYPD6B_uc002tww.1_Silent_p.P131P|LYPD6B_uc002twx.1_Silent_p.P131P	NM_177964	NP_808879	Q8NI32	LPD6B_HUMAN	LY6/PLAUR domain containing 6B	145	UPAR/Ly6.					anchored to membrane|plasma membrane					0																		---	---	---	---
KCNJ3	3760	broad.mit.edu	37	2	155566292	155566292	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155566292G>A	uc002tyv.1	+	2	1075	c.880G>A	c.(880-882)GAG>AAG	p.E294K	KCNJ3_uc010zce.1_Intron	NM_002239	NP_002230	P48549	IRK3_HUMAN	potassium inwardly-rectifying channel J3	294	Cytoplasmic (By similarity).				synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			upper_aerodigestive_tract(1)|pancreas(1)	2					Halothane(DB01159)													---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160255397	160255397	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160255397C>G	uc002uao.2	-	18	3259	c.2907G>C	c.(2905-2907)AAG>AAC	p.K969N	BAZ2B_uc002uap.2_Missense_Mutation_p.K933N|BAZ2B_uc002uaq.1_Missense_Mutation_p.K799N	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	969	Lys-rich.|Potential.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
RBMS1	5937	broad.mit.edu	37	2	161143571	161143571	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161143571T>G	uc002ubo.2	-	7	1109	c.665A>C	c.(664-666)AAG>ACG	p.K222T	RBMS1_uc002ubj.2_Missense_Mutation_p.K189T|RBMS1_uc002ubk.2_Missense_Mutation_p.K189T|RBMS1_uc002ubl.2_Missense_Mutation_p.K220T|RBMS1_uc002ubn.2_Missense_Mutation_p.K222T|RBMS1_uc002ubi.3_Missense_Mutation_p.K222T|RBMS1_uc002ubm.2_Missense_Mutation_p.K189T|RBMS1_uc002ubp.2_Missense_Mutation_p.K222T|RBMS1_uc010fox.2_Missense_Mutation_p.K222T	NM_016836	NP_058520	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting	222	RRM 2.				DNA replication|RNA processing	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding|single-stranded DNA binding				0																		---	---	---	---
SCN1A	6323	broad.mit.edu	37	2	166894563	166894563	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166894563A>G	uc010zcz.1	-	15	2654	c.2636T>C	c.(2635-2637)CTG>CCG	p.L879P	SCN1A_uc002udo.3_Missense_Mutation_p.L759P|SCN1A_uc010fpk.2_Missense_Mutation_p.L731P	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	890	II.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)													---	---	---	---
DFNB59	494513	broad.mit.edu	37	2	179325929	179325929	+	Silent	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179325929T>C	uc002umi.3	+	7	1343	c.987T>C	c.(985-987)TCT>TCC	p.S329S	DFNB59_uc002umj.3_Silent_p.S329S	NM_001042702	NP_001036167	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	329					sensory perception of sound						0			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179410691	179410691	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179410691C>T	uc010zfg.1	-	292	87792	c.87568G>A	c.(87568-87570)GTT>ATT	p.V29190I	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V22885I|TTN_uc010zfi.1_Missense_Mutation_p.V22818I|TTN_uc010zfj.1_Missense_Mutation_p.V22693I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	30117							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179446924	179446924	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179446924G>C	uc010zfg.1	-	264	58692	c.58468C>G	c.(58468-58470)CGC>GGC	p.R19490G	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R13185G|TTN_uc010zfi.1_Missense_Mutation_p.R13118G|TTN_uc010zfj.1_Missense_Mutation_p.R12993G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	20417							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179582536	179582536	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179582536C>T	uc010zfg.1	-	84	21557	c.21333G>A	c.(21331-21333)GCG>GCA	p.A7111A	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.A3772A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215854288	215854288	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215854288C>T	uc002vew.2	-	25	3902	c.3682G>A	c.(3682-3684)GAA>AAA	p.E1228K	ABCA12_uc002vev.2_Missense_Mutation_p.E910K|ABCA12_uc010zjn.1_Missense_Mutation_p.E155K	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	1228					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)														---	---	---	---
SPEG	10290	broad.mit.edu	37	2	220355192	220355192	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220355192A>T	uc010fwg.2	+	37	8983	c.8983A>T	c.(8983-8985)AAG>TAG	p.K2995*		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	2995	Protein kinase 2.	ATP (By similarity).			muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)														---	---	---	---
EPHA4	2043	broad.mit.edu	37	2	222347359	222347359	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222347359A>G	uc002vmq.2	-	5	1073	c.1031T>C	c.(1030-1032)GTG>GCG	p.V344A	EPHA4_uc002vmr.2_Missense_Mutation_p.V344A|EPHA4_uc010zlm.1_Missense_Mutation_p.V285A|EPHA4_uc010zln.1_Missense_Mutation_p.V344A	NM_004438	NP_004429	P54764	EPHA4_HUMAN	ephrin receptor EphA4 precursor	344	Extracellular (Potential).|Fibronectin type-III 1.					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)														---	---	---	---
FAM124B	79843	broad.mit.edu	37	2	225266260	225266260	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225266260T>G	uc002vnx.2	-	1	452	c.226A>C	c.(226-228)AGC>CGC	p.S76R	FAM124B_uc002vnw.2_Missense_Mutation_p.S76R	NM_001122779	NP_001116251	Q9H5Z6	F124B_HUMAN	hypothetical protein LOC79843 isoform a	76							protein binding			ovary(2)	2		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)														---	---	---	---
TM4SF20	79853	broad.mit.edu	37	2	228243973	228243973	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228243973G>A	uc002vpb.2	-	1	50	c.12C>T	c.(10-12)TGC>TGT	p.C4C		NM_024795	NP_079071	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	4	Cytoplasmic (Potential).					integral to membrane|plasma membrane					0		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)														---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230664083	230664083	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230664083G>A	uc002vpw.1	-	21	3107	c.2998C>T	c.(2998-3000)CTA>TTA	p.L1000L	TRIP12_uc002vpx.1_Silent_p.L1048L|TRIP12_uc002vpy.1_Silent_p.L730L|TRIP12_uc010zlz.1_Intron	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1000					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity	p.L1000L(1)		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)														---	---	---	---
PDCD1	5133	broad.mit.edu	37	2	242794868	242794868	+	Missense_Mutation	SNP	C	T	T	rs55679128		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242794868C>T	uc002wcq.3	-	2	409	c.341G>A	c.(340-342)CGG>CAG	p.R114Q	PDCD1_uc010fzs.2_Missense_Mutation_p.R45Q|PDCD1_uc010fzt.2_Intron	NM_005018	NP_005009	Q15116	PDCD1_HUMAN	programmed cell death 1 precursor	114	Ig-like V-type.|Extracellular (Potential).				apoptosis|humoral immune response|multicellular organismal development|T cell costimulation	integral to membrane	protein tyrosine phosphatase activity|signal transducer activity			ovary(1)	1		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219)														---	---	---	---
NKIRAS1	28512	broad.mit.edu	37	3	23942527	23942527	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23942527G>A	uc003ccj.2	-	4	510	c.108C>T	c.(106-108)TGC>TGT	p.C36C	NKIRAS1_uc003cck.2_Silent_p.C36C|NKIRAS1_uc003ccl.2_Silent_p.C36C|NKIRAS1_uc003ccm.2_Silent_p.C36C	NM_020345	NP_065078	Q9NYS0	KBRS1_HUMAN	kappa B-ras 1	36	Effector region.				I-kappaB kinase/NF-kappaB cascade|small GTPase mediated signal transduction	cytoplasm	GTP binding|GTPase activity				0																		---	---	---	---
STAB1	23166	broad.mit.edu	37	3	52554307	52554307	+	Splice_Site	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52554307G>A	uc003dej.2	+	52	5573	c.5499_splice	c.e52+1	p.A1833_splice	STAB1_uc003dek.1_Splice_Site|STAB1_uc003del.2_5'Flank	NM_015136	NP_055951			stabilin 1 precursor						cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77645801	77645801	+	Silent	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77645801T>C	uc003dpy.3	+	19	3397	c.2754T>C	c.(2752-2754)GAT>GAC	p.D918D	ROBO2_uc003dpz.2_Silent_p.D922D|ROBO2_uc011bgj.1_RNA|ROBO2_uc011bgk.1_Silent_p.D922D|ROBO2_uc003dqa.2_Silent_p.D45D	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2	918	Cytoplasmic (Potential).				apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)														---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	97202906	97202906	+	Intron	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97202906A>G	uc010how.1	+						EPHA6_uc011bgo.1_Intron|EPHA6_uc011bgp.1_Intron|EPHA6_uc003drs.3_Intron|EPHA6_uc003drr.3_Intron|EPHA6_uc003drt.2_Intron|EPHA6_uc010hox.1_Intron	NM_001080448	NP_001073917			EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16																		---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	97202913	97202913	+	Intron	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97202913A>G	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																		---	---	---	---
OR5H6	79295	broad.mit.edu	37	3	97983259	97983259	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97983259T>C	uc003dsi.1	+	1	131	c.131T>C	c.(130-132)TTC>TCC	p.F44S		NM_001005479	NP_001005479	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H,	44	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|large_intestine(1)	3																		---	---	---	---
IMPG2	50939	broad.mit.edu	37	3	100972575	100972575	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100972575T>C	uc003duq.1	-	11	1407	c.1204A>G	c.(1204-1206)AGT>GGT	p.S402G	IMPG2_uc011bhe.1_Missense_Mutation_p.S265G	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	402	Extracellular (Potential).				visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3																		---	---	---	---
IMPG2	50939	broad.mit.edu	37	3	100988348	100988348	+	Intron	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100988348A>C	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																		---	---	---	---
TIGIT	201633	broad.mit.edu	37	3	114026784	114026784	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114026784A>T	uc003ebg.1	+	4	575	c.541A>T	c.(541-543)AGA>TGA	p.R181*		NM_173799	NP_776160	Q495A1	TIGIT_HUMAN	T cell immunoreceptor with Ig and ITIM domains	181	Cytoplasmic (Potential).				negative regulation of interleukin-12 production|negative regulation of T cell activation|positive regulation of interleukin-10 production	cell surface|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
ADCY5	111	broad.mit.edu	37	3	123047546	123047546	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123047546C>T	uc003egh.1	-	6	1750	c.1750G>A	c.(1750-1752)GTC>ATC	p.V584I	ADCY5_uc003egg.1_Missense_Mutation_p.V217I|ADCY5_uc003egi.1_Missense_Mutation_p.V143I	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5	584	Guanylate cyclase 1.|Cytoplasmic (Potential).				activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)												OREG0015742	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PIK3R4	30849	broad.mit.edu	37	3	130403233	130403233	+	Intron	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130403233A>G	uc003enj.2	-							NM_014602	NP_055417			phosphoinositide-3-kinase, regulatory subunit 4						fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1)	12																		---	---	---	---
CPB1	1360	broad.mit.edu	37	3	148563398	148563398	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148563398G>C	uc003ewl.2	+	9	989	c.966G>C	c.(964-966)GAG>GAC	p.E322D		NM_001871	NP_001862	P15086	CBPB1_HUMAN	pancreatic carboxypeptidase B1 preproprotein	322					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)															---	---	---	---
HLTF	6596	broad.mit.edu	37	3	148765819	148765819	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148765819G>C	uc003ewq.1	-	17	2106	c.1888C>G	c.(1888-1890)CTT>GTT	p.L630V	HLTF_uc003ewr.1_Missense_Mutation_p.L630V|HLTF_uc003ews.1_Missense_Mutation_p.L629V|HLTF_uc010hve.1_Missense_Mutation_p.L629V	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor	630					chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)															---	---	---	---
AADACL2	344752	broad.mit.edu	37	3	151451949	151451949	+	Silent	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151451949T>C	uc003ezc.2	+	1	246	c.126T>C	c.(124-126)ACT>ACC	p.T42T	AADACL2_uc010hvn.2_5'UTR	NM_207365	NP_997248	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2 precursor	42						extracellular region|integral to membrane	carboxylesterase activity				0			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)															---	---	---	---
SI	6476	broad.mit.edu	37	3	164712183	164712183	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164712183G>T	uc003fei.2	-	41	4765	c.4703C>A	c.(4702-4704)CCC>CAC	p.P1568H		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	1568	Sucrase.|Lumenal.				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)			---	---	---	---
LRRIQ4	344657	broad.mit.edu	37	3	169540477	169540477	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169540477C>T	uc003fgb.2	+	1	768	c.768C>T	c.(766-768)CTC>CTT	p.L256L		NM_001080460	NP_001073929	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	256	LRR 10.										0																		---	---	---	---
USP13	8975	broad.mit.edu	37	3	179437723	179437723	+	Intron	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179437723G>A	uc003fkh.2	+						USP13_uc003fkf.2_Intron	NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
TP63	8626	broad.mit.edu	37	3	189455669	189455669	+	Intron	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189455669A>C	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)			---	---	---	---
APOD	347	broad.mit.edu	37	3	195295991	195295991	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195295991G>A	uc003fur.2	-	5	712	c.350C>T	c.(349-351)CCG>CTG	p.P117L		NM_001647	NP_001638	P05090	APOD_HUMAN	apolipoprotein D precursor	117					lipid metabolic process	extracellular space	lipid binding|lipid transporter activity|protein binding			ovary(2)	2	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)														---	---	---	---
SLIT2	9353	broad.mit.edu	37	4	20469422	20469422	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20469422G>A	uc003gpr.1	+	5	647	c.443G>A	c.(442-444)CGT>CAT	p.R148H	SLIT2_uc003gps.1_Missense_Mutation_p.R148H	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	148	LRR 4.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11																		---	---	---	---
CORIN	10699	broad.mit.edu	37	4	47788738	47788738	+	Intron	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47788738T>C	uc003gxm.2	-						CORIN_uc011bzf.1_Intron|CORIN_uc011bzg.1_Intron|CORIN_uc011bzh.1_Intron|CORIN_uc011bzi.1_Intron|CORIN_uc003gxn.3_Intron	NM_006587	NP_006578			corin						peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TXK	7294	broad.mit.edu	37	4	48116354	48116354	+	Intron	SNP	A	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48116354A>T	uc003gxx.3	-						TXK_uc003gxy.1_Intron	NM_003328	NP_003319			TXK tyrosine kinase							cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
C4orf14	84273	broad.mit.edu	37	4	57832867	57832867	+	Silent	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57832867G>T	uc003hck.2	-	5	1758	c.1683C>A	c.(1681-1683)TCC>TCA	p.S561S		NM_032313	NP_115689	Q8NC60	CD014_HUMAN	hypothetical protein LOC84273	561							GTP binding			ovary(1)|breast(1)	2	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
NAAA	27163	broad.mit.edu	37	4	76851622	76851622	+	Intron	SNP	C	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76851622C>G	uc003hjb.2	-						NAAA_uc003hja.2_Intron|NAAA_uc003hjc.3_Intron|NAAA_uc003hjd.3_Intron|NAAA_uc011cbq.1_Intron	NM_014435	NP_055250			N-acylethanolamine acid amidase isoform 1						lipid metabolic process	lysosome	hydrolase activity			skin(1)	1																		---	---	---	---
PPM1K	152926	broad.mit.edu	37	4	89199638	89199638	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89199638C>T	uc003hrm.3	-	2	488	c.98G>A	c.(97-99)CGG>CAG	p.R33Q	PPM1K_uc010ikp.1_Missense_Mutation_p.R33Q|PPM1K_uc003hrn.2_Missense_Mutation_p.R33Q	NM_152542	NP_689755	Q8N3J5	PPM1K_HUMAN	protein phosphatase 1K (PP2C domain containing)	33					protein dephosphorylation	mitochondrial matrix|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000192)														---	---	---	---
ADH4	127	broad.mit.edu	37	4	100063859	100063859	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100063859G>A	uc003hun.2	-	2	167	c.91C>T	c.(91-93)CCC>TCC	p.P31S	uc003hum.1_Intron|ADH4_uc011ced.1_Missense_Mutation_p.P50S	NM_000670	NP_000661	P08319	ADH4_HUMAN	class II alcohol dehydrogenase, pi subunit	31					alcohol catabolic process|cellular aldehyde metabolic process|ethanol oxidation|quinone cofactor metabolic process|retinol metabolic process|xenobiotic metabolic process	cytosol|microtubule cytoskeleton	alcohol dehydrogenase activity, zinc-dependent|all-trans retinal binding|benzaldehyde dehydrogenase activity|NAD binding|NADPH:quinone reductase activity|retinol binding|retinol dehydrogenase activity|zinc ion binding			skin(2)	2				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)	NADH(DB00157)													---	---	---	---
NDST3	9348	broad.mit.edu	37	4	119148127	119148127	+	Silent	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119148127C>A	uc003ibx.2	+	8	2212	c.1809C>A	c.(1807-1809)CCC>CCA	p.P603P	NDST3_uc011cgf.1_Silent_p.P522P	NM_004784	NP_004775	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan	603	Lumenal (Potential).|Heparan sulfate N-sulfotransferase 3.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1																		---	---	---	---
FABP2	2169	broad.mit.edu	37	4	120241895	120241895	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120241895C>T	uc003icw.2	-	2	229	c.170G>A	c.(169-171)CGA>CAA	p.R57Q		NM_000134	NP_000125	P12104	FABPI_HUMAN	intestinal fatty acid binding protein 2	57							fatty acid binding			ovary(1)	1																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126408501	126408501	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126408501T>C	uc003ifj.3	+	16	12818	c.12818T>C	c.(12817-12819)ATT>ACT	p.I4273T	FAT4_uc011cgp.1_Missense_Mutation_p.I2514T|FAT4_uc003ifi.1_Missense_Mutation_p.I1751T	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4273	Laminin G-like 2.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
NR3C2	4306	broad.mit.edu	37	4	149002531	149002531	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149002531C>T	uc003ilj.3	-	9	3253	c.2919G>A	c.(2917-2919)TCG>TCA	p.S973S	NR3C2_uc003ilk.3_Silent_p.S856S|NR3C2_uc010iph.2_RNA	NM_000901	NP_000892	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	973	Steroid-binding.				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)													---	---	---	---
TLR2	7097	broad.mit.edu	37	4	154625593	154625593	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154625593A>C	uc003inq.2	+	3	1753	c.1534A>C	c.(1534-1536)ACT>CCT	p.T512P	TLR2_uc003inr.2_Missense_Mutation_p.T512P|TLR2_uc003ins.2_Missense_Mutation_p.T512P	NM_003264	NP_003255	O60603	TLR2_HUMAN	toll-like receptor 2 precursor	512	LRR 14.|Extracellular (Potential).				cellular response to diacyl bacterial lipopeptide|cellular response to lipoteichoic acid|cellular response to triacyl bacterial lipopeptide|detection of diacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|I-kappaB phosphorylation|induction of apoptosis|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of interferon-beta 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 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|positive regulation of Wnt receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|integral to plasma membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	Gram-positive bacterial cell surface binding|lipopolysaccharide receptor activity|peptidoglycan binding|protein heterodimerization activity|transmembrane receptor activity|triacyl lipopeptide binding			ovary(1)|lung(1)|breast(1)	3	all_hematologic(180;0.093)	Renal(120;0.117)																---	---	---	---
SPATA4	132851	broad.mit.edu	37	4	177109269	177109269	+	Splice_Site	SNP	C	T	T	rs140274312	byFrequency;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177109269C>T	uc003iuo.1	-	5	914	c.805_splice	c.e5+1	p.P269_splice		NM_144644	NP_653245			spermatogenesis associated 4						apoptosis|spermatogenesis						0		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)														---	---	---	---
CMYA5	202333	broad.mit.edu	37	5	79024913	79024913	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79024913C>T	uc003kgc.2	+	2	397	c.325C>T	c.(325-327)CGG>TGG	p.R109W		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	109						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)														---	---	---	---
FAM170A	340069	broad.mit.edu	37	5	118969730	118969730	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118969730C>T	uc003ksm.2	+	3	497	c.287C>T	c.(286-288)CCT>CTT	p.P96L	FAM170A_uc003ksl.2_Missense_Mutation_p.P96L|FAM170A_uc003ksn.2_Missense_Mutation_p.P96L|FAM170A_uc003kso.2_Missense_Mutation_p.P49L	NM_182761	NP_877438	A1A519	F170A_HUMAN	family with sequence similarity 170, member A	96						intracellular	zinc ion binding			skin(1)	1																		---	---	---	---
ZNF474	133923	broad.mit.edu	37	5	121488615	121488615	+	Silent	SNP	T	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121488615T>A	uc003ksv.2	+	2	1306	c.930T>A	c.(928-930)CCT>CCA	p.P310P		NM_207317	NP_997200	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	310						intracellular	zinc ion binding				0		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)														---	---	---	---
TGFBI	7045	broad.mit.edu	37	5	135390426	135390426	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135390426C>T	uc003lbf.3	+	10	1447	c.1286C>T	c.(1285-1287)GCC>GTC	p.A429V	TGFBI_uc003lbg.3_Missense_Mutation_p.A162V|TGFBI_uc003lbh.3_Missense_Mutation_p.A255V|TGFBI_uc011cyb.1_Missense_Mutation_p.A255V|TGFBI_uc010jed.2_Missense_Mutation_p.A162V	NM_000358	NP_000349	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	429	FAS1 3.				angiogenesis|cell adhesion|cell proliferation|negative regulation of cell adhesion|response to stimulus|visual perception	extracellular space|proteinaceous extracellular matrix	integrin binding			breast(3)|ovary(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
KLHL3	26249	broad.mit.edu	37	5	136963998	136963998	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136963998G>A	uc010jek.2	-	13	2023	c.1579C>T	c.(1579-1581)CGG>TGG	p.R527W	KLHL3_uc011cyc.1_Missense_Mutation_p.R262W|KLHL3_uc003lbr.3_Missense_Mutation_p.R445W|KLHL3_uc011cyd.1_RNA	NM_017415	NP_059111	Q9UH77	KLHL3_HUMAN	kelch-like 3	527	Kelch 5.					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)														---	---	---	---
PCDHA3	56145	broad.mit.edu	37	5	140183050	140183050	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140183050G>T	uc003lhf.2	+	1	2268	c.2268G>T	c.(2266-2268)CAG>CAT	p.Q756H	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.Q756H	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	756	Cytoplasmic (Potential).|6 X 4 AA repeats of P-X-X-P.				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)															---	---	---	---
KIF4B	285643	broad.mit.edu	37	5	154394891	154394891	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154394891C>T	uc010jih.1	+	1	1632	c.1472C>T	c.(1471-1473)GCG>GTG	p.A491V		NM_001099293	NP_001092763	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	491	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)															---	---	---	---
GABRB2	2561	broad.mit.edu	37	5	160757981	160757981	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160757981A>C	uc003lys.1	-	9	1204	c.986T>G	c.(985-987)ATC>AGC	p.I329S	GABRB2_uc011deh.1_Missense_Mutation_p.I168S|GABRB2_uc003lyr.1_Missense_Mutation_p.I329S|GABRB2_uc003lyt.1_Missense_Mutation_p.I329S|GABRB2_uc010jiu.1_Missense_Mutation_p.I266S	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	329	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
LCP2	3937	broad.mit.edu	37	5	169683539	169683539	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169683539A>C	uc003man.1	-	17	1348	c.1141T>G	c.(1141-1143)TTC>GTC	p.F381V	LCP2_uc011des.1_Missense_Mutation_p.F176V|LCP2_uc011det.1_Missense_Mutation_p.F210V	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2	381					immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)														---	---	---	---
FLT4	2324	broad.mit.edu	37	5	180053156	180053156	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180053156C>T	uc003mma.3	-	9	1292	c.1213G>A	c.(1213-1215)GCT>ACT	p.A405T	FLT4_uc003mlz.3_Missense_Mutation_p.A405T|FLT4_uc003mmb.1_5'UTR|FLT4_uc011dgy.1_Missense_Mutation_p.A405T	NM_002020	NP_002011	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 2	405	Ig-like C2-type 4.|Extracellular (Potential).				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				---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17800348	17800348	+	Intron	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17800348G>T	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron	NM_022113	NP_071396			kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)															---	---	---	---
ZKSCAN4	387032	broad.mit.edu	37	6	28217559	28217559	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28217559C>A	uc003nks.1	-	2	721	c.477G>T	c.(475-477)TTG>TTT	p.L159F	ZKSCAN4_uc011dlb.1_Missense_Mutation_p.L4F	NM_019110	NP_061983	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	159					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
BTNL2	56244	broad.mit.edu	37	6	32362788	32362788	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32362788G>A	uc003obg.1	-	6	1093	c.1093C>T	c.(1093-1095)CCA>TCA	p.P365S	BTNL2_uc010jty.1_Missense_Mutation_p.P88S|BTNL2_uc010jtz.1_RNA|BTNL2_uc010jua.1_Missense_Mutation_p.P155S	NM_019602	NP_062548	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2	365	Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38890856	38890856	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38890856C>T	uc003ooe.1	+	70	10634	c.10034C>T	c.(10033-10035)ACG>ATG	p.T3345M	uc003oof.1_Intron	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38957837	38957837	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38957837G>T	uc003ooe.1	+	86	13052	c.12452G>T	c.(12451-12453)GGA>GTA	p.G4151V		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																		---	---	---	---
KCNK5	8645	broad.mit.edu	37	6	39163699	39163699	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39163699T>C	uc003oon.2	-	2	615	c.251A>G	c.(250-252)AAC>AGC	p.N84S		NM_003740	NP_003731	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	84					excretion	integral to plasma membrane	potassium channel activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2																		---	---	---	---
TREML2	79865	broad.mit.edu	37	6	41166041	41166041	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41166041T>G	uc010jxm.1	-	2	361	c.182A>C	c.(181-183)AAG>ACG	p.K61T		NM_024807	NP_079083	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid	61	Ig-like V-type.|Extracellular (Potential).				T cell activation	cell surface|integral to membrane|plasma membrane	protein binding|receptor activity			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
DST	667	broad.mit.edu	37	6	56422147	56422147	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56422147A>C	uc003pdf.2	-	53	8281	c.8253T>G	c.(8251-8253)AAT>AAG	p.N2751K	DST_uc003pcz.3_Missense_Mutation_p.N2573K|DST_uc011dxj.1_Missense_Mutation_p.N2602K|DST_uc011dxk.1_Missense_Mutation_p.N2613K|DST_uc003pcy.3_Missense_Mutation_p.N2247K	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	4659	Spectrin 5.				cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
ZNF451	26036	broad.mit.edu	37	6	57015612	57015612	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57015612C>T	uc003pdm.1	+	11	2928	c.2704C>T	c.(2704-2706)CAT>TAT	p.H902Y	ZNF451_uc003pdl.2_Missense_Mutation_p.H902Y|ZNF451_uc003pdn.1_Intron|uc003pdq.1_Intron|ZNF451_uc003pdk.1_Missense_Mutation_p.H902Y	NM_001031623	NP_001026794	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451 isoform 1	902					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|pancreas(1)	2	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)															---	---	---	---
EYS	346007	broad.mit.edu	37	6	66205311	66205311	+	5'UTR	SNP	T	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66205311T>A	uc011dxu.1	-	4					EYS_uc003peq.2_5'UTR|EYS_uc003per.1_5'UTR|EYS_uc010kaj.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																		---	---	---	---
CD109	135228	broad.mit.edu	37	6	74481144	74481144	+	Intron	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74481144T>G	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000			CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75811310	75811310	+	Intron	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75811310A>C	uc003phs.2	-						COL12A1_uc003pht.2_Intron	NM_004370	NP_004361			collagen, type XII, alpha 1 long isoform						cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87966559	87966559	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87966559T>C	uc003plm.3	+	8	3253	c.3212T>C	c.(3211-3213)ATT>ACT	p.I1071T		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	1071					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)														---	---	---	---
GJA10	84694	broad.mit.edu	37	6	90605201	90605201	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90605201T>A	uc011eaa.1	+	1	1014	c.1014T>A	c.(1012-1014)TGT>TGA	p.C338*		NM_032602	NP_115991	Q969M2	CXA10_HUMAN	gap junction protein, alpha 10	338	Cytoplasmic (Potential).				synaptic transmission	connexon complex|integral to membrane	gap junction channel activity				0		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)												OREG0004442	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=CX62|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	---	---	---	---
AIM1	202	broad.mit.edu	37	6	107009312	107009312	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107009312C>T	uc003prh.2	+	18	5338	c.4851C>T	c.(4849-4851)GTC>GTT	p.V1617V	AIM1_uc003pri.2_Silent_p.V421V	NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1	1617	Ricin B-type lectin.						sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)														---	---	---	---
PDE7B	27115	broad.mit.edu	37	6	136495026	136495026	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136495026C>T	uc003qgp.2	+	9	1106	c.803C>T	c.(802-804)ACA>ATA	p.T268I	uc003qgq.1_Intron|PDE7B_uc003qgr.2_Missense_Mutation_p.T320I	NM_018945	NP_061818	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B	268	Catalytic (By similarity).				signal transduction|synaptic transmission	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(1)	1	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Dyphylline(DB00651)|Ketotifen(DB00920)													---	---	---	---
STXBP5	134957	broad.mit.edu	37	6	147556374	147556374	+	Intron	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147556374A>G	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)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152782871	152782871	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152782871A>T	uc010kiw.2	-	21	2857	c.2255T>A	c.(2254-2256)ATT>AAT	p.I752N	SYNE1_uc003qot.3_Missense_Mutation_p.I759N|SYNE1_uc003qou.3_Missense_Mutation_p.I752N|SYNE1_uc010kjb.1_Missense_Mutation_p.I735N|SYNE1_uc003qow.2_Missense_Mutation_p.I47N|SYNE1_uc003qox.1_Missense_Mutation_p.I268N|SYNE1_uc003qoz.2_Missense_Mutation_p.I184N|SYNE1_uc003qoy.2_Missense_Mutation_p.I319N	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	752	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
OPRM1	4988	broad.mit.edu	37	6	154414576	154414576	+	Intron	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154414576A>G	uc003qpr.2	+						OPRM1_uc011efc.1_Intron|OPRM1_uc011efd.1_Intron|OPRM1_uc011efe.1_Intron|OPRM1_uc003qpo.1_Missense_Mutation_p.S446G|OPRM1_uc011eff.1_Intron|OPRM1_uc011efg.1_Intron|OPRM1_uc011efh.1_Intron|OPRM1_uc003qpq.1_Intron|OPRM1_uc003qpt.1_Intron|OPRM1_uc011efi.1_Intron|OPRM1_uc003qpp.2_Intron|OPRM1_uc003qps.2_Intron|OPRM1_uc010kjg.2_Intron	NM_000914	NP_000905			opioid receptor, mu 1 isoform MOR-1						behavior|negative regulation of cell proliferation|sensory perception	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	mu-opioid receptor activity|protein binding			ovary(1)	1		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tramadol(DB00193)													---	---	---	---
MAS1	4142	broad.mit.edu	37	6	160328572	160328572	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160328572C>A	uc003qsz.2	+	1	599	c.585C>A	c.(583-585)AGC>AGA	p.S195R		NM_002377	NP_002368	P04201	MAS_HUMAN	MAS1 oncogene	195	Helical; Name=5; (Potential).				anatomical structure morphogenesis|cell proliferation|protein kinase C signaling cascade	integral to plasma membrane	angiotensin type II receptor activity			ovary(2)|lung(2)	4		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.6e-06)														---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163735911	163735911	+	Silent	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163735911G>T	uc003qua.2	+	7	1007	c.783G>T	c.(781-783)GGG>GGT	p.G261G	PACRG_uc003qub.2_Silent_p.G222G|PACRG_uc003quc.2_Silent_p.G222G|LOC285796_uc011egh.1_Intron	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1	261											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)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	4247793	4247793	+	Silent	SNP	C	A	A	rs113117904	byFrequency	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4247793C>A	uc003smx.2	+	37	5416	c.5277C>A	c.(5275-5277)CCC>CCA	p.P1759P	SDK1_uc010kso.2_Silent_p.P1015P|SDK1_uc003smy.2_Silent_p.P246P	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	1759	Fibronectin type-III 11.				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)														---	---	---	---
HOXA13	3209	broad.mit.edu	37	7	27237911	27237911	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27237911G>A	uc003szb.1	-	2	1102	c.1073C>T	c.(1072-1074)ACG>ATG	p.T358M	uc003szc.1_5'Flank	NM_000522	NP_000513	P31271	HXA13_HUMAN	homeobox A13	358	Homeobox.				skeletal system development	nucleus	sequence-specific DNA binding			breast(1)	1								T	NUP98	AML								---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37256298	37256298	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37256298C>G	uc003tfk.1	-	11	1090	c.783G>C	c.(781-783)GAG>GAC	p.E261D	ELMO1_uc011kbc.1_Missense_Mutation_p.E165D|ELMO1_uc010kxg.1_Missense_Mutation_p.E261D	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	261					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																		---	---	---	---
TNS3	64759	broad.mit.edu	37	7	47384554	47384554	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47384554G>T	uc003tnv.2	-	19	2901	c.2534C>A	c.(2533-2535)CCA>CAA	p.P845Q	TNS3_uc003tnw.2_Missense_Mutation_p.P845Q	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3	845						focal adhesion	protein binding			ovary(4)	4																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48311574	48311574	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48311574A>C	uc003toq.2	+	17	2336	c.2311A>C	c.(2311-2313)AGT>CGT	p.S771R	ABCA13_uc010kyr.2_Missense_Mutation_p.S274R	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	771					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48506621	48506621	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48506621G>T	uc003toq.2	+	44	12909	c.12884G>T	c.(12883-12885)TGT>TTT	p.C4295F	ABCA13_uc010kys.1_Missense_Mutation_p.C1370F|ABCA13_uc010kyt.1_RNA|ABCA13_uc010kyu.1_Intron	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	4295					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48559880	48559880	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48559880C>T	uc003toq.2	+	53	14066	c.14041C>T	c.(14041-14043)CGA>TGA	p.R4681*	ABCA13_uc010kys.1_Nonsense_Mutation_p.R1756*|ABCA13_uc010kyt.1_RNA|ABCA13_uc010kyu.1_Nonsense_Mutation_p.R411*	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	4681					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
GRM3	2913	broad.mit.edu	37	7	86479841	86479841	+	Silent	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86479841T>G	uc003uid.2	+	5	3646	c.2547T>G	c.(2545-2547)ACT>ACG	p.T849T	GRM3_uc010lef.2_Missense_Mutation_p.W492G|GRM3_uc010leg.2_Silent_p.T721T|GRM3_uc010leh.2_Silent_p.T441T	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	849	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)													---	---	---	---
GIGYF1	64599	broad.mit.edu	37	7	100279796	100279796	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100279796G>A	uc003uwg.1	-	22	3833	c.2824C>T	c.(2824-2826)CGT>TGT	p.R942C		NM_022574	NP_072096	O75420	PERQ1_HUMAN	PERQ amino acid rich, with GYF domain 1	942										large_intestine(1)|central_nervous_system(1)	2	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)																	---	---	---	---
EPO	2056	broad.mit.edu	37	7	100320301	100320301	+	Silent	SNP	C	T	T	rs140683829	byFrequency	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100320301C>T	uc003uwi.2	+	4	442	c.261C>T	c.(259-261)GCC>GCT	p.A87A	EPO_uc011kkc.1_Silent_p.A87A	NM_000799	NP_000790	P01588	EPO_HUMAN	erythropoietin precursor	87					blood circulation|cellular hyperosmotic response|erythrocyte maturation|negative regulation of apoptosis|negative regulation of ion transmembrane transporter activity|negative regulation of sodium ion transport|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of Ras protein signal transduction|positive regulation of transcription, DNA-dependent|positive regulation of tyrosine phosphorylation of Stat5 protein|signal transduction	extracellular space	erythropoietin receptor binding|eukaryotic cell surface binding|hormone activity			central_nervous_system(2)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)				Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)													---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100349878	100349878	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100349878C>T	uc003uwj.2	+	14	2315	c.2150C>T	c.(2149-2151)CCC>CTC	p.P717L	ZAN_uc003uwk.2_Missense_Mutation_p.P717L|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	717	66 X heptapeptide repeats (approximate) (mucin-like domain).|Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)															---	---	---	---
SLC13A1	6561	broad.mit.edu	37	7	122787309	122787309	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122787309A>G	uc003vkm.2	-	7	741	c.716T>C	c.(715-717)CTT>CCT	p.L239P	SLC13A1_uc010lks.2_Missense_Mutation_p.L115P	NM_022444	NP_071889	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate	239	Helical; (Potential).					integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)													---	---	---	---
CNOT4	4850	broad.mit.edu	37	7	135048751	135048751	+	Silent	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135048751G>T	uc011kpy.1	-	10	1787	c.1695C>A	c.(1693-1695)CCC>CCA	p.P565P	CNOT4_uc003vss.2_Intron|CNOT4_uc011kpz.1_Silent_p.P562P|CNOT4_uc003vst.2_Intron	NM_001008225	NP_001008226	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					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																		---	---	---	---
EPHB6	2051	broad.mit.edu	37	7	142566366	142566366	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142566366C>T	uc011kst.1	+	15	2942	c.2155C>T	c.(2155-2157)CGG>TGG	p.R719W	EPHB6_uc011ksu.1_Missense_Mutation_p.R719W|EPHB6_uc003wbs.2_Missense_Mutation_p.R427W|EPHB6_uc003wbt.2_Missense_Mutation_p.R193W|EPHB6_uc003wbu.2_Missense_Mutation_p.R427W|EPHB6_uc003wbv.2_Missense_Mutation_p.R103W	NM_004445	NP_004436	O15197	EPHB6_HUMAN	ephrin receptor EphB6 precursor	719	Cytoplasmic (Potential).|Protein kinase.		R -> Q (in a colorectal cancer sample; somatic mutation).			extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1)	19	Melanoma(164;0.059)																	---	---	---	---
CLCN1	1180	broad.mit.edu	37	7	143048811	143048811	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143048811G>A	uc003wcr.1	+	23	2807	c.2720G>A	c.(2719-2721)TGG>TAG	p.W907*	CLCN1_uc011ktc.1_Nonsense_Mutation_p.W519*	NM_000083	NP_000074	P35523	CLCN1_HUMAN	chloride channel 1, skeletal muscle	907	Cytoplasmic (By similarity).				muscle contraction	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Melanoma(164;0.205)																	---	---	---	---
DLGAP2	9228	broad.mit.edu	37	8	1645406	1645406	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1645406G>A	uc003wpl.2	+	11	2747	c.2650G>A	c.(2650-2652)GAC>AAC	p.D884N	DLGAP2_uc003wpm.2_Missense_Mutation_p.D870N	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	963					neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2824082	2824082	+	Intron	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2824082G>T	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)														---	---	---	---
DEFA4	1669	broad.mit.edu	37	8	6794409	6794409	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6794409C>T	uc003wqu.1	-	2	64	c.13G>A	c.(13-15)GCC>ACC	p.A5T		NM_001925	NP_001916	P12838	DEF4_HUMAN	defensin, alpha 4 preproprotein	5					defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular space				large_intestine(1)	1				COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)														---	---	---	---
ZFHX4	79776	broad.mit.edu	37	8	77763428	77763428	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77763428C>T	uc003yav.2	+	10	4523	c.4136C>T	c.(4135-4137)GCG>GTG	p.A1379V	ZFHX4_uc003yau.1_Missense_Mutation_p.A1424V|ZFHX4_uc003yaw.1_Missense_Mutation_p.A1379V	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1379						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)			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104898096	104898096	+	Silent	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104898096T>G	uc003yls.2	+	2	844	c.603T>G	c.(601-603)TCT>TCG	p.S201S	RIMS2_uc003ylp.2_Silent_p.S423S|RIMS2_uc003ylw.2_Silent_p.S231S|RIMS2_uc003ylq.2_Silent_p.S231S|RIMS2_uc003ylr.2_Silent_p.S231S	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	454					intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding	p.S231S(1)		ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104924348	104924348	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104924348G>A	uc003yls.2	+	4	1335	c.1094G>A	c.(1093-1095)CGT>CAT	p.R365H	RIMS2_uc003ylp.2_Missense_Mutation_p.R587H|RIMS2_uc003ylw.2_Missense_Mutation_p.R395H|RIMS2_uc003ylq.2_Missense_Mutation_p.R395H|RIMS2_uc003ylr.2_Missense_Mutation_p.R442H|RIMS2_uc003ylt.2_5'UTR	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	665					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)			---	---	---	---
TMEM74	157753	broad.mit.edu	37	8	109796546	109796546	+	Missense_Mutation	SNP	C	T	T	rs145039251		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109796546C>T	uc003ymy.1	-	2	887	c.782G>A	c.(781-783)CGT>CAT	p.R261H	TMEM74_uc003ymx.2_Intron	NM_153015	NP_694560	Q96NL1	TMM74_HUMAN	transmembrane protein 74	261					autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)															---	---	---	---
ST3GAL1	6482	broad.mit.edu	37	8	134488086	134488086	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134488086C>T	uc003yuk.2	-	5	1011	c.182G>A	c.(181-183)TGC>TAC	p.C61Y	ST3GAL1_uc003yum.2_Missense_Mutation_p.C61Y	NM_173344	NP_775479	Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase	61	Lumenal (Potential).				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)															---	---	---	---
KHDRBS3	10656	broad.mit.edu	37	8	136594231	136594231	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136594231T>A	uc003yuv.2	+	6	1116	c.722T>A	c.(721-723)CTT>CAT	p.L241H	KHDRBS3_uc003yuw.2_Missense_Mutation_p.L241H|KHDRBS3_uc010mek.2_RNA	NM_006558	NP_006549	O75525	KHDR3_HUMAN	KH domain containing, RNA binding, signal	241	Interaction with SIAH1.			Missing: Complete loss of SIAH1-mediated degradation.	regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	SH3 domain binding			ovary(2)	2	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)															---	---	---	---
FOXD4	2298	broad.mit.edu	37	9	117584	117584	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117584C>T	uc003zfz.2	-	1	834	c.536G>A	c.(535-537)AGC>AAC	p.S179N		NM_207305	NP_997188	Q12950	FOXD4_HUMAN	forkhead box D4	179	Fork-head.				axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(1)	1	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)														---	---	---	---
DMRT3	58524	broad.mit.edu	37	9	990464	990464	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:990464C>T	uc003zgw.1	+	2	916	c.878C>T	c.(877-879)ACG>ATG	p.T293M		NM_021240	NP_067063	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor	293					cell differentiation|multicellular organismal development|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(2)|central_nervous_system(1)	3		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)														---	---	---	---
KIAA1432	57589	broad.mit.edu	37	9	5746060	5746060	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5746060G>A	uc003zji.2	+	10	1081	c.988G>A	c.(988-990)GTA>ATA	p.V330I	KIAA1432_uc003zjh.2_Missense_Mutation_p.V330I|KIAA1432_uc003zjl.3_Missense_Mutation_p.V330I|KIAA1432_uc003zjj.1_5'UTR	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a	409						integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)														---	---	---	---
TDRD7	23424	broad.mit.edu	37	9	100240763	100240763	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100240763C>A	uc004axj.2	+	13	2434	c.2209C>A	c.(2209-2211)CTG>ATG	p.L737M	TDRD7_uc011lux.1_Missense_Mutation_p.L663M|TDRD7_uc010msp.1_Translation_Start_Site|TDRD7_uc011luy.1_Missense_Mutation_p.L57M	NM_014290	NP_055105	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	737	Tudor 2.				lens fiber cell differentiation|lens morphogenesis in camera-type eye|posttranscriptional regulation of gene expression|spermatogenesis	chromatoid body	mRNA binding			ovary(2)|pancreas(1)	3		Acute lymphoblastic leukemia(62;0.158)																---	---	---	---
OR13C9	286362	broad.mit.edu	37	9	107379899	107379899	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107379899T>G	uc011lvr.1	-	1	587	c.587A>C	c.(586-588)GAG>GCG	p.E196A		NM_001001956	NP_001001956	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C,	196	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
OR1N1	138883	broad.mit.edu	37	9	125288701	125288701	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125288701C>T	uc004bmn.1	-	1	872	c.872G>A	c.(871-873)AGG>AAG	p.R291K		NM_012363	NP_036495	Q8NGS0	OR1N1_HUMAN	olfactory receptor, family 1, subfamily N,	291	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			upper_aerodigestive_tract(1)|breast(1)|skin(1)	3																		---	---	---	---
STRBP	55342	broad.mit.edu	37	9	125932229	125932229	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125932229T>A	uc004bns.2	-	6	917	c.487A>T	c.(487-489)ATA>TTA	p.I163L	STRBP_uc004bnt.2_5'UTR|STRBP_uc004bnu.2_Missense_Mutation_p.I149L|STRBP_uc004bnv.2_Missense_Mutation_p.I163L	NM_018387	NP_060857	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	163	DZF.				multicellular organismal development	cytoplasm|nucleus	DNA binding			breast(1)|skin(1)	2																		---	---	---	---
TBC1D13	54662	broad.mit.edu	37	9	131568560	131568560	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131568560G>A	uc010myj.2	+	11	1230	c.1107G>A	c.(1105-1107)GGG>GGA	p.G369G	TBC1D13_uc010myk.2_Silent_p.G244G|TBC1D13_uc010myl.2_Silent_p.G188G	NM_018201	NP_060671	Q9NVG8	TBC13_HUMAN	TBC1 domain family, member 13	369						intracellular	Rab GTPase activator activity				0																		---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137630633	137630633	+	Silent	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137630633A>G	uc004cfe.2	+	11	1855	c.1473A>G	c.(1471-1473)CAA>CAG	p.Q491Q		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	491	Interrupted collagenous region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137702118	137702118	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137702118G>A	uc004cfe.2	+	44	3874	c.3492G>A	c.(3490-3492)CCG>CCA	p.P1164P		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	1164	Triple-helical region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
FBXO18	84893	broad.mit.edu	37	10	5948320	5948320	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5948320A>G	uc001iis.2	+	3	573	c.478A>G	c.(478-480)AGG>GGG	p.R160G	FBXO18_uc001iir.2_Missense_Mutation_p.R86G|FBXO18_uc009xig.2_Missense_Mutation_p.R86G|FBXO18_uc001iit.2_Missense_Mutation_p.R211G	NM_178150	NP_835363	Q8NFZ0	FBX18_HUMAN	F-box only protein, helicase, 18 isoform 2	160	F-box.				DNA repair	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(2)|skin(1)	3																		---	---	---	---
ITGA8	8516	broad.mit.edu	37	10	15686083	15686083	+	Missense_Mutation	SNP	C	T	T	rs145062914	byFrequency	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15686083C>T	uc001ioc.1	-	13	1345	c.1345G>A	c.(1345-1347)GGA>AGA	p.G449R	ITGA8_uc010qcb.1_Missense_Mutation_p.G434R	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	449	Extracellular (Potential).|FG-GAP 7.				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6																		---	---	---	---
CUBN	8029	broad.mit.edu	37	10	16990490	16990490	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16990490G>A	uc001ioo.2	-	35	5248	c.5196C>T	c.(5194-5196)ACC>ACT	p.T1732T		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1732	CUB 11.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
THNSL1	79896	broad.mit.edu	37	10	25312685	25312685	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25312685C>T	uc001isi.3	+	3	862	c.533C>T	c.(532-534)TCT>TTT	p.S178F	ENKUR_uc001ish.1_Intron	NM_024838	NP_079114	Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1	178					threonine biosynthetic process		ATP binding|pyridoxal phosphate binding|shikimate kinase activity|threonine synthase activity			pancreas(1)	1					L-Threonine(DB00156)|Pyridoxal Phosphate(DB00114)													---	---	---	---
RBP3	5949	broad.mit.edu	37	10	48382196	48382196	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48382196C>T	uc001jez.2	-	4	3567	c.3453G>A	c.(3451-3453)GCG>GCA	p.A1151A		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	1151	4 X approximate tandem repeats.|4.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)													---	---	---	---
AGAP7	653268	broad.mit.edu	37	10	51465546	51465546	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51465546G>T	uc001jio.2	-	7	1036	c.910C>A	c.(910-912)CAT>AAT	p.H304N	PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron	NM_001077685	NP_001071153	Q5VUJ5	AGAP7_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH	304	PH.				regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
DKK1	22943	broad.mit.edu	37	10	54076463	54076463	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54076463A>G	uc001jjr.2	+	4	851	c.697A>G	c.(697-699)ATA>GTA	p.I233V	uc001jjq.1_5'Flank|uc009xox.1_5'Flank	NM_012242	NP_036374	O94907	DKK1_HUMAN	dickkopf homolog 1 precursor	233	DKK-type Cys-2.				negative regulation of peptidyl-serine phosphorylation|negative regulation of protein complex assembly|negative regulation of transcription from RNA polymerase II promoter|positive regulation of heart induction by negative regulation of canonical Wnt receptor signaling pathway|regulation of receptor internalization	extracellular space|plasma membrane	growth factor activity|low-density lipoprotein particle receptor binding|receptor antagonist activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3																		---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64975351	64975351	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64975351G>A	uc001jmn.2	-	6	1084	c.784C>T	c.(784-786)CGC>TGC	p.R262C	JMJD1C_uc001jml.2_Missense_Mutation_p.R43C|JMJD1C_uc001jmm.2_Translation_Start_Site|JMJD1C_uc010qiq.1_Missense_Mutation_p.R80C|JMJD1C_uc009xpi.2_Missense_Mutation_p.R80C|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc001jmp.1_Translation_Start_Site	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	262					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)																	---	---	---	---
GRID1	2894	broad.mit.edu	37	10	88123696	88123696	+	Splice_Site	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88123696A>G	uc001kdl.1	-	2	336	c.235_splice	c.e2+1	p.A79_splice	GRID1_uc009xsu.1_Splice_Site	NM_017551	NP_060021			glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)										Multiple Myeloma(13;0.14)			---	---	---	---
LDB1	8861	broad.mit.edu	37	10	103870394	103870394	+	Silent	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103870394C>A	uc009xwz.2	-	6	760	c.417G>T	c.(415-417)CTG>CTT	p.L139L	LDB1_uc001kuk.3_Silent_p.L103L|LDB1_uc001kul.3_Silent_p.L103L	NM_001113407	NP_001106878	Q86U70	LDB1_HUMAN	LIM domain binding 1 isoform 1	139					histone H3-K4 acetylation|negative regulation of erythrocyte differentiation|negative regulation of transcription, DNA-dependent|positive regulation of hemoglobin biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription elongation, DNA-dependent|transcription, DNA-dependent|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	nuclear chromatin|protein complex	LIM domain binding|protein homodimerization activity|transcription corepressor activity			large_intestine(1)	1		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)														---	---	---	---
BAG3	9531	broad.mit.edu	37	10	121436761	121436761	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121436761G>C	uc001lem.2	+	4	2001	c.1695G>C	c.(1693-1695)ATG>ATC	p.M565I	BAG3_uc001lel.2_Missense_Mutation_p.M564I	NM_004281	NP_004272	O95817	BAG3_HUMAN	BCL2-associated athanogene 3	565					anti-apoptosis|apoptosis|protein folding	cytosol				ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00187)|BRCA - Breast invasive adenocarcinoma(275;0.148)														---	---	---	---
EBF3	253738	broad.mit.edu	37	10	131665477	131665477	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131665477C>T	uc001lki.1	-	10	999	c.940G>A	c.(940-942)GTC>ATC	p.V314I		NM_001005463	NP_001005463	Q9H4W6	COE3_HUMAN	early B-cell factor 3	323	IPT/TIG.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|protein binding			central_nervous_system(1)|pancreas(1)	2		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)														---	---	---	---
OR52M1	119772	broad.mit.edu	37	11	4566687	4566687	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4566687C>T	uc010qyf.1	+	1	267	c.267C>T	c.(265-267)TTC>TTT	p.F89F		NM_001004137	NP_001004137	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M,	89	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
TRIM22	10346	broad.mit.edu	37	11	5729464	5729464	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5729464C>T	uc001mbr.2	+	6	1112	c.835C>T	c.(835-837)CGA>TGA	p.R279*	TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Nonsense_Mutation_p.R247*|TRIM22_uc009yes.2_Nonsense_Mutation_p.R275*|TRIM22_uc010qzm.1_Nonsense_Mutation_p.R107*|TRIM22_uc009yeu.2_Nonsense_Mutation_p.R90*|OR56B1_uc001mbs.1_5'UTR|OR56B1_uc009yev.1_5'UTR	NM_006074	NP_006065	Q8IYM9	TRI22_HUMAN	tripartite motif-containing 22	279					immune response|interspecies interaction between organisms|protein trimerization|response to virus	Cajal body|Golgi apparatus|nuclear speck	ligase activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding				0		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)														---	---	---	---
OR52E8	390079	broad.mit.edu	37	11	5878471	5878471	+	Silent	SNP	A	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5878471A>T	uc010qzr.1	-	1	462	c.462T>A	c.(460-462)GCT>GCA	p.A154A	TRIM5_uc001mbq.1_Intron	NM_001005168	NP_001005168	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E,	154	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
OR10A4	283297	broad.mit.edu	37	11	6898600	6898600	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6898600C>A	uc010rat.1	+	1	722	c.722C>A	c.(721-723)ACC>AAC	p.T241N		NM_207186	NP_997069	Q9H209	O10A4_HUMAN	olfactory receptor, family 10, subfamily A,	241	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)														---	---	---	---
ZNF215	7762	broad.mit.edu	37	11	6977491	6977491	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6977491T>G	uc001mey.2	+	7	1871	c.1283T>G	c.(1282-1284)CTT>CGT	p.L428R	ZNF215_uc010raw.1_3'UTR|ZNF215_uc010rax.1_Missense_Mutation_p.L190R|ZNF215_uc001mez.1_Intron	NM_013250	NP_037382	Q9UL58	ZN215_HUMAN	zinc finger protein 215	428	C2H2-type 2.				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)														---	---	---	---
RBMXL2	27288	broad.mit.edu	37	11	7111135	7111135	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7111135G>A	uc001mfc.2	+	1	971	c.784G>A	c.(784-786)GGC>AGC	p.G262S		NM_014469	NP_055284	O75526	HNRGT_HUMAN	testes-specific heterogenous nuclear	262	Arg/Gly/Pro-rich.					nucleus|ribonucleoprotein complex	nucleotide binding|RNA binding				0				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)														---	---	---	---
RIC3	79608	broad.mit.edu	37	11	8161528	8161528	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8161528A>G	uc001mgd.2	-	2	391	c.337T>C	c.(337-339)TAC>CAC	p.Y113H	RIC3_uc001mgb.2_5'Flank|RIC3_uc001mgc.2_Missense_Mutation_p.Y113H|RIC3_uc001mge.2_Intron|RIC3_uc010rbl.1_Missense_Mutation_p.Y63H|RIC3_uc010rbm.1_Missense_Mutation_p.Y113H|RIC3_uc009yfm.2_Missense_Mutation_p.Y113H|RIC3_uc009yfn.2_Intron|RIC3_uc001mgf.3_Missense_Mutation_p.Y113H	NM_024557	NP_078833	Q7Z5B4	RIC3_HUMAN	resistance to inhibitors of cholinesterase 3	113	Helical; (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				large_intestine(1)|ovary(1)|pancreas(1)	3				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)														---	---	---	---
KIF18A	81930	broad.mit.edu	37	11	28110147	28110147	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28110147C>T	uc001msc.2	-	6	1003	c.821G>A	c.(820-822)CGA>CAA	p.R274Q		NM_031217	NP_112494	Q8NI77	KI18A_HUMAN	kinesin family member 18A	274	Kinesin-motor.				blood coagulation|microtubule depolymerization|microtubule-based movement|mitotic metaphase plate congression|mitotic prometaphase|protein transport	caveola|cytosol|kinetochore microtubule|microtubule organizing center|nucleus|ruffle	actin binding|ATP binding|microtubule plus-end binding|plus-end-directed microtubule motor activity|tubulin-dependent ATPase activity|ubiquitin binding			ovary(2)	2																		---	---	---	---
PTPRJ	5795	broad.mit.edu	37	11	48157668	48157668	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48157668G>T	uc001ngp.3	+	9	2048	c.1693G>T	c.(1693-1695)GGT>TGT	p.G565C	PTPRJ_uc010rhr.1_Missense_Mutation_p.G10C	NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	565	Extracellular (Potential).|Fibronectin type-III 6.				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																		---	---	---	---
OR4A16	81327	broad.mit.edu	37	11	55110866	55110866	+	Silent	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55110866T>C	uc010rie.1	+	1	190	c.190T>C	c.(190-192)TTG>CTG	p.L64L		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	64	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.L64L(1)		large_intestine(2)|pancreas(1)	3																		---	---	---	---
OR5D14	219436	broad.mit.edu	37	11	55563846	55563846	+	Missense_Mutation	SNP	C	G	G	rs61896310	byFrequency;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55563846C>G	uc010rim.1	+	1	815	c.815C>G	c.(814-816)ACA>AGA	p.T272R		NM_001004735	NP_001004735	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D,	272	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3		all_epithelial(135;0.196)																---	---	---	---
P4HA3	283208	broad.mit.edu	37	11	73979186	73979186	+	Intron	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73979186T>G	uc001ouz.2	-						P4HA3_uc001ouy.3_Intron|P4HA3_uc010rrj.1_Intron	NM_182904	NP_878907			prolyl 4-hydroxylase, alpha III subunit							endoplasmic reticulum lumen	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			skin(1)	1	Breast(11;2.31e-05)																	---	---	---	---
CCDC82	79780	broad.mit.edu	37	11	96104293	96104293	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96104293T>C	uc009ywp.2	-	4	1336	c.1093A>G	c.(1093-1095)AGG>GGG	p.R365G	CCDC82_uc009ywq.2_Missense_Mutation_p.R365G|CCDC82_uc001pfx.3_Missense_Mutation_p.R365G|CCDC82_uc009ywr.2_Missense_Mutation_p.R365G	NM_024725	NP_079001	Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	365							protein binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)														---	---	---	---
PGR	5241	broad.mit.edu	37	11	100998748	100998748	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100998748G>T	uc001pgh.2	-	1	1797	c.1054C>A	c.(1054-1056)CCG>ACG	p.P352T	PGR_uc001pgi.2_Missense_Mutation_p.P352T|PGR_uc009yww.1_RNA|PGR_uc001pgj.2_RNA|PGR_uc009ywx.1_RNA|uc010rum.1_5'Flank	NM_000926	NP_000917	P06401	PRGR_HUMAN	progesterone receptor	352	Modulating, Pro-Rich.				cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			lung(1)|liver(1)|central_nervous_system(1)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)													---	---	---	---
TRPC6	7225	broad.mit.edu	37	11	101341968	101341968	+	Silent	SNP	A	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101341968A>T	uc001pgk.3	-	9	2780	c.2355T>A	c.(2353-2355)TCT>TCA	p.S785S	TRPC6_uc009ywy.2_Silent_p.S669S|TRPC6_uc009ywz.1_Silent_p.S730S	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	785	Cytoplasmic (Potential).				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)														---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106647283	106647283	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106647283C>T	uc001pjg.1	-	6	2108	c.1718G>A	c.(1717-1719)TGT>TAT	p.C573Y	GUCY1A2_uc010rvo.1_Missense_Mutation_p.C594Y|GUCY1A2_uc009yxn.1_Missense_Mutation_p.C573Y	NM_000855	NP_000846	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	573	Guanylate cyclase.				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)														---	---	---	---
TMPRSS13	84000	broad.mit.edu	37	11	117784603	117784603	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117784603T>G	uc001prs.1	-	5	791	c.698A>C	c.(697-699)AAG>ACG	p.K233T	TMPRSS13_uc009yzr.1_5'UTR|TMPRSS13_uc001prt.1_5'UTR|TMPRSS13_uc001pru.1_Missense_Mutation_p.K233T	NM_001077263	NP_001070731	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	228	Extracellular (Potential).|SRCR.				proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			pancreas(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)														---	---	---	---
OR10G8	219869	broad.mit.edu	37	11	123900575	123900575	+	Silent	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123900575T>G	uc001pzp.1	+	1	246	c.246T>G	c.(244-246)ACT>ACG	p.T82T		NM_001004464	NP_001004464	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G,	82	Extracellular (Potential).				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)														---	---	---	---
OR8B8	26493	broad.mit.edu	37	11	124310957	124310957	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124310957C>T	uc010sal.1	-	1	25	c.25G>A	c.(25-27)GTG>ATG	p.V9M		NM_012378	NP_036510	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B,	9	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)														---	---	---	---
KCNJ1	3758	broad.mit.edu	37	11	128709123	128709123	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128709123C>T	uc001qeo.1	-	2	1124	c.1073G>A	c.(1072-1074)TGC>TAC	p.C358Y	KCNJ1_uc001qep.1_Missense_Mutation_p.C339Y|KCNJ1_uc001qeq.1_Missense_Mutation_p.C339Y|KCNJ1_uc001qer.1_Missense_Mutation_p.C339Y|KCNJ1_uc001qes.1_Missense_Mutation_p.C339Y	NM_000220	NP_000211	P48048	IRK1_HUMAN	potassium inwardly-rectifying channel J1 isoform	358	Cytoplasmic (By similarity).				excretion	voltage-gated potassium channel complex	ATP binding|inward rectifier potassium channel activity			ovary(3)|breast(1)	4	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Acetohexamide(DB00414)|Chlorpropamide(DB00672)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolazamide(DB00839)|Tolbutamide(DB01124)													---	---	---	---
CD163	9332	broad.mit.edu	37	12	7635554	7635554	+	Intron	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7635554T>G	uc001qsz.3	-						CD163_uc001qta.3_Intron|CD163_uc009zfw.2_Intron	NM_004244	NP_004235			CD163 antigen isoform a						acute-phase response	extracellular region|integral to plasma membrane	protein binding|scavenger receptor activity			ovary(6)|pancreas(1)|skin(1)	8																		---	---	---	---
A2ML1	144568	broad.mit.edu	37	12	9013765	9013765	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9013765A>C	uc001quz.3	+	28	3472	c.3374A>C	c.(3373-3375)AAG>ACG	p.K1125T	A2ML1_uc001qva.1_Missense_Mutation_p.K705T|A2ML1_uc010sgm.1_Missense_Mutation_p.K625T	NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor	969						extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
CLEC2B	9976	broad.mit.edu	37	12	10005910	10005910	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10005910T>C	uc001qwn.2	-	5	1096	c.439A>G	c.(439-441)AGA>GGA	p.R147G		NM_005127	NP_005118	Q92478	CLC2B_HUMAN	C-type lectin, superfamily member 2	147	Extracellular (Potential).					integral to plasma membrane	sugar binding				0																		---	---	---	---
H2AFJ	55766	broad.mit.edu	37	12	14927445	14927445	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14927445A>G	uc009zia.2	+	1	176	c.41A>G	c.(40-42)AAG>AGG	p.K14R	H2AFJ_uc001rch.3_RNA	NM_177925	NP_808760	Q9BTM1	H2AJ_HUMAN	H2A histone family, member J	14					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)	1																		---	---	---	---
SLCO1A2	6579	broad.mit.edu	37	12	21427492	21427492	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21427492G>A	uc001rer.2	-	13	1955	c.1704C>T	c.(1702-1704)GGC>GGT	p.G568G	SLCO1A2_uc001res.2_Silent_p.G568G|SLCO1A2_uc010siq.1_Silent_p.G436G|SLCO1A2_uc010sio.1_Silent_p.G436G|SLCO1A2_uc010sip.1_Silent_p.G436G	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A	568	Helical; Name=11; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4																		---	---	---	---
IFLTD1	160492	broad.mit.edu	37	12	25672909	25672909	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25672909C>T	uc001rgs.2	-	6	986	c.836G>A	c.(835-837)CGA>CAA	p.R279Q	IFLTD1_uc001rgt.1_Missense_Mutation_p.R182Q|IFLTD1_uc010sji.1_Missense_Mutation_p.R300Q|IFLTD1_uc010sjj.1_Missense_Mutation_p.R216Q|IFLTD1_uc009zjc.2_Missense_Mutation_p.R260Q	NM_152590	NP_689803	Q8N9Z9	ILFT1_HUMAN	intermediate filament tail domain containing 1	279						intermediate filament	structural molecule activity			ovary(2)|central_nervous_system(1)	3	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26784902	26784902	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26784902G>A	uc001rhg.2	-	22	3248	c.2831C>T	c.(2830-2832)CCG>CTG	p.P944L		NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	944	Cytoplasmic (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
BIN2	51411	broad.mit.edu	37	12	51690922	51690922	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51690922A>G	uc001ryg.2	-	8	681	c.629T>C	c.(628-630)TTC>TCC	p.F210S	BIN2_uc009zlz.2_Missense_Mutation_p.F178S|BIN2_uc001ryh.2_Missense_Mutation_p.F86S|BIN2_uc010sng.1_Missense_Mutation_p.F184S	NM_016293	NP_057377	Q9UBW5	BIN2_HUMAN	bridging integrator 2	210	BAR.					cytoplasm	protein binding			ovary(1)	1																		---	---	---	---
OR6C6	283365	broad.mit.edu	37	12	55688572	55688572	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55688572T>C	uc010sph.1	-	1	445	c.445A>G	c.(445-447)ACT>GCT	p.T149A		NM_001005493	NP_001005493	A6NF89	OR6C6_HUMAN	olfactory receptor, family 6, subfamily C,	149	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|skin(1)	2																		---	---	---	---
MSRB3	253827	broad.mit.edu	37	12	65847509	65847509	+	Silent	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65847509T>G	uc001ssn.2	+	5	376	c.315T>G	c.(313-315)GGT>GGG	p.G105G	MSRB3_uc001ssm.2_Silent_p.G98G|MSRB3_uc009zqp.2_Silent_p.G98G	NM_198080	NP_932346	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3 isoform 1	105					protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)														---	---	---	---
PTPRB	5787	broad.mit.edu	37	12	70974880	70974880	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70974880G>A	uc001swb.3	-	8	1890	c.1860C>T	c.(1858-1860)TCC>TCT	p.S620S	PTPRB_uc010sto.1_Silent_p.S620S|PTPRB_uc010stp.1_Silent_p.S530S|PTPRB_uc001swc.3_Silent_p.S838S|PTPRB_uc001swa.3_Silent_p.S838S|PTPRB_uc001swd.3_Silent_p.S837S|PTPRB_uc009zrr.1_Silent_p.S717S	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	620	Fibronectin type-III 7.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)															---	---	---	---
KCNC2	3747	broad.mit.edu	37	12	75444607	75444607	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75444607A>C	uc001sxg.1	-	3	1722	c.1178T>G	c.(1177-1179)GTT>GGT	p.V393G	KCNC2_uc009zry.2_Missense_Mutation_p.V393G|KCNC2_uc001sxe.2_Missense_Mutation_p.V393G|KCNC2_uc001sxf.2_Missense_Mutation_p.V393G|KCNC2_uc010stw.1_Missense_Mutation_p.V393G	NM_139137	NP_631875	Q96PR1	KCNC2_HUMAN	Shaw-related voltage-gated potassium channel	393	Helical; Name=Segment S5; (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																		---	---	---	---
MYF6	4618	broad.mit.edu	37	12	81101532	81101532	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81101532T>G	uc001szf.1	+	1	87	c.34T>G	c.(34-36)TTC>GTC	p.F12V		NM_002469	NP_002460	P23409	MYF6_HUMAN	myogenic factor 6	12					muscle cell fate commitment|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|skeletal muscle tissue development	nucleoplasm	DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1																		---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85460604	85460604	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85460604T>C	uc001tac.2	+	10	2734	c.2623T>C	c.(2623-2625)TCT>CCT	p.S875P	LRRIQ1_uc001tab.1_Missense_Mutation_p.S875P	NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	875	LRR 3.									ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
LUM	4060	broad.mit.edu	37	12	91502040	91502040	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91502040G>A	uc001tbm.2	-	2	1106	c.717C>T	c.(715-717)AAC>AAT	p.N239N	LUM_uc001tbn.2_RNA	NM_002345	NP_002336	P51884	LUM_HUMAN	lumican precursor	239	LRR 8.				collagen fibril organization|visual perception	extracellular space|fibrillar collagen	collagen binding|extracellular matrix structural constituent			central_nervous_system(2)	2																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104146996	104146996	+	Splice_Site	SNP	A	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104146996A>T	uc001tjw.2	+	61	6767	c.6581_splice	c.e61-2	p.D2194_splice	STAB2_uc009zug.2_Splice_Site	NM_017564	NP_060034			stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
CCDC63	160762	broad.mit.edu	37	12	111336788	111336788	+	Missense_Mutation	SNP	G	A	A	rs116589141	by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111336788G>A	uc001trv.1	+	10	1396	c.1201G>A	c.(1201-1203)GGG>AGG	p.G401R	CCDC63_uc010sye.1_Missense_Mutation_p.G361R|CCDC63_uc001trw.1_Missense_Mutation_p.G316R	NM_152591	NP_689804	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	401	Potential.									skin(6)|ovary(1)|pancreas(1)	8																		---	---	---	---
CABP1	9478	broad.mit.edu	37	12	121098114	121098114	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121098114C>T	uc001tyu.2	+	3	868	c.801C>T	c.(799-801)ATC>ATT	p.I267I	CABP1_uc001tyv.2_Silent_p.I124I|CABP1_uc001tyw.2_Silent_p.I64I|CABP1_uc001tyx.2_Silent_p.I109I	NM_001033677	NP_001028849	Q9NZU7	CABP1_HUMAN	calcium binding protein 1 isoform 3	267	EF-hand 2.					cell cortex|cell junction|Golgi apparatus|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|calcium-dependent protein binding|enzyme inhibitor activity|protein binding			central_nervous_system(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
FZD10	11211	broad.mit.edu	37	12	130648917	130648917	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130648917C>T	uc001uii.2	+	1	1886	c.1430C>T	c.(1429-1431)GCG>GTG	p.A477V	uc001uig.1_5'Flank|uc001uih.1_5'Flank	NM_007197	NP_009128	Q9ULW2	FZD10_HUMAN	frizzled 10 precursor	477	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)														---	---	---	---
LATS2	26524	broad.mit.edu	37	13	21620053	21620053	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21620053G>T	uc009zzs.2	-	2	478	c.113C>A	c.(112-114)CCC>CAC	p.P38H	LATS2_uc001unr.3_Missense_Mutation_p.P38H	NM_014572	NP_055387	Q9NRM7	LATS2_HUMAN	LATS, large tumor suppressor, homolog 2	38					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)														---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28883047	28883047	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28883047T>G	uc001usb.3	-	28	3938	c.3653A>C	c.(3652-3654)AAG>ACG	p.K1218T	FLT1_uc010aap.2_Missense_Mutation_p.K223T|FLT1_uc010aaq.2_Missense_Mutation_p.K343T|FLT1_uc001usa.3_Missense_Mutation_p.K436T	NM_002019	NP_002010	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1 isoform 1	1218	Cytoplasmic (Potential).				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)													---	---	---	---
CCNA1	8900	broad.mit.edu	37	13	37016786	37016786	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37016786T>G	uc001uvr.3	+	9	1732	c.1382T>G	c.(1381-1383)GTT>GGT	p.V461G	CCNA1_uc010teo.1_Missense_Mutation_p.V417G|CCNA1_uc010abq.2_Missense_Mutation_p.V417G|CCNA1_uc010abp.2_Missense_Mutation_p.V417G|CCNA1_uc001uvs.3_Missense_Mutation_p.V460G|CCNA1_uc010abr.2_RNA	NM_003914	NP_003905	P78396	CCNA1_HUMAN	cyclin A1 isoform a	461					cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis	cytosol|microtubule cytoskeleton|nucleoplasm	protein kinase binding			lung(2)|skin(2)|ovary(1)	5		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)														---	---	---	---
TRPC4	7223	broad.mit.edu	37	13	38213209	38213209	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38213209T>G	uc001uws.2	-	10	2414	c.2179A>C	c.(2179-2181)ACT>CCT	p.T727P	TRPC4_uc010abv.2_Missense_Mutation_p.T307P|TRPC4_uc001uwt.2_Missense_Mutation_p.T727P|TRPC4_uc010tey.1_Missense_Mutation_p.T727P|TRPC4_uc010abw.2_Missense_Mutation_p.T554P|TRPC4_uc010abx.2_Missense_Mutation_p.T732P|TRPC4_uc010aby.2_Missense_Mutation_p.T662P	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	727	Binds to ITPR1, ITPR2 and ITPR3.|Cytoplasmic (Potential).				axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)														---	---	---	---
OLFM4	10562	broad.mit.edu	37	13	53624535	53624535	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53624535G>C	uc001vhl.2	+	5	1162	c.1162G>C	c.(1162-1164)GAT>CAT	p.D388H	OLFM4_uc001vhk.1_3'UTR	NM_006418	NP_006409	Q6UX06	OLFM4_HUMAN	olfactomedin 4 precursor	388	Olfactomedin-like.				cell adhesion	extracellular space				skin(1)	1		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)														---	---	---	---
OLFM4	10562	broad.mit.edu	37	13	53624775	53624775	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53624775G>C	uc001vhl.2	+	5	1402	c.1402G>C	c.(1402-1404)GAC>CAC	p.D468H	OLFM4_uc001vhk.1_3'UTR	NM_006418	NP_006409	Q6UX06	OLFM4_HUMAN	olfactomedin 4 precursor	468	Olfactomedin-like.				cell adhesion	extracellular space				skin(1)	1		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)														---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92346009	92346009	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92346009G>A	uc010tif.1	+	3	1260	c.894G>A	c.(892-894)TCG>TCA	p.S298S		NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor	298						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	92346147	92346147	+	Intron	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92346147C>A	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)																---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100511196	100511196	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100511196G>A	uc001vok.2	+	3	345	c.331G>A	c.(331-333)GTT>ATT	p.V111I	CLYBL_uc010tix.1_Missense_Mutation_p.V111I|CLYBL_uc010tiy.1_Missense_Mutation_p.V111I	NM_206808	NP_996531	Q8N0X4	CLYBL_HUMAN	citrate lyase beta like precursor	111					cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
PCCA	5095	broad.mit.edu	37	13	100861581	100861581	+	Intron	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100861581C>A	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron	NM_000282	NP_000273			propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)													---	---	---	---
OR4K14	122740	broad.mit.edu	37	14	20482607	20482607	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20482607G>A	uc010tky.1	-	1	746	c.746C>T	c.(745-747)ACG>ATG	p.T249M		NM_001004712	NP_001004712	Q8NGD5	OR4KE_HUMAN	olfactory receptor, family 4, subfamily K,	249	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|large_intestine(1)	3	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2e-06)	GBM - Glioblastoma multiforme(265;0.00124)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22964932	22964932	+	Intron	SNP	G	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22964932G>C	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wcx.3_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wdv.3_Intron|uc001wec.2_Intron|uc001wee.3_Intron|uc010tmt.1_Intron|uc010ajv.1_Intron|uc001weg.2_Intron|uc001weh.1_Intron|uc001wei.2_Intron|uc001wej.2_Intron|uc001wek.2_Intron|uc001wel.2_Intron|uc001wem.3_Intron|uc001wen.1_Intron|uc001weo.2_Intron|uc001wep.2_Intron|uc001weq.2_Missense_Mutation_p.R8T|uc001wer.2_5'Flank|uc001wet.2_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
RALGAPA1	253959	broad.mit.edu	37	14	36008780	36008780	+	3'UTR	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36008780G>A	uc001wti.2	-	41					RALGAPA1_uc010amp.2_RNA|RALGAPA1_uc001wtj.2_Missense_Mutation_p.R2074C|RALGAPA1_uc010tpv.1_3'UTR	NM_014990	NP_055805			Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4																		---	---	---	---
SYT16	83851	broad.mit.edu	37	14	62551035	62551035	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62551035C>T	uc001xfu.1	+	5	1753	c.1556C>T	c.(1555-1557)ACG>ATG	p.T519M	SYT16_uc010tse.1_Missense_Mutation_p.T77M	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like	519	C2 2.									central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)														---	---	---	---
ACOT4	122970	broad.mit.edu	37	14	74062207	74062207	+	Missense_Mutation	SNP	C	A	A	rs146020227		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74062207C>A	uc001xoo.2	+	3	1369	c.1115C>A	c.(1114-1116)GCT>GAT	p.A372D		NM_152331	NP_689544	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	372					acyl-CoA metabolic process|dicarboxylic acid metabolic process|long-chain fatty acid metabolic process|saturated monocarboxylic acid metabolic process|short-chain fatty acid metabolic process|succinyl-CoA metabolic process|unsaturated monocarboxylic acid metabolic process|very long-chain fatty acid metabolic process	peroxisome	carboxylesterase activity|palmitoyl-CoA hydrolase activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00331)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	80164147	80164147	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80164147G>A	uc001xun.2	+	15	3163	c.2672G>A	c.(2671-2673)GGA>GAA	p.G891E	NRXN3_uc001xum.1_RNA|NRXN3_uc001xup.2_RNA|NRXN3_uc001xuq.2_Missense_Mutation_p.G259E|NRXN3_uc010asw.2_Missense_Mutation_p.G289E|NRXN3_uc001xur.3_Missense_Mutation_p.G259E	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	1264	Extracellular (Potential).				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)														---	---	---	---
GALC	2581	broad.mit.edu	37	14	88450822	88450822	+	Silent	SNP	G	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88450822G>C	uc001xvt.2	-	5	897	c.498C>G	c.(496-498)GTC>GTG	p.V166V	GALC_uc010tvx.1_Silent_p.V140V|GALC_uc010tvy.1_Silent_p.V143V|GALC_uc010tvz.1_Silent_p.V110V|GALC_uc001xvu.1_Silent_p.V166V	NM_000153	NP_000144	P54803	GALC_HUMAN	galactosylceramidase isoform a precursor	166					carbohydrate metabolic process|galactosylceramide catabolic process	lysosome	cation binding|galactosylceramidase activity				0																		---	---	---	---
KIAA1409	57578	broad.mit.edu	37	14	94063714	94063714	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94063714T>G	uc001ybv.1	+	21	2752	c.2669T>G	c.(2668-2670)GTT>GGT	p.V890G	KIAA1409_uc001ybs.1_Missense_Mutation_p.V890G	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	1067						integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)														---	---	---	---
C15orf2	23742	broad.mit.edu	37	15	24922359	24922359	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24922359A>C	uc001ywo.2	+	1	1819	c.1345A>C	c.(1345-1347)AAA>CAA	p.K449Q		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	449	Pro-rich.				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)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	34021102	34021102	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34021102G>T	uc001zhi.2	+	47	7148	c.7078G>T	c.(7078-7080)GAC>TAC	p.D2360Y	RYR3_uc010bar.2_Missense_Mutation_p.D2360Y	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2360	4 X approximate repeats.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48782094	48782094	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48782094G>A	uc001zwx.1	-	25	3364	c.3036C>T	c.(3034-3036)CCC>CCT	p.P1012P		NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	1012					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)														---	---	---	---
ARIH1	25820	broad.mit.edu	37	15	72873082	72873082	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72873082C>A	uc002aut.3	+	12	1540	c.1226C>A	c.(1225-1227)GCA>GAA	p.A409E		NM_005744	NP_005735	Q9Y4X5	ARI1_HUMAN	ariadne ubiquitin-conjugating enzyme E2 binding	409					ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	86286744	86286744	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86286744C>G	uc002blv.1	+	36	8250	c.8080C>G	c.(8080-8082)CTG>GTG	p.L2694V	AKAP13_uc002blu.1_Missense_Mutation_p.L2698V|AKAP13_uc002blw.1_Missense_Mutation_p.L1159V|AKAP13_uc002blx.1_Missense_Mutation_p.L939V	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	2694	Interaction with ESR1.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88726669	88726669	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88726669C>T	uc002bme.1	-	4	537	c.375G>A	c.(373-375)AAG>AAA	p.K125K	NTRK3_uc002bmh.2_Silent_p.K125K|NTRK3_uc002bmf.1_Silent_p.K125K|NTRK3_uc010upl.1_Silent_p.K27K|NTRK3_uc010bnh.1_Silent_p.K125K|NTRK3_uc002bmg.2_Silent_p.K125K	NM_001012338	NP_001012338	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	125	LRR 1.|Extracellular (Potential).				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)			---	---	---	---
SV2B	9899	broad.mit.edu	37	15	91795076	91795076	+	Missense_Mutation	SNP	C	T	T	rs146271108	byFrequency	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91795076C>T	uc002bqv.2	+	2	870	c.479C>T	c.(478-480)GCG>GTG	p.A160V	SV2B_uc002bqt.2_Missense_Mutation_p.A160V|SV2B_uc010uqv.1_Missense_Mutation_p.A9V|SV2B_uc002bqu.3_RNA	NM_014848	NP_055663	Q7L1I2	SV2B_HUMAN	synaptic vesicle protein 2B homolog	160	Helical; (Potential).				neurotransmitter transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1)	8	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)															---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15111245	15111245	+	Missense_Mutation	SNP	C	T	T	rs142060473	byFrequency	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15111245C>T	uc002dda.3	+	11	1153	c.929C>T	c.(928-930)GCG>GTG	p.A310V	PDXDC1_uc010uzl.1_Missense_Mutation_p.A295V|PDXDC1_uc010uzm.1_Missense_Mutation_p.A219V|PDXDC1_uc002dcz.2_Missense_Mutation_p.A287V|PDXDC1_uc002ddb.3_Missense_Mutation_p.A283V|PDXDC1_uc010uzn.1_Missense_Mutation_p.A282V|PDXDC1_uc002ddc.2_Missense_Mutation_p.A310V	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain	310					carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
NTAN1	123803	broad.mit.edu	37	16	15132470	15132470	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15132470C>T	uc002ddd.2	-	9	719	c.714G>A	c.(712-714)GTG>GTA	p.V238V	PDXDC1_uc002ddc.2_Intron|NTAN1_uc010uzo.1_Silent_p.V133V	NM_173474	NP_775745	Q96AB6	NTAN1_HUMAN	N-terminal Asn amidase	238						cytoplasm					0																		---	---	---	---
KIAA0556	23247	broad.mit.edu	37	16	27789014	27789014	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27789014G>A	uc002dow.2	+	26	4659	c.4635G>A	c.(4633-4635)GAG>GAA	p.E1545E	KIAA0556_uc010vco.1_Silent_p.E47E	NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	1545										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8																		---	---	---	---
BCL7C	9274	broad.mit.edu	37	16	30904041	30904041	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30904041G>T	uc002dzv.2	-	4	442	c.308C>A	c.(307-309)TCG>TAG	p.S103*	BCL7C_uc002dzt.1_Nonsense_Mutation_p.S103*|uc002dzu.2_Intron|MIR762_hsa-mir-762|MI0003892_5'Flank	NM_004765	NP_004756	Q8WUZ0	BCL7C_HUMAN	B-cell CLL/lymphoma 7C	103					apoptosis						0			Colorectal(24;0.198)															---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	68912060	68912060	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68912060C>T	uc002ewi.3	+	6	1183	c.1171C>T	c.(1171-1173)CGA>TGA	p.R391*		NM_024562	NP_078838	Q9C0B7	TMCO7_HUMAN	transmembrane and coiled-coil domains 7	391						integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)														---	---	---	---
SRR	63826	broad.mit.edu	37	17	2224690	2224690	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2224690G>A	uc002fue.1	+	5	558	c.490G>A	c.(490-492)GGG>AGG	p.G164R	SRR_uc002fui.1_Missense_Mutation_p.G15R	NM_021947	NP_068766	Q9GZT4	SRR_HUMAN	serine racemase	164					D-serine biosynthetic process|L-serine metabolic process|protein homotetramerization|pyruvate biosynthetic process|response to lipopolysaccharide	cytoplasm|neuronal cell body|soluble fraction	ATP binding|calcium ion binding|D-serine ammonia-lyase activity|glycine binding|L-serine ammonia-lyase activity|magnesium ion binding|PDZ domain binding|protein homodimerization activity|pyridoxal phosphate binding|serine racemase activity|threonine racemase activity				0		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;3.24e-06)|READ - Rectum adenocarcinoma(1115;0.0649)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
KIAA0753	9851	broad.mit.edu	37	17	6526204	6526204	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6526204C>A	uc002gde.3	-	6	1461	c.1102G>T	c.(1102-1104)GAG>TAG	p.E368*	KIAA0753_uc010vtd.1_5'Flank|KIAA0753_uc010clo.2_Nonsense_Mutation_p.E69*|KIAA0753_uc010vte.1_Nonsense_Mutation_p.E69*	NM_014804	NP_055619	Q2KHM9	K0753_HUMAN	hypothetical protein LOC9851	368						centrosome					0				COAD - Colon adenocarcinoma(228;0.157)														---	---	---	---
TP53	7157	broad.mit.edu	37	17	7578403	7578403	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578403C>A	uc002gim.2	-	5	721	c.527G>T	c.(526-528)TGC>TTC	p.C176F	TP53_uc002gig.1_Missense_Mutation_p.C176F|TP53_uc002gih.2_Missense_Mutation_p.C176F|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.C44F|TP53_uc010cng.1_Missense_Mutation_p.C44F|TP53_uc002gii.1_Missense_Mutation_p.C44F|TP53_uc010cnh.1_Missense_Mutation_p.C176F|TP53_uc010cni.1_Missense_Mutation_p.C176F|TP53_uc002gij.2_Missense_Mutation_p.C176F|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.C83F|TP53_uc002gio.2_Missense_Mutation_p.C44F|TP53_uc010vug.1_Missense_Mutation_p.C137F	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	176	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).	Zinc.	CP -> FS (in a sporadic cancer; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in sporadic cancers; somatic mutation).|C -> F (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.C176F(102)|p.C176Y(56)|p.C176S(19)|p.C176W(11)|p.C176R(8)|p.C176fs*71(7)|p.0?(7)|p.C176*(6)|p.C176_R181delCPHHER(3)|p.R174fs*24(3)|p.C176G(3)|p.C176fs*5(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.K164_P219del(1)|p.C176fs*65(1)|p.C176_P177delCP(1)|p.V173fs*69(1)|p.C176fs*68(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.C44Y(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R42fs*24(1)|p.C83Y(1)|p.C176fs*72(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.C176del(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.C176fs*6(1)|p.R174fs*3(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)			111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			---	---	---	---
USP43	124739	broad.mit.edu	37	17	9580147	9580147	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9580147G>A	uc010cod.2	+	5	918	c.918G>A	c.(916-918)GTG>GTA	p.V306V	USP43_uc002gma.3_5'UTR|USP43_uc010vva.1_Silent_p.V306V|USP43_uc010coe.2_Silent_p.V103V	NM_153210	NP_694942	Q70EL4	UBP43_HUMAN	ubiquitin specific protease 43	306					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5																		---	---	---	---
MYH4	4622	broad.mit.edu	37	17	10359228	10359228	+	Intron	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10359228C>A	uc002gmn.2	-						uc002gml.1_Intron	NM_017533	NP_060003			myosin, heavy polypeptide 4, skeletal muscle						muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|skin(2)|central_nervous_system(1)	13																		---	---	---	---
MYOCD	93649	broad.mit.edu	37	17	12569500	12569500	+	5'UTR	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12569500C>A	uc002gnn.2	+	1					MYOCD_uc002gno.2_5'UTR	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)														---	---	---	---
PEX12	5193	broad.mit.edu	37	17	33904527	33904527	+	Silent	SNP	G	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33904527G>C	uc002hjp.2	-	2	826	c.210C>G	c.(208-210)CTC>CTG	p.L70L		NM_000286	NP_000277	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	70	Cytoplasmic (Potential).				protein import into peroxisome matrix	integral to peroxisomal membrane	protein C-terminus binding|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
HAP1	9001	broad.mit.edu	37	17	39888516	39888516	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39888516T>A	uc002hxm.1	-	3	692	c.680A>T	c.(679-681)AAG>ATG	p.K227M	JUP_uc010wfs.1_Intron|HAP1_uc002hxn.1_Missense_Mutation_p.K227M|HAP1_uc002hxo.1_Missense_Mutation_p.K235M|HAP1_uc002hxp.1_Missense_Mutation_p.K227M	NM_177977	NP_817084	P54257	HAP1_HUMAN	huntingtin-associated protein 1 isoform 2	227	HAP1 N-terminal.				brain development|protein localization|synaptic transmission	actin cytoskeleton	protein binding			ovary(2)	2		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)															---	---	---	---
RPL27	6155	broad.mit.edu	37	17	41150760	41150760	+	Intron	SNP	C	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41150760C>G	uc002icj.2	+						RPL27_uc002ick.2_5'UTR	NM_000988	NP_000979			ribosomal protein L27						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	structural constituent of ribosome				0		Breast(137;0.000717)|Ovarian(249;0.0776)		BRCA - Breast invasive adenocarcinoma(366;0.157)														---	---	---	---
LRRC59	55379	broad.mit.edu	37	17	48470250	48470250	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48470250G>A	uc002iqt.2	-	3	328	c.174C>T	c.(172-174)TTC>TTT	p.F58F		NM_018509	NP_060979	Q96AG4	LRC59_HUMAN	leucine rich repeat containing 59	58	Cytoplasmic (Potential).|LRR 2.					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)															---	---	---	---
MBTD1	54799	broad.mit.edu	37	17	49280159	49280159	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49280159G>A	uc002itr.3	-	10	1310	c.966C>T	c.(964-966)AGC>AGT	p.S322S	MBTD1_uc002itp.3_Silent_p.S158S|MBTD1_uc002itq.3_Silent_p.S322S	NM_017643	NP_060113	Q05BQ5	MBTD1_HUMAN	mbt domain containing 1	322	MBT 2.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)															---	---	---	---
ABCA8	10351	broad.mit.edu	37	17	66899439	66899439	+	Intron	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66899439T>C	uc002jhp.2	-						ABCA8_uc002jhq.2_Intron|ABCA8_uc010wqq.1_Intron|ABCA8_uc010wqr.1_Intron|ABCA8_uc002jhr.2_Intron	NM_007168	NP_009099			ATP-binding cassette, sub-family A member 8							integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)																	---	---	---	---
USP36	57602	broad.mit.edu	37	17	76818029	76818029	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76818029G>A	uc002jvz.1	-	7	1072	c.747C>T	c.(745-747)CTC>CTT	p.L249L	USP36_uc002jwa.1_Silent_p.L249L|USP36_uc002jwc.1_5'UTR	NM_025090	NP_079366	Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	249					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)															---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78931495	78931495	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78931495C>T	uc002jyt.1	+	29	4247	c.3442C>T	c.(3442-3444)CGG>TGG	p.R1148W	RPTOR_uc010wug.1_Missense_Mutation_p.R990W|RPTOR_uc002jyu.1_Missense_Mutation_p.R41W	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1	1148	WD 3.				cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6																		---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	6983216	6983216	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6983216C>T	uc002knm.2	-	40	5772	c.5678G>A	c.(5677-5679)AGA>AAA	p.R1893K	LAMA1_uc010wzj.1_Missense_Mutation_p.R1369K	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1893	Domain II and I.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
PSMA8	143471	broad.mit.edu	37	18	23724554	23724554	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23724554T>C	uc002kvq.2	+	2	248	c.134T>C	c.(133-135)CTT>CCT	p.L45P	PSMA8_uc002kvo.2_Intron|PSMA8_uc002kvp.2_Missense_Mutation_p.L45P|PSMA8_uc002kvr.2_Missense_Mutation_p.L19P	NM_144662	NP_653263	Q8TAA3	PSA7L_HUMAN	proteasome alpha 8 subunit isoform 1	45					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|M/G1 transition of mitotic cell cycle|mRNA metabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	threonine-type endopeptidase activity			skin(1)	1	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)															---	---	---	---
AQP4	361	broad.mit.edu	37	18	24442440	24442440	+	Silent	SNP	G	A	A	rs148022306		TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24442440G>A	uc002kwa.2	-	2	216	c.153C>T	c.(151-153)CTC>CTT	p.L51L	C18orf16_uc002kwb.2_5'Flank|C18orf16_uc010xbm.1_5'Flank|AQP4_uc002kvz.2_Silent_p.L29L	NM_001650	NP_001641	P55087	AQP4_HUMAN	aquaporin 4 isoform a	51	Helical; (Potential).				cellular response to interferon-gamma|excretion|nervous system development	cytoplasm|external side of plasma membrane|integral to plasma membrane	water channel activity				0	all_cancers(21;0.0172)|Lung NSC(5;0.00299)|all_lung(6;0.00747)|Ovarian(20;0.124)																	---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25565547	25565547	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25565547A>T	uc002kwg.2	-	12	2379	c.1920T>A	c.(1918-1920)GAT>GAA	p.D640E	CDH2_uc010xbn.1_Missense_Mutation_p.D609E	NM_001792	NP_001783	P19022	CADH2_HUMAN	cadherin 2, type 1 preproprotein	640	Extracellular (Potential).|Cadherin 5.				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																		---	---	---	---
NOL4	8715	broad.mit.edu	37	18	31599540	31599540	+	Silent	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31599540A>G	uc010dmi.2	-	6	1027	c.798T>C	c.(796-798)AAT>AAC	p.N266N	NOL4_uc010xbs.1_5'UTR|NOL4_uc002kxr.3_Silent_p.N102N|NOL4_uc010xbt.1_Silent_p.N192N|NOL4_uc010dmh.2_Silent_p.N192N|NOL4_uc010xbu.1_Silent_p.N266N|NOL4_uc002kxt.3_Silent_p.N266N|NOL4_uc010xbv.1_Silent_p.N15N|NOL4_uc010xbw.1_Silent_p.N152N	NM_003787	NP_003778	O94818	NOL4_HUMAN	nucleolar protein 4	266						nucleolus	RNA binding			ovary(3)	3																		---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42532418	42532418	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42532418T>A	uc010dni.2	+	4	3409	c.3113T>A	c.(3112-3114)TTC>TAC	p.F1038Y		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	1038						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
STARD6	147323	broad.mit.edu	37	18	51863496	51863496	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51863496G>A	uc010xdt.1	-	3	266	c.266C>T	c.(265-267)TCG>TTG	p.S89L		NM_139171	NP_631910	P59095	STAR6_HUMAN	START domain containing protein 6	89	START.				lipid transport		lipid binding			ovary(1)	1				Colorectal(16;0.021)|READ - Rectum adenocarcinoma(59;0.188)														---	---	---	---
SERPINB11	89778	broad.mit.edu	37	18	61388178	61388178	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61388178C>T	uc002ljk.3	+	8	794	c.732C>T	c.(730-732)AGC>AGT	p.S244S	SERPINB11_uc010xes.1_Silent_p.S69S|SERPINB11_uc010dqd.2_Silent_p.S130S|SERPINB11_uc002ljj.3_Silent_p.S130S|SERPINB11_uc010dqe.2_Silent_p.S43S|SERPINB11_uc010dqf.2_Intron	NM_080475	NP_536723	Q96P15	SPB11_HUMAN	serpin peptidase inhibitor, clade B, member 11	244					regulation of proteolysis	cytoplasm	serine-type endopeptidase inhibitor activity			breast(1)	1		Esophageal squamous(42;0.129)																---	---	---	---
DSEL	92126	broad.mit.edu	37	18	65180462	65180462	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65180462T>G	uc002lke.1	-	2	2638	c.1414A>C	c.(1414-1416)AGT>CGT	p.S472R		NM_032160	NP_115536	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	462						integral to membrane	isomerase activity|sulfotransferase activity			ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	6		Esophageal squamous(42;0.129)																---	---	---	---
ZNF177	7730	broad.mit.edu	37	19	9492343	9492343	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9492343C>A	uc002mli.2	+	12	1519	c.856C>A	c.(856-858)CAC>AAC	p.H286N	ZNF177_uc002mlj.2_Missense_Mutation_p.H236N|ZNF177_uc002mlk.2_Missense_Mutation_p.H286N	NM_003451	NP_003442	Q13360	ZN177_HUMAN	zinc finger protein 177	286	C2H2-type 6.				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
TYK2	7297	broad.mit.edu	37	19	10469974	10469974	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10469974G>A	uc002moc.3	-	15	2430	c.2052C>T	c.(2050-2052)ATC>ATT	p.I684I	TYK2_uc010dxe.2_Silent_p.I499I|TYK2_uc002mod.2_Silent_p.I684I	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2	684	Protein kinase 1.				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)															---	---	---	---
BRD4	23476	broad.mit.edu	37	19	15375503	15375503	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15375503C>T	uc002nar.2	-	6	1146	c.924G>A	c.(922-924)TCG>TCA	p.S308S	BRD4_uc002nas.2_Silent_p.S308S|BRD4_uc002nat.3_Silent_p.S308S|BRD4_uc002nau.3_Silent_p.S308S	NM_058243	NP_490597	O60885	BRD4_HUMAN	bromodomain-containing protein 4 isoform long	308					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						OREG0025319	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ZNF99	7652	broad.mit.edu	37	19	22940424	22940424	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22940424A>T	uc010xrh.1	-	5	2014	c.2014T>A	c.(2014-2016)TGT>AGT	p.C672S		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)																---	---	---	---
CD22	933	broad.mit.edu	37	19	35827132	35827132	+	Silent	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35827132C>T	uc010edt.2	+	4	683	c.606C>T	c.(604-606)AGC>AGT	p.S202S	CD22_uc010xst.1_Silent_p.S30S|CD22_uc010edu.2_Silent_p.S202S|CD22_uc010edv.2_Silent_p.S202S|CD22_uc002nzb.3_Silent_p.S202S|CD22_uc010edx.2_5'Flank	NM_001771	NP_001762	P20273	CD22_HUMAN	CD22 molecule precursor	202	Extracellular (Potential).|Ig-like C2-type 1.				cell adhesion		protein binding|sugar binding			ovary(5)|lung(3)|breast(1)	9	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		OspA lipoprotein(DB00045)													---	---	---	---
FFAR2	2867	broad.mit.edu	37	19	35941277	35941277	+	Missense_Mutation	SNP	G	A	A	rs61746520	byFrequency;by1000genomes	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35941277G>A	uc002nzg.2	+	2	741	c.661G>A	c.(661-663)GTG>ATG	p.V221M	FFAR2_uc010eea.2_Missense_Mutation_p.V221M	NM_005306	NP_005297	O15552	FFAR2_HUMAN	free fatty acid receptor 2	221	Helical; Name=6; (Potential).					integral to plasma membrane	G-protein coupled receptor activity|lipid binding			central_nervous_system(1)	1	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)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39075652	39075652	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39075652G>A	uc002oit.2	+	102	14846	c.14716G>A	c.(14716-14718)GCG>ACG	p.A4906T	RYR1_uc002oiu.2_Missense_Mutation_p.A4901T	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4906			A -> V (in CCD).		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)													---	---	---	---
ALDH16A1	126133	broad.mit.edu	37	19	49967198	49967198	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49967198C>T	uc002pnt.2	+	9	1302	c.1186C>T	c.(1186-1188)CAG>TAG	p.Q396*	ALDH16A1_uc010yar.1_Nonsense_Mutation_p.Q345*|ALDH16A1_uc010yas.1_Nonsense_Mutation_p.Q231*|ALDH16A1_uc010yat.1_Nonsense_Mutation_p.Q233*	NM_153329	NP_699160	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	396							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)														---	---	---	---
KLK15	55554	broad.mit.edu	37	19	51330316	51330316	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51330316G>A	uc002ptl.2	-	3	330	c.299C>T	c.(298-300)GCG>GTG	p.A100V	KLK15_uc002ptm.2_Missense_Mutation_p.A100V|KLK15_uc002ptn.2_Missense_Mutation_p.A100V|KLK15_uc002pto.2_Missense_Mutation_p.A99V|KLK15_uc010ych.1_RNA|KLK15_uc010yci.1_Missense_Mutation_p.A99V|KLK15_uc010eod.2_RNA	NM_017509	NP_059979	Q9H2R5	KLK15_HUMAN	kallikrein-related peptidase 15 isoform 4	100	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)|breast(1)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.0143)														---	---	---	---
ZNF610	162963	broad.mit.edu	37	19	52869647	52869647	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52869647C>T	uc002pyx.3	+	6	1422	c.1016C>T	c.(1015-1017)ACG>ATG	p.T339M	ZNF610_uc002pyy.3_Missense_Mutation_p.T339M|ZNF610_uc002pyz.3_Missense_Mutation_p.T296M|ZNF610_uc002pza.2_Missense_Mutation_p.T339M	NM_001161426	NP_001154898	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610 isoform a	339					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)	3				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)														---	---	---	---
ZNF578	147660	broad.mit.edu	37	19	53015375	53015375	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53015375G>A	uc002pzp.3	+	6	1985	c.1741G>A	c.(1741-1743)GAT>AAT	p.D581N		NM_001099694	NP_001093164	Q96N58	ZN578_HUMAN	zinc finger protein 578	356					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)														---	---	---	---
ZNF470	388566	broad.mit.edu	37	19	57089371	57089371	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57089371C>T	uc002qnl.3	+	6	2250	c.1574C>T	c.(1573-1575)GCG>GTG	p.A525V	ZNF470_uc010etn.2_Intron	NM_001001668	NP_001001668	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	525	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)														---	---	---	---
ZNF154	7710	broad.mit.edu	37	19	58213129	58213129	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58213129T>G	uc010euf.2	-	3	1428	c.1188A>C	c.(1186-1188)CAA>CAC	p.Q396H	ZNF776_uc002qpx.2_Intron|ZNF154_uc002qpy.2_RNA	NM_001085384	NP_001078853	Q13106	ZN154_HUMAN	zinc finger protein 154	396	C2H2-type 11.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)														---	---	---	---
TRIB3	57761	broad.mit.edu	37	20	368783	368783	+	Silent	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:368783G>T	uc002wdm.2	+	2	635	c.129G>T	c.(127-129)CTG>CTT	p.L43L	TRIB3_uc002wdn.2_Silent_p.L70L	NM_021158	NP_066981	Q96RU7	TRIB3_HUMAN	tribbles 3	43					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)														---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8628558	8628558	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8628558T>G	uc002wnb.2	+	6	479	c.476T>G	c.(475-477)CTT>CGT	p.L159R	PLCB1_uc010zrb.1_Missense_Mutation_p.L58R|PLCB1_uc010gbv.1_Missense_Mutation_p.L159R|PLCB1_uc002wmz.1_Missense_Mutation_p.L159R|PLCB1_uc002wna.2_Missense_Mutation_p.L159R|PLCB1_uc002wnc.1_Missense_Mutation_p.L58R	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	159					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																		---	---	---	---
SEL1L2	80343	broad.mit.edu	37	20	13868427	13868427	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13868427C>A	uc010gcf.2	-	8	815	c.733G>T	c.(733-735)GTG>TTG	p.V245L	SEL1L2_uc002woq.3_Missense_Mutation_p.V106L|SEL1L2_uc010zrl.1_Missense_Mutation_p.V245L|SEL1L2_uc002wor.2_RNA	NM_025229	NP_079505	Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 precursor	245	Sel1-like 4.|Extracellular (Potential).					integral to membrane	binding			ovary(2)	2																		---	---	---	---
ACSS1	84532	broad.mit.edu	37	20	24989960	24989960	+	Silent	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24989960G>A	uc002wub.2	-	13	2714	c.1836C>T	c.(1834-1836)CTC>CTT	p.L612L	ACSS1_uc002wuc.2_Silent_p.L610L|ACSS1_uc010gdc.2_Silent_p.L407L|ACSS1_uc002wud.1_RNA|ACSS1_uc002wua.2_Silent_p.L529L	NM_032501	NP_115890	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	612					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)													---	---	---	---
PLUNC	51297	broad.mit.edu	37	20	31830294	31830294	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31830294C>A	uc002wyv.2	+	8	802	c.732C>A	c.(730-732)AAC>AAA	p.N244K	PLUNC_uc002wyt.3_Missense_Mutation_p.N244K|PLUNC_uc002wyu.3_Missense_Mutation_p.N244K	NM_130852	NP_570913	Q9NP55	PLUNC_HUMAN	palate, lung and nasal epithelium associated	244					innate immune response	extracellular region	lipid binding				0																		---	---	---	---
NECAB3	63941	broad.mit.edu	37	20	32258548	32258548	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32258548C>A	uc002wzn.3	-	3	311	c.205G>T	c.(205-207)GTT>TTT	p.V69F	NECAB3_uc002wzm.3_Missense_Mutation_p.V69F|NECAB3_uc002wzo.3_RNA|NECAB3_uc002wzp.3_Missense_Mutation_p.V20F|NECAB3_uc002wzq.3_Missense_Mutation_p.V69F|NECAB3_uc002wzr.3_RNA|NECAB3_uc010geo.2_Missense_Mutation_p.V69F	NM_031232	NP_112509	Q96P71	NECA3_HUMAN	N-terminal EF-hand calcium binding protein 3	69	EF-hand.				antibiotic biosynthetic process|protein metabolic process|protein secretion|regulation of amyloid precursor protein biosynthetic process	endoplasmic reticulum membrane|Golgi cis cisterna|nucleus	calcium ion binding|oxidoreductase activity|protein binding			lung(1)	1																		---	---	---	---
MYH7B	57644	broad.mit.edu	37	20	33578886	33578886	+	Silent	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33578886G>T	uc002xbi.1	+	22	2363	c.2271G>T	c.(2269-2271)GGG>GGT	p.G757G		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	715	Myosin head-like.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00691)															---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	40877391	40877391	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40877391C>T	uc002xkg.2	-	14	2432	c.2248G>A	c.(2248-2250)GTG>ATG	p.V750M	PTPRT_uc010ggj.2_Missense_Mutation_p.V769M	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	750	Helical; (Potential).				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)																---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46256346	46256346	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46256346A>G	uc002xtk.2	+	7	779	c.574A>G	c.(574-576)AGC>GGC	p.S192G	NCOA3_uc010ght.1_Missense_Mutation_p.S192G|NCOA3_uc002xtl.2_Missense_Mutation_p.S192G|NCOA3_uc002xtm.2_Missense_Mutation_p.S192G|NCOA3_uc002xtn.2_Missense_Mutation_p.S192G|NCOA3_uc010zyc.1_5'UTR	NM_181659	NP_858045	Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3 isoform a	192					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																		---	---	---	---
BCAS4	55653	broad.mit.edu	37	20	49493052	49493052	+	Nonsense_Mutation	SNP	C	T	T	rs149433489	byFrequency	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49493052C>T	uc002xvq.2	+	6	680	c.616C>T	c.(616-618)CGA>TGA	p.R206*	BCAS4_uc002xvr.2_Silent_p.Y173Y|BCAS4_uc002xvs.2_Silent_p.Y128Y	NM_017843	NP_060313	Q8TDM0	BCAS4_HUMAN	breast carcinoma amplified sequence 4 isoform a	206						cytoplasm					0																		---	---	---	---
TFAP2C	7022	broad.mit.edu	37	20	55209271	55209271	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55209271C>T	uc002xya.2	+	5	1112	c.869C>T	c.(868-870)CCG>CTG	p.P290L	TFAP2C_uc010zzi.1_Missense_Mutation_p.P121L	NM_003222	NP_003213	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma	290					cell-cell signaling|male gonad development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Colorectal(105;0.229)															---	---	---	---
SYCP2	10388	broad.mit.edu	37	20	58490263	58490263	+	Intron	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58490263T>G	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)															---	---	---	---
MIR1-1	406904	broad.mit.edu	37	20	61151547	61151547	+	RNA	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61151547C>A	hsa-mir-1-1|MI0000651	+			c.35C>A			C20orf200_uc002ycy.2_5'Flank|C20orf200_uc002ycz.1_5'Flank|C20orf166_uc011aaj.1_Intron|uc011aak.1_RNA																	0																		---	---	---	---
PFKL	5211	broad.mit.edu	37	21	45742047	45742047	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45742047G>A	uc002zel.2	+	14	1429	c.1370G>A	c.(1369-1371)GGC>GAC	p.G457D	PFKL_uc002zek.2_Missense_Mutation_p.G504D|PFKL_uc002zem.2_Missense_Mutation_p.G44D|PFKL_uc002zen.2_Missense_Mutation_p.G44D	NM_002626	NP_002617	P17858	K6PL_HUMAN	liver phosphofructokinase	457					fructose 6-phosphate metabolic process|glycolysis|protein oligomerization	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|fructose-6-phosphate binding|identical protein binding|kinase binding|metal ion binding				0				Colorectal(79;0.0811)														---	---	---	---
CLTCL1	8218	broad.mit.edu	37	22	19195726	19195726	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19195726T>G	uc002zpb.2	-	22	3613	c.3538A>C	c.(3538-3540)ACC>CCC	p.T1180P	CLTCL1_uc011agv.1_Missense_Mutation_p.T1180P|CLTCL1_uc011agw.1_Missense_Mutation_p.T1180P|CLTCL1_uc011agt.1_5'Flank|CLTCL1_uc011agu.1_5'Flank|CLTCL1_uc010grm.1_Intron|CLTCL1_uc002zpe.2_Missense_Mutation_p.T140P|CLTCL1_uc002zpd.1_Intron	NM_007098	NP_009029	P53675	CLH2_HUMAN	clathrin, heavy polypeptide-like 1 isoform 1	1180	Proximal segment.|Heavy chain arm.				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)							T	?	ALCL								---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26231269	26231269	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26231269T>G	uc003abz.1	+	17	3317	c.3067T>G	c.(3067-3069)TTA>GTA	p.L1023V	MYO18B_uc003aca.1_Missense_Mutation_p.L904V|MYO18B_uc010guy.1_Missense_Mutation_p.L905V|MYO18B_uc010guz.1_Missense_Mutation_p.L904V|MYO18B_uc011aka.1_Missense_Mutation_p.L177V|MYO18B_uc011akb.1_Missense_Mutation_p.L536V	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1023	Myosin head-like.					nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32218770	32218770	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32218770G>T	uc003als.2	+	24	2240	c.2098G>T	c.(2098-2100)GGT>TGT	p.G700C	DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Missense_Mutation_p.G700C|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Missense_Mutation_p.G700C|DEPDC5_uc003alu.2_Missense_Mutation_p.G140C|DEPDC5_uc003alv.2_Intron|DEPDC5_uc011alw.1_Missense_Mutation_p.G21C|DEPDC5_uc011alt.1_Intron	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1	700					intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8																		---	---	---	---
ADSL	158	broad.mit.edu	37	22	40761054	40761054	+	Silent	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40761054C>A	uc003ayp.3	+	12	1421	c.1362C>A	c.(1360-1362)TCC>TCA	p.S454S	ADSL_uc003ays.3_Intron|ADSL_uc003ayq.3_Silent_p.S468S|ADSL_uc003ayr.3_Silent_p.S230S|ADSL_uc003ayt.3_Silent_p.S439S	NM_000026	NP_000017	P30566	PUR8_HUMAN	adenylosuccinate lyase isoform a	454					AMP biosynthetic process|protein tetramerization|purine base metabolic process	cytosol	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity			ovary(1)	1																		---	---	---	---
ASMT	438	broad.mit.edu	37	X	1761751	1761751	+	Silent	SNP	G	A	A	rs147532133	byFrequency	TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1761751G>A	uc004cqd.2	+	10	1111	c.966G>A	c.(964-966)CTG>CTA	p.L322L	ASMT_uc010ncy.2_Silent_p.L322L|ASMT_uc004cqe.2_Silent_p.L247L	NM_004043	NP_004034	P46597	HIOM_HUMAN	acetylserotonin O-methyltransferase	294					melatonin biosynthetic process|translation	cytosol	acetylserotonin O-methyltransferase activity|S-methyltransferase activity			skin(1)	1		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
EIF2S3	1968	broad.mit.edu	37	X	24078247	24078247	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24078247G>T	uc004dbc.2	+	5	447	c.426G>T	c.(424-426)ATG>ATT	p.M142I		NM_001415	NP_001406	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2,	142						cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			lung(1)	1																		---	---	---	---
MAGEB3	4114	broad.mit.edu	37	X	30254096	30254096	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30254096C>T	uc004dca.1	+	5	792	c.55C>T	c.(55-57)CGG>TGG	p.R19W		NM_002365	NP_002356	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	19											0																		---	---	---	---
DMD	1756	broad.mit.edu	37	X	31222074	31222074	+	Intron	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31222074T>G	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)																---	---	---	---
MAGEB16	139604	broad.mit.edu	37	X	35820678	35820678	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35820678A>G	uc010ngt.1	+	2	644	c.365A>G	c.(364-366)AAT>AGT	p.N122S		NM_001099921	NP_001093391	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	122	MAGE.									lung(3)|ovary(2)|breast(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	47663806	47663806	+	IGR	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47663806C>T								LOC100133957 (144030 upstream) : ZNF81 (32495 downstream)																																			---	---	---	---
BMP15	9210	broad.mit.edu	37	X	50659330	50659330	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50659330G>T	uc011mnw.1	+	2	902	c.902G>T	c.(901-903)CGC>CTC	p.R301L		NM_005448	NP_005439	O95972	BMP15_HUMAN	bone morphogenetic protein 15 precursor	301					female gamete generation|granulosa cell development|ovarian follicle development	extracellular space	cytokine activity|growth factor activity			ovary(2)	2	Ovarian(276;0.236)																	---	---	---	---
HEPH	9843	broad.mit.edu	37	X	65413355	65413355	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65413355A>C	uc011moz.1	+	8	1313	c.1253A>C	c.(1252-1254)AAG>ACG	p.K418T	HEPH_uc004dwn.2_Missense_Mutation_p.K418T|HEPH_uc004dwo.2_Missense_Mutation_p.K148T|HEPH_uc010nkr.2_Missense_Mutation_p.K418T|HEPH_uc011mpa.1_Missense_Mutation_p.K418T	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	415	Extracellular (Potential).|Plastocyanin-like 3.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9																		---	---	---	---
KIF4A	24137	broad.mit.edu	37	X	69615596	69615596	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69615596G>A	uc004dyg.2	+	21	2435	c.2308G>A	c.(2308-2310)GAT>AAT	p.D770N	KIF4A_uc010nkw.2_Missense_Mutation_p.D770N	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	770	Potential.|Interaction with PRC1.				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																		---	---	---	---
MAGEE1	57692	broad.mit.edu	37	X	75651189	75651189	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75651189T>C	uc004ecm.1	+	1	3073	c.2866T>C	c.(2866-2868)TTC>CTC	p.F956L		NM_020932	NP_065983	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	956	Interaction with DTNA (By similarity).					dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane				breast(3)|ovary(1)|pancreas(1)|skin(1)	6																		---	---	---	---
HDX	139324	broad.mit.edu	37	X	83724379	83724379	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83724379T>G	uc004eek.1	-	3	461	c.352A>C	c.(352-354)AGT>CGT	p.S118R	HDX_uc011mqv.1_Missense_Mutation_p.S118R|HDX_uc004eel.1_Missense_Mutation_p.S60R	NM_144657	NP_653258	Q7Z353	HDX_HUMAN	highly divergent homeobox	118						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
HDX	139324	broad.mit.edu	37	X	83730285	83730285	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83730285T>A	uc004eek.1	-	2	230	c.121A>T	c.(121-123)ACT>TCT	p.T41S	HDX_uc011mqv.1_Missense_Mutation_p.T41S|HDX_uc004eel.1_Intron	NM_144657	NP_653258	Q7Z353	HDX_HUMAN	highly divergent homeobox	41	Homeobox 1.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
PCDH11X	27328	broad.mit.edu	37	X	91132799	91132799	+	Silent	SNP	C	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91132799C>A	uc004efk.1	+	2	2405	c.1560C>A	c.(1558-1560)GGC>GGA	p.G520G	PCDH11X_uc004efl.1_Silent_p.G520G|PCDH11X_uc004efo.1_Silent_p.G520G|PCDH11X_uc010nmv.1_Silent_p.G520G|PCDH11X_uc004efm.1_Silent_p.G520G|PCDH11X_uc004efn.1_Silent_p.G520G|PCDH11X_uc004efh.1_Silent_p.G520G|PCDH11X_uc004efj.1_Silent_p.G520G	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	520	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2																		---	---	---	---
GUCY2F	2986	broad.mit.edu	37	X	108684691	108684691	+	Silent	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108684691T>G	uc004eod.3	-	7	1866	c.1590A>C	c.(1588-1590)GTA>GTC	p.V530V	GUCY2F_uc011msq.1_RNA	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	530	Cytoplasmic (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																		---	---	---	---
GLUD2	2747	broad.mit.edu	37	X	120182230	120182230	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120182230G>A	uc004eto.2	+	1	769	c.692G>A	c.(691-693)CGG>CAG	p.R231Q		NM_012084	NP_036216	P49448	DHE4_HUMAN	glutamate dehydrogenase 2 precursor	231					glutamate biosynthetic process|glutamate catabolic process	mitochondrial matrix	ADP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|leucine binding			pancreas(1)	1					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
IGSF1	3547	broad.mit.edu	37	X	130416654	130416654	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130416654T>G	uc004ewd.2	-	7	1248	c.1010A>C	c.(1009-1011)CAG>CCG	p.Q337P	IGSF1_uc004ewe.3_Missense_Mutation_p.Q326P|IGSF1_uc004ewf.2_Missense_Mutation_p.Q317P	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	337	Ig-like C2-type 4.|Extracellular (Potential).				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
GABRQ	55879	broad.mit.edu	37	X	151821296	151821296	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151821296A>T	uc004ffp.1	+	9	1471	c.1451A>T	c.(1450-1452)AAC>ATC	p.N484I		NM_018558	NP_061028	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) receptor, theta	484						cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|neurotransmitter transporter activity			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
CTAG2	30848	broad.mit.edu	37	X	153880762	153880762	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4284-01A-01D-1126-08	TCGA-BR-4284-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153880762C>T	uc004fmi.1	-	2	466	c.413G>A	c.(412-414)CGG>CAG	p.R138Q	CTAG2_uc004fmh.1_Intron	NM_020994	NP_066274	O75638	CTAG2_HUMAN	cancer/testis antigen 2 isoform LAGE-1b	138				R -> W (in Ref. 1; CAA11117).		centrosome				pancreas(1)	1	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
