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	ref_context	gc_content	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	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
Unknown	0	broad.mit.edu	37	1	1855262	1855262	+	Silent	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1855262G>A	uc001aik.2	-	7	1189	c.339C>T	c.(337-339)CAC>CAT	p.H113H	uc001ail.2_Silent_p.H113H					RecName: Full=Uncharacterized protein C1orf222;																		AGAGGCTTTCGTGGTCGGGGC	0.622													4	274	---	---	---	---	PASS
PTCHD2	57540	broad.mit.edu	37	1	11579864	11579864	+	Silent	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11579864C>T	uc001ash.3	+	9	2265	c.2127C>T	c.(2125-2127)CTC>CTT	p.L709L	PTCHD2_uc001asi.1_Silent_p.L709L	NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	709	Cytoplasmic (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GCGGCCATCTCATCGTGCAGC	0.677													6	16	---	---	---	---	PASS
FAM131C	348487	broad.mit.edu	37	1	16361925	16361925	+	Silent	SNP	G	A	A	rs146790110		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16361925G>A	uc010obz.1	-	7	781	c.591C>T	c.(589-591)AGC>AGT	p.S197S	CLCNKB_uc001axw.3_Intron	NM_182623	NP_872429	Q96AQ9	F131C_HUMAN	hypothetical protein LOC348487	197											0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		CGCTGGGAAGGCTGTCCTGAA	0.647													6	33	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16946407	16946407	+	RNA	SNP	T	G	G	rs10796418	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16946407T>G	uc010ocf.1	-	3		c.491A>C			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						AGCAATCTCCTCACTCAGCTG	0.672													5	29	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16974018	16974018	+	5'Flank	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974018A>G	uc001azg.1	-						CROCCL1_uc001azi.1_5'Flank|MST1P2_uc009vow.2_RNA|MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_RNA|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						CCGAGCGGCCATGGTGCTACA	0.637													4	75	---	---	---	---	PASS
ZBTB40	9923	broad.mit.edu	37	1	22843894	22843894	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22843894A>G	uc001bft.2	+	14	3281	c.2770A>G	c.(2770-2772)AGA>GGA	p.R924G	ZBTB40_uc001bfu.2_Missense_Mutation_p.R924G|ZBTB40_uc009vqi.1_Missense_Mutation_p.R812G	NM_001083621	NP_001077090	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	924	C2H2-type 5.				bone mineralization|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		CTATGTCTGCAGAGACTGTGG	0.547													9	64	---	---	---	---	PASS
MECR	51102	broad.mit.edu	37	1	29528492	29528492	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29528492T>C	uc001brq.1	-	6	755	c.719A>G	c.(718-720)GAG>GGG	p.E240G	MECR_uc001brp.1_Missense_Mutation_p.E164G|MECR_uc001brr.1_Missense_Mutation_p.E164G|MECR_uc001brs.1_RNA|MECR_uc001brt.1_Missense_Mutation_p.E164G|MECR_uc010ofz.1_Missense_Mutation_p.E240G	NM_016011	NP_057095	Q9BV79	MECR_HUMAN	trans-2-enoyl-CoA reductase, mitochondrial	240					fatty acid biosynthetic process	mitochondrion	trans-2-enoyl-CoA reductase (NADPH) activity|zinc ion binding			ovary(1)	1		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)		TCTTAGCTCCTCTTCTGTGAT	0.493													6	334	---	---	---	---	PASS
C1orf91	56063	broad.mit.edu	37	1	32681941	32681941	+	3'UTR	SNP	G	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32681941G>T	uc009vub.1	-	4					C1orf91_uc001buo.3_Intron|C1orf91_uc001bup.3_Intron|C1orf91_uc010oha.1_Intron|C1orf91_uc001buq.3_3'UTR			Q8WY98	TM234_HUMAN	RecName: Full=UPF0546 membrane protein C1orf91;							integral to membrane					0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				GGGCAGGCAAGGCTAATAGAC	0.582													12	12	---	---	---	---	PASS
KIAA0319L	79932	broad.mit.edu	37	1	35921629	35921629	+	Silent	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35921629T>C	uc001byx.2	-	10	1899	c.1641A>G	c.(1639-1641)AAA>AAG	p.K547K	KIAA0319L_uc001byw.2_5'Flank|KIAA0319L_uc010ohv.1_Silent_p.K189K	NM_024874	NP_079150	Q8IZA0	K319L_HUMAN	dyslexia susceptibility 2-like	547	PKD 3.|Extracellular (Potential).					cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCTCCACCACTTTCCCTTTGC	0.493													6	359	---	---	---	---	PASS
CDC14A	8556	broad.mit.edu	37	1	100964518	100964518	+	Silent	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100964518A>G	uc001dtg.3	+	15	1943	c.1455A>G	c.(1453-1455)CTA>CTG	p.L485L	CDC14A_uc010oui.1_Silent_p.L427L|CDC14A_uc001dtf.2_Silent_p.L485L|CDC14A_uc009wed.1_Silent_p.L192L|CDC14A_uc009wee.2_Silent_p.L485L	NM_003672	NP_003663	Q9UNH5	CC14A_HUMAN	CDC14 homolog A isoform 1	485					cell cycle|cell division|cell proliferation	centrosome|nucleus|spindle	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			large_intestine(1)	1		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		CCAGTTCTCTAGGGAACTTGA	0.463													31	90	---	---	---	---	PASS
KCNC4	3749	broad.mit.edu	37	1	110768720	110768720	+	Missense_Mutation	SNP	G	A	A	rs146310494		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110768720G>A	uc001dzh.2	+	3	1796	c.1739G>A	c.(1738-1740)CGA>CAA	p.R580Q	KCNC4_uc009wfr.2_Missense_Mutation_p.R580Q|KCNC4_uc001dzg.2_Missense_Mutation_p.R580Q|KCNC4_uc001dzi.2_RNA	NM_004978	NP_004969	Q03721	KCNC4_HUMAN	Shaw-related voltage-gated potassium channel	580	Cytoplasmic (Potential).				synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		TCCACCACTCGAGACAGAAAC	0.642													3	35	---	---	---	---	PASS
ATP1A1	476	broad.mit.edu	37	1	116939249	116939249	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116939249C>G	uc001ege.2	+	14	2205	c.1866C>G	c.(1864-1866)ATC>ATG	p.I622M	ATP1A1_uc010owv.1_Missense_Mutation_p.I591M|ATP1A1_uc010oww.1_Missense_Mutation_p.I622M|ATP1A1_uc010owx.1_Missense_Mutation_p.I591M|C1orf203_uc009whb.2_Intron	NM_000701	NP_000692	P05023	AT1A1_HUMAN	Na+/K+ -ATPase alpha 1 subunit isoform a	622	Cytoplasmic (Potential).				ATP biosynthetic process	melanosome|sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Captopril(DB01197)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Esomeprazole(DB00736)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Ouabain(DB01092)|Pantoprazole(DB00213)|Trichlormethiazide(DB01021)	ACCATCCAATCACAGCTAAAG	0.463													33	137	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144220850	144220850	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144220850T>G	uc010oxr.1	+	19	2227	c.2223T>G	c.(2221-2223)TGT>TGG	p.C741W	NBPF9_uc010oxn.1_Missense_Mutation_p.C612W|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Missense_Mutation_p.C529W|NBPF9_uc001ekg.1_Missense_Mutation_p.C41W|NBPF9_uc001ekk.1_Missense_Mutation_p.C285W|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Missense_Mutation_p.C41W|uc010oxz.1_Missense_Mutation_p.C529W	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						cytoplasm					0						TGGATAGATGTTATTCGACTC	0.493													4	8	---	---	---	---	PASS
THEM5	284486	broad.mit.edu	37	1	151824751	151824751	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151824751C>A	uc009wnd.2	-	2	440	c.308G>T	c.(307-309)GGA>GTA	p.G103V		NM_182578	NP_872384	Q8N1Q8	THEM5_HUMAN	thioesterase superfamily member 5	103							hydrolase activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AACTGCCAGTCCAGATGGGAG	0.532													55	61	---	---	---	---	PASS
GORAB	92344	broad.mit.edu	37	1	170521625	170521625	+	3'UTR	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170521625T>C	uc001gha.2	+	5					GORAB_uc009wvx.2_3'UTR|GORAB_uc001ghb.2_3'UTR|GORAB_uc001ghc.2_3'UTR|GORAB_uc001ghd.2_3'UTR	NM_152281	NP_689494	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting isoform a							Golgi apparatus|nucleus					0						TCTTTTGAGCTAATATGGTAT	0.368													4	130	---	---	---	---	PASS
CR1	1378	broad.mit.edu	37	1	207787831	207787831	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207787831G>T	uc001hfy.2	+	32	5448	c.5308G>T	c.(5308-5310)GAA>TAA	p.E1770*	CR1_uc001hfx.2_Nonsense_Mutation_p.E2220*	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	1770	Extracellular (Potential).|Sushi 27.				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3						TCCAGTGTGTGAACGTGAGTA	0.408													6	609	---	---	---	---	PASS
RCOR3	55758	broad.mit.edu	37	1	211487169	211487169	+	3'UTR	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211487169C>T	uc001hig.2	+	11					RCOR3_uc010psw.1_3'UTR|RCOR3_uc001hif.2_3'UTR|RCOR3_uc009xcz.2_RNA	NM_018254	NP_060724	Q9P2K3	RCOR3_HUMAN	REST corepressor 3 isoform d						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		CAGTGCTCATCTGACTGATGA	0.388													5	13	---	---	---	---	PASS
PTPN14	5784	broad.mit.edu	37	1	214656561	214656561	+	Intron	SNP	C	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214656561C>A	uc001hkk.1	-						PTPN14_uc010pty.1_Intron|uc010ptz.1_RNA	NM_005401	NP_005392	Q15678	PTN14_HUMAN	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)		GTCAGATCCTCCAATTAATAA	0.338													75	438	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215990345	215990345	+	Silent	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215990345T>C	uc001hku.1	-	48	9951	c.9564A>G	c.(9562-9564)GAA>GAG	p.E3188E		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3188	Extracellular (Potential).|Fibronectin type-III 18.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTACCTTAGCTTCAGAAGAAT	0.383										HNSCC(13;0.011)			5	145	---	---	---	---	PASS
SIPA1L2	57568	broad.mit.edu	37	1	232600698	232600698	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232600698C>T	uc001hvg.2	-	7	2866	c.2708G>A	c.(2707-2709)TGG>TAG	p.W903*	SIPA1L2_uc001hvf.2_5'Flank	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	903					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)|skin(1)	6		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				TCCAGATGTCCACCCAATCAC	0.418													4	155	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237664189	237664189	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237664189C>G	uc001hyl.1	+	21	2502	c.2382C>G	c.(2380-2382)TTC>TTG	p.F794L		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	794	Cytoplasmic (By similarity).|B30.2/SPRY 1.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TCGTTAGTTTCTCTGCAGGAA	0.423													138	556	---	---	---	---	PASS
ALK	238	broad.mit.edu	37	2	29455209	29455209	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29455209A>G	uc002rmy.2	-	15	3500	c.2593T>C	c.(2593-2595)TCC>CCC	p.S865P		NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	865	Gly-rich.|Extracellular (Potential).				protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	AGAACCGAGGAGTTATTCTCC	0.627			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				53	86	---	---	---	---	PASS
TACR1	6869	broad.mit.edu	37	2	75426105	75426105	+	5'UTR	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75426105C>T	uc002sng.2	-	1					TACR1_uc002snh.2_5'UTR	NM_001058	NP_001049	P25103	NK1R_HUMAN	tachykinin receptor 1 isoform long						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|detection of abiotic stimulus|mechanosensory behavior	integral to plasma membrane	protein binding			ovary(1)	1					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)	CACAACCCCCCTCTGCAGCAG	0.552													100	189	---	---	---	---	PASS
SAP130	79595	broad.mit.edu	37	2	128773981	128773981	+	Silent	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128773981T>C	uc002tpp.2	-	4	699	c.567A>G	c.(565-567)GCA>GCG	p.A189A	SAP130_uc002tpo.2_5'Flank|SAP130_uc010fmd.2_Silent_p.A189A|SAP130_uc002tpq.1_Silent_p.A163A	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b	189					histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		CACTGATTGTTGCCACAGGAA	0.448													6	178	---	---	---	---	PASS
IFIH1	64135	broad.mit.edu	37	2	163138009	163138009	+	Silent	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163138009T>C	uc002uce.2	-	7	1575	c.1353A>G	c.(1351-1353)GAA>GAG	p.E451E		NM_022168	NP_071451	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	451	Helicase ATP-binding.				detection of virus|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|regulation of apoptosis	cytosol|nucleus	ATP binding|DNA binding|double-stranded RNA binding|helicase activity|protein binding|ribonucleoprotein binding|zinc ion binding			ovary(1)	1						TATACACTGCTTCTTTGTTGG	0.348													7	477	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179483509	179483509	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179483509G>T	uc010zfg.1	-	200	39288	c.39064C>A	c.(39064-39066)CCA>ACA	p.P13022T	TTN_uc010zfh.1_Missense_Mutation_p.P6717T|TTN_uc010zfi.1_Missense_Mutation_p.P6650T|TTN_uc010zfj.1_Missense_Mutation_p.P6525T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	13949							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)			GCATCATATGGCACCACCATT	0.418													13	381	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179631234	179631234	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179631234G>A	uc010zfg.1	-	41	9801	c.9577C>T	c.(9577-9579)CGA>TGA	p.R3193*	TTN_uc010zfh.1_Nonsense_Mutation_p.R3147*|TTN_uc010zfi.1_Nonsense_Mutation_p.R3147*|TTN_uc010zfj.1_Nonsense_Mutation_p.R3147*|TTN_uc002umz.1_5'Flank|TTN_uc002unb.2_Nonsense_Mutation_p.R3193*	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3193							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)			TATTTGTGTCGTTCTTGAACT	0.423													72	334	---	---	---	---	PASS
PIKFYVE	200576	broad.mit.edu	37	2	209190047	209190047	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209190047A>G	uc002vcz.2	+	20	2670	c.2512A>G	c.(2512-2514)ACA>GCA	p.T838A	PIKFYVE_uc010fun.1_Missense_Mutation_p.T519A|PIKFYVE_uc002vcy.1_Missense_Mutation_p.T782A	NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type	838					cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10						CCTAGGCTGTACAATCAAGCT	0.393													5	302	---	---	---	---	PASS
DNPEP	23549	broad.mit.edu	37	2	220239735	220239735	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220239735C>A	uc010zlg.1	-	14	1355	c.1273G>T	c.(1273-1275)GTC>TTC	p.V425F	DNPEP_uc010zlf.1_RNA|DNPEP_uc002vle.2_Missense_Mutation_p.V417F|DNPEP_uc002vlf.1_Missense_Mutation_p.V403F|DNPEP_uc002vlh.2_Missense_Mutation_p.V364F|DNPEP_uc002vli.1_Missense_Mutation_p.V364F	NM_012100	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	407					peptide metabolic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	L-Glutamic Acid(DB00142)	TCATTCCGGACCATGAGATCC	0.577													27	49	---	---	---	---	PASS
DNPEP	23549	broad.mit.edu	37	2	220239736	220239736	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220239736C>A	uc010zlg.1	-	14	1354	c.1272G>T	c.(1270-1272)ATG>ATT	p.M424I	DNPEP_uc010zlf.1_RNA|DNPEP_uc002vle.2_Missense_Mutation_p.M416I|DNPEP_uc002vlf.1_Missense_Mutation_p.M402I|DNPEP_uc002vlh.2_Missense_Mutation_p.M363I|DNPEP_uc002vli.1_Missense_Mutation_p.M363I	NM_012100	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	406					peptide metabolic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	L-Glutamic Acid(DB00142)	CATTCCGGACCATGAGATCCT	0.582													28	50	---	---	---	---	PASS
SP140	11262	broad.mit.edu	37	2	231134601	231134601	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231134601T>A	uc002vql.2	+	14	1492	c.1377T>A	c.(1375-1377)TGT>TGA	p.C459*	SP140_uc010zma.1_RNA|SP140_uc002vqn.2_Nonsense_Mutation_p.C345*|SP140_uc002vqm.2_Nonsense_Mutation_p.C399*|SP140_uc010fxl.2_Nonsense_Mutation_p.C432*	NM_007237	NP_009168	Q13342	LY10_HUMAN	SP140 nuclear body protein isoform 1	459					defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		GTGTCATGTGTTTCTCAGAAG	0.507													5	329	---	---	---	---	PASS
PLCL2	23228	broad.mit.edu	37	3	17052098	17052098	+	Silent	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17052098A>G	uc011awc.1	+	5	1341	c.1236A>G	c.(1234-1236)GAA>GAG	p.E412E	PLCL2_uc010het.1_Intron|PLCL2_uc011awd.1_Silent_p.E294E	NM_001144382	NP_001137854	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2 isoform 1	420					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(2)|ovary(1)|lung(1)	4						TCGATCCAGAACATAAGAAGG	0.403													4	92	---	---	---	---	PASS
GOLGA4	2803	broad.mit.edu	37	3	37337696	37337696	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37337696A>G	uc003cgv.2	+	7	1104	c.800A>G	c.(799-801)GAT>GGT	p.D267G	GOLGA4_uc010hgr.1_Intron|GOLGA4_uc003cgw.2_Missense_Mutation_p.D289G|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_Missense_Mutation_p.D148G	NM_002078	NP_002069	Q13439	GOGA4_HUMAN	golgi autoantigen, golgin subfamily a, 4	267	Potential.|Glu-rich.				Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4						CCAGAAAGTGATGGAGAGCCA	0.328													5	137	---	---	---	---	PASS
CX3CR1	1524	broad.mit.edu	37	3	39307549	39307549	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39307549A>G	uc003cjl.2	-	2	544	c.452T>C	c.(451-453)CTA>CCA	p.L151P		NM_001337	NP_001328	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	151	Helical; Name=4; (Potential).				cell adhesion|cellular defense response|chemotaxis|interspecies interaction between organisms|response to wounding	integral to plasma membrane	chemokine receptor activity			lung(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)		CCAGACGCCTAGGCTGATGGT	0.552													4	94	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47098903	47098903	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47098903A>T	uc003cqs.2	-	15	6424	c.6371T>A	c.(6370-6372)TTG>TAG	p.L2124*	SETD2_uc003cqv.2_Nonsense_Mutation_p.L2191*|SETD2_uc003cqt.1_RNA	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2124	Potential.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTGCTCAAACAACTTCCGGCG	0.428			N|F|S|Mis		clear cell renal carcinoma								54	32	---	---	---	---	PASS
TREX1	11277	broad.mit.edu	37	3	48508682	48508682	+	Missense_Mutation	SNP	T	C	C	rs78948846		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48508682T>C	uc003ctj.2	+	2	2050	c.793T>C	c.(793-795)TGG>CGG	p.W265R	TREX1_uc010hjy.2_Missense_Mutation_p.W210R|TREX1_uc003ctk.2_Missense_Mutation_p.W71R|TREX1_uc010hjz.2_Missense_Mutation_p.W210R|TREX1_uc010hka.2_Missense_Mutation_p.W265R	NM_033629	NP_338599	Q9NSU2	TREX1_HUMAN	three prime repair exonuclease 1 isoform b	265					cell death|DNA recombination|DNA replication|mismatch repair	nuclear envelope	3'-5'-exodeoxyribonuclease activity|exodeoxyribonuclease III activity|metal ion binding|MutLalpha complex binding|MutSalpha complex binding|protein homodimerization activity|single-stranded DNA binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		CATCTGTCAGTGGAGACCACA	0.627								Direct_reversal_of_damage|Editing_and_processing_nucleases					23	16	---	---	---	---	PASS
DNAH1	25981	broad.mit.edu	37	3	52402795	52402795	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52402795C>A	uc011bef.1	+	37	6065	c.5804C>A	c.(5803-5805)GCC>GAC	p.A1935D		NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1935	AAA 2 (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CGGGCGGGGGCCATCACCTCC	0.582													25	20	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52598080	52598080	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52598080T>G	uc003des.2	-	23	3873	c.3861A>C	c.(3859-3861)GAA>GAC	p.E1287D	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.E1287D|PBRM1_uc003der.2_Missense_Mutation_p.E1255D|PBRM1_uc003det.2_Missense_Mutation_p.E1302D|PBRM1_uc003deu.2_Missense_Mutation_p.E1302D|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.E1287D|PBRM1_uc010hmk.1_Missense_Mutation_p.E1262D|PBRM1_uc003dey.2_Missense_Mutation_p.E1262D|PBRM1_uc003dez.1_Missense_Mutation_p.E1286D	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1287			E -> Q (found in a breast cancer cell line).		chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AGTAGTAAATTTCATCATCTA	0.353			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								249	184	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	3	126386192	126386192	+	Splice_Site	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126386192G>A	uc003eje.1	+	4	643	c.399_splice	c.e4+1	p.K133_splice						RecName: Full=Putative uncharacterized protein C3orf46;																		GCATCACAAGGTAGGTAACCA	0.622													3	27	---	---	---	---	PASS
KPNA4	3840	broad.mit.edu	37	3	160219829	160219829	+	3'UTR	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160219829C>T	uc003fdn.2	-	17						NM_002268	NP_002259	O00629	IMA4_HUMAN	karyopherin alpha 4						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			tatatatatacacacacacat	0.313													5	15	---	---	---	---	PASS
MCCC1	56922	broad.mit.edu	37	3	182740269	182740269	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182740269A>G	uc003fle.2	-	16	1942	c.1805T>C	c.(1804-1806)GTT>GCT	p.V602A	MCCC1_uc010hxi.2_RNA|MCCC1_uc011bqo.1_RNA|MCCC1_uc003flf.2_Missense_Mutation_p.V485A|MCCC1_uc003flg.2_Missense_Mutation_p.V493A|MCCC1_uc011bqp.1_Missense_Mutation_p.V555A	NM_020166	NP_064551	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	602					biotin metabolic process|leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	AACTCCATTAACAGAACATTT	0.353													152	101	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511310	195511310	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511310G>C	uc011bto.1	-	2	7601	c.7141C>G	c.(7141-7143)CAC>GAC	p.H2381D	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGGTGGTGTGACCTGAGGAT	0.592													3	37	---	---	---	---	PASS
CENPC1	1060	broad.mit.edu	37	4	68380027	68380027	+	Silent	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68380027A>G	uc003hdd.1	-	8	1392	c.1209T>C	c.(1207-1209)TAT>TAC	p.Y403Y	CENPC1_uc010ihj.1_RNA|CENPC1_uc010ihk.1_RNA|CENPC1_uc010ihm.1_Silent_p.Y403Y	NM_001812	NP_001803	Q03188	CENPC_HUMAN	centromere protein C 1	403					mitotic prometaphase	condensed chromosome kinetochore|condensed nuclear chromosome, centromeric region|cytosol	DNA binding			urinary_tract(1)|lung(1)	2						CATTCTTGGAATACATTTCAT	0.338													7	632	---	---	---	---	PASS
YTHDC1	91746	broad.mit.edu	37	4	69203460	69203460	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69203460T>G	uc003hdx.2	-	3	642	c.289A>C	c.(289-291)AAT>CAT	p.N97H	YTHDC1_uc003hdy.2_Missense_Mutation_p.N97H	NM_001031732	NP_001026902	Q96MU7	YTDC1_HUMAN	splicing factor YT521-B isoform 1	97										upper_aerodigestive_tract(1)|ovary(1)	2						TATTCCTCATTTTTATACTCT	0.378													370	416	---	---	---	---	PASS
MEPE	56955	broad.mit.edu	37	4	88766289	88766289	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88766289T>C	uc003hqy.2	+	4	308	c.269T>C	c.(268-270)TTC>TCC	p.F90S	MEPE_uc010ikn.2_5'UTR	NM_020203	NP_064588	Q9NQ76	MEPE_HUMAN	matrix, extracellular phosphoglycoprotein with	90					skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			ovary(1)|lung(1)|skin(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		CAAAATTATTTCACAAATAGA	0.338													5	174	---	---	---	---	PASS
FSTL5	56884	broad.mit.edu	37	4	162307412	162307412	+	Silent	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162307412G>A	uc003iqh.2	-	16	2467	c.2031C>T	c.(2029-2031)GTC>GTT	p.V677V	FSTL5_uc003iqi.2_Silent_p.V676V|FSTL5_uc010iqv.2_Silent_p.V667V|uc010iqu.1_RNA	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	677						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)		CGTCCACCATGACCTGTGGGG	0.493													46	169	---	---	---	---	PASS
LPCAT1	79888	broad.mit.edu	37	5	1483565	1483565	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1483565A>G	uc003jcm.2	-	6	821	c.704T>C	c.(703-705)GTT>GCT	p.V235A		NM_024830	NP_079106	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	235	Lumenal (Potential).				phospholipid biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		ATATCGTAAAACCACAGGCTG	0.562													5	93	---	---	---	---	PASS
MAP3K1	4214	broad.mit.edu	37	5	56152549	56152549	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56152549T>A	uc003jqw.3	+	2	1106	c.605T>A	c.(604-606)TTG>TAG	p.L202*		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase	202					cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		CACGAATGGTTGGAAAGGAGA	0.458													68	326	---	---	---	---	PASS
ADAMTS19	171019	broad.mit.edu	37	5	129037259	129037259	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129037259G>A	uc003kvb.1	+	20	3115	c.3115G>A	c.(3115-3117)GTG>ATG	p.V1039M	ADAMTS19_uc010jdh.1_RNA	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1039	TSP type-1 4.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		CTGCATGACCGTGTGGGAGGC	0.567													6	81	---	---	---	---	PASS
TCERG1	10915	broad.mit.edu	37	5	145843272	145843272	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145843272C>T	uc003lob.2	+	5	1091	c.1051C>T	c.(1051-1053)CCA>TCA	p.P351S	TCERG1_uc003loc.2_Missense_Mutation_p.P351S|TCERG1_uc011dbt.1_Missense_Mutation_p.P351S	NM_006706	NP_006697	O14776	TCRG1_HUMAN	transcription elongation regulator 1 isoform 1	351	Pro-rich.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGTACCTCAGCCAACAACAGC	0.512													49	197	---	---	---	---	PASS
ABT1	29777	broad.mit.edu	37	6	26598223	26598223	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26598223G>T	uc003nii.2	+	2	354	c.323G>T	c.(322-324)GGA>GTA	p.G108V		NM_013375	NP_037507	Q9ULW3	ABT1_HUMAN	activator of basal transcription 1	108	RRM.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleolus	DNA binding|nucleotide binding|protein binding|RNA binding|transcription coactivator activity			ovary(1)	1						TACACCGAGGGATGGGTGGAG	0.602													10	36	---	---	---	---	PASS
HLA-E	3133	broad.mit.edu	37	6	30459116	30459116	+	Silent	SNP	T	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30459116T>A	uc003nqg.2	+	4	851	c.813T>A	c.(811-813)CCT>CCA	p.P271P	HLA-E_uc011dmg.1_RNA|HLA-E_uc011dmh.1_Silent_p.P312P	NM_005516	NP_005507	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	271	Ig-like C1-type.|Alpha-3.|Extracellular (Potential).				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			central_nervous_system(4)|ovary(1)	5						TGGTGGTGCCTTCTGGAGAGG	0.627													6	13	---	---	---	---	PASS
CRISP1	167	broad.mit.edu	37	6	49814325	49814325	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49814325C>A	uc003ozw.2	-	5	422	c.343G>T	c.(343-345)GTA>TTA	p.V115L	CRISP1_uc003ozx.2_Missense_Mutation_p.V115L	NM_001131	NP_001122	P54107	CRIS1_HUMAN	acidic epididymal glycoprotein-like 1 isoform 1	115					fusion of sperm to egg plasma membrane	extracellular space					0	Lung NSC(77;0.0358)					ACTCCAATTACACTTGACCAT	0.408													10	567	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70831811	70831811	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70831811G>A	uc003pfc.1	+	17	1435	c.1318G>A	c.(1318-1320)GGA>AGA	p.G440R	COL19A1_uc010kam.1_Missense_Mutation_p.G336R	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	440					cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						AACTCTTGGTGGATATTATAA	0.254													4	208	---	---	---	---	PASS
PM20D2	135293	broad.mit.edu	37	6	89871594	89871594	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89871594T>A	uc003pmz.2	+	6	1236	c.1141T>A	c.(1141-1143)TAC>AAC	p.Y381N		NM_001010853	NP_001010853	Q8IYS1	P20D2_HUMAN	aminoacylase 1-like 2	381							hydrolase activity				0		all_cancers(76;9.47e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00813)		TACTGAACAGTACACTGAAGC	0.398													266	314	---	---	---	---	PASS
EPHA7	2045	broad.mit.edu	37	6	93973599	93973599	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93973599C>T	uc003poe.2	-	9	2018	c.1777G>A	c.(1777-1779)GAT>AAT	p.D593N	EPHA7_uc003pof.2_Missense_Mutation_p.D588N|EPHA7_uc011eac.1_Missense_Mutation_p.D593N	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	593	Cytoplasmic (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		AGCTCTTCATCGCCTTCTTGG	0.323													7	234	---	---	---	---	PASS
RPF2	84154	broad.mit.edu	37	6	111346663	111346663	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111346663C>T	uc003pun.2	+	10	818	c.799C>T	c.(799-801)CAT>TAT	p.H267Y	RPF2_uc003puo.2_Missense_Mutation_p.H204Y|uc003pup.1_5'Flank	NM_032194	NP_115570	Q9H7B2	RPF2_HUMAN	brix domain containing 1	267						nucleolus	protein binding			ovary(2)	2						TGGAAGGATTCATATGCAGAA	0.363													140	166	---	---	---	---	PASS
REV3L	5980	broad.mit.edu	37	6	111650862	111650862	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111650862T>C	uc003puy.3	-	25	8437	c.8114A>G	c.(8113-8115)AAG>AGG	p.K2705R	REV3L_uc003pux.3_Missense_Mutation_p.K2627R|REV3L_uc003puz.3_Missense_Mutation_p.K2627R|REV3L_uc003pva.1_RNA	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	2705					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CTTGTAAGCCTTCATTGACTG	0.388								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					6	299	---	---	---	---	PASS
PDE10A	10846	broad.mit.edu	37	6	165844947	165844947	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165844947T>C	uc003qun.2	-	9	918	c.677A>G	c.(676-678)AAT>AGT	p.N226S	PDE10A_uc011egj.1_RNA|PDE10A_uc011egk.1_Missense_Mutation_p.N156S|PDE10A_uc003quo.2_Missense_Mutation_p.N236S	NM_006661	NP_006652	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 2	226	GAF 1.				platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	CCAGGCAAGATTTGCTGTTGC	0.333													57	180	---	---	---	---	PASS
SDK1	221935	broad.mit.edu	37	7	4152925	4152925	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4152925C>T	uc003smx.2	+	24	3578	c.3439C>T	c.(3439-3441)CGA>TGA	p.R1147*	SDK1_uc010kso.2_Nonsense_Mutation_p.R423*	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	1147	Fibronectin type-III 5.				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)		CTTTAGATTTCGAATGAAGCA	0.537													36	230	---	---	---	---	PASS
STK31	56164	broad.mit.edu	37	7	23827688	23827688	+	Silent	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23827688T>C	uc003sws.3	+	21	2644	c.2577T>C	c.(2575-2577)AAT>AAC	p.N859N	STK31_uc003swt.3_Silent_p.N836N|STK31_uc011jze.1_Silent_p.N859N|STK31_uc010kuq.2_Silent_p.N836N|STK31_uc003swv.1_Silent_p.N25N	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a	859	Protein kinase.						ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						ATCAGAACAATGTATTTGCTT	0.358													12	394	---	---	---	---	PASS
PKD1L1	168507	broad.mit.edu	37	7	47924244	47924244	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47924244A>G	uc003tny.1	-	19	3217	c.3217T>C	c.(3217-3219)TAT>CAT	p.Y1073H		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	1073	Extracellular (Potential).|REJ.				cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						TCACTGTAATAGGCTTCAAAA	0.448													5	482	---	---	---	---	PASS
SBDS	51119	broad.mit.edu	37	7	66453154	66453154	+	3'UTR	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66453154G>A	uc003tvm.1	-	5						NM_016038	NP_057122	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome protein						bone marrow development|bone mineralization|leukocyte chemotaxis|mature ribosome assembly|mitotic spindle stabilization|positive regulation of translation|ribosomal large subunit biogenesis|rRNA processing	cytoplasm|nucleolus|nucleoplasm|spindle pole	microtubule binding|ribosome binding|rRNA binding			ovary(1)	1						TTTGCTTTAGGATTTAGACCC	0.363			Gene Conversion			AML|MDS			Shwachman-Diamond_syndrome				7	13	---	---	---	---	PASS
SBDS	51119	broad.mit.edu	37	7	66453155	66453155	+	3'UTR	SNP	A	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66453155A>T	uc003tvm.1	-	5						NM_016038	NP_057122	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome protein						bone marrow development|bone mineralization|leukocyte chemotaxis|mature ribosome assembly|mitotic spindle stabilization|positive regulation of translation|ribosomal large subunit biogenesis|rRNA processing	cytoplasm|nucleolus|nucleoplasm|spindle pole	microtubule binding|ribosome binding|rRNA binding			ovary(1)	1						TTGCTTTAGGATTTAGACCCC	0.358			Gene Conversion			AML|MDS			Shwachman-Diamond_syndrome				7	13	---	---	---	---	PASS
SBDS	51119	broad.mit.edu	37	7	66453159	66453159	+	3'UTR	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66453159A>G	uc003tvm.1	-	5						NM_016038	NP_057122	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome protein						bone marrow development|bone mineralization|leukocyte chemotaxis|mature ribosome assembly|mitotic spindle stabilization|positive regulation of translation|ribosomal large subunit biogenesis|rRNA processing	cytoplasm|nucleolus|nucleoplasm|spindle pole	microtubule binding|ribosome binding|rRNA binding			ovary(1)	1						TTTAGGATTTAGACCCCAGTT	0.353			Gene Conversion			AML|MDS			Shwachman-Diamond_syndrome				8	14	---	---	---	---	PASS
ABCB4	5244	broad.mit.edu	37	7	87042995	87042995	+	Silent	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87042995C>T	uc003uiv.1	-	22	2797	c.2721G>A	c.(2719-2721)GTG>GTA	p.V907V	ABCB4_uc003uiw.1_Silent_p.V907V|ABCB4_uc003uix.1_Silent_p.V907V	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	907	Cytoplasmic (By similarity).|ABC transmembrane type-1 2.				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					GGGTCAAAGACACAACTGTCC	0.338													7	574	---	---	---	---	PASS
ADAM22	53616	broad.mit.edu	37	7	87763727	87763727	+	Silent	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87763727A>G	uc003ujn.2	+	13	1240	c.1161A>G	c.(1159-1161)TTA>TTG	p.L387L	ADAM22_uc003ujk.1_Silent_p.L387L|ADAM22_uc003ujl.1_Silent_p.L387L|ADAM22_uc003ujm.2_Silent_p.L387L|ADAM22_uc003ujo.2_Silent_p.L387L|ADAM22_uc003ujp.1_Silent_p.L439L	NM_021723	NP_068369	Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22 isoform 1	387	Peptidase M12B.|Extracellular (Potential).				cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			AAAGAAAGTTAGCAAGTGGTA	0.299													6	683	---	---	---	---	PASS
TECPR1	25851	broad.mit.edu	37	7	97851019	97851019	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97851019C>G	uc003upg.2	-	23	3316	c.3111G>C	c.(3109-3111)AAG>AAC	p.K1037N		NM_015395	NP_056210	Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	1037						integral to membrane	protein binding			pancreas(1)	1						CGGACACCTGCTTCAGCCTCT	0.498													19	27	---	---	---	---	PASS
CYP3A5	1577	broad.mit.edu	37	7	99270247	99270247	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99270247T>C	uc003urq.2	-	4	361	c.274A>G	c.(274-276)ACA>GCA	p.T92A	ZNF498_uc003urn.2_Intron|CYP3A5_uc003urr.2_5'UTR|CYP3A5_uc011kiy.1_Missense_Mutation_p.T82A|CYP3A5_uc003urs.2_Intron|CYP3A5_uc010lgg.2_Intron|CYP3A5_uc003urt.2_Missense_Mutation_p.T92A	NM_000777	NP_000768	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A,	92					alkaloid catabolic process|drug catabolic process|oxidative demethylation|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				Alfentanil(DB00802)|Clopidogrel(DB00758)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Indinavir(DB00224)|Irinotecan(DB00762)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Mephenytoin(DB00532)|Midazolam(DB00683)|Mifepristone(DB00834)|Phenytoin(DB00252)|Quinine(DB00468)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Troleandomycin(DB01361)|Verapamil(DB00661)|Vincristine(DB00541)	ACTAGCACTGTTCTGATCACG	0.403													8	308	---	---	---	---	PASS
GPR85	54329	broad.mit.edu	37	7	112724772	112724772	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112724772G>A	uc010ljv.2	-	2	522	c.5C>T	c.(4-6)GCG>GTG	p.A2V	GPR85_uc003vgp.1_Missense_Mutation_p.A2V|GPR85_uc003vgq.2_Missense_Mutation_p.A2V|GPR85_uc010ljw.1_Missense_Mutation_p.A2V	NM_001146266	NP_001139738	P60893	GPR85_HUMAN	G protein-coupled receptor 85	2	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|central_nervous_system(1)	2						GCTATAGTTCGCCATAGATGG	0.398													18	58	---	---	---	---	PASS
FOXP2	93986	broad.mit.edu	37	7	114330058	114330058	+	3'UTR	SNP	A	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114330058A>T	uc003vhb.2	+	17					FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_3'UTR|FOXP2_uc003vha.2_3'UTR|FOXP2_uc011kmu.1_3'UTR|FOXP2_uc011kmv.1_3'UTR|FOXP2_uc010ljz.1_3'UTR	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8						TGAATATTTGACAAATTTTTA	0.403													24	45	---	---	---	---	PASS
CCDC136	64753	broad.mit.edu	37	7	128457873	128457873	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128457873C>T	uc003vnv.1	+	17	3792	c.3425C>T	c.(3424-3426)TCG>TTG	p.S1142L	CCDC136_uc003vnu.1_Missense_Mutation_p.S422L|CCDC136_uc003vnw.1_Missense_Mutation_p.S503L|CCDC136_uc003vnx.1_Intron|CCDC136_uc010llq.1_Intron|CCDC136_uc003vny.1_Intron	NM_022742	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	1142	Helical; (Potential).					integral to membrane	protein binding			ovary(2)	2						GTGGTCATCTCGGCTTTGCTC	0.557													45	507	---	---	---	---	PASS
UBE2H	7328	broad.mit.edu	37	7	129479130	129479130	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129479130T>A	uc003vpf.1	-	6	738	c.344A>T	c.(343-345)TAT>TTT	p.Y115F	UBE2H_uc003vpg.1_Missense_Mutation_p.Y84F	NM_003344	NP_003335	P62256	UBE2H_HUMAN	ubiquitin-conjugating enzyme E2H isoform 1	115					protein K11-linked ubiquitination|protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|ubiquitin-protein ligase activity			skin(1)	1	Melanoma(18;0.0435)					GGGGTTAGGATAGGCCAATAA	0.423													204	295	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142424604	142424604	+	Intron	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142424604G>A	uc011krr.1	+						uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc011ksg.1_Intron|uc011ksj.1_RNA					SubName: Full=V_segment translation product; Flags: Fragment;																		CCCCAAATATGTCCACTGCTG	0.458													15	27	---	---	---	---	PASS
ZDHHC2	51201	broad.mit.edu	37	8	17074722	17074722	+	3'UTR	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17074722C>T	uc003wxe.2	+	12						NM_016353	NP_057437	Q9UIJ5	ZDHC2_HUMAN	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)		TGAGACTTAACTCTTCAAGCA	0.289													4	260	---	---	---	---	PASS
XKR9	389668	broad.mit.edu	37	8	71646279	71646279	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71646279A>G	uc003xyq.2	+	5	1276	c.742A>G	c.(742-744)AAA>GAA	p.K248E	XKR9_uc010lze.2_Missense_Mutation_p.K248E|XKR9_uc010lzd.2_Missense_Mutation_p.K116E	NM_001011720	NP_001011720	Q5GH70	XKR9_HUMAN	XK, Kell blood group complex subunit-related	248						integral to membrane				ovary(1)|skin(1)	2	Breast(64;0.0716)		Epithelial(68;0.00301)|all cancers(69;0.0165)|OV - Ovarian serous cystadenocarcinoma(28;0.0524)|BRCA - Breast invasive adenocarcinoma(89;0.166)			ATGGGCATTTAAAAACAACAC	0.289													7	745	---	---	---	---	PASS
DENND3	22898	broad.mit.edu	37	8	142186848	142186848	+	Silent	SNP	C	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142186848C>A	uc003yvy.2	+	15	2732	c.2454C>A	c.(2452-2454)GCC>GCA	p.A818A	DENND3_uc010mep.2_Silent_p.A779A	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	818										ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			AGAAGCTGGCCGATGACCACA	0.602													55	53	---	---	---	---	PASS
ZNF251	90987	broad.mit.edu	37	8	145947453	145947453	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145947453A>G	uc003zdv.3	-	5	1848	c.1592T>C	c.(1591-1593)CTC>CCC	p.L531P		NM_138367	NP_612376	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	531					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		ATCTGCTGTGAGGCTGGAGCC	0.512													4	62	---	---	---	---	PASS
RLN2	6019	broad.mit.edu	37	9	5300128	5300128	+	Silent	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5300128A>G	uc003zja.1	-	2	528	c.528T>C	c.(526-528)TGT>TGC	p.C176C	RLN2_uc003ziz.1_3'UTR	NM_134441	NP_604390	P04090	REL2_HUMAN	relaxin 2 isoform 1 preproprotein	176					female pregnancy	extracellular region	hormone activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.0987)		ATCTTTTGGTACAACCAACAT	0.358													5	310	---	---	---	---	PASS
TESK1	7016	broad.mit.edu	37	9	35608911	35608911	+	Silent	SNP	G	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35608911G>C	uc003zxa.2	+	10	1389	c.1053G>C	c.(1051-1053)CGG>CGC	p.R351R	TESK1_uc003zwz.1_Intron|TESK1_uc010mks.2_Silent_p.R191R	NM_006285	NP_006276	Q15569	TESK1_HUMAN	testis-specific protein kinase 1	351					cell junction assembly|spermatogenesis	cytosol	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|breast(2)|lung(1)|ovary(1)|skin(1)	7			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CAGATCCCCGGCTTTCCCGAA	0.582													18	23	---	---	---	---	PASS
SHC3	53358	broad.mit.edu	37	9	91680466	91680466	+	Silent	SNP	A	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91680466A>C	uc004aqg.2	-	6	1120	c.813T>G	c.(811-813)GCT>GCG	p.A271A		NM_016848	NP_058544	Q92529	SHC3_HUMAN	src homology 2 domain-containing transforming	271	PID.			A -> T (in Ref. 4; AAH26314).	central nervous system development|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	protein binding|signal transducer activity			lung(3)|skin(1)	4						CAGGGTCCTTAGCCACATATG	0.453													53	124	---	---	---	---	PASS
RGS3	5998	broad.mit.edu	37	9	116246492	116246492	+	Silent	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116246492T>C	uc004bhq.2	+	7	809	c.600T>C	c.(598-600)GCT>GCC	p.A200A	RGS3_uc004bhr.2_Silent_p.A88A|RGS3_uc004bhs.2_Silent_p.A90A	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6	200	C2.				inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3						GAGACCCGGCTTTCCACGAGC	0.478													18	54	---	---	---	---	PASS
TUBBP5	643224	broad.mit.edu	37	9	141071456	141071456	+	Missense_Mutation	SNP	C	T	T	rs145186342	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141071456C>T	uc004com.2	+	4	1120	c.859C>T	c.(859-861)CGG>TGG	p.R287W	TUBBP5_uc010ncq.2_3'UTR					RecName: Full=Putative tubulin beta-4q chain;												0						CATCCCACCCCGGGGGCTAAA	0.488													3	70	---	---	---	---	PASS
SUV39H2	79723	broad.mit.edu	37	10	14941580	14941580	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14941580G>A	uc001inh.2	+	3	768	c.712G>A	c.(712-714)GAC>AAC	p.D238N	SUV39H2_uc001ing.2_Missense_Mutation_p.D118N|SUV39H2_uc001ini.2_Missense_Mutation_p.D238N|SUV39H2_uc001inj.2_Missense_Mutation_p.D238N|DCLRE1C_uc010qbx.1_Intron	NM_024670	NP_078946	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2	298	SET.				cell cycle|cell differentiation|chromatin assembly or disassembly|chromatin remodeling|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|chromosome, centromeric region|nucleus	histone methyltransferase activity (H3-K9 specific)|protein binding|zinc ion binding			breast(2)|ovary(1)	3						ACAGTTCTATGACAACAAGGG	0.398													47	159	---	---	---	---	PASS
SUV39H2	79723	broad.mit.edu	37	10	14941582	14941582	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14941582C>A	uc001inh.2	+	3	770	c.714C>A	c.(712-714)GAC>GAA	p.D238E	SUV39H2_uc001ing.2_Missense_Mutation_p.D118E|SUV39H2_uc001ini.2_Missense_Mutation_p.D238E|SUV39H2_uc001inj.2_Missense_Mutation_p.D238E|DCLRE1C_uc010qbx.1_Intron	NM_024670	NP_078946	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2	298	SET.				cell cycle|cell differentiation|chromatin assembly or disassembly|chromatin remodeling|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|chromosome, centromeric region|nucleus	histone methyltransferase activity (H3-K9 specific)|protein binding|zinc ion binding			breast(2)|ovary(1)	3						AGTTCTATGACAACAAGGGAA	0.398													51	161	---	---	---	---	PASS
ARHGAP12	94134	broad.mit.edu	37	10	32115240	32115240	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32115240T>C	uc001ivz.1	-	11	1792	c.1522A>G	c.(1522-1524)ACA>GCA	p.T508A	ARHGAP12_uc001ivy.1_Missense_Mutation_p.T454A|ARHGAP12_uc009xls.2_Missense_Mutation_p.T459A|ARHGAP12_uc001iwb.1_Missense_Mutation_p.T501A|ARHGAP12_uc001iwc.1_Missense_Mutation_p.T476A|ARHGAP12_uc009xlq.1_Missense_Mutation_p.T429A|ARHGAP12_uc001iwd.1_Missense_Mutation_p.T476A|ARHGAP12_uc009xlr.1_Missense_Mutation_p.T506A	NM_018287	NP_060757	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	508	PH.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		Prostate(175;0.0199)				ACCCAACTTGTGCTACTTCCT	0.348													5	241	---	---	---	---	PASS
CXCL12	6387	broad.mit.edu	37	10	44868551	44868551	+	3'UTR	SNP	T	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44868551T>A	uc001jbf.2	-	4						NM_000609	NP_000600	P48061	SDF1_HUMAN	chemokine (C-X-C motif) ligand 12 (stromal						blood circulation|cell adhesion|cellular calcium ion homeostasis|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|negative regulation of leukocyte apoptosis|positive regulation of monocyte chemotaxis|regulation of actin polymerization or depolymerization|response to virus	extracellular space	chemokine activity|growth factor activity|signal transducer activity				0					Dexamethasone(DB01234)	TAGTCTAAGCTGCTACGTGTC	0.408													8	3	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55892657	55892657	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55892657C>T	uc001jju.1	-	15	2290	c.1895G>A	c.(1894-1896)GGT>GAT	p.G632D	PCDH15_uc010qhq.1_Missense_Mutation_p.G637D|PCDH15_uc010qhr.1_Missense_Mutation_p.G632D|PCDH15_uc010qhs.1_Missense_Mutation_p.G644D|PCDH15_uc010qht.1_Missense_Mutation_p.G639D|PCDH15_uc010qhu.1_Missense_Mutation_p.G632D|PCDH15_uc001jjv.1_Missense_Mutation_p.G610D|PCDH15_uc010qhv.1_Missense_Mutation_p.G632D|PCDH15_uc010qhw.1_Missense_Mutation_p.G595D|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Missense_Mutation_p.G637D|PCDH15_uc010qhz.1_Missense_Mutation_p.G632D|PCDH15_uc010qia.1_Missense_Mutation_p.G610D|PCDH15_uc010qib.1_Missense_Mutation_p.G610D|PCDH15_uc001jjw.2_Missense_Mutation_p.G632D	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	632	Cadherin 6.|Extracellular (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				TAAAACAGCACCAACCCTCAT	0.338										HNSCC(58;0.16)			5	347	---	---	---	---	PASS
MYPN	84665	broad.mit.edu	37	10	69948821	69948821	+	Silent	SNP	C	A	A	rs149887823		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69948821C>A	uc001jnm.3	+	14	3048	c.2863C>A	c.(2863-2865)CGG>AGG	p.R955R	MYPN_uc001jnn.3_Silent_p.R680R|MYPN_uc001jno.3_Silent_p.R955R|MYPN_uc009xpt.2_Silent_p.R955R|MYPN_uc010qit.1_Silent_p.R661R|MYPN_uc010qiu.1_RNA	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin	955	Ig-like 3.|Interaction with ACTN.					nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5						CAAGCACTTCCGGGTCACAGA	0.473													4	151	---	---	---	---	PASS
BTAF1	9044	broad.mit.edu	37	10	93711186	93711186	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93711186G>A	uc001khr.2	+	5	525	c.427G>A	c.(427-429)GCA>ACA	p.A143T	BTAF1_uc009xua.1_RNA	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription	143					negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)				AGAGAGGATAGCACGCCAACG	0.353													5	302	---	---	---	---	PASS
ZDHHC13	54503	broad.mit.edu	37	11	19187855	19187855	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19187855G>T	uc001mpi.2	+	14	1502	c.1397G>T	c.(1396-1398)GGC>GTC	p.G466V	ZDHHC13_uc001mpj.2_Missense_Mutation_p.G336V	NM_019028	NP_061901	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC domain containing 13 isoform	466	DHHC-type.				positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|palmitoyltransferase activity|signal transducer activity|zinc ion binding				0						TGAGGTTTTGGCAACCATCAC	0.308													291	501	---	---	---	---	PASS
CKAP5	9793	broad.mit.edu	37	11	46784304	46784304	+	Silent	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46784304T>C	uc001ndi.1	-	31	4010	c.3900A>G	c.(3898-3900)GAA>GAG	p.E1300E	CKAP5_uc009ylg.1_Silent_p.E1186E|CKAP5_uc001ndj.1_Silent_p.E1300E|CKAP5_uc001ndh.1_Silent_p.E229E|SNORD67_uc001ndk.2_5'Flank	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein	1300	HEAT 8.				cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2						CATCCTTTGGTTCTCCAACCT	0.408													6	311	---	---	---	---	PASS
OR5F1	338674	broad.mit.edu	37	11	55761854	55761854	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55761854G>C	uc010riv.1	-	1	248	c.248C>G	c.(247-249)GCA>GGA	p.A83G		NM_003697	NP_003688	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F,	83	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2	Esophageal squamous(21;0.00448)					TAATAAATCTGCCAGCATCTT	0.458													28	60	---	---	---	---	PASS
CADM1	23705	broad.mit.edu	37	11	115080343	115080343	+	Silent	SNP	G	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115080343G>T	uc001ppi.3	-	8	1158	c.1029C>A	c.(1027-1029)ACC>ACA	p.T343T	CADM1_uc001ppf.3_Intron|CADM1_uc001ppk.3_Intron|CADM1_uc001ppj.3_Intron|CADM1_uc001pph.3_Silent_p.T95T	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1	343	Extracellular (Potential).			PPTTIPPPTTTTTTTTTTTTTILTIIT -> TTATTEPAVH GLTQLPNSAEELDSEDLS (in Ref. 3; BAC11657).	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)		tggtggtggtggttgttgtgg	0.269													5	161	---	---	---	---	PASS
ARHGEF12	23365	broad.mit.edu	37	11	120331458	120331458	+	Silent	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120331458C>T	uc001pxl.1	+	27	2612	c.2605C>T	c.(2605-2607)CTG>TTG	p.L869L	ARHGEF12_uc009zat.2_Silent_p.L850L|ARHGEF12_uc010rzn.1_Silent_p.L766L|ARHGEF12_uc009zau.1_Silent_p.L766L	NM_015313	NP_056128	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	869	DH.				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)		GGAAGATTTGCTGACATGGGT	0.323			T	MLL	AML								5	697	---	---	---	---	PASS
STT3A	3703	broad.mit.edu	37	11	125482500	125482500	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125482500T>C	uc001qcd.2	+	12	1333	c.1223T>C	c.(1222-1224)CTA>CCA	p.L408P	STT3A_uc001qce.2_Missense_Mutation_p.L408P|STT3A_uc010sbg.1_Missense_Mutation_p.L316P|STT3A_uc009zbn.2_Missense_Mutation_p.L130P	NM_152713	NP_689926	P46977	STT3A_HUMAN	integral membrane protein 1	408	Helical; (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity				0	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		CGTCTAATGCTAGTGTTGGCA	0.338													5	415	---	---	---	---	PASS
CD163L1	283316	broad.mit.edu	37	12	7520737	7520737	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7520737T>G	uc001qsy.2	-	17	4155	c.4129A>C	c.(4129-4131)ATT>CTT	p.I1377L	CD163L1_uc010sge.1_Missense_Mutation_p.I1387L	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	1377	Helical; (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|skin(2)|central_nervous_system(1)	11						AGAAATAGAATAAACAGAACC	0.393													194	311	---	---	---	---	PASS
SLC2A3	6515	broad.mit.edu	37	12	8082243	8082243	+	Intron	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8082243C>T	uc001qtr.2	-						SLC2A3_uc001qts.2_3'UTR	NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		AAGTGAAATACTTTAAGACAC	0.254													9	140	---	---	---	---	PASS
SLC2A3	6515	broad.mit.edu	37	12	8082245	8082245	+	Intron	SNP	T	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8082245T>G	uc001qtr.2	-						SLC2A3_uc001qts.2_3'UTR	NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		GTGAAATACTTTAAGACACGT	0.254													9	143	---	---	---	---	PASS
TAS2R7	50837	broad.mit.edu	37	12	10954390	10954390	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10954390C>T	uc001qyv.2	-	1	837	c.780G>A	c.(778-780)ATG>ATA	p.M260I		NM_023919	NP_076408	Q9NYW3	TA2R7_HUMAN	taste receptor, type 2, member 7	260	Extracellular (Potential).				sensory perception of taste	integral to membrane	taste receptor activity			skin(1)	1						CCGTCTCTGGCATAAAGTAGC	0.423													5	439	---	---	---	---	PASS
LRRK2	120892	broad.mit.edu	37	12	40745464	40745464	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40745464C>G	uc001rmg.3	+	44	6626	c.6505C>G	c.(6505-6507)CTG>GTG	p.L2169V	LRRK2_uc009zjw.2_Missense_Mutation_p.L1007V|LRRK2_uc001rmi.2_Missense_Mutation_p.L1002V	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2169					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)				AAGCATTTGGCTGGGCTGTGG	0.408													86	146	---	---	---	---	PASS
LRRK2	120892	broad.mit.edu	37	12	40745465	40745465	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40745465T>A	uc001rmg.3	+	44	6627	c.6506T>A	c.(6505-6507)CTG>CAG	p.L2169Q	LRRK2_uc009zjw.2_Missense_Mutation_p.L1007Q|LRRK2_uc001rmi.2_Missense_Mutation_p.L1002Q	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2169					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)				AGCATTTGGCTGGGCTGTGGG	0.408													87	144	---	---	---	---	PASS
RACGAP1P	83956	broad.mit.edu	37	12	45457990	45457990	+	RNA	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45457990T>C	uc001rol.2	-	1		c.1205A>G				NR_026583				Homo sapiens FKSG42 (FKSG42) mRNA, complete cds.												0						CCCAAGATCCTATACAGGCCT	0.463													5	309	---	---	---	---	PASS
FMNL3	91010	broad.mit.edu	37	12	50045173	50045173	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50045173C>T	uc001ruv.1	-	15	1898	c.1664G>A	c.(1663-1665)GGC>GAC	p.G555D	FMNL3_uc001ruw.1_Missense_Mutation_p.G504D|FMNL3_uc001rut.1_Missense_Mutation_p.G121D|FMNL3_uc001ruu.1_Missense_Mutation_p.G405D	NM_175736	NP_783863	Q8IVF7	FMNL3_HUMAN	formin-like 3 isoform 1	555					actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4						ACCTGACAGGCCCACTGTCAA	0.607													16	31	---	---	---	---	PASS
HNRNPA1	3178	broad.mit.edu	37	12	54675316	54675316	+	Intron	SNP	A	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54675316A>C	uc001sfl.2	+						CBX5_uc001sfk.3_5'Flank|CBX5_uc001sfi.3_5'Flank|HNRNPA1_uc001sfm.2_Intron|HNRNPA1_uc009zng.2_Intron|HNRNPA1_uc009znh.2_Intron|HNRNPA1_uc009zni.2_Intron|HNRNPA1_uc001sfn.2_Intron|HNRNPA1_uc001sfo.3_Intron|HNRNPA1_uc001sfp.1_5'UTR|HNRNPA1_uc009znj.1_5'Flank	NM_031157	NP_112420	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1						interspecies interaction between organisms|mRNA transport|nuclear import	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	nucleotide binding|protein binding|single-stranded DNA binding			skin(2)|ovary(1)	3						AAGCAGTAAAACAGCCGATTT	0.443													11	23	---	---	---	---	PASS
TIMELESS	8914	broad.mit.edu	37	12	56817448	56817448	+	Silent	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56817448C>T	uc001slf.2	-	17	2178	c.2010G>A	c.(2008-2010)GAG>GAA	p.E670E		NM_003920	NP_003911	Q9UNS1	TIM_HUMAN	timeless homolog	670	Glu-rich.				cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin				ovary(5)|breast(2)|pancreas(1)	8						cctcctcctcctcttcttctt	0.418													4	220	---	---	---	---	PASS
LRP1	4035	broad.mit.edu	37	12	57588207	57588207	+	Silent	SNP	C	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57588207C>A	uc001snd.2	+	49	8455	c.7989C>A	c.(7987-7989)ACC>ACA	p.T2663T	MIR1228_hsa-mir-1228|MI0006318_5'Flank	NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	2663	LDL-receptor class A 14.|Extracellular (Potential).				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GCGAGCGGACCTCACTCTGCT	0.662													8	13	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78591134	78591134	+	Silent	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78591134T>C	uc001syp.2	+	35	6572	c.6399T>C	c.(6397-6399)TCT>TCC	p.S2133S	NAV3_uc001syo.2_Silent_p.S2111S|NAV3_uc010sub.1_Silent_p.S1590S|NAV3_uc009zsf.2_Silent_p.S942S	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	2133						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						ATGTGGGCTCTCTGAGTGATA	0.323										HNSCC(70;0.22)			8	702	---	---	---	---	PASS
SNRPF	6636	broad.mit.edu	37	12	96259108	96259108	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96259108A>G	uc001tej.2	+	3	279	c.136A>G	c.(136-138)AAT>GAT	p.N46D		NM_003095	NP_003086	P62306	RUXF_HUMAN	small nuclear ribonucleoprotein polypeptide F	46					histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	protein binding|RNA binding				0						AAAGCTTGCAAATACAGAAGA	0.338													7	577	---	---	---	---	PASS
MTMR6	9107	broad.mit.edu	37	13	25841976	25841976	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25841976A>G	uc001uqf.3	-	3	564	c.245T>C	c.(244-246)GTT>GCT	p.V82A	MTMR6_uc001uqe.1_Missense_Mutation_p.V82A	NM_004685	NP_004676	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	82						cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)|skin(2)	4		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		TTCTCTGGGAACAATGAAATG	0.398													6	394	---	---	---	---	PASS
NUPL1	9818	broad.mit.edu	37	13	25914225	25914225	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25914225C>T	uc001uqi.2	+	16	1999	c.1753C>T	c.(1753-1755)CTT>TTT	p.L585F	NUPL1_uc001uqj.2_Missense_Mutation_p.L573F	NM_014089	NP_054808	Q9BVL2	NUPL1_HUMAN	nucleoporin like 1 isoform a	585					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore					0		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.0092)|Epithelial(112;0.0477)|OV - Ovarian serous cystadenocarcinoma(117;0.165)|GBM - Glioblastoma multiforme(144;0.244)		AGGACAACTCCTTCAGTTGAA	0.458													4	281	---	---	---	---	PASS
FRY	10129	broad.mit.edu	37	13	32768382	32768382	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32768382T>C	uc001utx.2	+	29	4190	c.3694T>C	c.(3694-3696)TAC>CAC	p.Y1232H	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	1232					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CACAGGTTCCTACCAACTTGC	0.423													5	368	---	---	---	---	PASS
LRCH1	23143	broad.mit.edu	37	13	47279205	47279205	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47279205T>C	uc001vbj.2	+	12	1639	c.1403T>C	c.(1402-1404)TTA>TCA	p.L468S	LRCH1_uc010acp.2_Missense_Mutation_p.L468S|LRCH1_uc001vbk.2_Missense_Mutation_p.L468S|LRCH1_uc001vbl.3_Missense_Mutation_p.L468S	NM_015116	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH)	468										ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		CTCTTTAGATTAAGCACAGAT	0.274													142	236	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106641994	106641994	+	RNA	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106641994C>T	uc010tyt.1	-	1021		c.24007G>A								Parts of antibodies, mostly variable regions.												0						CAGGTCCAGTCCATGGTGAGG	0.527													36	111	---	---	---	---	PASS
SNRPN	6638	broad.mit.edu	37	15	25222145	25222145	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25222145C>G	uc001ywp.1	+	10	1279	c.389C>G	c.(388-390)CCT>CGT	p.P130R	SNRPN_uc001ywq.1_Missense_Mutation_p.P130R|SNRPN_uc001ywr.1_Missense_Mutation_p.P130R|SNRPN_uc001yws.1_Missense_Mutation_p.P130R|SNRPN_uc001ywt.1_Missense_Mutation_p.P130R|SNRPN_uc001ywv.1_Missense_Mutation_p.P133R|SNRPN_uc001yww.1_Missense_Mutation_p.P130R|SNRPN_uc001ywx.1_Missense_Mutation_p.P130R|SNRPN_uc001ywz.1_Intron|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_3'UTR	NM_022807	NP_073718	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	130					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)		TTGGCAGGCCCTGTCCGAGGA	0.582									Prader-Willi_syndrome				23	66	---	---	---	---	PASS
HERC2	8924	broad.mit.edu	37	15	28499508	28499508	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28499508G>C	uc001zbj.2	-	20	3134	c.3028C>G	c.(3028-3030)CAG>GAG	p.Q1010E	HERC2_uc001zbl.1_Missense_Mutation_p.Q705E	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	1010					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TGTATGAGCTGAACCAGAGGC	0.313													65	186	---	---	---	---	PASS
PLA2G4F	255189	broad.mit.edu	37	15	42446638	42446638	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42446638T>C	uc001zoz.2	-	3	266	c.203A>G	c.(202-204)TAT>TGT	p.Y68C	PLA2G4F_uc010bcr.2_5'UTR|PLA2G4F_uc001zpa.2_5'UTR|PLA2G4F_uc010bcs.2_5'UTR	NM_213600	NP_998765	Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	68	C2.				phospholipid catabolic process	cytosol|lysosomal membrane	metal ion binding|phospholipase A2 activity			ovary(4)	4		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		CAGTTGCACATAGCAGTCGGC	0.607													4	72	---	---	---	---	PASS
TCF12	6938	broad.mit.edu	37	15	57565458	57565458	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57565458G>T	uc002aec.2	+	18	2188	c.1904G>T	c.(1903-1905)AGA>ATA	p.R635I	TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Missense_Mutation_p.R655I|TCF12_uc002aea.2_Missense_Mutation_p.R659I|TCF12_uc010bfs.2_Missense_Mutation_p.R56I|TCF12_uc002aeb.2_Missense_Mutation_p.R659I|TCF12_uc002aed.2_Missense_Mutation_p.R635I|TCF12_uc002aee.2_Missense_Mutation_p.R465I|TCF12_uc010bft.2_Missense_Mutation_p.R489I|TCF12_uc010ugo.1_Missense_Mutation_p.R399I|TCF12_uc010ugp.1_Missense_Mutation_p.R292I|TCF12_uc010ugq.1_Missense_Mutation_p.R269I	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b	635	Class A specific domain.				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)		CAGCAAGTCAGAGGTAAGTAG	0.423			T	TEC	extraskeletal myxoid chondrosarcoma								74	89	---	---	---	---	PASS
WDR93	56964	broad.mit.edu	37	15	90248827	90248827	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90248827T>C	uc002boj.2	+	4	640	c.539T>C	c.(538-540)CTA>CCA	p.L180P	WDR93_uc010bnr.2_Missense_Mutation_p.L180P	NM_020212	NP_064597	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	180					electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			GGACTTTACCTAGTCAAAGCC	0.338													6	532	---	---	---	---	PASS
ALDH1A3	220	broad.mit.edu	37	15	101434385	101434385	+	Intron	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101434385G>A	uc002bwn.3	+						ALDH1A3_uc010bpb.2_Intron|uc002bwo.1_RNA	NM_000693	NP_000684	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1A3						retinal metabolic process	cytoplasm	aldehyde dehydrogenase|protein homodimerization activity			central_nervous_system(2)|lung(1)|pancreas(1)	4	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		NADH(DB00157)|Vitamin A(DB00162)	GCAGACTGCTGGCAATCGAGT	0.507													10	10	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15100288	15100288	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15100288A>G	uc002dda.3	+	6	651	c.427A>G	c.(427-429)AGA>GGA	p.R143G	PDXDC1_uc010uzl.1_Missense_Mutation_p.R128G|PDXDC1_uc010uzm.1_Missense_Mutation_p.R52G|PDXDC1_uc010bvc.1_Missense_Mutation_p.R84G|PDXDC1_uc002dcz.2_Missense_Mutation_p.R143G|PDXDC1_uc002ddb.3_Missense_Mutation_p.R116G|PDXDC1_uc010uzn.1_Missense_Mutation_p.R115G|PDXDC1_uc002ddc.2_Missense_Mutation_p.R143G	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain	143					carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	CGAAGAGGAAAGAGAAGGACT	0.353													7	631	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	29127493	29127493	+	Intron	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29127493A>G	uc010vct.1	-						RRN3P2_uc002dsf.3_RNA|RRN3P2_uc002dsg.3_RNA|RRN3P2_uc010vdn.1_RNA					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		GCGGTTGGATAGCATTGAAGC	0.478													4	216	---	---	---	---	PASS
ORC6L	23594	broad.mit.edu	37	16	46729488	46729488	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46729488A>C	uc002eeh.2	+	5	524	c.464A>C	c.(463-465)AAA>ACA	p.K155T	ORC6L_uc010cbe.1_Missense_Mutation_p.K106T	NM_014321	NP_055136	Q9Y5N6	ORC6_HUMAN	origin recognition complex subunit 6	155					cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA binding|protein binding				0		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				CTAAAGCTGAAAGTGGATAAA	0.358													5	185	---	---	---	---	PASS
NFATC3	4775	broad.mit.edu	37	16	68224816	68224816	+	Silent	SNP	T	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68224816T>A	uc002evo.1	+	9	2454	c.2244T>A	c.(2242-2244)ATT>ATA	p.I748I	NFATC3_uc010vkl.1_Silent_p.I269I|NFATC3_uc010vkm.1_Silent_p.I269I|NFATC3_uc010vkn.1_Silent_p.I269I|NFATC3_uc010vko.1_Silent_p.I269I|NFATC3_uc010vkp.1_Silent_p.I269I|NFATC3_uc010vkq.1_Silent_p.I269I|NFATC3_uc002evl.2_Silent_p.I269I|NFATC3_uc002evk.2_Silent_p.I748I|NFATC3_uc002evm.1_Silent_p.I748I|NFATC3_uc002evn.1_Silent_p.I748I|NFATC3_uc010vkr.1_Silent_p.I269I|NFATC3_uc010vks.1_Silent_p.I269I|NFATC3_uc010vkt.1_Silent_p.I269I|NFATC3_uc010vku.1_Silent_p.I269I|NFATC3_uc010vkv.1_Silent_p.I269I|NFATC3_uc010vkw.1_Silent_p.I269I|NFATC3_uc010vkx.1_Silent_p.I269I|NFATC3_uc010vky.1_Silent_p.I269I|NFATC3_uc010vkz.1_Silent_p.I269I|NFATC3_uc010vla.1_Silent_p.I269I|NFATC3_uc010vlb.1_Silent_p.I269I|NFATC3_uc010vlc.1_Silent_p.I269I	NM_173165	NP_775188	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells,	748					inflammatory response|transcription from RNA polymerase II promoter	nucleolus|plasma membrane	DNA binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		GAAGTTTGATTTGCTCCATCC	0.473													63	87	---	---	---	---	PASS
GLG1	2734	broad.mit.edu	37	16	74530389	74530389	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74530389G>A	uc002fcy.3	-	5	978	c.928C>T	c.(928-930)CGG>TGG	p.R310W	GLG1_uc002fcx.2_Missense_Mutation_p.R310W|GLG1_uc002fcw.3_Missense_Mutation_p.R299W|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3	310	Cys-rich GLG1 4.|Extracellular (Potential).					Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						TATAAATGCCGGTCTAAGTGA	0.413													4	186	---	---	---	---	PASS
DHRS7C	201140	broad.mit.edu	37	17	9674867	9674867	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9674867A>G	uc010vvb.1	-	6	877	c.877T>C	c.(877-879)TTC>CTC	p.F293L	DHRS7C_uc010cof.2_Missense_Mutation_p.F292L	NM_001105571	NP_001099041	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	293						extracellular region	binding|oxidoreductase activity				0						GCGAAAAAGAACTCCGGGAAG	0.597													14	56	---	---	---	---	PASS
ZNF18	7566	broad.mit.edu	37	17	11887438	11887438	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11887438A>G	uc002gng.1	-	7	1348	c.743T>C	c.(742-744)GTC>GCC	p.V248A	ZNF18_uc002gnh.1_Missense_Mutation_p.V248A|ZNF18_uc002gni.1_Missense_Mutation_p.V248A	NM_144680	NP_653281	P17022	ZNF18_HUMAN	zinc finger protein 18	248	KRAB.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(1)	1				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)		ACCTCCTGAGACCATTTTCCC	0.443													7	612	---	---	---	---	PASS
SLFN12L	342615	broad.mit.edu	37	17	33802320	33802320	+	Silent	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33802320A>G	uc002hjn.2	-	5	2355	c.1476T>C	c.(1474-1476)GCT>GCC	p.A492A		NM_001145027	NP_001138499			schlafen family member 12-like											ovary(1)	1						AAATCAGAAGAGCATCACAGA	0.458													72	254	---	---	---	---	PASS
C17orf66	256957	broad.mit.edu	37	17	34182344	34182344	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34182344A>T	uc002hke.1	-	15	1585	c.1436T>A	c.(1435-1437)CTC>CAC	p.L479H	C17orf66_uc010wck.1_RNA|C17orf66_uc010wcl.1_Missense_Mutation_p.L439H	NM_152781	NP_689994	A2RTY3	CQ066_HUMAN	hypothetical protein LOC256957	479							binding			breast(2)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		ATATACAGAGAGAACCTTGTT	0.438													112	134	---	---	---	---	PASS
CCDC45	90799	broad.mit.edu	37	17	62506316	62506316	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62506316A>C	uc002jem.2	+	3	232	c.174A>C	c.(172-174)CAA>CAC	p.Q58H	CCDC45_uc002jen.2_RNA|CCDC45_uc010wqb.1_5'UTR	NM_138363	NP_612372	Q96GE4	CEP95_HUMAN	coiled-coil domain containing 45	58						centrosome|spindle pole	protein binding				0	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			CTAGGAGTCAAGAAGATGATG	0.413													90	415	---	---	---	---	PASS
UNC13D	201294	broad.mit.edu	37	17	73832900	73832900	+	Silent	SNP	A	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73832900A>T	uc002jpp.2	-	13	1535	c.1155T>A	c.(1153-1155)GGT>GGA	p.G385G	UNC13D_uc010wsk.1_Silent_p.G385G|UNC13D_uc002jpq.1_Silent_p.G35G|UNC13D_uc010dgq.1_Silent_p.G182G	NM_199242	NP_954712	Q70J99	UN13D_HUMAN	unc-13 homolog D	385	Interaction with RAB27A.				positive regulation of exocytosis|regulation of mast cell degranulation	exocytic vesicle|late endosome|lysosome|membrane|recycling endosome	protein binding			upper_aerodigestive_tract(1)|skin(1)	2			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCTTGAGCCGACCCTGGATCC	0.652									Familial_Hemophagocytic_Lymphohistiocytosis				74	74	---	---	---	---	PASS
SRP68	6730	broad.mit.edu	37	17	74060074	74060074	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74060074T>C	uc002jqk.1	-	4	579	c.544A>G	c.(544-546)ACC>GCC	p.T182A	SRP68_uc010wsu.1_Missense_Mutation_p.T81A|SRP68_uc002jql.1_Missense_Mutation_p.T144A	NM_014230	NP_055045	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	182					response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding			ovary(1)	1						TCTAATTTGGTCTTGGCATCC	0.433													6	335	---	---	---	---	PASS
SEC14L1	6397	broad.mit.edu	37	17	75212337	75212337	+	3'UTR	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75212337T>C	uc002jto.2	+	17					SEC14L1_uc010dhc.2_Intron|SEC14L1_uc010wth.1_3'UTR|SEC14L1_uc002jtm.2_3'UTR|SEC14L1_uc010wti.1_3'UTR	NM_003003	NP_002994	Q92503	S14L1_HUMAN	SEC14 (S. cerevisiae)-like 1 isoform a						transport	Golgi apparatus|integral to membrane	binding			ovary(2)	2						gtagggttcgtaggtagggtt	0.000													3	2	---	---	---	---	PASS
KIAA1012	22878	broad.mit.edu	37	18	29412138	29412138	+	Splice_Site	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29412138T>C	uc002kxc.3	-	28	4348	c.3984_splice	c.e28-1	p.S1328_splice	KIAA1012_uc002kxb.3_Splice_Site_p.S1274_splice|KIAA1012_uc002kxd.3_Splice_Site	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0						AAACAAAGGCTATGGAAGAAA	0.303													5	321	---	---	---	---	PASS
MYO5B	4645	broad.mit.edu	37	18	47500800	47500800	+	Silent	SNP	G	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47500800G>T	uc002leb.2	-	10	1530	c.1242C>A	c.(1240-1242)GGC>GGA	p.G414G	MYO5B_uc002lec.1_Silent_p.G413G	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	414	Myosin head-like.				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)		CCACAATCCAGCCGAACAACT	0.592													58	172	---	---	---	---	PASS
GTF2F1	2962	broad.mit.edu	37	19	6381619	6381619	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6381619G>C	uc002meq.2	-	8	1129	c.844C>G	c.(844-846)CAA>GAA	p.Q282E	GTF2F1_uc010xjb.1_Missense_Mutation_p.Q103E|GTF2F1_uc010xjc.1_Missense_Mutation_p.Q197E	NM_002096	NP_002087	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1,	282					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|response to virus|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cell junction|transcription factor TFIIF complex	catalytic activity|DNA binding|phosphatase activator activity|transcription coactivator activity|transcription factor binding				0						GGCTCTTCTTGGGAGCTACTG	0.697													21	33	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9087338	9087338	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9087338A>G	uc002mkp.2	-	1	4681	c.4477T>C	c.(4477-4479)TCC>CCC	p.S1493P		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	1493	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GAAGGTGTGGACATAGGTGGA	0.418													130	177	---	---	---	---	PASS
OR7D2	162998	broad.mit.edu	37	19	9297402	9297402	+	3'UTR	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9297402C>T	uc002mkz.1	+	1						NM_175883	NP_787079	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D,						regulation of transcription, DNA-dependent|sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|upper_aerodigestive_tract(1)	3						TGTGATGGATCCCTTGGCCCC	0.423													15	31	---	---	---	---	PASS
DNMT1	1786	broad.mit.edu	37	19	10250366	10250366	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10250366A>G	uc002mng.2	-	33	4066	c.3886T>C	c.(3886-3888)TTC>CTC	p.F1296L	DNMT1_uc002mne.2_RNA|DNMT1_uc002mnf.2_Missense_Mutation_p.F220L|DNMT1_uc010xlc.1_Missense_Mutation_p.F1312L|DNMT1_uc002mnh.2_Missense_Mutation_p.F1191L|DNMT1_uc010xld.1_Missense_Mutation_p.F1296L	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b	1296	Catalytic.|Interaction with the PRC2/EED-EZH2 complex (By similarity).				chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)	AGCACGCCGAAGGTGCACTGA	0.637													27	36	---	---	---	---	PASS
NFIX	4784	broad.mit.edu	37	19	13136046	13136046	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13136046G>T	uc010xmx.1	+	2	316	c.263G>T	c.(262-264)CGC>CTC	p.R88L	NFIX_uc002mwd.2_Missense_Mutation_p.R80L|NFIX_uc002mwe.2_Missense_Mutation_p.R72L|NFIX_uc002mwf.2_Missense_Mutation_p.R83L|NFIX_uc002mwg.1_Missense_Mutation_p.R79L			Q14938	NFIX_HUMAN	RecName: Full=Nuclear factor 1;	80	CTF/NF-I.				DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			GCCAAGCTGCGCAAGGACATC	0.657													13	22	---	---	---	---	PASS
GPI	2821	broad.mit.edu	37	19	34857121	34857121	+	Intron	SNP	T	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34857121T>A	uc002nvg.1	+						GPI_uc002nvf.2_Intron|GPI_uc010xrv.1_Intron|GPI_uc010xrw.1_Intron|GPI_uc010edl.1_Intron|GPI_uc002nvh.1_Silent_p.A302A	NM_000175	NP_000166	P06744	G6PI_HUMAN	glucose phosphate isomerase						angiogenesis|gluconeogenesis|glycolysis|hemostasis|humoral immune response	cytosol|extracellular space|nucleus|plasma membrane	cytokine activity|glucose-6-phosphate isomerase activity|growth factor activity			ovary(1)|kidney(1)	2	Esophageal squamous(110;0.162)					ACCACTGTGCTGGGTGGCCGC	0.617													24	22	---	---	---	---	PASS
CYP2A7	1549	broad.mit.edu	37	19	41533087	41533087	+	Intron	SNP	T	C	C	rs10426686	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41533087T>C	uc002opo.2	-						uc002ops.1_RNA	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CAGAGCCTCCTTGACGGCATC	0.647													6	88	---	---	---	---	PASS
LYPD5	284348	broad.mit.edu	37	19	44301842	44301842	+	Silent	SNP	G	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44301842G>T	uc002oxm.3	-	5	738	c.657C>A	c.(655-657)ACC>ACA	p.T219T	LYPD5_uc002oxn.3_Silent_p.T176T	NM_001031749	NP_001026919	Q6UWN5	LYPD5_HUMAN	LY6/PLAUR domain containing 5 isoform A	219						anchored to membrane|plasma membrane					0		Prostate(69;0.0352)				TGAAGGGCTGGGTCATGGATT	0.652													95	135	---	---	---	---	PASS
CEACAM20	125931	broad.mit.edu	37	19	45026873	45026873	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45026873C>T	uc010ejn.1	-	4	557	c.541G>A	c.(541-543)GAG>AAG	p.E181K	CEACAM20_uc010ejo.1_Missense_Mutation_p.E181K|CEACAM20_uc010ejp.1_Missense_Mutation_p.E181K|CEACAM20_uc010ejq.1_Missense_Mutation_p.E181K	NM_001102597	NP_001096067	Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion	181	Ig-like C2-type 2.|Extracellular (Potential).					integral to membrane				large_intestine(2)	2		Prostate(69;0.0352)				CTGGAGCCCTCCATCACCTCA	0.498													157	210	---	---	---	---	PASS
GRLF1	2909	broad.mit.edu	37	19	47491245	47491245	+	Splice_Site	SNP	G	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47491245G>C	uc010ekv.2	+	3	3827	c.3827_splice	c.e3-1	p.G1276_splice		NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1						axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)		TTTCTCCTCAGGACTGAGCAC	0.557													65	125	---	---	---	---	PASS
ZNF616	90317	broad.mit.edu	37	19	52619876	52619876	+	Silent	SNP	T	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52619876T>G	uc002pym.2	-	4	824	c.541A>C	c.(541-543)AGG>CGG	p.R181R	ZNF616_uc002pyn.2_RNA	NM_178523	NP_848618	Q08AN1	ZN616_HUMAN	zinc finger protein 616	181					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		GTTTTTTCCCTAATGTGTGGA	0.373													183	277	---	---	---	---	PASS
NLRP4	147945	broad.mit.edu	37	19	56388432	56388432	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56388432C>A	uc002qmd.3	+	8	3018	c.2596C>A	c.(2596-2598)CTG>ATG	p.L866M	NLRP4_uc002qmf.2_Missense_Mutation_p.L791M|NLRP4_uc010etf.2_Missense_Mutation_p.L641M	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	866	LRR 6.						ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		CAATCAAAACCTGAAGATTCT	0.473													7	546	---	---	---	---	PASS
CPXM1	56265	broad.mit.edu	37	20	2777900	2777900	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2777900T>G	uc002wgu.2	-	6	834	c.770A>C	c.(769-771)CAG>CCG	p.Q257P	CPXM1_uc010gas.2_Missense_Mutation_p.Q257P	NM_019609	NP_062555	Q96SM3	CPXM1_HUMAN	carboxypeptidase X, member 1 precursor	257	F5/8 type C.				cell adhesion|proteolysis		metallocarboxypeptidase activity|zinc ion binding			ovary(2)|skin(2)	4						GAGCCAGGTCTGGGGCAGCAG	0.662													33	68	---	---	---	---	PASS
ESF1	51575	broad.mit.edu	37	20	13756714	13756714	+	Silent	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13756714T>C	uc002woj.2	-	3	948	c.840A>G	c.(838-840)GAA>GAG	p.E280E	ESF1_uc002wok.1_Silent_p.E280E	NM_016649	NP_057733	Q9H501	ESF1_HUMAN	ABT1-associated protein	280	Asp-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1						cctcttcatcttcatcctcct	0.234													7	730	---	---	---	---	PASS
ZNF334	55713	broad.mit.edu	37	20	45130663	45130663	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45130663C>T	uc002xsc.2	-	5	1499	c.1315G>A	c.(1315-1317)GGA>AGA	p.G439R	ZNF334_uc002xsa.2_Missense_Mutation_p.G462R|ZNF334_uc002xsb.2_Missense_Mutation_p.G401R|ZNF334_uc002xsd.2_Missense_Mutation_p.G401R|ZNF334_uc010ghl.2_Missense_Mutation_p.G438R	NM_018102	NP_060572	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334 isoform a	439	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)				AAAAATTTTCCACATTGACTG	0.378													5	195	---	---	---	---	PASS
BRWD1	54014	broad.mit.edu	37	21	40568620	40568620	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40568620T>G	uc002yxk.1	-	41	6514	c.6375A>C	c.(6373-6375)GAA>GAC	p.E2125D	BRWD1_uc010goc.1_Missense_Mutation_p.E768D|BRWD1_uc002yxl.2_Missense_Mutation_p.E2125D	NM_018963	NP_061836	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2125					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TCCTTTTTACTTCCTTCTCTG	0.413													109	332	---	---	---	---	PASS
MYO18B	84700	broad.mit.edu	37	22	26272193	26272193	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26272193T>G	uc003abz.1	+	24	4368	c.4118T>G	c.(4117-4119)GTG>GGG	p.V1373G	MYO18B_uc003aca.1_Missense_Mutation_p.V1254G|MYO18B_uc010guy.1_Missense_Mutation_p.V1255G|MYO18B_uc010guz.1_Missense_Mutation_p.V1254G|MYO18B_uc011aka.1_Missense_Mutation_p.V527G|MYO18B_uc011akb.1_Missense_Mutation_p.V886G	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1373						nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						CAGAAGAATGTGGCTGTGTTC	0.567													31	38	---	---	---	---	PASS
PES1	23481	broad.mit.edu	37	22	30973095	30973095	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30973095G>A	uc003aij.1	-	15	1779	c.1705C>T	c.(1705-1707)CGG>TGG	p.R569W	PES1_uc003aik.1_Missense_Mutation_p.R564W|PES1_uc003ail.1_Missense_Mutation_p.R552W|PES1_uc003aim.1_Missense_Mutation_p.R568W|PES1_uc003ain.1_Missense_Mutation_p.R430W|PES1_uc003aio.1_Missense_Mutation_p.R430W	NM_014303	NP_055118	O00541	PESC_HUMAN	pescadillo homolog 1, containing BRCT domain	569	Required for 28S ribosomal RNA processing.				cell proliferation|maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|regulation of cell cycle	chromosome|nucleoplasm|PeBoW complex|preribosome, large subunit precursor	protein binding				0						TGGGCTTTCCGCTTCTCCGCC	0.617													15	33	---	---	---	---	PASS
RFPL2	10739	broad.mit.edu	37	22	32587136	32587136	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32587136C>G	uc003amg.3	-	5	1696	c.760G>C	c.(760-762)GAC>CAC	p.D254H	RFPL2_uc003ame.3_Missense_Mutation_p.D193H|RFPL2_uc003amf.3_Missense_Mutation_p.D164H|RFPL2_uc003amh.3_Missense_Mutation_p.D164H	NM_001098527	NP_001091997	O75678	RFPL2_HUMAN	ret finger protein-like 2 isoform 2	254	B30.2/SPRY.						zinc ion binding			skin(1)	1						ACTCCCAGGTCCCATTCTGTG	0.582													74	140	---	---	---	---	PASS
CYP2D6	1565	broad.mit.edu	37	22	42522550	42522550	+	3'UTR	SNP	G	A	A	rs142105976	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42522550G>A	uc003bce.2	-	9					uc003bcd.1_Intron|CYP2D6_uc010gyu.2_3'UTR|CYP2D6_uc003bcf.2_3'UTR	NM_000106	NP_000097	Q6NWU0	Q6NWU0_HUMAN	cytochrome P450, family 2, subfamily D,								electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen			breast(1)|skin(1)	2						TGGCTAGGGAGCAGGCTGGGG	0.582													3	48	---	---	---	---	PASS
MOV10L1	54456	broad.mit.edu	37	22	50530474	50530474	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50530474T>C	uc003bjj.2	+	2	225	c.142T>C	c.(142-144)TGC>CGC	p.C48R	MOV10L1_uc003bjk.3_Missense_Mutation_p.C48R|MOV10L1_uc011arp.1_Missense_Mutation_p.C28R|MOV10L1_uc010han.2_Missense_Mutation_p.C28R	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1	48					germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GACAAGGTACTGCAGCGATTA	0.448													7	596	---	---	---	---	PASS
DLG3	1741	broad.mit.edu	37	X	69722142	69722142	+	3'UTR	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69722142T>C	uc004dyi.1	+	19					DLG3_uc004dyj.1_3'UTR|DLG3_uc011mpn.1_3'UTR	NM_021120	NP_066943	Q92796	DLG3_HUMAN	synapse-associated protein 102 isoform a						axon guidance|negative regulation of cell proliferation|synaptic transmission	plasma membrane	guanylate kinase activity			large_intestine(1)|pancreas(1)	2	Renal(35;0.156)					AACCATTCTCTTGTGAACAGA	0.433													5	109	---	---	---	---	PASS
GPRASP1	9737	broad.mit.edu	37	X	101912721	101912721	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101912721T>C	uc004ejj.3	+	5	4681	c.3880T>C	c.(3880-3882)TTT>CTT	p.F1294L	GPRASP1_uc004eji.3_Missense_Mutation_p.F1294L|GPRASP1_uc010nod.2_Missense_Mutation_p.F1294L	NM_014710	NP_055525	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting	1294	OPRD1-binding.					cytoplasm	protein binding			ovary(1)|lung(1)	2						CAAAACAAGGTTTCATGTTTT	0.368													5	100	---	---	---	---	PASS
IGSF1	3547	broad.mit.edu	37	X	130407781	130407781	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130407781C>T	uc004ewd.2	-	20	4238	c.4000G>A	c.(4000-4002)GTT>ATT	p.V1334I	IGSF1_uc004ewe.3_Missense_Mutation_p.V1328I|IGSF1_uc004ewf.2_Missense_Mutation_p.V1314I	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	1334	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						TATATTGGAACGGGCAGTTCC	0.483													9	305	---	---	---	---	PASS
FAM3A	60343	broad.mit.edu	37	X	153735234	153735234	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153735234C>T	uc004fls.1	-	9	878	c.601G>A	c.(601-603)GTG>ATG	p.V201M	FAM3A_uc004flt.1_Missense_Mutation_p.V215M|FAM3A_uc011mzp.1_Missense_Mutation_p.V184M|FAM3A_uc004flu.1_Missense_Mutation_p.V198M|FAM3A_uc011mzq.1_Missense_Mutation_p.V201M|FAM3A_uc004flw.1_Missense_Mutation_p.V201M	NM_021806	NP_068578	P98173	FAM3A_HUMAN	family 3, member A protein precursor	201						extracellular region				large_intestine(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)					CTGTTCTTCACGTGCTGTGGG	0.602													18	30	---	---	---	---	PASS
GNB1	2782	broad.mit.edu	37	1	1823513	1823513	+	5'Flank	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1823513delG	uc001aif.2	-						GNB1_uc009vky.2_5'Flank|uc001aig.1_Intron	NM_002074	NP_002065	P62873	GBB1_HUMAN	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)		CCACCTGCCTGGGCCTTCATC	0.652													4	2	---	---	---	---	
KIAA0562	9731	broad.mit.edu	37	1	3750216	3750216	+	Intron	DEL	C	-	-	rs35801288		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3750216delC	uc001aky.2	-						KIAA0562_uc010nzm.1_Intron	NM_014704	NP_055519	O60308	CE104_HUMAN	glycine-, glutamate-,							centriole	binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_epithelial(116;3.96e-21)|all_lung(118;2.74e-08)|Lung NSC(185;6.4e-06)|Breast(487;0.00066)|Renal(390;0.00121)|Hepatocellular(190;0.00335)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.031)|Lung SC(97;0.0548)|Medulloblastoma(700;0.212)		Epithelial(90;6.85e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.59e-22)|GBM - Glioblastoma multiforme(42;3.16e-16)|Colorectal(212;2.01e-05)|COAD - Colon adenocarcinoma(227;7.99e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000389)|Kidney(185;0.000513)|STAD - Stomach adenocarcinoma(132;0.00709)|KIRC - Kidney renal clear cell carcinoma(229;0.00714)|Lung(427;0.137)		ATAAAAAAAACATTGGAAAAA	0.279													4	6	---	---	---	---	
SLC2A5	6518	broad.mit.edu	37	1	9129815	9129815	+	5'UTR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9129815delG	uc001apo.2	-	1					SLC2A5_uc010nzz.1_5'Flank|SLC2A5_uc010oaa.1_5'UTR|SLC2A5_uc010oab.1_Intron|SLC2A5_uc010oac.1_5'Flank|SLC2A5_uc001app.3_5'UTR	NM_003039	NP_003030	P22732	GTR5_HUMAN	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)		CTAAGTAAGTGGGTGCCCCCT	0.468													4	2	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15018544	15018544	+	Intron	DEL	A	-	-	rs34394371		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15018544delA	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						CAGTAGTGGtaaaaaaaaaaa	0.294													19	12	---	---	---	---	
DDI2	84301	broad.mit.edu	37	1	15946364	15946364	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15946364delA	uc001awx.1	+						DDI2_uc001aww.2_Intron	NM_032341	NP_115717	Q5TDH0	DDI2_HUMAN	DNA-damage inducible protein 2						proteolysis		aspartic-type endopeptidase activity				0		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		AGGGCTTGGGAAAAGACAGAG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20420333	20420333	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20420333delG								PLA2G5 (1940 upstream) : PLA2G2D (18108 downstream)																							tcccacctcagcctccagagt	0.000													15	20	---	---	---	---	
EIF4G3	8672	broad.mit.edu	37	1	21359950	21359950	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21359950delA	uc001bec.2	-						EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beg.2_Intron|EIF4G3_uc010odk.1_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751	O43432	IF4G3_HUMAN	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)		TTCTGAACTTAAAAAAAAAAA	0.254													3	3	---	---	---	---	
ZDHHC18	84243	broad.mit.edu	37	1	27179541	27179541	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27179541delA	uc001bnb.2	+							NM_032283	NP_115659	Q9NUE0	ZDH18_HUMAN	zinc finger, DHHC-type containing 18							integral to membrane	zinc ion binding				0		all_cancers(24;5.82e-22)|all_epithelial(13;9.91e-20)|Colorectal(325;0.000147)|Breast(348;0.000706)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;5.71e-53)|Epithelial(14;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(117;1.53e-29)|Colorectal(126;1.9e-09)|COAD - Colon adenocarcinoma(152;4.2e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000548)|STAD - Stomach adenocarcinoma(196;0.00065)|KIRC - Kidney renal clear cell carcinoma(1967;0.000779)|GBM - Glioblastoma multiforme(114;0.0265)|READ - Rectum adenocarcinoma(331;0.0455)|Lung(427;0.163)|LUSC - Lung squamous cell carcinoma(448;0.237)		CTCATTGTAGAAAAAAAAAAT	0.438											OREG0013274	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	3	---	---	---	---	
LCK	3932	broad.mit.edu	37	1	32738451	32738452	+	Intron	DEL	TG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32738451_32738452delTG	uc001bux.2	+						LCK_uc001buy.2_5'Flank|LCK_uc001buz.2_5'Flank|LCK_uc010ohc.1_5'Flank|LCK_uc001bva.2_5'Flank	NM_005356	NP_005347	P06239	LCK_HUMAN	lymphocyte-specific protein tyrosine kinase						activation of caspase activity|cellular zinc ion homeostasis|induction of apoptosis|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of T cell receptor signaling pathway|regulation of defense response to virus by virus|release of sequestered calcium ion into cytosol|response to drug|T cell costimulation|T cell differentiation|T cell receptor signaling pathway|viral reproduction	cytosol|Golgi apparatus|membrane raft|pericentriolar material|plasma membrane	ATP binding|ATPase binding|CD4 receptor binding|CD8 receptor binding|glycoprotein binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein kinase binding|protein serine/threonine phosphatase activity|SH2 domain binding			lung(3)|central_nervous_system(2)|ovary(1)	6		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)	AGGGGATGCCtgtgtgtgtgtg	0.094			T	TRB@	T-ALL								4	2	---	---	---	---	
KIAA0319L	79932	broad.mit.edu	37	1	35976870	35976870	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35976870delA	uc001byx.2	-						KIAA0319L_uc010ohw.1_Intron|KIAA0319L_uc001byz.2_Intron|KIAA0319L_uc010ohx.1_Intron	NM_024874	NP_079150	Q8IZA0	K319L_HUMAN	dyslexia susceptibility 2-like							cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TACTGGGGGGAAAAAAAAACA	0.383													8	4	---	---	---	---	
PSMB2	5690	broad.mit.edu	37	1	36076590	36076590	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36076590delT	uc001bzf.1	-						PSMB2_uc001bzd.1_Intron|PSMB2_uc010ohz.1_Intron|PSMB2_uc001bzg.1_Intron	NM_002794	NP_002785	P49721	PSB2_HUMAN	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)	AAATGGATGATTTTTTTTTTC	0.388													4	2	---	---	---	---	
CLSPN	63967	broad.mit.edu	37	1	36212163	36212163	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36212163delT	uc001bzi.2	-						CLSPN_uc009vux.2_Intron	NM_022111	NP_071394	Q9HAW4	CLSPN_HUMAN	claspin						activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation	nucleoplasm	anaphase-promoting complex binding|DNA binding			breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				gcctggctaattttttttttt	0.000													7	4	---	---	---	---	
RNF220	55182	broad.mit.edu	37	1	45060756	45060756	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45060756delG	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620	Q5VTB9	RN220_HUMAN	ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						ctaggagcttggtagaaatgc	0.124											OREG0013443	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
TTC39A	22996	broad.mit.edu	37	1	51781011	51781011	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51781011delA	uc001csl.2	-						TTC39A_uc001csk.2_Intron|TTC39A_uc010ond.1_Intron|TTC39A_uc010one.1_Intron|TTC39A_uc010onf.1_Intron|TTC39A_uc001csn.2_Intron|TTC39A_uc001cso.1_Intron|TTC39A_uc009vyy.1_Intron	NM_001080494	NP_001073963	Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A isoform 2								binding			skin(1)	1						CTCAAACCTCAGGCACTCCAA	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56926141	56926142	+	IGR	INS	-	GATA	GATA	rs149606739	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56926141_56926142insGATA								None (None upstream) : PPAP2B (34291 downstream)																							GTGgatggatggatagatagat	0.134													2	4	---	---	---	---	
C8B	732	broad.mit.edu	37	1	57412101	57412101	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57412101delA	uc001cyp.2	-						C8B_uc010oon.1_Intron|C8B_uc010ooo.1_Intron	NM_000066	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide						complement activation, alternative pathway|complement activation, classical pathway|cytolysis	membrane attack complex				central_nervous_system(2)|large_intestine(1)|ovary(1)	4						TAAACTCTGGAAAAAAAGCCG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	63467380	63467380	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63467380delG								ATG4C (137331 upstream) : FOXD3 (321350 downstream)																							TTGGTTGGTTGGGGGTGGTGA	0.493													4	2	---	---	---	---	
PDE4B	5142	broad.mit.edu	37	1	66820809	66820809	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66820809delT	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.2_Intron|PDE4B_uc001dcp.2_Intron|PDE4B_uc001dcq.2_Intron|PDE4B_uc009was.2_Intron	NM_001037341	NP_001032418	Q07343	PDE4B_HUMAN	phosphodiesterase 4B isoform 1						signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)	AAGATGCTTCTTTTTTTTTCT	0.244													4	2	---	---	---	---	
MIER1	57708	broad.mit.edu	37	1	67394273	67394274	+	Intron	DEL	CA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67394273_67394274delCA	uc001dde.2	+						MIER1_uc001dda.3_Intron|MIER1_uc010opf.1_Intron|MIER1_uc009way.2_Intron|MIER1_uc001ddc.2_Intron|MIER1_uc001ddh.2_Intron|MIER1_uc001ddf.2_Intron|MIER1_uc001ddg.2_Intron|MIER1_uc010opg.1_Intron|MIER1_uc001ddj.1_5'Flank|MIER1_uc001ddi.2_5'Flank	NM_001077700	NP_001071168	Q8N108	MIER1_HUMAN	mesoderm induction early response 1 isoform b						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)	1						TCTTTGCCTTCAGCTCTTTTCA	0.366													8	4	---	---	---	---	
MIER1	57708	broad.mit.edu	37	1	67394276	67394277	+	Intron	DEL	CT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67394276_67394277delCT	uc001dde.2	+						MIER1_uc001dda.3_Intron|MIER1_uc010opf.1_Intron|MIER1_uc009way.2_Intron|MIER1_uc001ddc.2_Intron|MIER1_uc001ddh.2_Intron|MIER1_uc001ddf.2_Intron|MIER1_uc001ddg.2_Intron|MIER1_uc010opg.1_Intron|MIER1_uc001ddj.1_5'Flank|MIER1_uc001ddi.2_5'Flank	NM_001077700	NP_001071168	Q8N108	MIER1_HUMAN	mesoderm induction early response 1 isoform b						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)	1						TTGCCTTCAGCTCTTTTCATTA	0.361													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	68091456	68091456	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68091456delC								SERBP1 (195333 upstream) : GADD45A (59427 downstream)																							ACCTGAGAATCCACCTGGCAC	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	69488281	69488282	+	IGR	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69488281_69488282insA								DEPDC1 (525482 upstream) : LRRC7 (544586 downstream)																							TGTCAGAGGAGAAAAAAAACAG	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	69947325	69947326	+	IGR	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69947325_69947326insT								DEPDC1 (984526 upstream) : LRRC7 (85542 downstream)																							GTTTGCAGTTCTTTTTTTAAAT	0.267													4	2	---	---	---	---	
ANKRD13C	81573	broad.mit.edu	37	1	70784893	70784894	+	Intron	DEL	GA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70784893_70784894delGA	uc001dex.3	-						ANKRD13C_uc009wbk.2_Intron	NM_030816	NP_110443	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C						protein retention in ER lumen|regulation of anoikis|regulation of receptor biosynthetic process	endoplasmic reticulum membrane|perinuclear region of cytoplasm	receptor binding				0						TTAAAATCTTGACTAGCACATA	0.361													4	2	---	---	---	---	
C1orf173	127254	broad.mit.edu	37	1	75078706	75078706	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75078706delA	uc001dgg.2	-						uc001dgh.2_Intron|C1orf173_uc001dgi.3_Intron	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254											ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						agctaaaaacaaaaaaaaaag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	83318066	83318066	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83318066delT								LPHN2 (859960 upstream) : None (None downstream)																							tttgggatcatttttccattg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	83824691	83824691	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83824691delT								None (None upstream) : TTLL7 (510368 downstream)																							agcctctgacttttttttgta	0.000													4	2	---	---	---	---	
COL24A1	255631	broad.mit.edu	37	1	86398928	86398929	+	Intron	INS	-	T	T	rs138714068	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86398928_86398929insT	uc001dlj.2	-						COL24A1_uc001dli.2_Intron|COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	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)		AAATTACTCTATTCAGTATCTA	0.312													4	5	---	---	---	---	
CLCA1	1179	broad.mit.edu	37	1	86942465	86942466	+	Intron	INS	-	T	T	rs146043808	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86942465_86942466insT	uc001dlt.2	+						CLCA1_uc001dls.1_Intron	NM_001285	NP_001276	A8K7I4	CLCA1_HUMAN	chloride channel accessory 1 precursor						calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		CTCCTTTTTTCTTTTTTTTTAA	0.351													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	87681667	87681667	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87681667delA								LOC339524 (46783 upstream) : LMO4 (112484 downstream)																							AAATAAAACCAAAAATAGACA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	90790974	90790974	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90790974delC								ZNF326 (296880 upstream) : BARHL2 (386606 downstream)																							gagtctgtttcctgatctgtt	0.060													4	2	---	---	---	---	
TMEM56	148534	broad.mit.edu	37	1	95658793	95658793	+	3'UTR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95658793delA	uc001drb.2	+	7					RWDD3_uc001drd.3_Intron|uc001dre.1_Intron|TMEM56_uc001drc.2_3'UTR	NM_152487	NP_689700	Q96MV1	TMM56_HUMAN	transmembrane protein 56							integral to membrane					0		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.133)		TAAAGCACAGAAAAAAAAAGG	0.294													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	99996329	99996329	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99996329delA								LPPR4 (221193 upstream) : PALMD (115102 downstream)																							ATGATAAGCCAAAAAAAAAAA	0.343													3	3	---	---	---	---	
FNDC7	163479	broad.mit.edu	37	1	109273041	109273041	+	Intron	DEL	A	-	-	rs34848956		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109273041delA	uc001dvx.2	+						FNDC7_uc010ova.1_Intron	NM_001144937	NP_001138409	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7							extracellular region				ovary(1)|skin(1)	2		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		TCTTATTCTGAAAAAAAAAAA	0.299													3	5	---	---	---	---	
SARS	6301	broad.mit.edu	37	1	109768111	109768111	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109768111delT	uc001dwu.1	+						SARS_uc001dwt.1_Intron|SARS_uc001dwv.1_Intron|SARS_uc001dww.1_Intron|SARS_uc001dwx.1_Intron|SARS_uc009wfa.1_Intron|SARS_uc001dwy.1_Intron	NM_006513	NP_006504	P49591	SYSC_HUMAN	seryl-tRNA synthetase						seryl-tRNA aminoacylation|tRNA processing	cytosol	ATP binding|protein binding|RNA binding|serine-tRNA ligase activity			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0301)|Lung(183;0.0677)|COAD - Colon adenocarcinoma(174;0.116)|Epithelial(280;0.233)	L-Serine(DB00133)	CAGCTGGGTATTTTTTGAAGC	0.438													4	2	---	---	---	---	
C1orf162	128346	broad.mit.edu	37	1	112019172	112019173	+	Intron	INS	-	T	T	rs34481842		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112019172_112019173insT	uc001ebe.2	+							NM_174896	NP_777556	Q8NEQ5	CA162_HUMAN	hypothetical protein LOC128346							integral to membrane				ovary(1)	1		all_cancers(81;0.00116)|all_epithelial(167;0.000761)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0236)|Colorectal(144;0.0286)|all cancers(265;0.0572)|Epithelial(280;0.0862)|COAD - Colon adenocarcinoma(174;0.112)|LUSC - Lung squamous cell carcinoma(189;0.134)		AACATATGAGATTTTTTTTTTT	0.332													4	2	---	---	---	---	
MAGI3	260425	broad.mit.edu	37	1	114136298	114136298	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114136298delA	uc001edk.2	+						MAGI3_uc001edh.3_Intron|MAGI3_uc001edi.3_Intron|MAGI3_uc010owm.1_Intron|MAGI3_uc001edj.2_Intron	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3						apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTGTCCACTAAGCAATGAGA	0.328													4	2	---	---	---	---	
CD58	965	broad.mit.edu	37	1	117107615	117107619	+	Intron	DEL	CCCAC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117107615_117107619delCCCAC	uc001egm.2	-						CD58_uc001egn.2_Intron|CD58_uc010owy.1_Intron|CD58_uc001egp.3_Intron	NM_001779	NP_001770	P19256	LFA3_HUMAN	CD58 molecule isoform 1						blood coagulation|cell-cell adhesion|leukocyte migration	anchored to membrane|integral to plasma membrane	protein binding				0	Lung SC(450;0.225)	all_cancers(81;0.000363)|all_lung(203;0.000118)|all_epithelial(167;0.000149)|Lung NSC(69;0.000577)		Lung(183;0.0086)|LUSC - Lung squamous cell carcinoma(189;0.0528)|Colorectal(144;0.0775)|all cancers(265;0.109)|Epithelial(280;0.118)|COAD - Colon adenocarcinoma(174;0.121)		ctaatgcaagcccacaccaaatcct	0.132													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143504744	143504745	+	IGR	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143504744_143504745insT								None (None upstream) : LOC100286793 (142894 downstream)																							accatcagttgtttgttataaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143514187	143514187	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143514187delA								None (None upstream) : LOC100286793 (133452 downstream)																							CAGAGTCTCCAAAAAAAAATT	0.378													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144989456	144989456	+	Intron	DEL	T	-	-	rs139479913		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144989456delT	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emg.1_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GCCTTGTCAGTTTTTCAATTT	0.368			T	PDGFRB	MPD								4	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145056066	145056066	+	Intron	DEL	T	-	-	rs2500363		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145056066delT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						AGAAAAAAAATATATTGCTGC	0.100													4	3	---	---	---	---	
NOS1AP	9722	broad.mit.edu	37	1	162324998	162324999	+	Frame_Shift_Ins	INS	-	GG	GG			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162324998_162324999insGG	uc001gbv.2	+	7	1004_1005	c.617_618insGG	c.(616-618)GAGfs	p.E206fs	NOS1AP_uc010pkr.1_Frame_Shift_Ins_p.E201fs|NOS1AP_uc010pks.1_RNA|NOS1AP_uc001gbw.2_Frame_Shift_Ins_p.E201fs	NM_014697	NP_055512	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor	206					regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			ACTGGAGCCGAGAGGGCCTCCA	0.554													34	25	---	---	---	---	
ILDR2	387597	broad.mit.edu	37	1	166943910	166943910	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166943910delC	uc001gdx.1	-							NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor							integral to membrane				ovary(1)	1						AAGGTTCCATCCCCATCTTCT	0.502													4	2	---	---	---	---	
GPR161	23432	broad.mit.edu	37	1	168056573	168056574	+	Intron	DEL	GT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168056573_168056574delGT	uc001gfc.2	-						GPR161_uc001gfb.2_Intron|GPR161_uc010pll.1_Intron|GPR161_uc010plm.1_Intron|GPR161_uc009wvo.2_Intron|GPR161_uc001gfd.2_Intron|GPR161_uc010pln.1_Intron	NM_153832	NP_722561	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161 isoform 2						multicellular organismal development	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_hematologic(923;0.215)					ACACgtgtgggtgtgtgtgtgt	0.337													5	3	---	---	---	---	
C1orf105	92346	broad.mit.edu	37	1	172399347	172399348	+	Intron	DEL	AA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172399347_172399348delAA	uc001gik.2	+						PIGC_uc001gii.1_Intron|PIGC_uc001gij.1_Intron	NM_139240	NP_640333	O95561	CA105_HUMAN	hypothetical protein LOC92346											skin(1)	1						GTTTAAATATAAGAGACTGACT	0.396													0	6	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	185765846	185765847	+	Intron	DEL	AC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185765846_185765847delAC	uc001grq.1	+							NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						atacatatatacacacactgca	0.000													4	2	---	---	---	---	
C1orf27	54953	broad.mit.edu	37	1	186370598	186370599	+	Intron	INS	-	TCTG	TCTG	rs142302628	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186370598_186370599insTCTG	uc001grw.2	+						C1orf27_uc010poq.1_Intron|C1orf27_uc010por.1_Intron	NM_017847	NP_060317	Q5SWX8	ODR4_HUMAN	odorant response abnormal 4 isoform 1							integral to membrane	oxidoreductase activity|zinc ion binding			ovary(1)	1						TCGTCCGtctttctgtctgtct	0.045													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193782121	193782121	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193782121delT								CDC73 (558181 upstream) : None (None downstream)																							TTTTATAGTATTTTTTTACAT	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	194747827	194747828	+	IGR	DEL	GT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194747827_194747828delGT								None (None upstream) : None (None downstream)																							AAATGGAATGGTGACTGCATAG	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	201327484	201327484	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201327484delG								PKP1 (25369 upstream) : TNNT2 (659 downstream)																							ATCAGGAATTGGGGGAAATTC	0.547													4	2	---	---	---	---	
KLHDC8A	55220	broad.mit.edu	37	1	205320730	205320731	+	Intron	INS	-	AAA	AAA	rs143420341		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205320730_205320731insAAA	uc001hcf.1	-						KLHDC8A_uc010prg.1_Intron|KLHDC8A_uc001hcg.1_Intron	NM_018203	NP_060673	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A											ovary(1)	1	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CTGTAATAGTCaaaaaaaaaaa	0.188													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	210369139	210369139	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210369139delC								SYT14 (31508 upstream) : C1orf133 (35665 downstream)																							gctacctagtccccaaaccaa	0.114													4	2	---	---	---	---	
SUSD4	55061	broad.mit.edu	37	1	223466362	223466362	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223466362delG	uc001hnx.2	-						SUSD4_uc001hny.3_Intron|SUSD4_uc010puw.1_Intron|SUSD4_uc001hnz.2_Intron|SUSD4_uc010pux.1_Intron	NM_017982	NP_060452	Q5VX71	SUSD4_HUMAN	sushi domain containing 4 isoform a							integral to membrane					0				GBM - Glioblastoma multiforme(131;0.0611)		ATCTGAGCCTGGCCTTGAGGA	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	223695942	223695942	+	IGR	DEL	C	-	-	rs10907389	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223695942delC								C1orf65 (127130 upstream) : CAPN8 (19030 downstream)																							ACTGTTTGCTCATTGTCTCCC	0.582													4	2	---	---	---	---	
WNT9A	7483	broad.mit.edu	37	1	228114840	228114840	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228114840delG	uc001hri.2	-							NM_003395	NP_003386	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family,						anterior/posterior pattern formation|axis specification|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|cornea development in camera-type eye|embryonic arm morphogenesis|embryonic skeletal joint morphogenesis|endoderm development|iris morphogenesis|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|neuron differentiation|positive regulation of smoothened signaling pathway|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|G-protein-coupled receptor binding|signal transducer activity			central_nervous_system(1)|pancreas(1)	2		Prostate(94;0.0405)				ATGAGCCCTCGGAGTTGAGCC	0.617													4	2	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237427391	237427392	+	Intron	INS	-	CA	CA	rs148961062	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237427391_237427392insCA	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	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)			acatgcacatgcacacacacac	0.342													3	3	---	---	---	---	
PLD5	200150	broad.mit.edu	37	1	242652677	242652678	+	Intron	INS	-	A	A	rs143262290		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242652677_242652678insA	uc001hzn.1	-						PLD5_uc001hzo.1_Intron			Q8N7P1	PLD5_HUMAN	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)			TACATTTGATTAAAAAAAAAAA	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	242981793	242981793	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242981793delA								PLD5 (293795 upstream) : CEP170 (305938 downstream)																							AAGCAAAAGCAAGAAATAAAT	0.388													4	2	---	---	---	---	
C1orf100	200159	broad.mit.edu	37	1	244538931	244538931	+	Intron	DEL	G	-	-	rs141977606		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244538931delG	uc001iah.2	+						C1orf100_uc001iai.2_Intron	NM_001012970	NP_001012988	Q5SVJ3	CA100_HUMAN	hypothetical protein LOC200159												0	all_cancers(71;3.94e-05)|all_epithelial(71;0.000138)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|all_lung(81;0.0736)|Ovarian(71;0.0761)|Lung NSC(105;0.103)		all cancers(7;8.19e-08)|GBM - Glioblastoma multiforme(7;2.05e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.000984)			AACTGTTAATGTTTTTTTTTT	0.244													3	8	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246258503	246258503	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246258503delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	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)		ATACAACTTCATACTTCTTTC	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	249240212	249240212	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249240212delT								PGBD2 (26868 upstream) : None (None downstream)																							agggttagggttagggtaggg	0.000													4	2	---	---	---	---	
COLEC11	78989	broad.mit.edu	37	2	3658787	3658790	+	Intron	DEL	AAAC	-	-	rs79891538		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3658787_3658790delAAAC	uc002qya.2	+						COLEC11_uc002qxz.2_Intron|COLEC11_uc002qyb.2_Intron|COLEC11_uc002qyc.2_Intron|COLEC11_uc010ewo.2_Intron|COLEC11_uc010ewp.2_Intron|COLEC11_uc010ewq.2_Intron|COLEC11_uc010ewr.2_Intron|COLEC11_uc010ews.2_Intron	NM_024027	NP_076932	Q9BWP8	COL11_HUMAN	collectin sub-family member 11 isoform a							collagen	mannose binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		CGTAACTTCAAAACAAACAAACAA	0.495													0	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4703685	4703685	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4703685delT	uc002qyi.2	-											Homo sapiens cDNA, FLJ97272.																		agacctactcttaactactat	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10276089	10276089	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10276089delT								RRM2 (4543 upstream) : C2orf48 (5420 downstream)																							TAGTCATGTGTTTTTTTTTTA	0.473													4	2	---	---	---	---	
HPCAL1	3241	broad.mit.edu	37	2	10464454	10464454	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10464454delA	uc002raj.2	+						HPCAL1_uc002rak.2_Intron|HPCAL1_uc002ral.2_Intron|HPCAL1_uc010exe.2_5'Flank	NM_002149	NP_002140	P37235	HPCL1_HUMAN	hippocalcin-like 1								calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)		AGGTCAGGCTAACAGTGATGT	0.343													4	2	---	---	---	---	
GREB1	9687	broad.mit.edu	37	2	11754965	11754966	+	Intron	INS	-	T	T	rs142142931	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11754965_11754966insT	uc002rbk.1	+						GREB1_uc002rbp.1_Intron	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1							integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		ctgCAAGCCCCTTTTTTATCTG	0.228													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18850733	18850733	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18850733delA								NT5C1B (79895 upstream) : OSR1 (700514 downstream)																							AGAGTCTTTGAAATGAACTAG	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	21485213	21485213	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21485213delC								APOB (218268 upstream) : None (None downstream)																							TTCTTTCAGTCCCGAATTTAT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	22892831	22892832	+	IGR	DEL	AG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22892831_22892832delAG								None (None upstream) : KLHL29 (862623 downstream)																							GGTGCTTCTCAGAGGAGTAATC	0.421													4	2	---	---	---	---	
EFR3B	22979	broad.mit.edu	37	2	25344834	25344834	+	Intron	DEL	T	-	-	rs80150843		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25344834delT	uc010eyh.2	+						EFR3B_uc002rfw.2_Intron	NM_014971	NP_055786	Q9Y2G0	EFR3B_HUMAN	EFR3 homolog B								binding				0						GTGGtttctgttttttttttt	0.264													9	4	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29610008	29610008	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29610008delT	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	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)	CCATCTGGACTTTAGGAAGTC	0.378			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				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	32277038	32277038	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32277038delT								MEMO1 (12176 upstream) : SPAST (11642 downstream)																							aagcactgagtttctgatgag	0.000													4	2	---	---	---	---	
SLC30A6	55676	broad.mit.edu	37	2	32438096	32438096	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32438096delT	uc002roe.1	+						SLC30A6_uc002rof.1_Intron|SLC30A6_uc010ymw.1_Intron|SLC30A6_uc010ezr.1_Intron|SLC30A6_uc002rog.1_Intron|SLC30A6_uc010ezs.1_Intron|SLC30A6_uc002roh.1_Intron	NM_017964	NP_060434	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter),							Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					tacctcagccttcccagtagc	0.000													4	2	---	---	---	---	
YIPF4	84272	broad.mit.edu	37	2	32523031	32523031	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32523031delT	uc002rok.2	+							NM_032312	NP_115688	Q9BSR8	YIPF4_HUMAN	Yip1 domain family, member 4							endoplasmic reticulum|integral to membrane	protein binding				0	Acute lymphoblastic leukemia(172;0.155)					TAGTAAACACTTTTTTTTTGC	0.279													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34574179	34574180	+	IGR	INS	-	TGTGTG	TGTGTG	rs139010289	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34574179_34574180insTGTGTG								MYADML (620895 upstream) : None (None downstream)																							gtgtgtgtgtttgtgtgtgtgt	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35889441	35889442	+	IGR	INS	-	A	A	rs144572465	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35889441_35889442insA								None (None upstream) : CRIM1 (693955 downstream)																							AGCAGATATTTAAAAAAAACAC	0.287													5	5	---	---	---	---	
CRIM1	51232	broad.mit.edu	37	2	36776050	36776050	+	3'UTR	DEL	T	-	-	rs11309348		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36776050delT	uc002rpd.2	+	17						NM_016441	NP_057525	Q9NZV1	CRIM1_HUMAN	cysteine-rich motor neuron 1 precursor						nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				TGACCAAGTGTTTTCTTAGAA	0.418													8	5	---	---	---	---	
HEATR5B	54497	broad.mit.edu	37	2	37245868	37245868	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37245868delG	uc002rpp.1	-							NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)				CAGAAAACTAGGAAGAAGAGA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37973206	37973207	+	IGR	DEL	TT	-	-	rs68002671		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37973206_37973207delTT								CDC42EP3 (73880 upstream) : FAM82A1 (179255 downstream)																							TATGGCTTTCTTTTTTTTTCTA	0.238													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37984142	37984142	+	IGR	DEL	T	-	-	rs112508808		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37984142delT								CDC42EP3 (84816 upstream) : FAM82A1 (168320 downstream)																							TATTACATTCTTTTCCCCATT	0.408													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38088492	38088492	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38088492delC								CDC42EP3 (189166 upstream) : FAM82A1 (63970 downstream)																							AAGAGTGACTCCCATGTGATG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	40122975	40122975	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40122975delA								THUMPD2 (116559 upstream) : SLC8A1 (216312 downstream)																							AGGTTCTGTGAGGGCGGTCTC	0.353													4	2	---	---	---	---	
SRBD1	55133	broad.mit.edu	37	2	45641925	45641926	+	Intron	DEL	AT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45641925_45641926delAT	uc002rus.2	-						SRBD1_uc010yoc.1_Intron	NM_018079	NP_060549	Q8N5C6	SRBD1_HUMAN	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)			acacacacacatagtgtgtata	0.025													4	2	---	---	---	---	
SRBD1	55133	broad.mit.edu	37	2	45641953	45641954	+	Intron	DEL	AT	-	-	rs147495372		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45641953_45641954delAT	uc002rus.2	-						SRBD1_uc010yoc.1_Intron	NM_018079	NP_060549	Q8N5C6	SRBD1_HUMAN	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)			gtacacacacatatagtgtgta	0.025													4	2	---	---	---	---	
TTC7A	57217	broad.mit.edu	37	2	47243649	47243650	+	Intron	INS	-	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47243649_47243650insG	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_Intron|TTC7A_uc002rvq.2_Intron|TTC7A_uc002rvr.2_Intron	NM_020458	NP_065191	Q9ULT0	TTC7A_HUMAN	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)			AGGACTAGGCAGGGAAAGATCT	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	51281539	51281539	+	IGR	DEL	T	-	-	rs67950375		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51281539delT								NRXN1 (21865 upstream) : None (None downstream)																							TAGTTACTGCTTAGGCATGAG	0.328													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	53588764	53588764	+	IGR	DEL	A	-	-	rs11125485	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53588764delA								None (None upstream) : ASB3 (308354 downstream)																							gtttttttttaattcgatatt	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	53693958	53693959	+	IGR	DEL	GA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53693958_53693959delGA								None (None upstream) : ASB3 (203159 downstream)																							ggtaggtagggagagagagaga	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	56182725	56182725	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56182725delT	uc002rzk.2	+											Homo sapiens, clone IMAGE:3873411, mRNA.																		GATGCTGGGATtttttttttt	0.234													11	5	---	---	---	---	
PEX13	5194	broad.mit.edu	37	2	61268963	61268963	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61268963delG	uc002sau.3	+							NM_002618	NP_002609	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13						cerebral cortex cell migration|fatty acid alpha-oxidation|locomotory behavior|microtubule-based peroxisome localization|neuron migration|protein import into peroxisome matrix, docking|suckling behavior	integral to peroxisomal membrane|membrane fraction	protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)			GGGAAAGATAGGAGTTAAATG	0.378													4	2	---	---	---	---	
COMMD1	150684	broad.mit.edu	37	2	62202706	62202706	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62202706delT	uc002sbp.2	+							NM_152516	NP_689729	Q8N668	COMD1_HUMAN	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)			aattatatgatttttttATAT	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	62482598	62482599	+	IGR	DEL	CA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62482598_62482599delCA								B3GNT2 (30734 upstream) : TMEM17 (244757 downstream)																							TAAATTGCACCACACACACACG	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66433295	66433296	+	IGR	DEL	TG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66433295_66433296delTG								SPRED2 (773639 upstream) : MEIS1 (229236 downstream)																							CTCTCACTCATGTGTGTGTGTG	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67878152	67878152	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67878152delC								ETAA1 (240619 upstream) : C1D (391181 downstream)																							AAGCAAGCGGCCAGAAGCACC	0.517											OREG0014656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
AAK1	22848	broad.mit.edu	37	2	69723406	69723406	+	Intron	DEL	T	-	-	rs72223816		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69723406delT	uc002sfp.2	-						AAK1_uc010fdk.2_Intron|AAK1_uc010yqm.1_Intron	NM_014911	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0						ATCTGGCCCGttttttttttt	0.204													4	3	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71863642	71863642	+	Intron	DEL	G	-	-	rs71403000		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71863642delG	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron|DYSF_uc010yqy.1_Intron|DYSF_uc010yqz.1_Intron	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						ttgagcatctggaaggagaga	0.000													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	72162830	72162831	+	IGR	DEL	CC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72162830_72162831delCC								DYSF (248938 upstream) : CYP26B1 (193536 downstream)																							CACTGACTCTcccagggaagag	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73400282	73400285	+	IGR	DEL	CACA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73400282_73400285delCACA								RAB11FIP5 (60136 upstream) : NOTO (29101 downstream)																							tagcagacaccacacacacacaca	0.172													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73851205	73851207	+	IGR	DEL	TCC	-	-	rs112833082		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73851205_73851207delTCC								ALMS1 (14159 upstream) : NAT8 (16643 downstream)																							CAGCTTCTGGtcctcctcctcct	0.340													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	75837707	75837707	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75837707delT								FAM176A (40859 upstream) : MRPL19 (36202 downstream)																							GAAAGCAGGGTTTTCCATGCC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82227492	82227492	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82227492delA								None (None upstream) : None (None downstream)																							GGGACTATATAAGAAAAATCC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85544589	85544590	+	IGR	INS	-	CAACA	CAACA	rs140958510	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85544589_85544590insCAACA								TCF7L1 (7085 upstream) : TGOLN2 (557 downstream)																							GCTACTGAAAGCAGGCAGCCAG	0.559													4	4	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87327733	87327733	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87327733delC	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						caggaaagttccccaatatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90451278	90451278	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90451278delT	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		ACTGACCTTATTTTTTTTTAC	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96085114	96085115	+	IGR	DEL	AG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96085114_96085115delAG								FAHD2A (6236 upstream) : TRIM43 (172651 downstream)																							ATCTAGAGACAGAGAGAGAGAG	0.337													4	2	---	---	---	---	
FER1L5	90342	broad.mit.edu	37	2	97353460	97353461	+	Intron	INS	-	GGGAA	GGGAA	rs138874749	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97353460_97353461insGGGAA	uc010fia.2	+						FER1L5_uc002sws.3_Intron	NM_001113382	NP_001106853	A0AVI2	FR1L5_HUMAN	fer-1-like 5 isoform 2							integral to membrane				ovary(1)	1						AGGGCTCAGGGGGGAAGGGGCA	0.653													12	6	---	---	---	---	
FAM178B	51252	broad.mit.edu	37	2	97610676	97610676	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97610676delT	uc002sxl.3	-						FAM178B_uc002sxk.3_Intron	NM_001122646	NP_001116118	Q8IXR5	F178B_HUMAN	hypothetical protein LOC51252 isoform A												0						GGTTCCTGCCTCCCCACATCC	0.413													4	2	---	---	---	---	
ANKRD36	375248	broad.mit.edu	37	2	97856287	97856287	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97856287delA	uc010yva.1	+						ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron|ANKRD36_uc002sxq.1_Intron	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36												0						CAAGTTAAAGAGCATGATGAA	0.383													4	3	---	---	---	---	
AFF3	3899	broad.mit.edu	37	2	100603371	100603371	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100603371delG	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						AGTAAACTTAGGAAACAAGTG	0.403													4	2	---	---	---	---	
NPAS2	4862	broad.mit.edu	37	2	101478820	101478820	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101478820delT	uc002tap.1	+						NPAS2_uc010yvt.1_Intron	NM_002518	NP_002509	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2						central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4						TTGGTTGGGGTTTTTTTTGCC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103913375	103913376	+	IGR	DEL	CA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103913375_103913376delCA								TMEM182 (479239 upstream) : None (None downstream)																							acacacacaccacacacacaca	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107678370	107678370	+	IGR	DEL	A	-	-	rs71379797		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107678370delA								ST6GAL2 (174807 upstream) : LOC729121 (761150 downstream)																							TAAATGATTTAAAAAAGGAAA	0.224													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108882580	108882580	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108882580delT								SULT1C3 (774 upstream) : SULT1C2 (22515 downstream)																							TTTTTTATACTTTTTTTTAAA	0.318													4	2	---	---	---	---	
PTPN4	5775	broad.mit.edu	37	2	120591258	120591258	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120591258delT	uc002tmf.1	+							NM_002830	NP_002821	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity			ovary(2)	2					Alendronate(DB00630)	ctcggactaattttttttttt	0.000													4	4	---	---	---	---	
MYO7B	4648	broad.mit.edu	37	2	128341532	128341533	+	Intron	DEL	GT	-	-	rs150669299		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128341532_128341533delGT	uc002top.2	+							NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB							apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		AGGAGAGAGAGTGTGCAGGAAT	0.515													8	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129984025	129984026	+	IGR	DEL	GT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129984025_129984026delGT								HS6ST1 (907854 upstream) : LOC389033 (696409 downstream)																							AGACAGACAGGTGAAAGGGGGA	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131643862	131643862	+	Intron	DEL	T	-	-	rs113150360		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131643862delT	uc002try.1	+											Homo sapiens cDNA FLJ45181 fis, clone BRAWH3047644, highly  similar to Homo sapiens Rho guanine nucleotide exchange factor (GEF) 4 (ARHGEF4).																		ctcattgctgtttttttttgc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132364941	132364942	+	IGR	INS	-	G	G	rs145918909	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132364941_132364942insG								CCDC74A (73704 upstream) : C2orf27A (115122 downstream)																							CCATGACCTGTGTGAGTCACAG	0.446													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132817202	132817204	+	IGR	DEL	AGA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132817202_132817204delAGA								C2orf27B (257968 upstream) : NCRNA00164 (87960 downstream)																							CTTATCAAGGAGAAGAACTCAAG	0.310													6	3	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	133647118	133647118	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133647118delA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						GGATCAGAACAAAAAAAAAAT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134526339	134526339	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134526339delA								NCKAP5 (200308 upstream) : MGAT5 (485491 downstream)																							tgtattctccaagcctagcac	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134637629	134637629	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134637629delC								NCKAP5 (311598 upstream) : MGAT5 (374201 downstream)																							GTGATAGTGTCCAGTAGAATT	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	137053825	137053825	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137053825delT								CXCR4 (178100 upstream) : THSD7B (469290 downstream)																							ttatgcaatgttttttttctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	139113308	139113308	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139113308delT								HNMT (339375 upstream) : SPOPL (146042 downstream)																							CAGAACACAGTATAATCCCAT	0.313													4	2	---	---	---	---	
ARHGAP15	55843	broad.mit.edu	37	2	144390754	144390755	+	Intron	INS	-	TG	TG	rs142921229	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144390754_144390755insTG	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	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)		TTGCTTTTTAATGTGTGTGTGT	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146549019	146549019	+	IGR	DEL	A	-	-	rs77796370	byFrequency	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146549019delA								None (None upstream) : PABPC1P2 (795606 downstream)																							GGATTTGATTAAAAAAAAATA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	147592035	147592035	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147592035delA								PABPC1P2 (243478 upstream) : None (None downstream)																							TTTTGCTTACAAAAAAAAACC	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	150559887	150559887	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150559887delC								MMADHC (115557 upstream) : RND3 (764825 downstream)																							AGCAAGCATTCCAAGGAATTT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	151579204	151579205	+	IGR	INS	-	C	C	rs143458454	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151579204_151579205insC								RND3 (235024 upstream) : RBM43 (525524 downstream)																							TTTTAAGCTGGCCTGTAATGTT	0.282													4	2	---	---	---	---	
GALNT13	114805	broad.mit.edu	37	2	155309867	155309868	+	3'UTR	DEL	CA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155309867_155309868delCA	uc002tyr.3	+	13					GALNT13_uc002tyt.3_3'UTR|GALNT13_uc010fod.2_3'UTR|uc002tyu.1_Intron	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	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						catacacatgcacacacacaca	0.000													4	2	---	---	---	---	
SCN2A	6326	broad.mit.edu	37	2	166151105	166151105	+	Intron	DEL	C	-	-	rs111503921		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166151105delC	uc002udc.2	+						SCN2A_uc002udd.2_Intron|SCN2A_uc002ude.2_5'Flank	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha						myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)	ATTTAAATGACAACTCTGACT	0.318													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	170271964	170271964	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170271964delA								LRP2 (52842 upstream) : BBS5 (64042 downstream)																							tctgggttccaaaagctgaac	0.100													4	2	---	---	---	---	
OLA1	29789	broad.mit.edu	37	2	174943425	174943425	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174943425delA	uc002uih.2	-						OLA1_uc002uii.2_Intron|OLA1_uc010fqq.2_Intron|OLA1_uc002uij.2_Intron|OLA1_uc002uik.2_Intron|OLA1_uc010fqr.2_Intron	NM_013341	NP_037473	Q9NTK5	OLA1_HUMAN	Obg-like ATPase 1 isoform 1						ATP catabolic process	cytoplasm	ATP binding|GTP binding|hydrolase activity|protein binding			ovary(1)|breast(1)	2						GAAATTATTTACAATTACTTA	0.229													3	3	---	---	---	---	
OLA1	29789	broad.mit.edu	37	2	174943427	174943427	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174943427delA	uc002uih.2	-						OLA1_uc002uii.2_Intron|OLA1_uc010fqq.2_Intron|OLA1_uc002uij.2_Intron|OLA1_uc002uik.2_Intron|OLA1_uc010fqr.2_Intron	NM_013341	NP_037473	Q9NTK5	OLA1_HUMAN	Obg-like ATPase 1 isoform 1						ATP catabolic process	cytoplasm	ATP binding|GTP binding|hydrolase activity|protein binding			ovary(1)|breast(1)	2						AATTATTTACAATTACTTAAA	0.229													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177504623	177504624	+	5'Flank	INS	-	AT	AT	rs149030178	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177504623_177504624insAT	uc002ukz.1	-						uc002ula.1_Intron					Homo sapiens hypothetical gene supported by BC013438, mRNA (cDNA clone IMAGE:3899073), partial cds.																		CTCCATCACACGTGTGTTCTCT	0.416													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181492463	181492464	+	IGR	INS	-	GATA	GATA	rs138913199	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181492463_181492464insGATA								CWC22 (620623 upstream) : UBE2E3 (352648 downstream)																							caggtaaataggatagatagat	0.000													5	3	---	---	---	---	
UBE2E3	10477	broad.mit.edu	37	2	181912680	181912681	+	Intron	INS	-	T	T	rs140398116	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181912680_181912681insT	uc002unq.1	+						UBE2E3_uc002unr.1_Intron|UBE2E3_uc010fri.1_Intron	NM_182678	NP_872619	Q969T4	UB2E3_HUMAN	ubiquitin-conjugating enzyme E2E 3						protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|regulation of growth	cytoplasm|nucleolus	ATP binding|protein binding|ubiquitin-protein ligase activity			ovary(1)	1						tcattaggtcgtttcattgtac	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	182253379	182253380	+	Intron	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182253379_182253380insT	uc002uns.1	+											Homo sapiens cDNA FLJ43011 fis, clone BRTHA2015853.																		ACATACTAAGATTTTTTTTTAT	0.282													4	2	---	---	---	---	
CERKL	375298	broad.mit.edu	37	2	182403223	182403234	+	Intron	DEL	GCCTCTAGAACA	-	-	rs3217651		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182403223_182403234delGCCTCTAGAACA	uc002unx.2	-						CERKL_uc002uny.2_Intron|CERKL_uc010zfm.1_Intron|CERKL_uc002unz.2_Intron|CERKL_uc002uoa.2_Intron|CERKL_uc002uob.2_Intron|CERKL_uc002uoc.2_Intron|CERKL_uc010frk.2_Intron|CERKL_uc002unw.2_Intron	NM_001030311	NP_001025482	Q49MI3	CERKL_HUMAN	ceramide kinase-like isoform b						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis	endoplasmic reticulum|endoplasmic reticulum|Golgi apparatus|Golgi apparatus|nucleolus|nucleolus	diacylglycerol kinase activity			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.088)			agtcagttatgcctctagaacacccatgtcta	0.038													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	185916592	185916593	+	IGR	INS	-	T	T	rs142456109	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185916592_185916593insT								ZNF804A (112380 upstream) : None (None downstream)																							tgcctgtttggttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	185949870	185949871	+	IGR	INS	-	AC	AC	rs147185920	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185949870_185949871insAC								ZNF804A (145658 upstream) : None (None downstream)																							GCTCCCCCAATACACACACATA	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	194134768	194134768	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194134768delT								PCGEM1 (493147 upstream) : None (None downstream)																							AAaattctggttttcacactt	0.159													4	2	---	---	---	---	
ANKRD44	91526	broad.mit.edu	37	2	198085368	198085368	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198085368delA	uc002uuc.2	-						ANKRD44_uc002uub.2_Intron|ANKRD44_uc010zgw.1_Intron|ANKRD44_uc002uud.1_Intron	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44								protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TTTCTGGGGGAAAAAAAATGG	0.368													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	199792819	199792819	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199792819delA								PLCL1 (778213 upstream) : SATB2 (341405 downstream)																							AAGCTTCTGGAAAAAAAAAAT	0.418													4	2	---	---	---	---	
PLEKHM3	389072	broad.mit.edu	37	2	208745591	208745592	+	Intron	INS	-	T	T	rs145968682	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208745591_208745592insT	uc002vcl.2	-							NM_001080475	NP_001073944	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M,						intracellular signal transduction		metal ion binding			ovary(1)	1						cataagaagtctttttttttac	0.000													4	3	---	---	---	---	
PIKFYVE	200576	broad.mit.edu	37	2	209218261	209218262	+	Intron	INS	-	TC	TC	rs145304645	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209218261_209218262insTC	uc002vcz.2	+							NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type						cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10						GACTATTTGCATCTCTCTCTTT	0.322													4	2	---	---	---	---	
CPS1	1373	broad.mit.edu	37	2	211359725	211359725	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211359725delG	uc010fur.2	+							NM_001122633	NP_001116105	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform a						carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		cttttggggtggggttctgtc	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221348585	221348586	+	IGR	INS	-	CA	CA	rs7419815	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221348585_221348586insCA								SLC4A3 (841884 upstream) : EPHA4 (934163 downstream)																							tttcattcatttattcattcat	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221348586	221348587	+	IGR	INS	-	TC	TC	rs7419815	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221348586_221348587insTC								SLC4A3 (841885 upstream) : EPHA4 (934162 downstream)																							ttcattcatttattcattcatt	0.193													4	2	---	---	---	---	
EPHA4	2043	broad.mit.edu	37	2	222324271	222324272	+	Intron	DEL	AC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222324271_222324272delAC	uc002vmq.2	-						EPHA4_uc002vmr.2_Intron|EPHA4_uc010zlm.1_Intron|EPHA4_uc010zln.1_Intron	NM_004438	NP_004429	P54764	EPHA4_HUMAN	ephrin receptor EphA4 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(6)|large_intestine(2)|central_nervous_system(2)|urinary_tract(1)|skin(1)	12		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		CCTTCTCCCAacacacacacag	0.332													4	2	---	---	---	---	
COL4A4	1286	broad.mit.edu	37	2	227961879	227961881	+	Intron	DEL	AAG	-	-	rs66929856		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227961879_227961881delAAG	uc010zlt.1	-							NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor						axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TCCCATTGCCAAGAAGAATGCTT	0.340													3	3	---	---	---	---	
COL4A3	1285	broad.mit.edu	37	2	228132877	228132877	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228132877delA	uc002vom.1	+						COL4A3_uc002von.1_Intron|COL4A3_uc002voo.1_Intron|COL4A3_uc002vop.1_Intron|uc002voq.1_Intron|uc002vor.1_Intron	NM_000091	NP_000082	Q01955	CO4A3_HUMAN	alpha 3 type IV collagen isoform 1 precursor						activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		AGGTGAAGttacagagccctt	0.239													4	2	---	---	---	---	
PID1	55022	broad.mit.edu	37	2	230107103	230107103	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230107103delA	uc002vps.3	-						PID1_uc002vpt.3_Intron|PID1_uc002vpu.3_Intron	NM_017933	NP_060403	Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1							cytoplasm				breast(3)|skin(1)	4		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)		GGTCCAAAAGAAAAACCCGTG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	231755962	231755962	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231755962delA	uc002vre.2	+											Homo sapiens hypothetical protein LOC151484, mRNA (cDNA clone IMAGE:5180745), partial cds.																		tctaaaaaagaaaaaaaaaaa	0.224													4	2	---	---	---	---	
ARMC9	80210	broad.mit.edu	37	2	232195569	232195569	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232195569delT	uc002vrq.3	+						ARMC9_uc002vrp.3_Intron|ARMC9_uc002vrr.1_Intron	NM_025139	NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9								binding			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		tttggggggctttttttgttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	235589296	235589296	+	IGR	DEL	C	-	-	rs5839555		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235589296delC								ARL4C (183603 upstream) : SH3BP4 (271332 downstream)																							TAGGTTGACACCTGTGCATAA	0.502													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239578936	239578936	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239578936delT								ASB1 (218046 upstream) : TWIST2 (177737 downstream)																							TAGTTTCTTCTTTTTTTTTTC	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	241086417	241086418	+	IGR	DEL	TG	-	-	rs72074872		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241086417_241086418delTG								OTOS (6344 upstream) : GPC1 (288697 downstream)																							GCCTGAAGAAtgtgtgtgtgtg	0.252													4	2	---	---	---	---	
C3orf24	115795	broad.mit.edu	37	3	10146617	10146621	+	Intron	DEL	TTATT	-	-	rs113292025		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10146617_10146621delTTATT	uc003buz.2	-						C3orf24_uc003bva.1_Intron	NM_173472	NP_775743	Q96PS1	CC024_HUMAN	hypothetical protein LOC115795												0				OV - Ovarian serous cystadenocarcinoma(96;0.196)		ATATTAGTAAttattttattttatt	0.180													2	6	---	---	---	---	
NKIRAS1	28512	broad.mit.edu	37	3	23940963	23940963	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23940963delT	uc003ccj.2	-						NKIRAS1_uc003cck.2_Intron|NKIRAS1_uc003ccl.2_Intron|NKIRAS1_uc003ccm.2_Intron	NM_020345	NP_065078	Q9NYS0	KBRS1_HUMAN	kappa B-ras 1						I-kappaB kinase/NF-kappaB cascade|small GTPase mediated signal transduction	cytoplasm	GTP binding|GTPase activity				0						TTGTTTTTTGTTTTTTTTCTA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	26545110	26545110	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26545110delA								OXSM (709086 upstream) : LRRC3B (119190 downstream)																							aatatggcttaagaagatgtg	0.005													4	2	---	---	---	---	
OSBPL10	114884	broad.mit.edu	37	3	31992659	31992659	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31992659delA	uc003cev.2	-						OSBPL10_uc011axf.1_Intron	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10						lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)		tcaccaggataaaaaatttgt	0.000													4	2	---	---	---	---	
CNOT10	25904	broad.mit.edu	37	3	32756889	32756889	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32756889delG	uc003cfc.1	+						CNOT10_uc011axi.1_Intron|CNOT10_uc003cfd.1_Intron|CNOT10_uc003cfe.1_Intron|CNOT10_uc010hfv.1_Intron|CNOT10_uc011axj.1_Intron|CNOT10_uc010hfw.1_Intron	NM_015442	NP_056257	Q9H9A5	CNOTA_HUMAN	CCR4-NOT transcription complex, subunit 10						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2						ATGGTGTGCTGGAGACCTTTC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	34997616	34997616	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34997616delA								None (None upstream) : ARPP21 (683465 downstream)																							AGGAAATGATAACTAGAAAGT	0.373													4	2	---	---	---	---	
ARPP21	10777	broad.mit.edu	37	3	35824912	35824912	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35824912delT	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc011axy.1_Intron|ARPP21_uc003cgf.2_Intron|ARPP21_uc003cgg.2_Intron	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD							cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3						TATTCTTGTGTTTTTTTTTTA	0.378													4	2	---	---	---	---	
ITGA9	3680	broad.mit.edu	37	3	37561894	37561894	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37561894delT	uc003chd.2	+						ITGA9_uc003chc.2_Intron	NM_002207	NP_002198	Q13797	ITA9_HUMAN	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)		ccaccatttatttatccacga	0.114													4	2	---	---	---	---	
TRAK1	22906	broad.mit.edu	37	3	42251012	42251012	+	Intron	DEL	A	-	-	rs71994031		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42251012delA	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron|TRAK1_uc011azj.1_Intron|TRAK1_uc003cla.2_Intron	NM_001042646	NP_001036111	Q9UPV9	TRAK1_HUMAN	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						ATTTTACTTTAAAAAAAAAAT	0.403													5	3	---	---	---	---	
DNAH12	201625	broad.mit.edu	37	3	57431722	57431725	+	Intron	DEL	AAAT	-	-	rs113596741		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57431722_57431725delAAAT	uc003dit.2	-							NM_178504	NP_848599	Q6ZR08	DYH12_HUMAN	dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2						caaaaaCATAaaataaataaataa	0.152													18	8	---	---	---	---	
FHIT	2272	broad.mit.edu	37	3	60962478	60962478	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60962478delG	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003	P49789	FHIT_HUMAN	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)		CTTTTACCATGGAGGCAGGGA	0.323			T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	64870831	64870831	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64870831delA	uc003dml.2	+											Homo sapiens cDNA FLJ25194 fis, clone REC04095.																		TTCAGAAATGAAAAAAAAAAA	0.343													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	76535687	76535687	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76535687delA								ZNF717 (701017 upstream) : ROBO2 (553607 downstream)																							ATTTTTTTCCAAAAAAATGTT	0.353													4	2	---	---	---	---	
ROBO1	6091	broad.mit.edu	37	3	79184624	79184624	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79184624delA	uc003dqe.2	-							NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	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)		GATCCAGCTTAAAGTTTCCAG	0.179													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90457358	90457358	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90457358delA								EPHA3 (926076 upstream) : None (None downstream)																							ctgctctatcaaaagaaaggt	0.000													4	2	---	---	---	---	
NFKBIZ	64332	broad.mit.edu	37	3	101574899	101574899	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101574899delT	uc003dvp.2	+						NFKBIZ_uc003dvo.2_Intron|NFKBIZ_uc010hpo.2_Intron|NFKBIZ_uc003dvq.2_Intron	NM_031419	NP_113607	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(2)	2						AAGCCCAGAAttttttttttt	0.184													8	4	---	---	---	---	
LOC344595	344595	broad.mit.edu	37	3	106968825	106968825	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106968825delT	uc010hpq.2	+						uc003dwh.1_RNA	NR_028302				Homo sapiens cDNA FLJ31372 fis, clone NB9N42000281.												0						cttggtggccttagtgaattg	0.149													4	2	---	---	---	---	
MYH15	22989	broad.mit.edu	37	3	108203165	108203166	+	Intron	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108203165_108203166insT	uc003dxa.1	-							NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						AAGAGTATAGATTTTTTTAAAT	0.351													4	2	---	---	---	---	
ZDHHC23	254887	broad.mit.edu	37	3	113673485	113673485	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113673485delT	uc003eau.2	+						ZDHHC23_uc003eav.2_Intron|ZDHHC23_uc003eaw.1_5'Flank	NM_173570	NP_775841	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC domain containing 23							integral to membrane	acyltransferase activity|zinc ion binding			ovary(2)	2						ACTTGTGGGGTTTTTTTTTTC	0.303													3	4	---	---	---	---	
PARP15	165631	broad.mit.edu	37	3	122296897	122296898	+	Intron	INS	-	T	T	rs35358934		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122296897_122296898insT	uc003efm.2	+						PARP15_uc003efn.2_Intron	NM_001113523	NP_001106995	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	NAD+ ADP-ribosyltransferase activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)	5				GBM - Glioblastoma multiforme(114;0.0531)		catttctggtggtttttttttt	0.238													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	129717844	129717844	+	IGR	DEL	G	-	-	rs139899778		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129717844delG								TRH (21068 upstream) : ALG1L2 (82830 downstream)																							AAAAAAAAAAGGAAGcagtct	0.184													5	5	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131981564	131981564	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131981564delT	uc003eom.2	-							NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						ATCAGAGGTATTGGTCTGCTT	0.284													4	2	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131999971	131999971	+	Intron	DEL	G	-	-	rs67821960		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131999971delG	uc003eom.2	-							NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						AAAACCATGAGAAAAAATTCA	0.149													1	5	---	---	---	---	
NPHP3	27031	broad.mit.edu	37	3	132438748	132438749	+	Intron	DEL	AT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132438748_132438749delAT	uc003epe.1	-						NCRNA00119_uc003epg.1_5'Flank|NPHP3_uc003epf.1_Intron|NCRNA00119_uc010htu.1_5'Flank	NM_153240	NP_694972	Q7Z494	NPHP3_HUMAN	nephrocystin 3						maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1						atatatatacatatatatatat	0.248													14	13	---	---	---	---	
ARMC8	25852	broad.mit.edu	37	3	138014950	138014950	+	3'UTR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138014950delT	uc003esa.1	+	23					TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_3'UTR|ARMC8_uc011bmg.1_3'UTR|ARMC8_uc011bmh.1_3'UTR|ARMC8_uc003esb.1_3'UTR|ARMC8_uc003esc.1_3'UTR|ARMC8_uc003esf.1_3'UTR	NM_015396	NP_056211	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8 isoform 2								binding				0						TTTGTTTTGGTTTTTTTTTCT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144637276	144637277	+	IGR	DEL	TG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144637276_144637277delTG								C3orf58 (926067 upstream) : None (None downstream)																							GTTCTGAGTTtgtgtgtgtgtg	0.327													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	146588662	146588662	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146588662delT								PLSCR5 (264659 upstream) : ZIC4 (515175 downstream)																							tttaaaatagttttttttaat	0.000													4	2	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	171013290	171013291	+	Intron	INS	-	C	C	rs34976926	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171013290_171013291insC	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	Q9UKE5	TNIK_HUMAN	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)			ACATCTCCTGTCCCCCAACTGC	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176968094	176968094	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176968094delA								TBL1XR1 (53046 upstream) : None (None downstream)																							AGCTGGTGGGAAAAAAGATTG	0.323													4	2	---	---	---	---	
FYTTD1	84248	broad.mit.edu	37	3	197504101	197504101	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197504101delG	uc003fyi.2	+						FYTTD1_uc011bui.1_Intron|FYTTD1_uc011buj.1_Intron|FYTTD1_uc011buk.1_Intron	NM_032288	NP_115664	Q96QD9	UIF_HUMAN	forty-two-three domain containing 1 isoform 1						mRNA export from nucleus	nuclear speck	mRNA binding|protein binding				0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)		TGTTTTTTATGTTTTAAAAAT	0.234													4	2	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	67784	67784	+	Intron	DEL	T	-	-	rs146895580		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67784delT	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_RNA|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		ggattgCttcttttttttttt	0.005													3	3	---	---	---	---	
LOC348926	348926	broad.mit.edu	37	4	3951121	3951122	+	Intron	INS	-	TGTC	TGTC	rs71636744		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3951121_3951122insTGTC	uc011bvu.1	-						LOC348926_uc003ghn.2_Intron	NR_024253				Homo sapiens hypothetical protein LOC348926, mRNA (cDNA clone IMAGE:4546485), partial cds.												0						cgttttcACTTTGTGCAGGAAG	0.297													8	5	---	---	---	---	
PPP2R2C	5522	broad.mit.edu	37	4	6501375	6501375	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6501375delT	uc011bwd.1	-						PPP2R2C_uc011bwe.1_Intron	NM_181876	NP_870991	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein						signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4						GAGGAGATGATTTTTTTTGTC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	30713682	30713682	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30713682delT								None (None upstream) : PCDH7 (8355 downstream)																							tttgctttgattagacattgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	31498952	31498952	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31498952delT								PCDH7 (350531 upstream) : None (None downstream)																							tcattttgcctggtattttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49246088	49246088	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49246088delA								CWH43 (181995 upstream) : None (None downstream)																							AAAAACAAACAAAAAAAAATG	0.249													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49533889	49533889	+	IGR	DEL	T	-	-	rs56205126	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49533889delT								CWH43 (469796 upstream) : None (None downstream)																							gaaaaaaaaattagcgggtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49642355	49642355	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49642355delA								CWH43 (578262 upstream) : None (None downstream)																							aatggaatggaatttaatgga	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	71166315	71166316	+	IGR	INS	-	G	G	rs146966041	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71166315_71166316insG								CSN3 (49172 upstream) : C4orf35 (34355 downstream)																							ACAACAACTGAGTTGCCATCCC	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	85302829	85302829	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85302829delA								AGPAT9 (775804 upstream) : NKX6-1 (111607 downstream)																							ggatactatgaaaaaaaaagc	0.164													4	2	---	---	---	---	
CDS1	1040	broad.mit.edu	37	4	85566802	85566802	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85566802delA	uc011ccv.1	+							NM_001263	NP_001254	Q92903	CDS1_HUMAN	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)		ACTAAGAGTTAAAAAGGGAGA	0.209													4	2	---	---	---	---	
ARHGAP24	83478	broad.mit.edu	37	4	86469029	86469029	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86469029delA	uc003hpk.2	+						ARHGAP24_uc003hpi.1_Intron|ARHGAP24_uc003hpj.2_Intron	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	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)		acttctacctactagtttttg	0.000													4	2	---	---	---	---	
BANK1	55024	broad.mit.edu	37	4	102644412	102644412	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102644412delA	uc003hvx.3	+							NM_001083907	NP_001077376	Q8NDB2	BANK1_HUMAN	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)		TCCAGAGGTTAAAAAAAAGAA	0.333													4	2	---	---	---	---	
SGMS2	166929	broad.mit.edu	37	4	108821035	108821035	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108821035delA	uc003hyl.3	+						uc003hym.1_Intron|SGMS2_uc003hyn.2_Intron|SGMS2_uc003hyo.2_Intron	NM_001136258	NP_001129730	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2						sphingomyelin biosynthetic process	integral to Golgi membrane|integral to plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			lung(1)	1				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)	Choline(DB00122)	CTTTTGTGCTAAAAAAATGTA	0.264													4	2	---	---	---	---	
CFI	3426	broad.mit.edu	37	4	110693737	110693738	+	Intron	INS	-	T	T	rs35970339		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110693737_110693738insT	uc003hzr.3	-						CFI_uc011cft.1_Intron|CFI_uc003hzs.3_Intron	NM_000204	NP_000195	P05156	CFAI_HUMAN	complement factor I preproprotein						complement activation, classical pathway|innate immune response|proteolysis	extracellular space|membrane	scavenger receptor activity|serine-type endopeptidase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		GAATTTGATCGttttttttttt	0.074													4	2	---	---	---	---	
MAD2L1	4085	broad.mit.edu	37	4	120983988	120983988	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120983988delG	uc003idl.2	-						MAD2L1_uc003idm.2_Intron	NM_002358	NP_002349	Q13257	MD2L1_HUMAN	MAD2-like 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of apoptosis|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of mitotic cell cycle spindle assembly checkpoint	condensed chromosome kinetochore|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity				0						atgttaaagaggggatctaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	124540287	124540287	+	IGR	DEL	T	-	-	rs112449259		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124540287delT								SPRY1 (215380 upstream) : LOC285419 (31135 downstream)																							ATGAAACACATTTTTTTTTTT	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	130685097	130685097	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130685097delT	uc003igv.2	-											Homo sapiens cDNA clone IMAGE:5265890.																		CTTAGAATGGTTCTGTCTAAC	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	133293548	133293549	+	IGR	DEL	CA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133293548_133293549delCA								None (None upstream) : PCDH10 (776921 downstream)																							cacaccacaccacacacacaca	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	148523443	148523443	+	IGR	DEL	A	-	-	rs80028214		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148523443delA								EDNRA (57337 upstream) : TMEM184C (15096 downstream)																							TTAGTACAAGAAAAAAAAAAT	0.438													4	2	---	---	---	---	
ARHGAP10	79658	broad.mit.edu	37	4	148847118	148847118	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148847118delA	uc003ilf.2	+						ARHGAP10_uc003ilg.2_Intron	NM_024605	NP_078881	A1A4S6	RHG10_HUMAN	Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		ttgctctaggagacaccatct	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	176178001	176178002	+	IGR	DEL	AA	-	-	rs77250187		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176178001_176178002delAA								ADAM29 (278671 upstream) : GPM6A (376087 downstream)																							ctggagcaacaaaagagtgccc	0.124													0	6	---	---	---	---	
GPM6A	2823	broad.mit.edu	37	4	176571312	176571312	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176571312delC	uc003iuf.2	-						GPM6A_uc011ckj.1_Intron|GPM6A_uc003iug.2_Intron|GPM6A_uc003iuh.2_Intron	NM_201591	NP_963885	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 2							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		TTCTGCTTTTCCCCCCGTACA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	184290500	184290500	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184290500delT								WWC2 (48573 upstream) : CDKN2AIP (75289 downstream)																							GCAAGTCAGGTGGTGTTAGGG	0.537													4	2	---	---	---	---	
SNX25	83891	broad.mit.edu	37	4	186184601	186184601	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186184601delA	uc003ixh.2	+							NM_031953	NP_114159	Q9H3E2	SNX25_HUMAN	sorting nexin 25						cell communication|protein transport	endosome membrane	phosphatidylinositol binding|signal transducer activity			ovary(2)|breast(2)|pancreas(1)	5		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		GGCTTATTCTAAAAATTTCCT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190100530	190100533	+	IGR	DEL	GCAG	-	-	rs142848430		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190100530_190100533delGCAG								None (None upstream) : FRG1 (761441 downstream)																							CTGATGCCACGCAGGCCGCTTTCG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190554100	190554101	+	IGR	INS	-	G	G	rs146405111		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190554100_190554101insG								None (None upstream) : FRG1 (307873 downstream)																							TGAAGAAATGACTCGGGACAAA	0.267													0	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190555504	190555505	+	IGR	INS	-	A	A	rs143138382		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190555504_190555505insA								None (None upstream) : FRG1 (306469 downstream)																							tctttggtgtcggGGGGAATGA	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190585061	190585062	+	IGR	DEL	AT	-	-	rs148561031		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190585061_190585062delAT								None (None upstream) : FRG1 (276912 downstream)																							TTTGAAACACATGTGTAGGAAT	0.351													10	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190642249	190642249	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190642249delA								None (None upstream) : FRG1 (219725 downstream)																							CAGATGAACCAGGAGTGTGAC	0.557													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190834817	190834818	+	Intron	DEL	TG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190834817_190834818delTG	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		gtggtttcactgtgcctcctcc	0.173													3	3	---	---	---	---	
TRIP13	9319	broad.mit.edu	37	5	895604	895610	+	Intron	DEL	ACTTATC	-	-	rs34308287		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:895604_895610delACTTATC	uc003jbr.2	+						BRD9_uc003jbn.2_5'Flank|BRD9_uc011cmb.1_5'Flank|BRD9_uc003jbo.2_5'Flank|BRD9_uc003jbq.2_5'Flank|BRD9_uc011cmc.1_5'Flank|TRIP13_uc010ite.1_Intron	NM_004237	NP_004228	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13						double-strand break repair|reciprocal meiotic recombination|synaptonemal complex assembly|transcription from RNA polymerase II promoter		ATP binding|identical protein binding|nucleoside-triphosphatase activity|transcription cofactor activity				0			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			CCTAAGGAAGACTTATCACTTACAGCA	0.478													3	3	---	---	---	---	
SLC6A3	6531	broad.mit.edu	37	5	1418975	1418978	+	Intron	DEL	ATCC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1418975_1418978delATCC	uc003jck.2	-							NM_001044	NP_001035	Q01959	SC6A3_HUMAN	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)	tccatccattatccatccatccat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2140199	2140200	+	IGR	DEL	CT	-	-	rs112976869		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2140199_2140200delCT								IRX4 (257319 upstream) : IRX2 (606081 downstream)																							CACACACACActctctctctct	0.406													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3310509	3310510	+	IGR	DEL	TC	-	-	rs148686327		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3310509_3310510delTC								C5orf38 (554997 upstream) : IRX1 (285658 downstream)																							GAGGCTGCAATCTCTCTGTCCT	0.460													4	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3744872	3744873	+	IGR	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3744872_3744873insA								IRX1 (143356 upstream) : None (None downstream)																							TGAAGATACATAAAAAAAAAAT	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4877980	4877980	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4877980delT								None (None upstream) : LOC340094 (156492 downstream)																							GGATGGGTACTTTTTTTTTTT	0.398													3	3	---	---	---	---	
SEMA5A	9037	broad.mit.edu	37	5	9171288	9171288	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9171288delT	uc003jek.2	-							NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						AATTCTGTCCTTTTTTTTCTT	0.408													4	2	---	---	---	---	
DNAH5	1767	broad.mit.edu	37	5	13837670	13837670	+	Intron	DEL	A	-	-	rs113448786		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13837670delA	uc003jfd.2	-							NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					ctatcttctcaaaaaaaaaaa	0.005									Kartagener_syndrome				7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	31068909	31068910	+	IGR	DEL	TT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31068909_31068910delTT								None (None upstream) : CDH6 (124886 downstream)																							GAATAAAAACTTTTTAAAATCA	0.342													4	5	---	---	---	---	
PDZD2	23037	broad.mit.edu	37	5	31870304	31870304	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31870304delG	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc011cnx.1_Intron	NM_178140	NP_835260	O15018	PDZD2_HUMAN	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						CACCTGCTGAGGGAAAAGGGC	0.333													4	2	---	---	---	---	
ZFR	51663	broad.mit.edu	37	5	32399914	32399914	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32399914delA	uc003jhr.1	-							NM_016107	NP_057191	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein						multicellular organismal development	chromosome|cytoplasm|nucleus	DNA binding|RNA binding|zinc ion binding				0				STAD - Stomach adenocarcinoma(35;0.19)		AAAAGTTAGCAAAAAAAAAAT	0.299													9	4	---	---	---	---	
IL7R	3575	broad.mit.edu	37	5	35860711	35860711	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35860711delT	uc003jjs.2	+						IL7R_uc011coo.1_Intron|IL7R_uc011cop.1_Intron	NM_002185	NP_002176	P16871	IL7RA_HUMAN	interleukin 7 receptor precursor						immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)|skin(1)	5	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			TTATGATGGATTTTTTTTTTC	0.318													4	2	---	---	---	---	
NUP155	9631	broad.mit.edu	37	5	37292320	37292320	+	Intron	DEL	T	-	-	rs34382591		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37292320delT	uc003jku.1	-						NUP155_uc003jkt.1_Intron|NUP155_uc010iuz.1_Intron	NM_153485	NP_705618	O75694	NU155_HUMAN	nucleoporin 155kDa isoform 1						carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CATTTGAAGAttttttttttt	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	39569592	39569592	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39569592delA								DAB2 (144257 upstream) : None (None downstream)																							CCAGCCAGCCAAAAATGCTCA	0.448													4	2	---	---	---	---	
CARD6	84674	broad.mit.edu	37	5	40852067	40852067	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40852067delA	uc003jmg.2	+							NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6						apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5						catctctattaaaaaaaaaaa	0.000													8	4	---	---	---	---	
EMB	133418	broad.mit.edu	37	5	49729073	49729073	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49729073delT	uc003jom.2	-						EMB_uc010ivr.2_Intron	NM_198449	NP_940851	Q6PCB8	EMB_HUMAN	embigin precursor							integral to membrane					0	Lung SC(58;0.218)	Lung NSC(810;0.0795)				ACAGACAAGGTTTTTTTTTTA	0.353													2	4	---	---	---	---	
ITGA1	3672	broad.mit.edu	37	5	52082683	52082683	+	5'Flank	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52082683delT	uc003jou.2	+						ITGA1_uc003jov.2_5'Flank|PELO_uc003jos.2_5'Flank|PELO_uc003jot.1_5'Flank	NM_181501	NP_852478	P56199	ITA1_HUMAN	integrin, alpha 1 precursor						axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TTCAACCTCCTTGGGTCTGCC	0.388													4	2	---	---	---	---	
HSPB3	8988	broad.mit.edu	37	5	53751384	53751385	+	5'Flank	INS	-	A	A	rs143819651	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53751384_53751385insA	uc003jph.1	+							NM_006308	NP_006299	Q12988	HSPB3_HUMAN	heat shock 27kDa protein 3						cell death|response to heat|response to unfolded protein	cytoplasm|nucleus					0		Lung NSC(810;0.00104)				GTGCTAAATGCACTGGGAAACA	0.446													3	5	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59512339	59512339	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59512339delA	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron|PDE4D_uc003jse.1_Intron	NM_006203	NP_006194	Q08499	PDE4D_HUMAN	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)	agcatagattaaaaaacagaa	0.040													4	2	---	---	---	---	
SV2C	22987	broad.mit.edu	37	5	75512919	75512919	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75512919delG	uc003kei.1	+							NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		ACAGCACACTGGGCCTCATCT	0.502													4	2	---	---	---	---	
F2R	2149	broad.mit.edu	37	5	76026029	76026029	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76026029delT	uc003ken.3	+							NM_001992	NP_001983	P25116	PAR1_HUMAN	coagulation factor II receptor precursor						activation of caspase activity|anatomical structure morphogenesis|connective tissue replacement involved in inflammatory response wound healing|negative regulation of cell proliferation|platelet activation|positive regulation of blood coagulation|positive regulation of cell migration|positive regulation of collagen biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JAK-STAT cascade|positive regulation of MAPKKK cascade|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of transcription, DNA-dependent|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	caveola|extracellular region|Golgi apparatus|integral to plasma membrane|platelet dense tubular network	receptor binding|thrombin receptor activity			ovary(3)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)	Streptokinase(DB00086)	acttcagttcttttatcttta	0.000													4	2	---	---	---	---	
BHMT	635	broad.mit.edu	37	5	78415277	78415277	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78415277delG	uc003kfu.3	+						BHMT_uc011cti.1_Intron	NM_001713	NP_001704	Q93088	BHMT1_HUMAN	betaine-homocysteine methyltransferase						protein methylation|regulation of homocysteine metabolic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	ATAGAGAAAAGGGTTCAACCT	0.358													76	44	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	88496003	88496003	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88496003delT								MEF2C (296134 upstream) : None (None downstream)																							ggatctggcctggggctgggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	89466081	89466081	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89466081delA								None (None upstream) : CETN3 (223450 downstream)																							ACATGCACACAAAAAATGCTC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	91821715	91821715	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91821715delT								None (None upstream) : FLJ42709 (923350 downstream)																							CAATTTGGTATTTTTTTTTTT	0.348													3	3	---	---	---	---	
FBXL17	64839	broad.mit.edu	37	5	107553141	107553141	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107553141delT	uc011cvc.1	-						FBXL17_uc003kon.3_Intron	NM_001163315	NP_001156787	Q9UF56	FXL17_HUMAN	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)		caccggcaactttttttttga	0.020													4	2	---	---	---	---	
PJA2	9867	broad.mit.edu	37	5	108735001	108735001	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108735001delA	uc003kos.3	-							NM_014819	NP_055634	O43164	PJA2_HUMAN	praja 2, RING-H2 motif containing						long-term memory|regulation of protein kinase A signaling cascade	cell junction|endoplasmic reticulum membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	ligase activity|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		aacaagagacaaagggcttgt	0.000													4	2	---	---	---	---	
CAMK4	814	broad.mit.edu	37	5	110599589	110599590	+	Intron	INS	-	T	T	rs140886406	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110599589_110599590insT	uc011cvj.1	+						CAMK4_uc003kpf.2_Intron|CAMK4_uc010jbv.2_Intron	NM_001744	NP_001735	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission	cytosol|nucleoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(3)|lung(2)	5		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		TTTTAAAGCACTTTCATAGTAT	0.282													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	114389018	114389018	+	IGR	DEL	G	-	-	rs147728306		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114389018delG								KCNN2 (556822 upstream) : TRIM36 (71449 downstream)																							gaagaagggtgggaggaaagg	0.000													4	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	117115221	117115221	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117115221delT								None (None upstream) : None (None downstream)																							AGCTTTCCTCTTTTTTTTTTA	0.423													9	4	---	---	---	---	
DMXL1	1657	broad.mit.edu	37	5	118560918	118560918	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118560918delT	uc003ksd.2	+						DMXL1_uc010jcl.1_Intron|DMXL1_uc010jcm.1_Intron	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	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)		ATTTTATTACTTTTTTTCAGT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	119574499	119574499	+	IGR	DEL	A	-	-	rs79061867		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119574499delA								FAM170A (602983 upstream) : PRR16 (225520 downstream)																							ATTTGCTAATAAAAAAAAAAG	0.308													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	125129430	125129431	+	IGR	DEL	TT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125129430_125129431delTT								None (None upstream) : GRAMD3 (566357 downstream)																							GATTTGAGTCTTTTTTTTTTTT	0.297													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	125305331	125305331	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125305331delT								None (None upstream) : GRAMD3 (390457 downstream)																							TGTATGTTTATTACAGTAGAT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129116190	129116190	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129116190delA								ADAMTS19 (41814 upstream) : CHSY3 (124333 downstream)																							cagaaaagacaaaaaaaaaaa	0.000													7	5	---	---	---	---	
CHSY3	337876	broad.mit.edu	37	5	129477598	129477599	+	Intron	INS	-	CTCT	CTCT	rs146968423	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129477598_129477599insCTCT	uc003kvd.2	+							NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3							Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		GGTGGAGCTCCCTCTGCTGGAG	0.495													10	6	---	---	---	---	
FSTL4	23105	broad.mit.edu	37	5	132816483	132816483	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132816483delG	uc003kyn.1	-							NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	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)			TCATGATCCTGAAGAAATGCT	0.458													4	2	---	---	---	---	
PKD2L2	27039	broad.mit.edu	37	5	137244280	137244280	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137244280delA	uc003lby.2	+						PKD2L2_uc003lbw.1_Intron|PKD2L2_uc003lbx.2_Intron|PKD2L2_uc011cyi.1_Intron	NM_014386	NP_055201	Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2							integral to membrane	calcium ion binding|ion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			actccatctcaaaaaaaaaaa	0.159													12	6	---	---	---	---	
NR3C1	2908	broad.mit.edu	37	5	142689517	142689517	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142689517delT	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	P04150	GCR_HUMAN	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)	CCCATTTTTATTGGGCAGTAA	0.294													56	33	---	---	---	---	
NR3C1	2908	broad.mit.edu	37	5	142760625	142760625	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142760625delA	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	P04150	GCR_HUMAN	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)	agactccaccaaaaaaatatt	0.000													4	2	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148380729	148380730	+	3'UTR	DEL	AC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148380729_148380730delAC	uc003lpu.2	-	17					SH3TC2_uc003lpp.1_Intron|SH3TC2_uc010jgw.2_3'UTR|SH3TC2_uc003lps.2_RNA|SH3TC2_uc003lpt.2_3'UTR|SH3TC2_uc010jgx.2_3'UTR	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGAAAATGAacacacacacac	0.277													4	2	---	---	---	---	
GEMIN5	25929	broad.mit.edu	37	5	154292267	154292267	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154292267delA	uc003lvx.3	-						GEMIN5_uc011ddk.1_Intron	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5						ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCTAAGTAACAAAAAAAAAAA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157681339	157681339	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157681339delC								CLINT1 (395171 upstream) : EBF1 (441585 downstream)																							ATCCGAGCTGCCCCCAGGGTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157906773	157906773	+	IGR	DEL	C	-	-	rs2963458	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157906773delC								CLINT1 (620605 upstream) : EBF1 (216151 downstream)																							TTTCTTTTTTCTTTTTTTTTT	0.264													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	158816377	158816377	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158816377delT								IL12B (58896 upstream) : LOC285627 (59187 downstream)																							gacaagaggattttttttttt	0.000													4	2	---	---	---	---	
ATP10B	23120	broad.mit.edu	37	5	160088194	160088194	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160088194delA	uc003lym.1	-						ATP10B_uc003lyp.2_Intron|ATP10B_uc011deg.1_Intron|ATP10B_uc003lyo.2_Intron	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			actctgtctcaaaaaaaaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	160336291	160336292	+	IGR	DEL	TG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160336291_160336292delTG								ATP10B (57072 upstream) : LOC285629 (22496 downstream)																							CAGCCAATGCTGTGTGTGTGTG	0.327													4	2	---	---	---	---	
WWC1	23286	broad.mit.edu	37	5	167862007	167862007	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167862007delA	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron|WWC1_uc003lzw.2_Intron|WWC1_uc010jjf.1_Intron	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		gagcaactggaaaaaaaaatg	0.000													6	3	---	---	---	---	
PANK3	79646	broad.mit.edu	37	5	167993043	167993044	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167993043_167993044delTG	uc003lzz.1	-	3	909_910	c.609_610delCA	c.(607-612)GACAACfs	p.D203fs		NM_024594	NP_078870	Q9H999	PANK3_HUMAN	pantothenate kinase 3	203_204					coenzyme A biosynthetic process	cytoplasm|nucleus	ATP binding|pantothenate kinase activity			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0441)|all_lung(126;0.0909)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0989)|OV - Ovarian serous cystadenocarcinoma(192;0.147)|Epithelial(171;0.188)		CGTTTATAGTTGTCTTTGGAAT	0.391													219	118	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	171229042	171229042	+	IGR	DEL	A	-	-	rs74575831		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171229042delA								FGF18 (344880 upstream) : FBXW11 (59514 downstream)																							gtctcaaaacaaaaaaaaaTT	0.020													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173993591	173993591	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173993591delG								HMP19 (457410 upstream) : MSX2 (157984 downstream)																							AGAGTAGGTTGGGGGCATGAA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174824116	174824116	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174824116delA								MSX2 (666215 upstream) : DRD1 (43560 downstream)																							TTCTGGTGGGAAAAAAAAGTG	0.498													3	3	---	---	---	---	
ZNF454	285676	broad.mit.edu	37	5	178380140	178380141	+	Intron	INS	-	ATT	ATT	rs138429463		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178380140_178380141insATT	uc003mjo.1	+						ZNF454_uc010jkz.1_Intron|ZNF454_uc003mjp.2_Intron	NM_182594	NP_872400	Q8N9F8	ZN454_HUMAN	zinc finger protein 454						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|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)	all cancers(165;0.234)		cagttttagacatgtattgaat	0.000													1	7	---	---	---	---	
EXOC2	55770	broad.mit.edu	37	6	529405	529409	+	Intron	DEL	AAAGA	-	-	rs10608942		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:529405_529409delAAAGA	uc003mtd.2	-						EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein						exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GAGGGCTGGCAAAGAAAAGTCTTCT	0.483													4	7	---	---	---	---	
C6orf201	404220	broad.mit.edu	37	6	4106204	4106204	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4106204delA	uc003mwa.3	+						C6orf201_uc003mvz.3_Intron|C6orf201_uc011dhw.1_Intron|C6orf201_uc003mwb.3_Intron	NM_001085401	NP_001078870	Q7Z4U5	CF201_HUMAN	hypothetical protein LOC404220												0	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				acaaggtatgaaaattcaaag	0.000													4	2	---	---	---	---	
LYRM4	57128	broad.mit.edu	37	6	5152856	5152859	+	Intron	DEL	CCTC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5152856_5152859delCCTC	uc003mwp.2	-						LYRM4_uc010jnu.2_Intron|LYRM4_uc003mwq.2_Intron|uc003mwn.1_Intron	NM_020408	NP_065141	Q9HD34	LYRM4_HUMAN	LYR motif containing 4 isoform 1							mitochondrion|nucleus					0	Ovarian(93;0.11)	all_hematologic(90;0.0901)				GTACACGCTTCCTCCCTCAGCCCC	0.544													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	9974072	9974073	+	Intron	INS	-	C	C	rs145281637	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9974072_9974073insC	uc003myn.2	-						uc010joi.1_Intron|uc010joj.1_Intron|uc003myp.1_Intron					RecName: Full=Orofacial cleft 1 candidate gene 1 protein; AltName: Full=Orofacial clefting chromosomal breakpoint region candidate 1 protein;																		CCCATTTACCTCCAGCTGAATA	0.421													4	4	---	---	---	---	
RANBP9	10048	broad.mit.edu	37	6	13691880	13691880	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13691880delT	uc003nbb.2	-						RANBP9_uc003nba.2_Intron	NM_005493	NP_005484	Q96S59	RANB9_HUMAN	RAN binding protein 9						axon guidance|microtubule nucleation|protein complex assembly	cytosol|microtubule associated complex|nucleus	Ran GTPase binding			lung(1)|skin(1)	2	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			AAACTCAGtgttttttttttg	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14227327	14227327	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14227327delA								CD83 (90181 upstream) : None (None downstream)																							ACCAAGGATGAAAAAAAAAAC	0.289													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	20506047	20506047	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20506047delC								E2F3 (12102 upstream) : CDKAL1 (28641 downstream)																							TTCCTCCAGGCCCTTTGTCCA	0.458													4	3	---	---	---	---	
HLA-G	3135	broad.mit.edu	37	6	29954179	29954179	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29954179delA	uc011dmb.1	+							NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						gaagcttcataagacacaaca	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	33307389	33307389	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33307389delT								DAXX (16596 upstream) : LYPLA2P1 (25126 downstream)																							GCTTTGCCTCTTTTTTTTTTT	0.368													12	6	---	---	---	---	
MTCH1	23787	broad.mit.edu	37	6	36951167	36951171	+	Intron	DEL	TCCAG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36951167_36951171delTCCAG	uc003ond.1	-						MTCH1_uc003onc.1_Intron|MTCH1_uc010jwo.1_Intron|MTCH1_uc003one.3_Intron|MTCH1_uc011dtt.1_Intron	NM_014341	NP_055156	Q9NZJ7	MTCH1_HUMAN	mitochondrial carrier homolog 1						activation of caspase activity|neuronal ion channel clustering|positive regulation of apoptosis|regulation of signal transduction|transport	integral to membrane|mitochondrial inner membrane	protein binding				0						GCTGTCCTTATCCAGTTTAGTCAAC	0.395													3	3	---	---	---	---	
TBC1D22B	55633	broad.mit.edu	37	6	37260256	37260257	+	Intron	INS	-	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37260256_37260257insC	uc003onn.2	+						TBC1D22B_uc010jwt.2_Intron	NM_017772	NP_060242	Q9NU19	TB22B_HUMAN	TBC1 domain family, member 22B							intracellular	Rab GTPase activator activity				0			OV - Ovarian serous cystadenocarcinoma(102;0.241)			TATCCTCCCCACCCCCCCGCCT	0.386													4	2	---	---	---	---	
KCNK5	8645	broad.mit.edu	37	6	39164982	39164983	+	Intron	INS	-	A	A	rs142769651	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39164982_39164983insA	uc003oon.2	-							NM_003740	NP_003731	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5						excretion	integral to plasma membrane	potassium channel activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2						CAGAGGGAGACAAAAAAAACCT	0.446													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	40178422	40178422	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40178422delC								MOCS1 (276168 upstream) : TDRG1 (167741 downstream)																							ctgcccagctcccccacttca	0.174													4	2	---	---	---	---	
TRERF1	55809	broad.mit.edu	37	6	42195938	42195939	+	3'UTR	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42195938_42195939insT	uc003osd.2	-	18					TRERF1_uc011duq.1_3'UTR|TRERF1_uc003osb.2_3'UTR|TRERF1_uc003osc.2_3'UTR|TRERF1_uc003ose.2_3'UTR	NM_033502	NP_277037	Q96PN7	TREF1_HUMAN	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)			AAGAAATAGGATTTTTTTTTCT	0.327													12	6	---	---	---	---	
UBR2	23304	broad.mit.edu	37	6	42652345	42652345	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42652345delA	uc011dur.1	+						UBR2_uc011dus.1_Intron|UBR2_uc003osh.2_Intron|UBR2_uc011dut.1_Intron|UBR2_uc011duu.1_5'Flank	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	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)			aaacaaaaacaaaaaaAAAAC	0.194													11	6	---	---	---	---	
RCAN2	10231	broad.mit.edu	37	6	46331172	46331172	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46331172delT	uc003oyc.1	-						RCAN2_uc003oyd.1_Intron			Q14206	RCAN2_HUMAN	SubName: Full=cDNA, FLJ92723, highly similar to Homo sapiens Down syndrome critical region gene 1-like 1 (DSCR1L1), mRNA;						calcium-mediated signaling|central nervous system development		nucleotide binding|protein phosphatase 2B binding				0						TAAAAATGTATTTTTTTTCTT	0.294													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57231358	57231359	+	Intron	INS	-	TG	TG	rs148204817		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57231358_57231359insTG	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	NM_000947	NP_000938	P49643	PRI2_HUMAN	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)		ATGCTGACGACTGTGAAACTAG	0.500													5	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57282780	57282780	+	Intron	DEL	T	-	-	rs11318624		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57282780delT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	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)		ACAAAGATTATAAATCATTAT	0.294													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57323077	57323077	+	Intron	DEL	G	-	-	rs67240761		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57323077delG	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	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)		aagcattgcaggaaaaaaaca	0.000													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57345003	57345004	+	Intron	INS	-	ATTTA	ATTTA	rs140856200	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57345003_57345004insATTTA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	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)		AGTACATTTGTATTTAGTAAGC	0.292													6	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57379495	57379496	+	Intron	INS	-	TA	TA	rs146172325		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57379495_57379496insTA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	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)		GCACAAACTTTTAGTTCACTGA	0.337													6	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57452282	57452285	+	Intron	DEL	TCTA	-	-	rs142927118		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57452282_57452285delTCTA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	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)		AGCTGTTCTTTCTATCTAAGTCAC	0.333													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57473359	57473359	+	Intron	DEL	T	-	-	rs1830753		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57473359delT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	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)		tgtctgaaaataaaaacataa	0.045													4	3	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65459499	65459499	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65459499delA	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						CGACTATTCTAAAAAAAAACA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	70296366	70296367	+	IGR	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70296366_70296367insA								BAI3 (196964 upstream) : LMBRD1 (89384 downstream)																							CAACCAAACTTAAAAAAAAAAA	0.307													3	3	---	---	---	---	
DDX43	55510	broad.mit.edu	37	6	74122242	74122243	+	Intron	INS	-	GT	GT			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74122242_74122243insGT	uc003pgw.2	+							NM_018665	NP_061135	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43							intracellular	ATP binding|ATP-dependent RNA helicase activity|RNA binding			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4						agagagagagagtgtgtgtgtg	0.134													3	5	---	---	---	---	
MYO6	4646	broad.mit.edu	37	6	76558432	76558432	+	Intron	DEL	T	-	-	rs11343853		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76558432delT	uc003pih.1	+						MYO6_uc003pig.1_Intron|MYO6_uc003pii.1_Intron	NM_004999	NP_004990	Q9UM54	MYO6_HUMAN	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)		TTCTGAGCTCTGTTTTGAACA	0.274													4	5	---	---	---	---	
ME1	4199	broad.mit.edu	37	6	84015287	84015287	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84015287delC	uc003pjy.2	-						ME1_uc011dzb.1_Intron|ME1_uc011dzc.1_Intron	NM_002395	NP_002386	P48163	MAOX_HUMAN	cytosolic malic enzyme 1						carbohydrate metabolic process|cellular lipid metabolic process|malate metabolic process|NADP biosynthetic process|response to carbohydrate stimulus|response to hormone stimulus	cytosol	ADP binding|electron carrier activity|malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|manganese ion binding|NAD binding|NADP binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)	NADH(DB00157)	aaggaacatgccttgagagtt	0.000													2	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	91353336	91353336	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91353336delT								MAP3K7 (56429 upstream) : None (None downstream)																							TACAGGTTGGTTTACTGGCTT	0.448													4	2	---	---	---	---	
GPR63	81491	broad.mit.edu	37	6	97269930	97269930	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97269930delA	uc010kcl.2	-						GPR63_uc003pou.2_Intron	NM_001143957	NP_001137429	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63							integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		ACACACACTTAAAAAAAAAAA	0.338													4	3	---	---	---	---	
PREP	5550	broad.mit.edu	37	6	105849495	105849496	+	Intron	INS	-	C	C	rs148929617	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105849495_105849496insC	uc003prc.2	-							NM_002726	NP_002717	P48147	PPCE_HUMAN	prolyl endopeptidase						proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	AAAGGAAACAACCTTTAAACCA	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	107189956	107189956	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107189956delG	uc003pro.1	-						uc003prn.1_Intron					Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1534000.																		TAACTTCCAAGCAGGAAGATG	0.279													4	2	---	---	---	---	
GSTM2P1	442245	broad.mit.edu	37	6	111368833	111368834	+	5'Flank	INS	-	TT	TT			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111368833_111368834insTT	uc003puq.2	-							NR_002932				Homo sapiens chromosome 1 truncated glutathione S-transferase M1 mRNA, complete cds.												0						cctgggataaattccacttgat	0.074													3	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	111974739	111974740	+	IGR	INS	-	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111974739_111974740insG								TRAF3IP2 (47265 upstream) : FYN (7747 downstream)																							CCCACTATTCAAAACAAGTACT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	115975670	115975670	+	IGR	DEL	A	-	-	rs67195690		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115975670delA								None (None upstream) : FRK (287023 downstream)																							TCTGACCAGTAAAAAAAAAAA	0.279													4	2	---	---	---	---	
SLC35F1	222553	broad.mit.edu	37	6	118418802	118418802	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118418802delT	uc003pxx.3	+							NM_001029858	NP_001025029	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1						transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)		TGAAGATTGCTTTATGCAGGA	0.403													4	2	---	---	---	---	
SAMD3	154075	broad.mit.edu	37	6	130542490	130542490	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130542490delG	uc003qbv.2	-						SAMD3_uc003qbx.2_Intron|SAMD3_uc003qbw.2_Intron	NM_001017373	NP_001017373	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3 isoform											ovary(1)	1				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)		TGACTAAAAAGGAAAAACGCA	0.090													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145407013	145407013	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145407013delT								UTRN (232845 upstream) : EPM2A (539433 downstream)																							gtcttcaaaatttttacctca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156629421	156629421	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156629421delA								MIR1202 (361408 upstream) : ARID1B (469665 downstream)																							AAACACTTGGAAAAATATTAA	0.333													4	2	---	---	---	---	
TULP4	56995	broad.mit.edu	37	6	158895552	158895552	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158895552delC	uc003qrf.2	+						TULP4_uc011efo.1_Intron|TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1						intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		ctcctctcagccaggcctctg	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165338125	165338125	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165338125delT								None (None upstream) : C6orf118 (355030 downstream)																							CAGGAAGAGGTTTTAGGTTAT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168451876	168451879	+	IGR	DEL	CCCT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168451876_168451879delCCCT								KIF25 (6107 upstream) : FRMD1 (4586 downstream)																							AATCCGCTGGCCCTCCCTCCCTCT	0.598													4	2	---	---	---	---	
MICALL2	79778	broad.mit.edu	37	7	1498817	1498818	+	Intron	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1498817_1498818insA	uc003skj.3	-							NM_182924	NP_891554	Q8IY33	MILK2_HUMAN	MICAL-like 2 isoform 1							cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		AGGCAGGACTTACATGAGGTCG	0.668													50	26	---	---	---	---	
EIF3B	8662	broad.mit.edu	37	7	2413039	2413040	+	Intron	DEL	GT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2413039_2413040delGT	uc003slx.2	+						EIF3B_uc003sly.2_Intron|EIF3B_uc003sma.2_Intron|EIF3B_uc003smb.2_5'Flank	NM_003751	NP_003742	P55884	EIF3B_HUMAN	eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	nucleotide binding|protein complex scaffold|translation initiation factor activity				0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		TAGGCGTGGGGTGTGTGTGTGT	0.609													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	2755553	2755554	+	IGR	DEL	CA	-	-	rs148928057		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2755553_2755554delCA								AMZ1 (484 upstream) : GNA12 (12189 downstream)																							ACGGTTCTTTCAGTTTTTAAAC	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	3116390	3116393	+	IGR	DEL	TGTA	-	-	rs60293270		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3116390_3116393delTGTA								CARD11 (32811 upstream) : SDK1 (224687 downstream)																							tgtgtgtgtgtgtatatatatatc	0.221													4	2	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	3677254	3677254	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3677254delA	uc003smx.2	+							NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	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)		CAGTAAACCTAAGGCAAGGCT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	6684379	6684379	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6684379delA								ZNF853 (20460 upstream) : ZNF12 (43685 downstream)																							CAAGTTCCAGAAAGGTCCGAG	0.358													4	2	---	---	---	---	
THSD7A	221981	broad.mit.edu	37	7	11441208	11441208	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11441208delT	uc003ssf.3	-							NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		ccatgcataattttttttttg	0.000										HNSCC(18;0.044)			5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	13899630	13899630	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13899630delG								None (None upstream) : ETV1 (31228 downstream)																							TATAGCATCTGGGACTATGGC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	15154669	15154670	+	IGR	INS	-	A	A	rs71549914		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15154669_15154670insA								DGKB (212119 upstream) : TMEM195 (85273 downstream)																							taagatgttacaaaaaaaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	17066184	17066185	+	IGR	INS	-	ATT	ATT	rs150486487	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17066184_17066185insATT								AGR3 (144571 upstream) : AHR (272091 downstream)																							AAACCTCTCTCAGTTGCTATCC	0.446													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25445988	25445988	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25445988delA								NPVF (177883 upstream) : MIR148A (543551 downstream)																							agaaaTTAGCAAAAAATACAA	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	34221553	34221553	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34221553delC								BMPER (27442 upstream) : AAA1 (168482 downstream)																							gctctgttctccacacttcat	0.000													4	2	---	---	---	---	
AOAH	313	broad.mit.edu	37	7	36556076	36556077	+	Intron	DEL	CA	-	-	rs71983755		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36556076_36556077delCA	uc003tfh.3	-						AOAH_uc010kxf.2_Intron|AOAH_uc011kba.1_Intron	NM_001637	NP_001628	P28039	AOAH_HUMAN	acyloxyacyl hydrolase precursor						inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity			skin(1)	1						gcacggataccacacacacaca	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	37861358	37861359	+	Intron	INS	-	A	A	rs151118719	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37861358_37861359insA	uc003tfl.2	+											Homo sapiens, clone IMAGE:3881224, mRNA.																		CTTTATTGGGGAAAAAAAATAG	0.252													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41860851	41860851	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41860851delT								LOC285954 (41877 upstream) : GLI3 (139699 downstream)																							atttttgtgctttttcctcat	0.000													4	2	---	---	---	---	
GLI3	2737	broad.mit.edu	37	7	42017541	42017541	+	Intron	DEL	T	-	-	rs68006817		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42017541delT	uc011kbh.1	-						GLI3_uc011kbg.1_Intron	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						AGTCCTGAAGTTTTTTTTTTT	0.373									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome		OREG0018015	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	3	---	---	---	---	
HECW1	23072	broad.mit.edu	37	7	43210621	43210621	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43210621delT	uc003tid.1	+						HECW1_uc011kbi.1_Intron|HECW1_uc003tie.1_Intron	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						TTTCGCTTCCTTACAAAAGCT	0.438													4	2	---	---	---	---	
PKD1L1	168507	broad.mit.edu	37	7	47869356	47869356	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47869356delC	uc003tny.1	-						C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_5'Flank	NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1						cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						caactactcaccaggcatggc	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52639714	52639714	+	IGR	DEL	C	-	-	rs75437694		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52639714delC								None (None upstream) : POM121L12 (463635 downstream)																							ataagacactcccagttctat	0.119													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	53016480	53016481	+	IGR	INS	-	AAACA	AAACA	rs140057665	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53016480_53016481insAAACA								None (None upstream) : POM121L12 (86868 downstream)																							aaagttgaaataaacaaaacaa	0.000													4	2	---	---	---	---	
VOPP1	81552	broad.mit.edu	37	7	55637615	55637615	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55637615delC	uc003tqs.2	-						VOPP1_uc011kcr.1_Intron	NM_030796	NP_110423	Q96AW1	VOPP1_HUMAN	EGFR-coamplified and overexpressed protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic vesicle membrane|endosome|integral to organelle membrane	signal transducer activity				0						CACAAGGCCACCCCTTAATTT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56546028	56546031	+	IGR	DEL	TGTG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56546028_56546031delTGTG								PSPH (361938 upstream) : DKFZp434L192 (17885 downstream)																							TGTGTACACCtgtgtgtgtgtgtg	0.377													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57626766	57626766	+	IGR	DEL	A	-	-	rs145469174		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57626766delA								ZNF716 (93501 upstream) : None (None downstream)																							TCACAAATAGAAATGTTTTCT	0.189													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57924142	57924143	+	IGR	DEL	AG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57924142_57924143delAG								ZNF716 (390877 upstream) : None (None downstream)																							AAGAAGAATCAGAGGTAAATTA	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61077032	61077032	+	IGR	DEL	A	-	-	rs74858662		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61077032delA								None (None upstream) : None (None downstream)																							tctctcttttaaaaaagctag	0.015													2	4	---	---	---	---	
VKORC1L1	154807	broad.mit.edu	37	7	65341022	65341023	+	Intron	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65341022_65341023insT	uc003tul.2	+						VKORC1L1_uc011kds.1_Intron	NM_173517	NP_775788	Q8N0U8	VKORL_HUMAN	vitamin K epoxide reductase complex, subunit							integral to membrane					0		Lung NSC(55;0.197)			Menadione(DB00170)|Warfarin(DB00682)	GTCCTCTATTATTTTGGGGAGG	0.327													4	2	---	---	---	---	
TPST1	8460	broad.mit.edu	37	7	65715473	65715474	+	Intron	DEL	TG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65715473_65715474delTG	uc003tuw.2	+						TPST1_uc010kzy.2_Intron|TPST1_uc010kzz.2_Intron|TPST1_uc010laa.2_Intron	NM_003596	NP_003587	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1						inflammatory response|peptidyl-tyrosine sulfation	Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity				0						ttattgattatgtgaccttgag	0.084													4	2	---	---	---	---	
LOC729156	729156	broad.mit.edu	37	7	66304731	66304731	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66304731delT	uc003tvj.1	-							NR_003934				Homo sapiens cDNA FLJ36054 fis, clone TESTI2018290.												0						TTTCTTTCCCttttttttttt	0.438													13	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67670191	67670191	+	IGR	DEL	A	-	-	rs80180743		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67670191delA								STAG3L4 (883679 upstream) : None (None downstream)																							catctcaaataaaaaaaaaaG	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68728248	68728249	+	IGR	DEL	CT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68728248_68728249delCT								None (None upstream) : AUTS2 (335656 downstream)																							AAGCTGATTCCTCTCTCTCTCT	0.282													7	4	---	---	---	---	
STYXL1	51657	broad.mit.edu	37	7	75633413	75633413	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75633413delT	uc003uej.3	-						STYXL1_uc003uef.2_Intron|STYXL1_uc011kgf.1_Intron|STYXL1_uc011kgg.1_Intron|STYXL1_uc003ueh.2_Intron|STYXL1_uc003uek.3_Intron|STYXL1_uc003uel.2_Intron|STYXL1_uc003uem.2_Intron|STYXL1_uc010ldg.1_Intron|STYXL1_uc010ldh.1_Intron|STYXL1_uc003uen.1_Intron	NM_016086	NP_057170	Q9Y6J8	STYL1_HUMAN	map kinase phosphatase-like protein MK-STYX						intracellular signal transduction|protein dephosphorylation	intracellular	protein binding|protein tyrosine/serine/threonine phosphatase activity				0						GACCCttgtctttttttttgt	0.080													4	2	---	---	---	---	
CCDC146	57639	broad.mit.edu	37	7	76921953	76921953	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76921953delG	uc003uga.2	+						CCDC146_uc010ldp.2_Intron|CCDC146_uc003ugc.2_Intron	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				aaaaaaaaaagaaCATCCCTT	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	79485077	79485078	+	IGR	INS	-	T	T	rs144130238	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79485077_79485078insT								MAGI2 (402187 upstream) : GNAI1 (279062 downstream)																							AGATTATAAAACCAACACTCAT	0.252													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84104493	84104493	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84104493delT								SEMA3A (280276 upstream) : SEMA3D (520381 downstream)																							GTGTGTTTTGTTTTTTTTTTA	0.383													4	2	---	---	---	---	
PEX1	5189	broad.mit.edu	37	7	92148504	92148504	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92148504delG	uc003uly.2	-						PEX1_uc011khr.1_Intron|PEX1_uc010ley.2_Intron|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_5'Flank	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1						microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			GTGTGTGTATGTTTTGGATGG	0.179													38	19	---	---	---	---	
ZNF3	7551	broad.mit.edu	37	7	99665438	99665438	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99665438delA	uc003usp.2	-							NM_017715	NP_060185	P17036	ZNF3_HUMAN	zinc finger protein 3 isoform 1						cell differentiation|leukocyte activation|multicellular organismal development	nucleus	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			CTACAATCTCAACTCTGAAAA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	109531268	109531268	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109531268delT								None (None upstream) : EIF3IP1 (68016 downstream)																							AAATATTTGGTGAAAATTATT	0.328													4	2	---	---	---	---	
IMMP2L	83943	broad.mit.edu	37	7	110646772	110646772	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110646772delA	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938	Q96T52	IMP2L_HUMAN	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)		AACCACTGCTAACAGGCTCTC	0.333													4	2	---	---	---	---	
DOCK4	9732	broad.mit.edu	37	7	111510264	111510264	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111510264delA	uc003vfx.2	-						DOCK4_uc003vfw.2_Intron|DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	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)				AGGCCAAGGTAATTTTTTTTC	0.373													4	2	---	---	---	---	
DOCK4	9732	broad.mit.edu	37	7	111845827	111845828	+	Intron	INS	-	AC	AC	rs149233596	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111845827_111845828insAC	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	Q8N1I0	DOCK4_HUMAN	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)				CTTCCAACTTGacacacacaca	0.554													15	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	115510017	115510017	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115510017delT								MDFIC (850754 upstream) : TFEC (65185 downstream)																							CACTTTCCCCTTACATGCCAG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	123307869	123307869	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123307869delA								LMOD2 (3722 upstream) : WASL (14132 downstream)																							CCAGTCTGGGAAAAAAAAGTC	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	124432106	124432107	+	5'Flank	INS	-	AC	AC	rs142678970	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124432106_124432107insAC	uc003vlj.1	-											Homo sapiens cDNA clone IMAGE:40146631.																		AGCACATAAAAacacacacaca	0.312													4	3	---	---	---	---	
UBE2H	7328	broad.mit.edu	37	7	129589593	129589593	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129589593delC	uc003vpf.1	-						UBE2H_uc003vpg.1_Intron	NM_003344	NP_003335	P62256	UBE2H_HUMAN	ubiquitin-conjugating enzyme E2H isoform 1						protein K11-linked ubiquitination|protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|ubiquitin-protein ligase activity			skin(1)	1	Melanoma(18;0.0435)					TCTCTCCCTACCCCCACACTG	0.498													4	2	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	132185854	132185855	+	Intron	INS	-	GT	GT	rs147796984	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132185854_132185855insGT	uc003vra.3	-						PLXNA4_uc003vrc.2_Intron|PLXNA4_uc003vrb.2_Intron	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						CTGCATGAGGCGTGTGTGTGTG	0.446													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	132415248	132415248	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132415248delT								PLXNA4 (81801 upstream) : CHCHD3 (54376 downstream)																							accttatacattttggcattg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	135028139	135028139	+	IGR	DEL	C	-	-	rs142364632	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135028139delC								STRA8 (84897 upstream) : CNOT4 (18414 downstream)																							ACTAATCCATCAACCAACACC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	135028140	135028140	+	IGR	DEL	A	-	-	rs5887730		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135028140delA								STRA8 (84898 upstream) : CNOT4 (18413 downstream)																							CTAATCCATCAACCAACACCA	0.542													4	2	---	---	---	---	
PTN	5764	broad.mit.edu	37	7	136967873	136967873	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136967873delG	uc003vtq.2	-						PTN_uc010lmx.2_Intron|PTN_uc003vtr.1_Intron	NM_002825	NP_002816	P21246	PTN_HUMAN	pleiotrophin						nervous system development|positive regulation of cell division|positive regulation of cell proliferation|transmembrane receptor protein tyrosine phosphatase signaling pathway	endoplasmic reticulum|extracellular space	growth factor activity|heparin binding|protein phosphatase inhibitor activity			upper_aerodigestive_tract(1)|pancreas(1)	2						CACACTGCTAGGAAGTGTCCA	0.458													3	3	---	---	---	---	
SLC37A3	84255	broad.mit.edu	37	7	140049238	140049238	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140049238delA	uc003vvo.2	-						SLC37A3_uc003vvp.2_Intron|SLC37A3_uc010lnh.2_Intron|SLC37A3_uc011kqz.1_Intron	NM_207113	NP_996996	Q8NCC5	SPX3_HUMAN	solute carrier family 37 (glycerol-3-phosphate						carbohydrate transport|transmembrane transport	integral to membrane				ovary(3)	3	Melanoma(164;0.0142)					CCTTGAGGGGAAAAAAATGCT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142109808	142109809	+	Intron	INS	-	T	T	rs34134616		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142109808_142109809insT	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		ACCCTCAGGGATTCTGTATAGT	0.525													4	4	---	---	---	---	
TRPV5	56302	broad.mit.edu	37	7	142633073	142633073	+	5'Flank	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142633073delA	uc003wby.1	-						TRPV5_uc003wbz.2_5'Flank	NM_019841	NP_062815	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel,						protein tetramerization	apical plasma membrane|integral to plasma membrane	calcium channel activity			ovary(3)|central_nervous_system(2)|skin(1)	6	Melanoma(164;0.059)					AAAGTTAAGTAAAAAAAAAAA	0.388													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	143435250	143435251	+	Intron	INS	-	T	T	rs139306514	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143435250_143435251insT	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																		ttatgaaatacttttttttcca	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	144138020	144138020	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144138020delA								NOBOX (30700 upstream) : TPK1 (11023 downstream)																							aattctttggaaaaaataaaa	0.000													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146067680	146067683	+	Intron	DEL	AATT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146067680_146067683delAATT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	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)			ccaaactgtgaattaatatagcct	0.000										HNSCC(39;0.1)			5	7	---	---	---	---	
GIMAP8	155038	broad.mit.edu	37	7	150157359	150157359	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150157359delA	uc003whj.2	+							NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8							endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		tcctctgctgaagtcaccctt	0.000													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151971449	151971450	+	Intron	INS	-	C	C	rs79820593		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151971449_151971450insC	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	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)		AGACTCACAGAAAAAAACACAA	0.287			N		medulloblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155212228	155212229	+	IGR	INS	-	CA	CA	rs139957162	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155212228_155212229insCA								INSIG1 (110286 upstream) : EN2 (38595 downstream)																							acatgaacacccacacacacac	0.149													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	156213273	156213273	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156213273delG								SHH (608306 upstream) : C7orf4 (119912 downstream)																							CTGTGTGTCTGGTGTACCATG	0.458													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158105230	158105231	+	Intron	DEL	AT	-	-	rs10566610		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158105230_158105231delAT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	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)		CTGCACACACATGTGCTCCAGT	0.282													2	4	---	---	---	---	
FBXO25	26260	broad.mit.edu	37	8	417342	417342	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:417342delA	uc003wox.2	+						FBXO25_uc003woy.2_Intron|FBXO25_uc003woz.2_Intron|FBXO25_uc003wpa.2_Intron	NM_183421	NP_904357	Q8TCJ0	FBX25_HUMAN	F-box only protein 25 isoform 1							nucleus|SCF ubiquitin ligase complex	actin binding|ubiquitin-protein ligase activity			lung(1)	1		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)		AACTTTCCCCAAAAAAATCTG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	1172746	1172746	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1172746delG								ERICH1 (491520 upstream) : DLGAP2 (276823 downstream)																							gacgggctctgctggtgagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2233738	2233738	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2233738delT								MYOM2 (140359 upstream) : CSMD1 (559138 downstream)																							CAACGTCCTATTTTTTTTTCC	0.428													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2269794	2269795	+	IGR	INS	-	T	T	rs146279030	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2269794_2269795insT								MYOM2 (176415 upstream) : CSMD1 (523081 downstream)																							cctcCTAtttattttttttgga	0.079													3	3	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3205827	3205828	+	Intron	INS	-	T	T	rs140023053	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3205827_3205828insT	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc003wqe.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	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)		TAGATCAGTGATTTTTTTTTAT	0.302													18	8	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3445034	3445034	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3445034delA	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	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)		GGGGAAACATAAATAGATGCT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	9225905	9225905	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9225905delT								PPP1R3B (216821 upstream) : TNKS (187540 downstream)																							TCAGCAGCCCTTTGAGTGCAC	0.438													4	2	---	---	---	---	
EFHA2	286097	broad.mit.edu	37	8	16961724	16961724	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16961724delG	uc003wxd.2	+							NM_181723	NP_859074	Q86XE3	EFHA2_HUMAN	EF-hand domain family, member A2							integral to membrane	calcium ion binding			skin(1)	1				Colorectal(111;0.0686)|COAD - Colon adenocarcinoma(73;0.239)		TAAAATGTGAGCTTTATTTTA	0.224													4	3	---	---	---	---	
PSD3	23362	broad.mit.edu	37	8	18470533	18470534	+	Intron	INS	-	ACA	ACA	rs137963515	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18470533_18470534insACA	uc003wza.2	-						PSD3_uc003wyx.3_Intron|PSD3_uc003wyy.2_Intron|PSD3_uc003wyz.2_Intron	NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	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)		CAGGTCAGAACACAAGAGCATG	0.450													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20341289	20341289	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20341289delC								LZTS1 (228486 upstream) : None (None downstream)																							CTTCAGCCATCCTCAGTGAGA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20659304	20659304	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20659304delC								LZTS1 (546501 upstream) : GFRA2 (890226 downstream)																							AAGCACAATGCCCCAGGCAAG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	22117815	22117815	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22117815delC								POLR3D (9136 upstream) : PIWIL2 (14995 downstream)																							cgcctgtaatcccagcactct	0.000													4	2	---	---	---	---	
R3HCC1	203069	broad.mit.edu	37	8	23144953	23144954	+	5'Flank	INS	-	G	G			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23144953_23144954insG	uc003xdf.2	+						R3HCC1_uc011kzt.1_5'Flank	NM_001136108	NP_001129580	Q9Y3T6	R3HC1_HUMAN	R3H domain and coiled-coil containing 1								nucleic acid binding|nucleotide binding			central_nervous_system(1)|skin(1)	2						TGATAGTGGCTGCCCAACCCAG	0.495													3	3	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	31661598	31661598	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31661598delC	uc003xip.2	+							NM_013962	NP_039256	Q02297	NRG1_HUMAN	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)		attgtcttttcccagtctcca	0.000													4	2	---	---	---	---	
ADAM18	8749	broad.mit.edu	37	8	39486649	39486649	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39486649delT	uc003xni.2	+						ADAM18_uc010lww.2_Intron|ADAM18_uc010lwx.2_Intron	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	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)			TATGTTTATGTTTTTTTTTTC	0.323													11	5	---	---	---	---	
AGPAT6	137964	broad.mit.edu	37	8	41479074	41479076	+	3'UTR	DEL	TGC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41479074_41479076delTGC	uc003xnz.2	+	13						NM_178819	NP_848934	Q86UL3	GPAT4_HUMAN	lysophosphatidic acid acyltransferase zeta						acyl-CoA metabolic process|lactation|phosphatidylcholine biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|membrane fraction	glycerol-3-phosphate O-acyltransferase activity				0	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			TAGATTTTTATGCTGCTGCTGAT	0.552													4	2	---	---	---	---	
TCEA1	6917	broad.mit.edu	37	8	54922592	54922593	+	Intron	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54922592_54922593insA	uc003xru.2	-						TCEA1_uc003xrv.2_Intron|TCEA1_uc011ldw.1_Intron|TCEA1_uc003xrw.1_Intron	NM_006756	NP_006747	P23193	TCEA1_HUMAN	transcription elongation factor A 1 isoform 1						positive regulation of viral transcription|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|translation elongation factor activity|zinc ion binding				0		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			TGACTGGTGCTAAAAAAAAAAG	0.332			T	PLAG1	salivary adenoma								3	3	---	---	---	---	
CLVS1	157807	broad.mit.edu	37	8	62321508	62321509	+	Intron	DEL	AG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62321508_62321509delAG	uc003xuh.2	+						CLVS1_uc003xui.2_Intron|CLVS1_uc010lyp.2_Intron	NM_173519	NP_775790	Q8IUQ0	CLVS1_HUMAN	retinaldehyde binding protein 1-like 1						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5						TCAAATCCTCAGGCCACTCATC	0.391													1	5	---	---	---	---	
CNBD1	168975	broad.mit.edu	37	8	88034440	88034440	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88034440delG	uc003ydy.2	+							NM_173538	NP_775809	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1											ovary(3)	3						cagcggagaagggaatgtctg	0.000													4	2	---	---	---	---	
OSGIN2	734	broad.mit.edu	37	8	90922897	90922898	+	Intron	INS	-	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90922897_90922898insC	uc003yeg.2	+						OSGIN2_uc003yeh.2_Intron	NM_004337	NP_004328	Q9Y236	OSGI2_HUMAN	oxidative stress induced growth inhibitor family						germ cell development|meiosis						0			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TGTTTCATTTTCCCCCTTACCT	0.401													4	2	---	---	---	---	
DPY19L4	286148	broad.mit.edu	37	8	95790462	95790463	+	Intron	INS	-	A	A	rs35068675		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95790462_95790463insA	uc003ygx.2	+							NM_181787	NP_861452	Q7Z388	D19L4_HUMAN	dpy-19-like 4							integral to membrane				ovary(2)	2	Breast(36;3.85e-06)					gactttgtctcaaaaaaaaaaa	0.114													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	97212566	97212566	+	IGR	DEL	A	-	-	rs77884243		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97212566delA								GDF6 (39546 upstream) : UQCRB (26744 downstream)																							gctttagcagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
BAALC	79870	broad.mit.edu	37	8	104224753	104224753	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104224753delA	uc003yld.2	+						BAALC_uc003yle.2_Intron|uc003ylf.2_Intron|BAALC_uc003ylg.2_5'Flank|BAALC_uc010mcc.2_5'Flank	NM_024812	NP_079088	Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic isoform 1							centrosome|membrane|nucleus					0			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)			aatttatcccaaggaagtaat	0.015													4	2	---	---	---	---	
RIMS2	9699	broad.mit.edu	37	8	104826652	104826652	+	Intron	DEL	A	-	-	rs68142003	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104826652delA	uc003ylp.2	+							NM_001100117	NP_001093587	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			taaaaaaaCTAAAAAAAAAAA	0.139										HNSCC(12;0.0054)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	106017058	106017058	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106017058delA								LRP12 (415838 upstream) : ZFPM2 (314089 downstream)																							GCGACTTCAGAAAAAAAAAAT	0.333													4	2	---	---	---	---	
ZFPM2	23414	broad.mit.edu	37	8	106526816	106526816	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106526816delT	uc003ymd.2	+							NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2						blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			agcgcattgcttttccttgcc	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	118634556	118634556	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118634556delT								MED30 (82057 upstream) : EXT1 (177046 downstream)																							aatgactcaatttttttttaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	126412328	126412330	+	IGR	DEL	GTG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126412328_126412330delGTG								NSMCE2 (32961 upstream) : TRIB1 (30233 downstream)																							ggctgttcctgtgtctcctccca	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134815498	134815498	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134815498delA								ST3GAL1 (231315 upstream) : ZFAT (674535 downstream)																							gtataaaaagaaaaaaaaaaT	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139987228	139987228	+	IGR	DEL	A	-	-	rs5895565		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139987228delA								COL22A1 (60992 upstream) : KCNK9 (625854 downstream)																							tgtataatggaaaaaaaaggt	0.000													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	140369798	140369798	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140369798delC								COL22A1 (443562 upstream) : KCNK9 (243284 downstream)																							AGGGCAAATACCCACAAAGCT	0.483													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141381729	141381730	+	Intron	INS	-	A	A	rs143137472	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141381729_141381730insA	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						tcagggtttacaaaagttttct	0.109													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	145938025	145938025	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145938025delT								ARHGAP39 (26831 upstream) : ZNF251 (8270 downstream)																							GACATGTTGCTTCCGGGCTCC	0.428													4	2	---	---	---	---	
KDM4C	23081	broad.mit.edu	37	9	7013568	7013568	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7013568delG	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						TATATGAACAGACATATAGAA	0.348													4	2	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	8355434	8355434	+	Intron	DEL	T	-	-	rs143508576		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8355434delT	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	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)		ATGGTTGACCTTTTAGTTCGA	0.308										TSP Lung(15;0.13)			4	2	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	8436344	8436345	+	Intron	INS	-	A	A	rs146664020	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8436344_8436345insA	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	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)		aaaataaaaataaaaaaCAGAA	0.144										TSP Lung(15;0.13)			5	3	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	9711927	9711927	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9711927delG	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	P23468	PTPRD_HUMAN	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)		GTTGTTCACTGGGAAAATAAG	0.388										TSP Lung(15;0.13)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	12385872	12385873	+	IGR	INS	-	A	A	rs143684433	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12385872_12385873insA								None (None upstream) : TYRP1 (307513 downstream)																							TATAGACCTGGAAAAAAGAAAG	0.327													1	5	---	---	---	---	
MTAP	4507	broad.mit.edu	37	9	21967162	21967163	+	Intron	INS	-	A	A	rs144944498		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21967162_21967163insA	uc003zpi.1	+						C9orf53_uc011lnm.1_RNA	NM_002451	NP_002442	Q13126	MTAP_HUMAN	5'-methylthioadenosine phosphorylase						nucleoside metabolic process	cytoplasm	phosphorylase activity|S-methyl-5-thioadenosine phosphorylase activity			central_nervous_system(1)	1		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)	Adenine(DB00173)	GCGTGTACCCTAAAAAAAAAAA	0.302													3	3	---	---	---	---	
LINGO2	158038	broad.mit.edu	37	9	28166159	28166160	+	Intron	DEL	AT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28166159_28166160delAT	uc003zqu.1	-						LINGO2_uc010mjf.1_Intron|LINGO2_uc003zqv.1_Intron	NM_152570	NP_689783	Q7L985	LIGO2_HUMAN	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)		GGTACAGAGCATATAAGGATGa	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66245063	66245064	+	IGR	INS	-	T	T	rs74614480		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66245063_66245064insT								FAM74A4 (750677 upstream) : LOC442421 (251406 downstream)																							aattgcgaatatgctgaaacaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68410449	68410451	+	Intron	DEL	CTT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68410449_68410451delCTT	uc004aew.1	+						uc004aex.2_5'Flank					Homo sapiens cDNA, FLJ98602.																		ttagattttacttcttctttctt	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	81535865	81535865	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81535865delT								PSAT1 (590858 upstream) : TLE4 (651013 downstream)																							ttgttcttcatttgattcctt	0.000													4	2	---	---	---	---	
SEMA4D	10507	broad.mit.edu	37	9	92099561	92099562	+	Intron	DEL	GT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92099561_92099562delGT	uc004aqp.1	-							NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1						anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2						TATATAtgtagtgtgtgtgtgg	0.040													4	2	---	---	---	---	
TXN	7295	broad.mit.edu	37	9	113007320	113007322	+	Intron	DEL	GAA	-	-	rs144802558		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113007320_113007322delGAA	uc004bep.1	-						TXN_uc004beq.1_Intron	NM_003329	NP_003320	P10599	THIO_HUMAN	thioredoxin						cell proliferation|cell-cell signaling|cellular component movement|electron transport chain|glycerol ether metabolic process|nucleobase, nucleoside and nucleotide interconversion|positive regulation of DNA binding|regulation of protein import into nucleus, translocation|response to radiation|signal transduction|transcription, DNA-dependent|transport	cytosol|extracellular region|nucleoplasm	electron carrier activity|protein binding|protein disulfide oxidoreductase activity				0				OV - Ovarian serous cystadenocarcinoma(323;7.36e-07)		TATTCTCAATGAAGAAGTTTTAT	0.345													6	4	---	---	---	---	
PPP6C	5537	broad.mit.edu	37	9	127913971	127913972	+	Intron	DEL	GT	-	-	rs73668905	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127913971_127913972delGT	uc004bpg.3	-						PPP6C_uc010mwv.2_Intron|PPP6C_uc010mww.2_Intron|PPP6C_uc011lzr.1_Intron	NM_002721	NP_002712	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2						GCTTGCTCCAGTGTAGCTTTCT	0.416													8	4	---	---	---	---	
RALGPS1	9649	broad.mit.edu	37	9	129868538	129868538	+	Intron	DEL	A	-	-	rs36083212		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129868538delA	uc004bqo.1	+						RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron|ANGPTL2_uc004bqr.1_Intron|ANGPTL2_uc010mxg.1_Intron	NM_014636	NP_055451	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1						GCCCAAGGGCACGTTTTACCC	0.438													4	2	---	---	---	---	
NUP188	23511	broad.mit.edu	37	9	131718489	131718490	+	Intron	INS	-	GC	GC	rs60109270		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131718489_131718490insGC	uc004bws.1	+						NUP188_uc004bwq.1_Intron	NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	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						tgtgtgtgtgtgcgtgtgtgtg	0.233													11	9	---	---	---	---	
MED27	9442	broad.mit.edu	37	9	134956404	134956404	+	5'Flank	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134956404delG	uc004cbe.1	-						MED27_uc004cbf.1_5'Flank|MED27_uc011mco.1_5'Flank|MED27_uc004cbg.3_5'Flank	NM_004269	NP_004260	Q6P2C8	MED27_HUMAN	mediator complex subunit 27						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleolus|transcription factor complex	protein binding|transcription coactivator activity			skin(1)	1		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		tagaggagctggggttgcata	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	6462502	6462502	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6462502delT								PFKFB3 (184997 upstream) : PRKCQ (6603 downstream)																							cactcccgccttttttttggt	0.000													4	2	---	---	---	---	
GATA3	2625	broad.mit.edu	37	10	8106259	8106265	+	Intron	DEL	TCTTTTC	-	-	rs60280763		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8106259_8106265delTCTTTTC	uc001ika.2	+						GATA3_uc001ijz.2_Intron	NM_002051	NP_002042	P23771	GATA3_HUMAN	GATA binding protein 3 isoform 2						aortic valve morphogenesis|blood coagulation|canonical Wnt receptor signaling pathway involved in metanephric kidney development|cardiac right ventricle morphogenesis|cell fate determination|cellular response to interferon-alpha|cellular response to interleukin-4|cellular response to tumor necrosis factor|defense response|ear development|lymphocyte migration|male gonad development|mesenchymal to epithelial transition|mesonephros development|negative regulation of cell cycle|negative regulation of cell motility|negative regulation of cell proliferation involved in mesonephros development|negative regulation of endothelial cell apoptosis|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation|negative regulation of inflammatory response|negative regulation of mammary gland epithelial cell proliferation|nephric duct formation|norepinephrine biosynthetic process|pharyngeal system development|phosphatidylinositol 3-kinase cascade|positive regulation of endothelial cell migration|positive regulation of interleukin-13 secretion|positive regulation of interleukin-4 production|positive regulation of interleukin-5 secretion|positive regulation of protein kinase B signaling cascade|positive regulation of T cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription regulatory region DNA binding|positive regulation of ureteric bud formation|regulation of cellular response to X-ray|regulation of cytokine biosynthetic process|regulation of nephron tubule epithelial cell differentiation|response to estrogen stimulus|response to virus|sympathetic nervous system development|T cell receptor signaling pathway|TOR signaling cascade|ureteric bud formation|uterus development|ventricular septum development	nuclear chromatin|nucleolus|nucleoplasm	core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|E-box binding|HMG box domain binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription coactivator activity|transcription factor binding|zinc ion binding			breast(17)|ovary(3)|central_nervous_system(2)	22						tttctttctttcttttcttcttcttct	0.329			F|N|S		breast		HDR syndrome (HYPOPARATHYROIDISM|SENSORINEURAL DEAFNESS|AND RENAL DISEASE)						7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10099763	10099764	+	5'Flank	INS	-	CTC	CTC	rs145339341	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10099763_10099764insCTC	uc001ikd.1	+											Homo sapiens cDNA clone IMAGE:5265675.																		TGCCCCTGCTTCTCCTGTATCA	0.223													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10277663	10277663	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10277663delG								None (None upstream) : SFTA1P (548739 downstream)																							gtacagatctggtcaagaaat	0.085													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14058486	14058487	+	Intron	DEL	TT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14058486_14058487delTT	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						CATCTGCCTCTTCCTGTCTGTT	0.475													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14089598	14089598	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14089598delC	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						TCCTCCTGTTCCCAGAACCCA	0.393													4	2	---	---	---	---	
FAM188A	80013	broad.mit.edu	37	10	15891040	15891041	+	Intron	DEL	GT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15891040_15891041delGT	uc001iod.1	-						FAM188A_uc001ioe.1_Intron|FAM188A_uc001iof.1_Intron	NM_024948	NP_079224	Q9H8M7	F188A_HUMAN	chromosome 10 open reading frame 97						apoptosis	nucleus	calcium ion binding			ovary(1)	1						actagtgcaggtgaagagagac	0.040													4	2	---	---	---	---	
CACNB2	783	broad.mit.edu	37	10	18718920	18718920	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18718920delA	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc010qcl.1_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron|CACNB2_uc001ipw.2_Intron|CACNB2_uc001ipx.2_Intron|CACNB2_uc009xkb.1_Intron|CACNB2_uc010qcm.1_Intron|CACNB2_uc001ipz.2_Intron|CACNB2_uc001ipy.2_Intron|CACNB2_uc010qcn.1_Intron|CACNB2_uc010qco.1_Intron|CACNB2_uc001iqa.2_Intron	NM_201596	NP_963890	Q08289	CACB2_HUMAN	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)	aaaacaaaacaaaaaaaGTCA	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31374516	31374516	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31374516delC								ZNF438 (53650 upstream) : LOC220930 (230942 downstream)																							AGTCATGGAACCCATTCTATT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42657140	42657140	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42657140delT								None (None upstream) : LOC441666 (170175 downstream)																							AGCATTTTAGTAcagtcacac	0.174													4	3	---	---	---	---	
ZNF488	118738	broad.mit.edu	37	10	48373058	48373059	+	3'UTR	DEL	CA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48373058_48373059delCA	uc001jex.2	+	2					ZNF488_uc001jey.2_3'UTR	NM_153034	NP_694579	Q96MN9	ZN488_HUMAN	zinc finger protein 488						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						atccattgtccacacacacaca	0.000													3	3	---	---	---	---	
FRMPD2	143162	broad.mit.edu	37	10	49449647	49449647	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49449647delG	uc001jgi.2	-						FRMPD2_uc001jgh.2_Intron|FRMPD2_uc001jgj.2_Intron	NM_001018071	NP_001018081	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2 isoform 3						tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding			large_intestine(1)	1				Kidney(211;0.201)		ccctgtctctgggttagcttg	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	59905729	59905730	+	IGR	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59905729_59905730insA								None (None upstream) : IPMK (49888 downstream)																							ATCAAGACAATTCAAATTTTGA	0.401													4	2	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	68128170	68128170	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68128170delT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	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						CTTCTGGATCTTTTTTTTTTC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	69634691	69634691	+	IGR	DEL	A	-	-	rs34328489		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69634691delA								DNAJC12 (36754 upstream) : SIRT1 (9736 downstream)																							AAAGAGGGAGAAAAAAAAAag	0.214													4	2	---	---	---	---	
AP3M1	26985	broad.mit.edu	37	10	75896174	75896174	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75896174delA	uc001jwf.2	-						AP3M1_uc001jwg.2_Intron|AP3M1_uc001jwh.2_Intron|AP3M1_uc010qla.1_Intron	NM_207012	NP_996895	Q9Y2T2	AP3M1_HUMAN	adaptor-related protein complex 3, mu 1 subunit						protein targeting to lysosome|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus|lysosome	protein binding				0	Prostate(51;0.0112)					GGTGTTTTAGAAAAAAAAAAA	0.279													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81281499	81281499	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81281499delA								EIF5AL1 (5309 upstream) : SFTPA2 (34110 downstream)																							AAGCAGAGAGAGGGAAAGGAA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81281503	81281503	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81281503delA								EIF5AL1 (5313 upstream) : SFTPA2 (34106 downstream)																							AGAGAGAGGGAAAGGAAGGAG	0.428													4	2	---	---	---	---	
BTAF1	9044	broad.mit.edu	37	10	93724358	93724358	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93724358delT	uc001khr.2	+						BTAF1_uc001khs.1_Intron|BTAF1_uc001kht.1_5'Flank	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)				CTCTGTGAACTTTTTTTTTGT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	96625948	96625948	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96625948delT								CYP2C19 (13278 upstream) : CYP2C9 (72467 downstream)																							TACTTACTAGTTTTTTTTTTG	0.393													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	101244990	101244991	+	IGR	INS	-	A	A	rs143092129	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101244990_101244991insA								GOT1 (54460 upstream) : NKX2-3 (47699 downstream)																							AGCTCTCTTCCAGTCCATTCCA	0.535													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102428382	102428383	+	IGR	DEL	AC	-	-	rs66647935		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102428382_102428383delAC								HIF1AN (114702 upstream) : PAX2 (77085 downstream)																							CAACCCTCCAacacacacacac	0.361													2	4	---	---	---	---	
C10orf76	79591	broad.mit.edu	37	10	103789686	103789686	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103789686delT	uc009xwy.1	-						C10orf76_uc001kui.2_Intron	NM_024541	NP_078817	Q5T2E6	CJ076_HUMAN	hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		tgtttgtttgttttttttttt	0.159													9	4	---	---	---	---	
VTI1A	143187	broad.mit.edu	37	10	114427612	114427612	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114427612delT	uc001kzy.2	+						VTI1A_uc001kzz.2_Intron	NM_145206	NP_660207	Q96AJ9	VTI1A_HUMAN	SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		AGCAGAATCATTAACATTACT	0.353													4	2	---	---	---	---	
GFRA1	2674	broad.mit.edu	37	10	117909837	117909837	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117909837delA	uc001lcj.2	-						GFRA1_uc001lci.2_Intron|GFRA1_uc009xyr.2_Intron	NM_005264	NP_005255	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1 isoform a						axon guidance	anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity			ovary(1)|pancreas(1)	2		Lung NSC(174;0.21)		all cancers(201;0.0337)		GCTCTTCCTTAAAAAAAAACT	0.473													4	2	---	---	---	---	
WDR11	55717	broad.mit.edu	37	10	122640169	122640169	+	Intron	DEL	A	-	-	rs72385528		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122640169delA	uc010qtf.1	+						WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2							integral to membrane					0						agaccatctcaaaaaaaaaaa	0.179													9	5	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127583479	127583480	+	Intron	INS	-	AG	AG	rs146232148		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127583479_127583480insAG	uc001ljg.1	-						FANK1_uc010quk.1_5'Flank|FANK1_uc001ljh.3_5'Flank|FANK1_uc009yan.2_5'Flank	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TGCTGATCTTTATACTTTCTGT	0.356													4	3	---	---	---	---	
FRG2B	441581	broad.mit.edu	37	10	135439939	135439940	+	Intron	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135439939_135439940insA	uc010qvg.1	-							NM_001080998	NP_001074467	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B							nucleus					0		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		ACACATTTCTCAAGTCCCCTGA	0.480													23	11	---	---	---	---	
IFITM2	10581	broad.mit.edu	37	11	308885	308886	+	Intron	INS	-	C	C	rs5789178		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:308885_308886insC	uc001lox.3	+							NM_006435	NP_006426	Q01629	IFM2_HUMAN	interferon induced transmembrane protein 2						response to virus|type I interferon-mediated signaling pathway	integral to membrane|plasma membrane	protein binding				0		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		GAGAGTCTGAGCCGGGTGAGGA	0.639													3	6	---	---	---	---	
MUC2	4583	broad.mit.edu	37	11	1086555	1086555	+	Intron	DEL	T	-	-	rs12225981		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1086555delT	uc001lsx.1	+							NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor							inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GACTGTGGGCTGGGGCCATGG	0.502													9	5	---	---	---	---	
TH	7054	broad.mit.edu	37	11	2194824	2194824	+	5'Flank	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2194824delG	uc001lvq.2	-						TH_uc001lvp.2_5'Flank|TH_uc001lvr.2_5'Flank|TH_uc010qxj.1_5'Flank|TH_uc001lvs.2_5'Flank|TH_uc001lvt.2_5'Flank	NM_199292	NP_954986	P07101	TY3H_HUMAN	tyrosine hydroxylase isoform a						dopamine biosynthetic process from tyrosine|embryonic camera-type eye morphogenesis|epinephrine biosynthetic process|eye photoreceptor cell development|heart morphogenesis|hormone biosynthetic process|learning|locomotory behavior|memory|neurotransmitter biosynthetic process|neurotransmitter secretion|norepinephrine biosynthetic process|pigmentation|regulation of heart contraction|response to ethanol|response to hypoxia|synaptic transmission, dopaminergic|visual perception	cytosol|internal side of plasma membrane|melanosome membrane|nucleus|perikaryon|smooth endoplasmic reticulum	protein binding|tyrosine 3-monooxygenase activity				0		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	gaacATCCCTGGGGGCAGGGA	0.343											OREG0020678	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
RPL27A	6157	broad.mit.edu	37	11	8704976	8704977	+	Intron	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8704976_8704977insA	uc001mgs.3	+						SNORA3_uc001mgq.1_5'Flank|SNORA45_uc001mgr.1_5'Flank	NM_000990	NP_000981	P46776	RL27A_HUMAN	ribosomal protein L27a						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0				Epithelial(150;3.24e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAGTTCTAAGGAATTTCACATC	0.426													4	2	---	---	---	---	
GALNTL4	374378	broad.mit.edu	37	11	11435614	11435614	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11435614delC	uc001mjo.2	-							NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		tttccttcatcccctacattc	0.000													4	2	---	---	---	---	
LDHC	3948	broad.mit.edu	37	11	18471590	18471590	+	Intron	DEL	T	-	-	rs77905030		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18471590delT	uc001mon.3	+						LDHC_uc001mom.3_Intron|LDHC_uc009yhp.2_Intron|LDHC_uc001moo.3_Intron|LDHC_uc009yhq.2_Intron|LDHC_uc009yhr.2_Intron	NM_017448	NP_059144	P07864	LDHC_HUMAN	L-lactate dehydrogenase C						glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)	ACTGGGTGTCTTTTTTTTTTT	0.428													3	5	---	---	---	---	
PTPN5	84867	broad.mit.edu	37	11	18779155	18779155	+	Intron	DEL	C	-	-	rs5790049		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18779155delC	uc001mpd.2	-						PTPN5_uc001mpb.2_Intron|PTPN5_uc001mpc.2_Intron|PTPN5_uc001mpe.2_Intron|PTPN5_uc010rdj.1_Intron|PTPN5_uc001mpf.2_Intron|PTPN5_uc010rdk.1_Intron	NM_006906	NP_008837	P54829	PTN5_HUMAN	protein-tyrosine-phosphatase non-receptor 5							integral to membrane	phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(2)	2						ctagAACtggctaaggtgact	0.005													6	3	---	---	---	---	
NAV2	89797	broad.mit.edu	37	11	20004504	20004504	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20004504delC	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						GCTCAGCTGACCCTGTTTCAG	0.383													4	2	---	---	---	---	
PRMT3	10196	broad.mit.edu	37	11	20413462	20413462	+	Intron	DEL	T	-	-	rs11351468		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20413462delT	uc001mqb.2	+						PRMT3_uc001mqc.2_Intron|PRMT3_uc010rdn.1_Intron	NM_005788	NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3 isoform 1								zinc ion binding				0						AATGTGGATCTTAATTTTCCA	0.294													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	20603531	20603532	+	IGR	DEL	TC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20603531_20603532delTC								PRMT3 (72654 upstream) : SLC6A5 (17414 downstream)																							AGGTGCAAGATCTCTCTCTCTC	0.450													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	25919594	25919594	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25919594delT								LUZP2 (815412 upstream) : ANO3 (291235 downstream)																							AAAAAAGTGCTTtttttttgg	0.174													3	3	---	---	---	---	
DCDC1	341019	broad.mit.edu	37	11	31366695	31366695	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31366695delT	uc001msv.2	-						DCDC1_uc001msu.1_Intron	NM_181807	NP_861523	P59894	DCDC1_HUMAN	doublecortin domain containing 1						intracellular signal transduction					skin(1)	1	Lung SC(675;0.225)					tcaaaggccattttttaaaaa	0.000													4	2	---	---	---	---	
QSER1	79832	broad.mit.edu	37	11	32998372	32998372	+	3'UTR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32998372delT	uc001mty.2	+	13					QSER1_uc001mtz.1_Intron	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1											ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					AAAGTAACGATTTTTTTTTTC	0.333													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	33444609	33444609	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33444609delG								HIPK3 (68670 upstream) : C11orf41 (119268 downstream)																							TTTCTTTGCTGGTTTGGCCTT	0.144													4	2	---	---	---	---	
PAMR1	25891	broad.mit.edu	37	11	35495755	35495755	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35495755delT	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2						GGATGTTTGCTTTTTTCTGAA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	39928961	39928961	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39928961delA								None (None upstream) : LRRC4C (206792 downstream)																							ACTTGTCAGGAAAAAAAAAAA	0.373													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44790040	44790040	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44790040delT								CD82 (148727 upstream) : TSPAN18 (91839 downstream)																							tgttccaggattttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	47670226	47670226	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47670226delG								MTCH2 (6020 upstream) : AGBL2 (10919 downstream)																							CTAAGGATCTGGGTTGCTAGG	0.368													4	2	---	---	---	---	
SYT7	9066	broad.mit.edu	37	11	61329550	61329551	+	Intron	DEL	AC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61329550_61329551delAC	uc001nrv.2	-						SYT7_uc009ynr.2_Intron	NM_004200	NP_004191	O43581	SYT7_HUMAN	synaptotagmin VII							cell junction|integral to membrane|synaptic vesicle membrane	transporter activity			ovary(3)|pancreas(1)	4						gcacgcacgtacacacacacac	0.139													4	2	---	---	---	---	
STX5	6811	broad.mit.edu	37	11	62598291	62598291	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62598291delA	uc001nvh.2	-						STX5_uc010rmi.1_Intron|STX5_uc009yoh.2_Intron|STX5_uc001nvi.2_Intron|STX5_uc010rmj.1_Intron|STX5_uc001nvj.2_Intron	NM_003164	NP_003155	Q13190	STX5_HUMAN	syntaxin 5						intracellular protein transport|retrograde transport, endosome to Golgi|vesicle targeting	ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane|nucleus|SNARE complex	protein N-terminus binding|SNAP receptor activity			ovary(1)|breast(1)	2						GATTCCTCACAAAAAAAAGTC	0.463													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	62715165	62715165	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62715165delT								CHRM1 (26153 upstream) : SLC22A6 (28905 downstream)																							GCCTATTAAGTTTTTTATGCT	0.423													4	2	---	---	---	---	
FERMT3	83706	broad.mit.edu	37	11	63990997	63990997	+	3'UTR	DEL	C	-	-	rs34304595		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63990997delC	uc001nyl.2	+	15					FERMT3_uc001nym.2_3'UTR|NUDT22_uc009ypd.2_5'Flank|NUDT22_uc001nyp.3_5'Flank|NUDT22_uc009ype.2_5'Flank|NUDT22_uc001nyq.3_5'Flank	NM_178443	NP_848537	Q86UX7	URP2_HUMAN	fermitin family homolog 3 long form						integrin activation|leukocyte cell-cell adhesion|platelet aggregation|regulation of cell-cell adhesion mediated by integrin	cell junction|cell projection|podosome	integrin binding			ovary(1)	1						CTGCTCACCACCCTGTCACAG	0.662													9	4	---	---	---	---	
RHOD	29984	broad.mit.edu	37	11	66831930	66831930	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66831930delG	uc001ojv.2	+							NM_014578	NP_055393	O00212	RHOD_HUMAN	ras homolog D precursor						regulation of small GTPase mediated signal transduction|Rho protein signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity				0						GGGGCGCATTGGGGCATTCTG	0.303													4	2	---	---	---	---	
LRP5	4041	broad.mit.edu	37	11	68115834	68115834	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68115834delG	uc001ont.2	+						LRP5_uc009ysg.2_Intron	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein						adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7						ATGAACCCGTGGGGGGGTTGG	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	68951676	68951676	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68951676delT								TPCN2 (21769 upstream) : MYEOV (109946 downstream)																							ttttcttttcttttttttgag	0.000													4	2	---	---	---	---	
DHCR7	1717	broad.mit.edu	37	11	71157105	71157105	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71157105delG	uc001oqk.2	-						DHCR7_uc001oql.2_Intron	NM_001163817	NP_001157289	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase						cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|nuclear outer membrane	7-dehydrocholesterol reductase activity|protein binding			ovary(1)|liver(1)	2					NADH(DB00157)	gcaggggcaagtcccaagagg	0.000									Smith-Lemli-Opitz_syndrome				2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71529536	71529550	+	IGR	DEL	AGGGGTATCAGGAAA	-	-	rs3952333		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71529536_71529550delAGGGGTATCAGGAAA								FAM86C (17260 upstream) : DEFB108B (14696 downstream)																							TAGTCTTCACAGGGGTATCAGGAAAAGAGTCAGCA	0.335													5	4	---	---	---	---	
FCHSD2	9873	broad.mit.edu	37	11	72549650	72549650	+	3'UTR	DEL	A	-	-	rs113447165		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72549650delA	uc009ytl.2	-	20					FCHSD2_uc010rrg.1_3'UTR|FCHSD2_uc001oth.3_3'UTR|ATG16L2_uc009ytj.1_Intron	NM_014824	NP_055639	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2								protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			AAATGACAACAAAAAAAAAAG	0.453													14	7	---	---	---	---	
FCHSD2	9873	broad.mit.edu	37	11	72811908	72811909	+	Intron	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72811908_72811909insT	uc009ytl.2	-						FCHSD2_uc010rrg.1_Intron|FCHSD2_uc001oth.3_Intron|FCHSD2_uc001oti.2_Intron	NM_014824	NP_055639	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2								protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			TCTACGTGGGATTTTTTTTTTT	0.312													5	3	---	---	---	---	
C2CD3	26005	broad.mit.edu	37	11	73861201	73861201	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73861201delA	uc001ouu.2	-						C2CD3_uc001ouv.2_Intron	NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3							centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)					ttcCTTTTGTAAAAAAAAAAA	0.050													1	5	---	---	---	---	
KCNE3	10008	broad.mit.edu	37	11	74170756	74170756	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74170756delC	uc001ovc.2	-						KCNE3_uc001ovd.2_Intron	NM_005472	NP_005463	Q9Y6H6	KCNE3_HUMAN	potassium voltage-gated channel, Isk-related							integral to membrane	voltage-gated potassium channel activity			ovary(1)	1	Breast(11;2.86e-06)					GCCTTCCCTTCCCCCCAGCAC	0.488													4	2	---	---	---	---	
SLCO2B1	11309	broad.mit.edu	37	11	74815575	74815576	+	Intron	DEL	AT	-	-	rs34275576		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74815575_74815576delAT	uc010rrp.1	+									O94956	SO2B1_HUMAN	Homo sapiens mRNA for KIAA0880 protein, partial cds.						sodium-independent organic anion transport	integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|breast(1)	2					Ergoloid mesylate(DB01049)	atGTGTAAACATGTGAAAATAT	0.262													15	14	---	---	---	---	
PICALM	8301	broad.mit.edu	37	11	85696723	85696723	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85696723delA	uc001pbm.2	-						PICALM_uc001pbl.2_Intron|PICALM_uc001pbn.2_Intron|PICALM_uc010rtl.1_Intron|PICALM_uc010rtk.1_Intron|PICALM_uc001pbo.1_Intron	NM_007166	NP_009097	Q13492	PICAL_HUMAN	phosphatidylinositol-binding clathrin assembly						clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				CTCTTTACATAAAAAGCGAAT	0.303			T	MLLT10|MLL	TALL|AML|								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	87066101	87066101	+	IGR	DEL	T	-	-	rs5793248		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87066101delT								TMEM135 (31533 upstream) : RAB38 (780330 downstream)																							AATGGACACATTTTTTTTTTC	0.453													3	4	---	---	---	---	
NOX4	50507	broad.mit.edu	37	11	89075998	89075999	+	Intron	DEL	AG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89075998_89075999delAG	uc001pct.2	-						NOX4_uc009yvr.2_Intron|NOX4_uc001pcu.2_Intron|NOX4_uc001pcw.2_Intron|NOX4_uc001pcx.2_Intron|NOX4_uc001pcv.2_Intron|NOX4_uc009yvo.2_Intron|NOX4_uc010rtu.1_Intron|NOX4_uc009yvp.2_Intron|NOX4_uc010rtv.1_Intron|NOX4_uc009yvq.2_Intron	NM_016931	NP_058627	Q9NPH5	NOX4_HUMAN	NADPH oxidase 4 isoform a						cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation	endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus	electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				TGTGTGAGACAGAGAGAGAGAG	0.272													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	89989684	89989684	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89989684delA								CHORDC1 (33152 upstream) : MIR1261 (612605 downstream)																							AGCAGTGGGCAAGTATGTGGC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	90226797	90226798	+	IGR	INS	-	TCT	TCT	rs144566527	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90226797_90226798insTCT								CHORDC1 (270265 upstream) : MIR1261 (375491 downstream)																							ATAGCCCCCACTCTTCTTTGTT	0.475													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	90864448	90864449	+	IGR	DEL	CT	-	-	rs141373601		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90864448_90864449delCT								MIR1261 (262078 upstream) : None (None downstream)																							GGAAATGGGACTCTCTTTGTAT	0.361													4	3	---	---	---	---	
C11orf54	28970	broad.mit.edu	37	11	93486742	93486742	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93486742delC	uc009ywi.2	+						C11orf54_uc001pee.1_Intron|C11orf54_uc001pef.2_Intron|C11orf54_uc001peg.2_Intron|C11orf54_uc001peh.2_Intron|C11orf54_uc001pei.2_Intron|C11orf54_uc001pej.2_Intron|C11orf54_uc001pek.2_5'Flank	NM_014039	NP_054758	Q9H0W9	CK054_HUMAN	hypothetical protein LOC28970							nucleus	hydrolase activity, acting on ester bonds|protein binding|zinc ion binding				0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				ATTTGTAAAACTTTATGATAA	0.318													68	36	---	---	---	---	
C11orf54	28970	broad.mit.edu	37	11	93486744	93486746	+	Intron	DEL	TTA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93486744_93486746delTTA	uc009ywi.2	+						C11orf54_uc001pee.1_Intron|C11orf54_uc001pef.2_Intron|C11orf54_uc001peg.2_Intron|C11orf54_uc001peh.2_Intron|C11orf54_uc001pei.2_Intron|C11orf54_uc001pej.2_Intron|C11orf54_uc001pek.2_5'Flank	NM_014039	NP_054758	Q9H0W9	CK054_HUMAN	hypothetical protein LOC28970							nucleus	hydrolase activity, acting on ester bonds|protein binding|zinc ion binding				0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TTGTAAAACTTTATGATAATGGA	0.320													70	36	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	93932944	93932947	+	IGR	DEL	TGAT	-	-	rs137910271		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93932944_93932947delTGAT								PANX1 (17809 upstream) : FOLR4 (105856 downstream)																							GTTGATTAACTGATTGATTGATTC	0.407													5	3	---	---	---	---	
MRE11A	4361	broad.mit.edu	37	11	94175708	94175708	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94175708delG	uc001peu.2	-						MRE11A_uc001pev.2_Intron|MRE11A_uc009ywj.2_Intron	NM_005591	NP_005582	P49959	MRE11_HUMAN	meiotic recombination 11 homolog A isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase	Mre11 complex|nucleoplasm	3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity			breast(4)|lung(1)	5		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				AGGTAAAGGTGGGTAATCTAC	0.214								Homologous_recombination	Ataxia-Telangiectasia-Like_Disorder				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	101485551	101485551	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101485551delG								TRPC6 (30892 upstream) : ANGPTL5 (275855 downstream)																							catggaagatggggggacagg	0.000													4	2	---	---	---	---	
AASDHPPT	60496	broad.mit.edu	37	11	105950677	105950677	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105950677delG	uc001pjc.1	+						KBTBD3_uc001pja.2_5'Flank|KBTBD3_uc001pjb.2_5'Flank|KBTBD3_uc009yxm.2_5'Flank|AASDHPPT_uc010rvn.1_Intron	NM_015423	NP_056238	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde						macromolecule biosynthetic process|pantothenate metabolic process	cytosol	holo-[acyl-carrier-protein] synthase activity|magnesium ion binding|protein binding				0		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		AATATTAAGTGAAATTTTTTT	0.249													4	2	---	---	---	---	
ARHGAP20	57569	broad.mit.edu	37	11	110561521	110561521	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110561521delA	uc001pkz.1	-						ARHGAP20_uc001pky.1_Intron|ARHGAP20_uc009yyb.1_Intron|ARHGAP20_uc001pla.1_Intron	NM_020809	NP_065860	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)|kidney(2)	5		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		TAGGATAGTTAAAAAAAAAAC	0.308													9	5	---	---	---	---	
ALG9	79796	broad.mit.edu	37	11	111669318	111669318	+	Intron	DEL	A	-	-	rs78440181		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111669318delA	uc001pmb.2	-						ALG9_uc001ply.2_Intron|ALG9_uc001plz.2_Intron|ALG9_uc010rwm.1_Intron|ALG9_uc010rwn.1_Intron|ALG9_uc010rwo.1_Intron	NM_001077690	NP_001071158	Q9H6U8	ALG9_HUMAN	asparagine-linked glycosylation 9 protein						dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,2-mannosyltransferase activity			large_intestine(1)|ovary(1)	2		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)		TGCTTCAAAGAAAAAAAAATC	0.353													4	2	---	---	---	---	
NCAM1	4684	broad.mit.edu	37	11	113024175	113024176	+	Intron	INS	-	GA	GA	rs139651919	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113024175_113024176insGA	uc009yyq.1	+						NCAM1_uc001pno.2_Intron	NM_001076682	NP_001070150	P13591	NCAM1_HUMAN	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)		agacagagagtgagagagagag	0.361													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	117831569	117831569	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117831569delA								TMPRSS13 (31454 upstream) : IL10RA (25537 downstream)																							cccaaagcacaaaaatatgca	0.000													4	2	---	---	---	---	
POU2F3	25833	broad.mit.edu	37	11	120187585	120187585	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120187585delT	uc001pxc.2	+						POU2F3_uc010rzk.1_Intron|POU2F3_uc010rzl.1_Intron|POU2F3_uc001pxe.1_Intron|POU2F3_uc001pxf.1_5'Flank	NM_014352	NP_055167	Q9UKI9	PO2F3_HUMAN	POU transcription factor						negative regulation by host of viral transcription	cytoplasm	sequence-specific DNA binding			ovary(1)|skin(1)	2		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)		CTTCTTGTTCTTTTTCTCCTA	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	121610191	121610191	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121610191delT								SORL1 (105720 upstream) : LOC399959 (349620 downstream)																							ATTTGTTTGCttttttttttg	0.025													4	3	---	---	---	---	
PUS3	83480	broad.mit.edu	37	11	125764947	125764947	+	Intron	DEL	T	-	-	rs144232833		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125764947delT	uc001qcy.2	-						HYLS1_uc009zbv.2_Intron|HYLS1_uc001qcx.3_Intron	NM_031307	NP_112597	Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3							nucleus	RNA binding			ovary(1)	1	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)		ATGCTAtttcttttttttttt	0.184													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	126968956	126968957	+	Intron	INS	-	A	A	rs146410503	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126968956_126968957insA	uc001qeg.1	+											Homo sapiens cDNA FLJ37868 fis, clone BRSSN2017297.																		GCCCTACAGTGAAAAAAAAAAT	0.441													3	3	---	---	---	---	
B3GAT1	27087	broad.mit.edu	37	11	134277866	134277867	+	Intron	INS	-	T	T	rs145508957		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134277866_134277867insT	uc001qhq.2	-						B3GAT1_uc001qhr.2_Intron	NM_018644	NP_061114	Q9P2W7	B3GA1_HUMAN	beta-1,3-glucuronyltransferase 1						carbohydrate metabolic process	Golgi membrane|integral to membrane	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity|metal ion binding			ovary(1)	1	all_hematologic(175;0.127)	all_cancers(12;1.39e-23)|all_epithelial(12;7.17e-17)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|Medulloblastoma(222;0.0125)|all_neural(223;0.0137)|Esophageal squamous(93;0.0559)		Epithelial(10;2.58e-11)|all cancers(11;5.75e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.000879)|Lung(977;0.0864)		TGGTGTCAAGATTTTTTTTTTT	0.342													4	2	---	---	---	---	
KDM5A	5927	broad.mit.edu	37	12	393122	393123	+	3'UTR	DEL	AA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:393122_393123delAA	uc001qif.1	-	28					KDM5A_uc001qie.1_3'UTR	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						CACACAAAAGAAAAAAGAGCCA	0.401			T 	NUP98	AML								4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2175475	2175476	+	Intron	DEL	GA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2175475_2175476delGA	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	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	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)	AGCCATTGGGGAGAGAGAGAGC	0.510													4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2300133	2300133	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2300133delT	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	Q13936	CAC1C_HUMAN	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)	gtgccagtcatttcctgcaag	0.000													4	2	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6062399	6062399	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6062399delA	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	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)	ctcaagaaagaaaaaaaaaaG	0.159													3	3	---	---	---	---	
IFFO1	25900	broad.mit.edu	37	12	6658357	6658357	+	Intron	DEL	A	-	-	rs72489368		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6658357delA	uc001qpd.1	-						IFFO1_uc001qoy.2_Intron|IFFO1_uc001qpa.1_5'Flank|IFFO1_uc001qpb.1_Intron|IFFO1_uc001qpe.1_Intron|IFFO1_uc010sfe.1_Intron|IFFO1_uc001qpf.1_Intron|IFFO1_uc001qoz.1_5'Flank|IFFO1_uc001qpc.1_Intron|IFFO1_uc001qpg.2_5'Flank	NM_080730	NP_542768	Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan isoform 2							intermediate filament					0						TGACTCAACTAAAAAAAAAAA	0.428													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8968022	8968027	+	IGR	DEL	AAACCC	-	-	rs113104838		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8968022_8968027delAAACCC								RIMKLB (32337 upstream) : A2ML1 (7123 downstream)																							GGAGATTATTAAACCCTGGACATTTC	0.417													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8968028	8968029	+	IGR	INS	-	GGTG	GGTG	rs146218175		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8968028_8968029insGGTG								RIMKLB (32343 upstream) : A2ML1 (7121 downstream)																							TATTAAACCCTGGACATTTCCT	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	10267110	10267110	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10267110delA								CLEC1A (15505 upstream) : CLEC7A (2266 downstream)																							CTAGGATCAGAAAAAAAGGCA	0.299													4	2	---	---	---	---	
GABARAPL1	23710	broad.mit.edu	37	12	10365540	10365540	+	5'UTR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10365540delC	uc001qxs.2	+	1					GABARAPL1_uc010shb.1_5'UTR|GABARAPL1_uc001qxt.2_RNA|GABARAPL1_uc001qxu.2_5'Flank	NM_031412	NP_113600	Q9H0R8	GBRL1_HUMAN	GABA(A) receptor-associated protein like 1							autophagic vacuole|endoplasmic reticulum|Golgi apparatus|membrane|microtubule	beta-tubulin binding|GABA receptor binding				0						TCCTCTACCTCCAGGCAGGCT	0.652													4	2	---	---	---	---	
ETV6	2120	broad.mit.edu	37	12	11905743	11905743	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11905743delA	uc001qzz.2	+							NM_001987	NP_001978	P41212	ETV6_HUMAN	ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				ATGACATGTTAAAAAAAAAAG	0.378			T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	14345029	14345029	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14345029delA								GRIN2B (212007 upstream) : ATF7IP (173582 downstream)																							AAACGAAAACAAAAAAGGCAG	0.453													4	2	---	---	---	---	
RERG	85004	broad.mit.edu	37	12	15319497	15319499	+	Intron	DEL	TGG	-	-	rs142727831	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15319497_15319499delTGG	uc001rcs.2	-						RERG_uc001rct.2_Intron|RERG_uc010shu.1_Intron	NM_032918	NP_116307	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor						negative regulation of cell growth|negative regulation of cell proliferation|response to hormone stimulus|small GTPase mediated signal transduction	cytosol|membrane|nucleus	estrogen receptor binding|GDP binding|GTP binding|GTPase activity			lung(1)	1						gtggtggtgttggtggtggtggt	0.128													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	17192904	17192905	+	IGR	DEL	AC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17192904_17192905delAC								LMO3 (430146 upstream) : None (None downstream)																							ctcagaagaaacacacacacac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	17229265	17229265	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17229265delA								LMO3 (466507 upstream) : None (None downstream)																							gggtttctgtaaaaaaaaagg	0.080													4	2	---	---	---	---	
FAR2	55711	broad.mit.edu	37	12	29339397	29339398	+	Intron	DEL	CT	-	-	rs142241097		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29339397_29339398delCT	uc001ris.3	+							NM_018099	NP_060569	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2						ether lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor				0						ATTTTGTCTCCTCTGATCTTTT	0.381													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31207731	31207732	+	Intron	DEL	AC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31207731_31207732delAC	uc001rjq.1	-											Homo sapiens cDNA FLJ39041 fis, clone NT2RP7010109.																		gaacttgtgtacacacacacag	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	39022490	39022491	+	IGR	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39022490_39022491insT								ALG10B (298963 upstream) : CPNE8 (23511 downstream)																							AAGTAGTAGAATTTTTGTTAAA	0.267													4	2	---	---	---	---	
LRRK2	120892	broad.mit.edu	37	12	40724839	40724839	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40724839delT	uc001rmg.3	+						LRRK2_uc009zjw.2_Intron|LRRK2_uc001rmi.2_Intron	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	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)				TCAATTAGAATTTTTTTTTGT	0.338													4	2	---	---	---	---	
ARID2	196528	broad.mit.edu	37	12	46299067	46299067	+	3'UTR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46299067delA	uc001ros.1	+	21					ARID2_uc009zkg.1_3'UTR|ARID2_uc009zkh.1_3'UTR|ARID2_uc001rou.1_3'UTR	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		aagaaaaaggaaaaaaaaaaa	0.333													3	4	---	---	---	---	
HDAC7	51564	broad.mit.edu	37	12	48176607	48176608	+	3'UTR	DEL	AC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48176607_48176608delAC	uc010slo.1	-	26					HDAC7_uc009zku.2_RNA|HDAC7_uc001rqe.2_3'UTR|HDAC7_uc001rqj.3_3'UTR|HDAC7_uc001rqk.3_3'UTR	NM_015401	NP_056216	Q8WUI4	HDAC7_HUMAN	histone deacetylase 7 isoform a						negative regulation of interleukin-2 production|negative regulation of osteoblast differentiation|positive regulation of cell migration involved in sprouting angiogenesis|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.137)		CCTAGGAAAGacacacacacac	0.248													6	3	---	---	---	---	
CACNB3	784	broad.mit.edu	37	12	49212875	49212875	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49212875delG	uc001rsl.1	+						CACNB3_uc010slx.1_Intron|CACNB3_uc010sly.1_Intron|CACNB3_uc010slz.1_Intron|CACNB3_uc001rsk.1_Intron	NM_000725	NP_000716	P54284	CACB3_HUMAN	calcium channel, voltage-dependent, beta 3						axon guidance|membrane depolarization|synaptic transmission	cytosol|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0					Verapamil(DB00661)	AGGGTTTGTAGGGGGGCGCTC	0.617													6	5	---	---	---	---	
LASS5	91012	broad.mit.edu	37	12	50528687	50528687	+	Intron	DEL	A	-	-	rs3830643		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50528687delA	uc001rwd.3	-						LASS5_uc001rwc.2_Intron|LASS5_uc001rwe.3_Intron|LASS5_uc001rwf.3_Intron|LASS5_uc010smq.1_Intron	NM_147190	NP_671723	Q8N5B7	CERS5_HUMAN	LAG1 homolog, ceramide synthase 5						ceramide biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity				0						ACAGAGAAAGATATATAAATC	0.388													3	9	---	---	---	---	
FAM186A	121006	broad.mit.edu	37	12	50745374	50745374	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50745374delA	uc001rwl.2	-	4	5379	c.5241delT	c.(5239-5241)GCTfs	p.A1747fs	FAM186A_uc010smt.1_Frame_Shift_Del_p.A1525fs	NM_001145475	NP_001138947	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1747											0						AGGACTTCTCAGCAGTAGGAG	0.507													125	62	---	---	---	---	
SP1	6667	broad.mit.edu	37	12	53795308	53795309	+	Intron	INS	-	T	T	rs148315788	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53795308_53795309insT	uc001scw.2	+						SP1_uc010sog.1_Intron	NM_138473	NP_612482	P08047	SP1_HUMAN	Sp1 transcription factor isoform a						positive regulation by host of viral transcription|positive regulation of transcription from RNA polymerase II promoter	cytoplasm	double-stranded DNA binding|histone deacetylase binding|HMG box domain binding|protein C-terminus binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(357;0.00527)		AGCAATGATACTGGCAAGACAT	0.243													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54344292	54344292	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54344292delT								HOXC13 (3965 upstream) : HOXC12 (4422 downstream)																							TTTGATGTGATTTTTTTTTTT	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55047805	55047806	+	IGR	INS	-	ACA	ACA	rs144571470	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55047805_55047806insACA								DCD (5656 upstream) : MUCL1 (200493 downstream)																							CTGTATCTGGGCGGACATAAGG	0.510													8	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55169341	55169341	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55169341delG								DCD (127192 upstream) : MUCL1 (78958 downstream)																							gtcttgctctgggatgatgtc	0.000													4	2	---	---	---	---	
RBMS2	5939	broad.mit.edu	37	12	56921616	56921616	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56921616delT	uc001sln.2	+						RBMS2_uc010sqp.1_Intron|RBMS2_uc010sqq.1_Intron|RBMS2_uc009zou.2_Intron	NM_002898	NP_002889	Q15434	RBMS2_HUMAN	RNA binding motif, single stranded interacting						RNA processing	nucleus	nucleotide binding|RNA binding				0						GGATATGCCCTTTGGTTGCTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	59833086	59833086	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59833086delT								LRIG3 (518824 upstream) : SLC16A7 (156762 downstream)																							aattttagaatttttttttct	0.000													4	2	---	---	---	---	
PPM1H	57460	broad.mit.edu	37	12	63170251	63170251	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63170251delT	uc001srk.3	-							NM_020700	NP_065751	Q9ULR3	PPM1H_HUMAN	protein phosphatase 1H (PP2C domain containing)								phosphoprotein phosphatase activity			lung(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		gaaggcagggtttttttgatc	0.065													4	2	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	66762370	66762370	+	Intron	DEL	G	-	-	rs146810333		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66762370delG	uc001stk.2	-						GRIP1_uc001stj.2_Intron	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		ACTGTGGCTTGGGTTATCTTC	0.478													4	2	---	---	---	---	
PAWR	5074	broad.mit.edu	37	12	79996354	79996354	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79996354delA	uc001syx.2	-							NM_002583	NP_002574	Q96IZ0	PAWR_HUMAN	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						gcaagatgggaaaaaaaaata	0.000													5	3	---	---	---	---	
C12orf26	84190	broad.mit.edu	37	12	82855497	82855498	+	Intron	INS	-	G	G	rs78653888		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82855497_82855498insG	uc001szq.2	+							NM_032230	NP_115606	Q8N6Q8	CL026_HUMAN	hypothetical protein LOC84190												0						GGCAAAAAAAAATCAAGGAATG	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	83664811	83664811	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83664811delA								TMTC2 (136748 upstream) : None (None downstream)																							TACAGGTTAGAAAAAAAAAGT	0.299													4	2	---	---	---	---	
CEP290	80184	broad.mit.edu	37	12	88471899	88471899	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88471899delA	uc001tar.2	-						CEP290_uc001taq.2_Intron	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						CGACTTTGAGAAAAAAAAAAA	0.269													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	90304006	90304007	+	IGR	INS	-	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90304006_90304007insC								LOC338758 (198278 upstream) : None (None downstream)																							ggacatcttttccctttcaaac	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96974947	96974947	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96974947delA	uc001ter.1	+											Homo sapiens cDNA FLJ31514 fis, clone NT2RI1000164.																		GTTATGAAGTAATTTCTGATG	0.308													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	100161184	100161184	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100161184delA	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		ACAAATGTTTAAAAAAAAAAC	0.303													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102366533	102366534	+	IGR	DEL	CT	-	-	rs145038047		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102366533_102366534delCT								DRAM1 (49134 upstream) : CCDC53 (40184 downstream)																							gatatctgtactctcagcaata	0.000													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	105370462	105370462	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105370462delT								SLC41A2 (47990 upstream) : C12orf45 (9636 downstream)																							aaatttCATCTTTTTTTGACC	0.269													4	2	---	---	---	---	
ALDH1L2	160428	broad.mit.edu	37	12	105463801	105463801	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105463801delA	uc001tlc.2	-						ALDH1L2_uc009zup.2_Intron	NM_001034173	NP_001029345	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2						10-formyltetrahydrofolate catabolic process|biosynthetic process	mitochondrion	acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity|phosphopantetheine binding			skin(1)	1						tgctctatgcaaaaaaaaagt	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108799642	108799642	+	IGR	DEL	A	-	-	rs75566384		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108799642delA								CMKLR1 (66548 upstream) : FICD (109409 downstream)																							ggagtggaggaaaaaaaaaac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108913381	108913382	+	IGR	DEL	TA	-	-	rs59843862		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108913381_108913382delTA								FICD (1 upstream) : SART3 (2609 downstream)																							GTTTTAGTTTTAAAAAAAAAAA	0.297													5	3	---	---	---	---	
MYL2	4633	broad.mit.edu	37	12	111358113	111358113	+	Intron	DEL	T	-	-	rs3216816		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111358113delT	uc001try.3	-						MYL2_uc001trx.3_5'Flank	NM_000432	NP_000423	P10916	MLRV_HUMAN	slow cardiac myosin regulatory light chain 2						cardiac myofibril assembly|heart contraction|muscle filament sliding|negative regulation of cell growth|regulation of striated muscle contraction|ventricular cardiac muscle tissue morphogenesis	cytosol|myosin complex|sarcomere	actin monomer binding|calcium ion binding|myosin heavy chain binding|structural constituent of muscle			ovary(1)	1						AACTCTCTTATTTTGTGTTTG	0.463													8	7	---	---	---	---	
RASAL1	8437	broad.mit.edu	37	12	113554164	113554164	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113554164delA	uc001tum.1	-						RASAL1_uc010syp.1_Intron|RASAL1_uc001tul.2_Intron|RASAL1_uc001tun.1_Intron|RASAL1_uc010syq.1_Intron|RASAL1_uc001tuo.3_Intron|RASAL1_uc010syr.1_Intron	NM_004658	NP_004649	O95294	RASL1_HUMAN	RAS protein activator like 1						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	metal ion binding|phospholipid binding|Ras GTPase activator activity			ovary(2)|skin(2)	4						tactctgtctaaaaaaaaaaa	0.194													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114872901	114872902	+	IGR	INS	-	AC	AC	rs140903478	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114872901_114872902insAC								TBX5 (26654 upstream) : TBX3 (235157 downstream)																							GGCGTATGCATACACACACACA	0.386													5	3	---	---	---	---	
TBX3	6926	broad.mit.edu	37	12	115111365	115111365	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115111365delG	uc001tvt.1	-						TBX3_uc001tvu.1_Intron	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2						anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding			ovary(2)|skin(1)	3	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		AGGAAAGGCTGGAGGAATCAA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115413185	115413185	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115413185delT								TBX3 (291216 upstream) : MED13L (983198 downstream)																							AAAGCAAAGATTTTTTTTTTT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126471851	126471852	+	IGR	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126471851_126471852insT								TMEM132B (328262 upstream) : LOC100128554 (455175 downstream)																							gaaaaagtgtatttttttctgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127575324	127575325	+	IGR	DEL	AT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127575324_127575325delAT								LOC100128554 (617994 upstream) : None (None downstream)																							ttaaacccacatataccctagg	0.129													4	2	---	---	---	---	
GPR133	283383	broad.mit.edu	37	12	131446374	131446374	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131446374delA	uc001uit.3	+						GPR133_uc010tbm.1_Intron	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		attttgctttaaaaaaaaatc	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131814739	131814742	+	IGR	DEL	TCCA	-	-	rs72419588		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131814739_131814742delTCCA								LOC116437 (117264 upstream) : SFRS8 (380893 downstream)																							ttctctctcttccatccatccatc	0.074													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131814753	131814754	+	IGR	DEL	CA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131814753_131814754delCA								LOC116437 (117278 upstream) : SFRS8 (380881 downstream)																							tccatccatccatccatccatc	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131814756	131814757	+	IGR	DEL	CC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131814756_131814757delCC								LOC116437 (117281 upstream) : SFRS8 (380878 downstream)																							atccatccatccatccatccat	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132127620	132127620	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132127620delC								LOC116437 (430145 upstream) : SFRS8 (68015 downstream)																							caggagtcagcccctgtggct	0.010													4	2	---	---	---	---	
SAP18	10284	broad.mit.edu	37	13	21714654	21714654	+	5'UTR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21714654delA	uc001uns.2	+	1						NM_005870	NP_005861	O00422	SAP18_HUMAN	Sin3A-associated protein, 18kDa						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|plasma membrane	protein binding|transcription corepressor activity				0		all_cancers(29;2.16e-20)|all_epithelial(30;2.97e-18)|all_lung(29;4.58e-16)|Lung SC(185;0.0262)|Breast(139;0.147)		all cancers(112;9.79e-05)|Epithelial(112;0.000292)|OV - Ovarian serous cystadenocarcinoma(117;0.00276)|Lung(94;0.0941)		GGCCGACTATAAAGTGTCGAG	0.667													24	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22880301	22880301	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22880301delG								FGF9 (601661 upstream) : SGCG (874759 downstream)																							gtgtgagggtgggggagatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	23262163	23262163	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23262163delT								FGF9 (983523 upstream) : SGCG (492897 downstream)																							ctgcagttacttttttttttt	0.000													4	2	---	---	---	---	
ATP8A2	51761	broad.mit.edu	37	13	26273981	26273981	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26273981delT	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron|ATP8A2_uc010aaj.1_Intron	NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	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)		CCTGGGAAGGTTTTTTTTTTT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27525527	27525527	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27525527delC								GPR12 (190605 upstream) : USP12 (116911 downstream)																							acaggaaccactgcgctcagc	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	29379733	29379733	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29379733delT								SLC46A3 (86583 upstream) : MTUS2 (219015 downstream)																							atatagctgctttttgggatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	29472478	29472478	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29472478delA								SLC46A3 (179328 upstream) : MTUS2 (126270 downstream)																							ATACATGGCCAAAAACACTAT	0.433													4	2	---	---	---	---	
HMGB1	3146	broad.mit.edu	37	13	31166911	31166911	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31166911delA	uc001usz.2	-							NM_002128	NP_002119	P09429	HMGB1_HUMAN	high-mobility group box 1						base-excision repair, DNA ligation|dendritic cell chemotaxis|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|inflammatory response to antigenic stimulus|innate immune response|myeloid dendritic cell activation|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|neuron projection development|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of DNA binding|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	cell surface|condensed chromosome|extracellular space|nucleolus|nucleoplasm	chemoattractant activity|cytokine activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|repressing transcription factor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		CTTCAAACTTAAAAAACATTT	0.259													4	2	---	---	---	---	
C13orf26	122046	broad.mit.edu	37	13	31537397	31537397	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31537397delA	uc001uti.2	+							NM_152325	NP_689538	Q8N6G2	CM026_HUMAN	hypothetical protein LOC122046											ovary(2)|skin(1)	3		Lung SC(185;0.0281)		all cancers(112;0.0176)|Epithelial(112;0.0768)|OV - Ovarian serous cystadenocarcinoma(117;0.0852)		ACTCCAGTGGAAAAGAAACCC	0.463													4	2	---	---	---	---	
B3GALTL	145173	broad.mit.edu	37	13	31837525	31837525	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31837525delT	uc010aaz.2	+						B3GALTL_uc001utn.3_Intron	NM_194318	NP_919299	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like						fucose metabolic process	endoplasmic reticulum membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		TTTGAACACATTTTTGACTCC	0.408													4	2	---	---	---	---	
FRY	10129	broad.mit.edu	37	13	32868431	32868431	+	Intron	DEL	T	-	-	rs11400232		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32868431delT	uc001utx.2	+						FRY_uc010tdw.1_Intron|FRY_uc001utz.2_Intron|FRY_uc010tdx.1_Intron	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CATAAGATCCTTTTTTTTTCC	0.353													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	34830541	34830544	+	IGR	DEL	GTGT	-	-	rs71862357		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34830541_34830544delGTGT								RFC3 (289847 upstream) : NBEA (685912 downstream)																							TGGGgtatgcgtgtgtgtgtgtgt	0.382													4	2	---	---	---	---	
DCLK1	9201	broad.mit.edu	37	13	36361419	36361419	+	Intron	DEL	T	-	-	rs10718386		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36361419delT	uc001uvf.2	-						DCLK1_uc001uve.3_Intron|DCLK1_uc010teh.1_Intron|DCLK1_uc010abk.2_Intron	NM_004734	NP_004725	O15075	DCLK1_HUMAN	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)		ACCAGTGGAATTTTTTTTTTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	37144898	37144899	+	IGR	DEL	AG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37144898_37144899delAG								CCNA1 (127880 upstream) : C13orf36 (103150 downstream)																							gtttaggaatagagagaggtag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	41352244	41352244	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41352244delT								MRPS31 (6897 upstream) : SLC25A15 (11303 downstream)																							CATGGtttcctttttcatcat	0.045													4	2	---	---	---	---	
DGKH	160851	broad.mit.edu	37	13	42730146	42730146	+	Intron	DEL	A	-	-	rs145203018		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42730146delA	uc001uyl.1	+						DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_Intron|DGKH_uc010tfi.1_Intron|DGKH_uc010tfj.1_Intron|DGKH_uc001uyn.1_Intron|DGKH_uc001uyo.1_Intron|DGKH_uc001uyp.2_Intron	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		ACTACTGTCTAAAAAAAAAAA	0.303													5	3	---	---	---	---	
AKAP11	11215	broad.mit.edu	37	13	42870850	42870854	+	Intron	DEL	AAGTT	-	-	rs67350560		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42870850_42870854delAAGTT	uc001uys.1	+							NM_016248	NP_057332	Q9UKA4	AKA11_HUMAN	A-kinase anchor protein 11						intracellular protein kinase cascade	microtubule organizing center	protein kinase A binding|protein phosphatase 1 binding			ovary(1)|central_nervous_system(1)	2		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		AAATTTCATAAAGTTAAGTTAAGAC	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	43194653	43194654	+	IGR	DEL	TG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43194653_43194654delTG								TNFSF11 (12504 upstream) : C13orf30 (161032 downstream)																							acATCTGGACTGTGTGTGTGTG	0.193													4	2	---	---	---	---	
TSC22D1	8848	broad.mit.edu	37	13	45067210	45067210	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45067210delA	uc001uzn.3	-						TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358	Q15714	T22D1_HUMAN	TSC22 domain family, member 1 isoform 1						transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		acacacaaacaaaaaaatgag	0.050													4	2	---	---	---	---	
ZC3H13	23091	broad.mit.edu	37	13	46584872	46584872	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46584872delA	uc010tfw.1	-						ZC3H13_uc001vas.1_Intron|ZC3H13_uc001vat.1_Intron	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13								nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		tctcttatacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	48922817	48922817	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48922817delT	uc001vcb.2	+						RB1_uc010acs.1_Intron	NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(5)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TTTTTCTTAATTTTTTTTTTT	0.204		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	58809670	58809672	+	IGR	DEL	GAC	-	-	rs60471785		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58809670_58809672delGAC								PCDH17 (506605 upstream) : None (None downstream)																							ATAAAATGATGACAATTATATGC	0.374													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	60753106	60753106	+	IGR	DEL	T	-	-	rs67313590		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60753106delT								DIAPH3 (14987 upstream) : TDRD3 (217485 downstream)																							tacttttctcttttttttttt	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	72898133	72898133	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72898133delT								DACH1 (456803 upstream) : C13orf37 (384362 downstream)																							AATTGTCAGCTTTTTTTTTAC	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	77554890	77554890	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77554890delA								BTF3L1 (51667 upstream) : CLN5 (11169 downstream)																							GCTGGAGGACAAAAAAAAAAT	0.453											OREG0022450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
MYCBP2	23077	broad.mit.edu	37	13	77783326	77783326	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77783326delC	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		GATCATCTGTCCCATTGCTAC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85648513	85648513	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85648513delA								None (None upstream) : SLITRK6 (718409 downstream)																							ATCCATTGTCAAAAAAAAGGC	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	87387905	87387906	+	IGR	DEL	AC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87387905_87387906delAC								None (None upstream) : SLITRK5 (936964 downstream)																							ggatggttcaacacacacacat	0.000													4	2	---	---	---	---	
GPC5	2262	broad.mit.edu	37	13	92702575	92702575	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92702575delT	uc010tif.1	+							NM_004466	NP_004457	P78333	GPC5_HUMAN	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)				CTTCTCTATATTTTTTTTAAA	0.303													3	3	---	---	---	---	
NALCN	259232	broad.mit.edu	37	13	102031250	102031250	+	Intron	DEL	T	-	-	rs140952985		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102031250delT	uc001vox.1	-						NALCN_uc001voy.2_Intron|NALCN_uc001voz.2_Intron|NALCN_uc001vpa.2_Intron	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AATATCACTATTTTTTTTTTC	0.318													3	3	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102671006	102671026	+	Intron	DEL	CTCCTCTTCCAGCCCTGAGGT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102671006_102671026delCTCCTCTTCCAGCCCTGAGGT	uc001vpf.2	-							NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GCCCTGAGGCCTCCTCTTCCAGCCCTGAGGTCACTTATCCA	0.330													32	29	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	104634495	104634496	+	IGR	INS	-	TG	TG	rs138790049	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104634495_104634496insTG								SLC10A2 (915299 upstream) : None (None downstream)																							ctctctctctatgtgtgtgtgt	0.000													2	5	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	108440734	108440735	+	Intron	DEL	TC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108440734_108440735delTC	uc001vql.2	-						uc001vqm.2_RNA	NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						TCTGACATCATCTCTCTCTCTC	0.351													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	110202063	110202063	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110202063delT								MYO16 (341708 upstream) : IRS2 (204123 downstream)																							AACTTGCTCCTTTTTTTTTAA	0.373													4	2	---	---	---	---	
PCID2	55795	broad.mit.edu	37	13	113833642	113833643	+	Intron	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113833642_113833643insT	uc010tju.1	-						PCID2_uc001vtb.2_Intron|PCID2_uc010tjv.1_Intron|PCID2_uc010tjw.1_Intron|PCID2_uc001vte.2_Intron|PCID2_uc001vtd.2_Intron|PCID2_uc001vtf.2_Intron	NM_001127203	NP_001120675	Q5JVF3	PCID2_HUMAN	PCI domain containing 2						negative regulation of apoptosis|negative regulation of cysteine-type endopeptidase activity|positive regulation of mitotic cell cycle spindle assembly checkpoint|positive regulation of transcription, DNA-dependent|regulation of mRNA stability|spleen development		protein binding				0	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)			ttaaggttcggttttttttttc	0.183													4	2	---	---	---	---	
RNASE12	493901	broad.mit.edu	37	14	21058840	21058840	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21058840delC	uc001vxt.2	-	1	143	c.43delG	c.(43-45)GAAfs	p.E15fs	RNASE11_uc010ahv.2_5'Flank|RNASE11_uc010ahx.2_5'Flank|RNASE11_uc010ahw.2_5'Flank|RNASE11_uc001vxs.2_5'Flank|uc001vxu.1_RNA	NM_001024822	NP_001019993	Q5GAN4	RNS12_HUMAN	ribonuclease, RNase A family, 12 (non-active)	15						extracellular region	nucleic acid binding|pancreatic ribonuclease activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(95;0.00238)		Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.013)		ACCTCATTTTCCCAGAACAGA	0.428													227	107	---	---	---	---	
METT11D1	64745	broad.mit.edu	37	14	21461952	21461952	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21461952delA	uc001vyn.2	+						METT11D1_uc001vym.2_Intron|METT11D1_uc001vyo.2_Intron|METT11D1_uc001vyp.2_Intron|METT11D1_uc001vyq.2_Intron	NM_022734	NP_073571	Q9H7H0	MET17_HUMAN	methyltransferase 11 domain containing 1 isoform						translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)		TTTTTTTTTTAGGAGTTGTAA	0.179													4	2	---	---	---	---	
JUB	84962	broad.mit.edu	37	14	23443221	23443223	+	Intron	DEL	CTT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23443221_23443223delCTT	uc001whz.2	-						JUB_uc001why.2_Intron	NM_032876	NP_116265	Q96IF1	JUB_HUMAN	ajuba isoform 1						cell cycle|gene silencing by miRNA|positive regulation of protein complex assembly	cell-cell junction|cytoplasmic mRNA processing body|microtubule organizing center	alpha-catenin binding|zinc ion binding				0	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.0122)		CCCATTTCCACTTCTTCTCCAGC	0.512											OREG0022591	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	98	47	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	54013110	54013110	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54013110delT								DDHD1 (393064 upstream) : BMP4 (403347 downstream)																							gtttgactgattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	62904357	62904357	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62904357delT								FLJ43390 (307125 upstream) : KCNH5 (269590 downstream)																							gttttattcattttttttggt	0.000													4	2	---	---	---	---	
JDP2	122953	broad.mit.edu	37	14	75918553	75918554	+	Intron	INS	-	TG	TG	rs5809708		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75918553_75918554insTG	uc010asj.2	+						JDP2_uc010tvb.1_Intron|JDP2_uc010tvc.1_Intron|JDP2_uc001xrq.2_Intron	NM_001135047	NP_001128519	Q8WYK2	JDP2_HUMAN	Jun dimerization protein 2 isoform a							nucleus	sequence-specific DNA binding				0				BRCA - Breast invasive adenocarcinoma(234;0.0296)		gtttcctcatctaaaatctagg	0.233													4	3	---	---	---	---	
C14orf145	145508	broad.mit.edu	37	14	80972186	80972189	+	Intron	DEL	TCAT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80972186_80972189delTCAT	uc001xux.2	-						C14orf145_uc010asz.1_Intron	NM_152446	NP_689659	Q6ZU80	CE128_HUMAN	hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)		cttctttcactcattcattcattc	0.137													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98029330	98029331	+	IGR	DEL	AC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98029330_98029331delAC								VRK1 (681380 upstream) : C14orf64 (362616 downstream)																							AGCAACAGAGACAGCGTGGTGG	0.515													2	4	---	---	---	---	
HHIPL1	84439	broad.mit.edu	37	14	100123087	100123088	+	Intron	INS	-	G	G	rs141123292		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100123087_100123088insG	uc010avs.2	+						HHIPL1_uc001ygl.1_Intron	NM_001127258	NP_001120730	Q96JK4	HIPL1_HUMAN	HHIP-like protein 1 isoform a						carbohydrate metabolic process	extracellular region|membrane	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding|scavenger receptor activity			skin(2)	2		Melanoma(154;0.128)				cactccagcctggtgacagagc	0.000													9	5	---	---	---	---	
YY1	7528	broad.mit.edu	37	14	100744094	100744095	+	3'UTR	DEL	AA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100744094_100744095delAA	uc001ygy.1	+	5					uc001ygz.1_5'Flank	NM_003403	NP_003394	P25490	TYY1_HUMAN	YY1 transcription factor						cell differentiation|cellular response to UV|double-strand break repair via homologous recombination|negative regulation of transcription from RNA polymerase II promoter|response to UV-C|spermatogenesis	Ino80 complex|nuclear matrix|plasma membrane	four-way junction DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding				0		Melanoma(154;0.152)				AGTAAAAATTAAAAAAAAAAAA	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	102222574	102222574	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102222574delG								C14orf72 (23714 upstream) : PPP2R5C (5561 downstream)																							ttagggatttgggaggaaaaa	0.154													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106779485	106779485	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106779485delG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						TGTGTCACTTGGGGGGAAGCA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20054370	20054371	+	IGR	INS	-	AAA	AAA	rs76558337		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20054370_20054371insAAA								None (None upstream) : GOLGA6L6 (682723 downstream)																							aagaaagaaaggaagaaagaaa	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20054371	20054372	+	IGR	INS	-	A	A	rs76558337		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20054371_20054372insA								None (None upstream) : GOLGA6L6 (682722 downstream)																							agaaagaaaggaagaaagaaag	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20454214	20454214	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20454214delT								None (None upstream) : GOLGA6L6 (282880 downstream)																							ACCCTCAAGCtttttttttct	0.264													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20866851	20866852	+	IGR	INS	-	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20866851_20866852insC								GOLGA8C (85825 upstream) : BCL8 (3204 downstream)																							TGAGCACATTTCCCCTATTTAA	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21086017	21086022	+	IGR	DEL	TTTCTA	-	-	rs74736528		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21086017_21086022delTTTCTA								POTEB (14040 upstream) : NF1P1 (35999 downstream)																							gtcatcattgtttctatttgtatttg	0.019													4	2	---	---	---	---	
LOC646214	646214	broad.mit.edu	37	15	21934898	21934899	+	RNA	INS	-	C	C	rs60809088		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21934898_21934899insC	uc010tzj.1	-	1		c.5841_5842insG				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						AATTATTTTTTATTCATGATTT	0.361													4	2	---	---	---	---	
LOC646214	646214	broad.mit.edu	37	15	21940266	21940267	+	RNA	INS	-	A	A	rs150817229		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21940266_21940267insA	uc010tzj.1	-	1		c.473_474insT				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						ACAAAGAGTATAAAAAACAAAA	0.307													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21968357	21968357	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21968357delA								LOC646214 (27618 upstream) : CXADRP2 (46063 downstream)																							AAGCGATGACAAAAAAAAATC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23140656	23140660	+	IGR	DEL	AAAGG	-	-	rs144644532		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23140656_23140660delAAAGG								NIPA1 (53813 upstream) : WHAMML1 (47071 downstream)																							GTAAAAAAAAAAAGGAAGAATACAT	0.263													4	2	---	---	---	---	
FMN1	342184	broad.mit.edu	37	15	33256051	33256052	+	Intron	DEL	GC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33256051_33256052delGC	uc001zhf.3	-							NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	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)		TTTGCCATCTGCCACTCAAAAC	0.327													4	2	---	---	---	---	
ATPBD4	89978	broad.mit.edu	37	15	35815313	35815314	+	Intron	DEL	CC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35815313_35815314delCC	uc001zja.2	-						ATPBD4_uc001ziz.2_Intron|ATPBD4_uc001zjb.2_Intron	NM_080650	NP_542381	Q7L8W6	ATBD4_HUMAN	ATP binding domain 4 isoform 1												0		all_epithelial(112;2.11e-09)|Lung NSC(122;2.38e-08)|all_lung(180;3.65e-07)		all cancers(64;9.9e-19)|GBM - Glioblastoma multiforme(113;2.01e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)		aaattaccgtccagaaatattg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37964869	37964869	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37964869delG								MEIS2 (571369 upstream) : TMCO5A (261958 downstream)																							GAAGTGTTCTGGAATACCTGA	0.433													4	2	---	---	---	---	
TGM5	9333	broad.mit.edu	37	15	43528260	43528262	+	Intron	DEL	TTC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43528260_43528262delTTC	uc001zrd.1	-						TGM5_uc001zrc.1_Intron|TGM5_uc001zre.1_Intron	NM_201631	NP_963925	O43548	TGM5_HUMAN	transglutaminase 5 isoform 1						epidermis development|peptide cross-linking	cytoplasm	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(1)	1		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	accattagcattcttcttcttct	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	44504208	44504208	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44504208delT								FRMD5 (16779 upstream) : CASC4 (76721 downstream)																							ctaggctctgttttaagtgct	0.114													4	2	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	47935197	47935198	+	Intron	DEL	GA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47935197_47935198delGA	uc001zvw.2	+							NM_020858	NP_065909	Q8NFY4	SEM6D_HUMAN	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)		tggaaatagggagagagagaga	0.262													4	2	---	---	---	---	
NARG2	79664	broad.mit.edu	37	15	60769310	60769310	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60769310delA	uc002agp.2	-						uc002ags.1_5'Flank|NARG2_uc002ago.2_Intron|NARG2_uc010bgk.2_Intron|NARG2_uc002agr.1_Intron	NM_024611	NP_078887	Q659A1	NARG2_HUMAN	NMDA receptor regulated 2 isoform a							nucleus				ovary(1)|lung(1)	2						GCATTTATCCAAAAAACTATA	0.328													4	2	---	---	---	---	
IGDCC4	57722	broad.mit.edu	37	15	65674194	65674194	+	3'UTR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65674194delC	uc002aou.1	-	20					IGDCC4_uc002aot.1_3'UTR	NM_020962	NP_066013	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member							integral to membrane|plasma membrane				ovary(1)|pancreas(1)|skin(1)	3						TGAGAAATGGCCACTTTCTTA	0.328													4	2	---	---	---	---	
GLCE	26035	broad.mit.edu	37	15	69518820	69518820	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69518820delA	uc002ary.1	+							NM_015554	NP_056369	O94923	GLCE_HUMAN	D-glucuronyl C5-epimerase						heparan sulfate proteoglycan biosynthetic process|heparin biosynthetic process	Golgi membrane|integral to membrane	UDP-glucuronate 5'-epimerase activity			ovary(2)	2						AGTCACTCCTAAAATGTAGCG	0.348													4	2	---	---	---	---	
LOC145837	145837	broad.mit.edu	37	15	69840980	69840983	+	Intron	DEL	TGAG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69840980_69840983delTGAG	uc002asf.1	+						LOC145837_uc002asg.1_Intron|LOC145837_uc010bij.1_Intron					Homo sapiens cDNA clone IMAGE:5189446.												0						AGTGCGTGCATGAGTGAGTGAGTG	0.534													4	2	---	---	---	---	
ST20	400410	broad.mit.edu	37	15	80212023	80212023	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80212023delT	uc002bfa.3	-							NM_001100880	NP_001094350	Q9HBF5	ST20_HUMAN	cervical cancer suppressor-1												0						gaaagggaagttttgaacatt	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	83742375	83742376	+	IGR	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83742375_83742376insA								BTBD1 (6269 upstream) : TM6SF1 (33948 downstream)																							aagagcatttgaaaaaaatact	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	83768979	83768979	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83768979delC								BTBD1 (32873 upstream) : TM6SF1 (7345 downstream)																							ATCTGCCCAGCCCCACTCTTC	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84919884	84919887	+	IGR	DEL	GAGT	-	-	rs139438768		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84919884_84919887delGAGT								LOC388152 (20964 upstream) : GOLGA6L5 (127851 downstream)																							GAATACATAGGAgtgagtgagtga	0.275													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	85841053	85841053	+	IGR	DEL	C	-	-	rs5814189		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85841053delC								PDE8A (158683 upstream) : AKAP13 (82818 downstream)																							aacaatgtatccccatttctt	0.050													1	6	---	---	---	---	
FURIN	5045	broad.mit.edu	37	15	91413865	91413866	+	Intron	DEL	TT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91413865_91413866delTT	uc002bpu.1	+							NM_002569	NP_002560	P09958	FURIN_HUMAN	furin preproprotein						cell proliferation|negative regulation of low-density lipoprotein particle receptor catabolic process|negative regulation of transforming growth factor-beta1 production|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|Notch signaling pathway|peptide biosynthetic process|peptidyl-glutamic acid carboxylation|post-translational protein modification|secretion by cell|signal peptide processing|transforming growth factor beta receptor signaling pathway|viral assembly, maturation, egress, and release	cell surface|Golgi lumen|Golgi membrane|integral to membrane|membrane raft|plasma membrane|trans-Golgi network|trans-Golgi network transport vesicle	metal ion binding|nerve growth factor binding|peptide binding|protease binding|serine-type endopeptidase activity|serine-type endopeptidase inhibitor activity			central_nervous_system(4)|lung(2)|breast(1)	7	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CCTTCTTTTCTTTCTCAGCTCA	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	91631984	91631984	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91631984delT								VPS33B (66151 upstream) : SV2B (11199 downstream)																							ATTTTCTTTATTTTTTtttct	0.015													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93076817	93076817	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93076817delT								C15orf32 (32470 upstream) : LOC100144604 (34231 downstream)																							ttgaattgcctttttttttcc	0.080													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96403822	96403823	+	IGR	INS	-	GAT	GAT	rs149421414	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96403822_96403823insGAT								LOC145820 (352748 upstream) : NR2F2 (465334 downstream)																							atgatgacgaagatgatgatga	0.243													2	4	---	---	---	---	
LOC91948	91948	broad.mit.edu	37	15	98302955	98302955	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98302955delT	uc002buh.1	-						LOC91948_uc002bug.1_Intron	NR_024173				SubName: Full=Putative uncharacterized protein ENSP00000381347;												0						AGAAGCCTAGTTTTTTTAACT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98738489	98738489	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98738489delA								ARRDC4 (221422 upstream) : FAM169B (241902 downstream)																							GAGGCAAAAGAAAAAAAAAGT	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	101250299	101250300	+	IGR	INS	-	GG	GG			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101250299_101250300insGG								ASB7 (58397 upstream) : ALDH1A3 (169709 downstream)																							gctagaggtgacaatgatggtg	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	880161	880176	+	IGR	DEL	GCTGGGCTGCTGGGCT	-	-	rs11275697		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:880161_880176delGCTGGGCTGCTGGGCT								PRR25 (16301 upstream) : LMF1 (23459 downstream)																							GTGAGTGGACgctgggctgctgggctgctgggctgc	0.481													4	4	---	---	---	---	
LMF1	64788	broad.mit.edu	37	16	1008906	1008907	+	Intron	INS	-	AC	AC	rs151030762	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1008906_1008907insAC	uc002ckj.2	-						LMF1_uc010brh.2_Intron|LMF1_uc010bri.2_Intron|LMF1_uc002ckk.2_Intron|LMF1_uc010uuu.1_Intron|LMF1_uc010uuv.1_Intron	NM_022773	NP_073610	Q96S06	LMF1_HUMAN	lipase maturation factor 1							endoplasmic reticulum membrane|integral to membrane					0		Hepatocellular(780;0.00308)				caaaaaaacaaaacaaaaaaaa	0.000													4	3	---	---	---	---	
C16orf91	283951	broad.mit.edu	37	16	1479062	1479064	+	Intron	DEL	GCA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1479062_1479064delGCA	uc010uvd.1	-							NM_001010878	NP_001010878	Q4G0I0	CSMT1_HUMAN	hypothetical protein LOC283951							integral to membrane					0						CTCACCTGGGGCATGGGCTCCCT	0.665													4	4	---	---	---	---	
TCEB2	6923	broad.mit.edu	37	16	2825271	2825271	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2825271delT	uc002crn.2	-						TCEB2_uc002crm.2_Intron	NM_007108	NP_009039	Q15370	ELOB_HUMAN	elongin B isoform a						positive regulation of viral transcription|protein complex assembly|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|nucleoplasm	protein binding				0						TGGTTGCTTCTTTTTTAAAAA	0.299													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8411662	8411662	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8411662delC								A2BP1 (648322 upstream) : TMEM114 (207841 downstream)																							CTGCTTTCCACCCCCGTATTG	0.478													4	2	---	---	---	---	
RSL1D1	26156	broad.mit.edu	37	16	11945582	11945583	+	5'Flank	INS	-	GC	GC			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11945582_11945583insGC	uc002dbp.1	-						RSL1D1_uc010buv.1_5'Flank|RSL1D1_uc010uyw.1_5'Flank|RSL1D1_uc010buw.2_5'Flank	NM_015659	NP_056474	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1						regulation of protein localization|translation	large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0						TTTCTCCAGCTTTCCATGAGCT	0.564													4	3	---	---	---	---	
RSL1D1	26156	broad.mit.edu	37	16	11945587	11945588	+	5'Flank	DEL	AT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11945587_11945588delAT	uc002dbp.1	-						RSL1D1_uc010buv.1_5'Flank|RSL1D1_uc010uyw.1_5'Flank|RSL1D1_uc010buw.2_5'Flank	NM_015659	NP_056474	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1						regulation of protein localization|translation	large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0						CCAGCTTTCCATGAGCTGTGGG	0.564													4	3	---	---	---	---	
RUNDC2A	84127	broad.mit.edu	37	16	12142009	12142009	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12142009delT	uc002dbw.1	+							NM_032167	NP_115543	Q9HA26	RUN2A_HUMAN	RUN domain containing 2A											ovary(1)	1						TCATGGGAGGttttttttttt	0.264			T	CIITA	PMBL|Hodgkin Lymphona|								6	4	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12660558	12660559	+	Intron	DEL	TC	-	-	rs149439743	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12660558_12660559delTC	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						GTAAGTGGGGTCCCCCATCCTT	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	16701472	16701472	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16701472delC								LOC339047 (257035 upstream) : XYLT1 (494711 downstream)																							TGGAATCTGGCAGCATGGGGC	0.443													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22654097	22654097	+	IGR	DEL	G	-	-	rs5816181		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22654097delG								LOC653786 (65911 upstream) : HS3ST2 (171763 downstream)																							CATAGATTTTGTGGGAGCTTC	0.453													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26852871	26852871	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26852871delT								HS3ST4 (703863 upstream) : C16orf82 (225348 downstream)																							GGGAGGGTCATTTTTTTTTTC	0.378													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32841458	32841459	+	IGR	INS	-	GGA	GGA			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32841458_32841459insGGA								TP53TG3B (152580 upstream) : SLC6A10P (47338 downstream)																							agctgtcttggggagatttgca	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33048951	33048951	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33048951delT								SLC6A10P (152488 upstream) : MIR1826 (916557 downstream)																							tacaagtcaatggcttttagt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33521341	33521341	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33521341delT								SLC6A10P (624878 upstream) : MIR1826 (444167 downstream)																							acccctaaactggcagttggt	0.095													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49018758	49018758	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49018758delT								N4BP1 (374638 upstream) : CBLN1 (293453 downstream)																							AAGCAAGCTCttttttttttt	0.254													4	3	---	---	---	---	
ZNF423	23090	broad.mit.edu	37	16	49628554	49628554	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49628554delC	uc002efs.2	-						ZNF423_uc010vgn.1_Intron	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	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)				ACACAAAGCACAGAAAGAAGC	0.308													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	50940202	50940203	+	IGR	INS	-	CATCA	CATCA	rs147105528	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50940202_50940203insCATCA								CYLD (104356 upstream) : SALL1 (229683 downstream)																							CCAGCCTTCTGcatcacatcac	0.500													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	53568345	53568348	+	IGR	DEL	GAGT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53568345_53568348delGAGT								AKTIP (31175 upstream) : RPGRIP1L (65475 downstream)																							GGCCTATTCAGAGTGAGTGAGTGG	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54442409	54442410	+	IGR	INS	-	T	T	rs148193484	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54442409_54442410insT								IRX3 (122031 upstream) : IRX5 (522701 downstream)																							CAGGGTGGTGATGGAGGCATGA	0.411													5	9	---	---	---	---	
SLC6A2	6530	broad.mit.edu	37	16	55731636	55731636	+	Intron	DEL	A	-	-	rs35434599		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55731636delA	uc002eif.2	+						SLC6A2_uc010ccd.2_Intron|SLC6A2_uc002eig.2_Intron|SLC6A2_uc002eih.2_Intron|SLC6A2_uc002eii.2_Intron|SLC6A2_uc002eij.2_Intron	NM_001043	NP_001034	P23975	SC6A2_HUMAN	solute carrier family 6 member 2						synaptic transmission	integral to plasma membrane|membrane fraction	norepinephrine:sodium symporter activity			lung(4)|ovary(2)|pancreas(2)	8				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Atomoxetine(DB00289)|Bethanidine(DB00217)|Bupropion(DB01156)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Diethylpropion(DB00937)|Doxepin(DB01142)|Duloxetine(DB00476)|Ergotamine(DB00696)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Maprotiline(DB00934)|Mazindol(DB00579)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GCCTGAGAACAGGACAGAAAT	0.547													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	58348882	58348882	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58348882delG								PRSS54 (19931 upstream) : GINS3 (77416 downstream)																							ctagttttgagggatagagtt	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	65675397	65675397	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65675397delG								LOC283867 (65194 upstream) : CDH5 (725128 downstream)																							ttcatgtgctggtgtttcttg	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	67045848	67045848	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67045848delT								CES8 (2191 upstream) : CBFB (17202 downstream)																							tttcctgaactttttcagcta	0.169													4	2	---	---	---	---	
ZFHX3	463	broad.mit.edu	37	16	73011494	73011495	+	Intron	INS	-	A	A	rs147952180	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73011494_73011495insA	uc002fck.2	-						ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	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)				TCAGTGGGGGGAAAAAAATCAC	0.475													4	2	---	---	---	---	
WDR59	79726	broad.mit.edu	37	16	74938198	74938198	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74938198delA	uc002fdh.1	-						WDR59_uc002fdf.1_5'UTR|WDR59_uc002fdg.1_Intron	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59											ovary(1)|breast(1)	2						ttacagacataaaaaattcaa	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77616269	77616270	+	IGR	INS	-	AACCGTGGA	AACCGTGGA	rs11281281		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77616269_77616270insAACCGTGGA								ADAMTS18 (147258 upstream) : NUDT7 (140141 downstream)																							ATCATTTTCTGAATGTATGCTT	0.431													3	3	---	---	---	---	
PLCG2	5336	broad.mit.edu	37	16	81969516	81969516	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81969516delA	uc002fgt.2	+							NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2						intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8						GTGATAGTTTAAAAAAAAAAG	0.413													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	85538627	85538628	+	IGR	INS	-	CGC	CGC	rs150749476	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85538627_85538628insCGC								FAM92B (392513 upstream) : KIAA0182 (106401 downstream)																							ACACATGTGCACGCACACACAG	0.515													4	5	---	---	---	---	
C16orf74	404550	broad.mit.edu	37	16	85765298	85765298	+	Intron	DEL	T	-	-	rs33921613		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85765298delT	uc002fjc.3	-							NM_206967	NP_996850	Q96GX8	CP074_HUMAN	MGC17624 protein												0						TGTGATGTCAttttttttttt	0.249													3	4	---	---	---	---	
ZNF469	84627	broad.mit.edu	37	16	88494070	88494070	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88494070delG	uc002fku.2	+	1	192	c.192delG	c.(190-192)CAGfs	p.Q64fs		NM_001127464	NP_001120936	Q96JG9	ZN469_HUMAN	zinc finger protein 469	64	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CCGAGGCCCAGCCAAGGCAGG	0.731													4	2	---	---	---	---	
INPP5K	51763	broad.mit.edu	37	17	1410457	1410466	+	Intron	DEL	GATCAGCACA	-	-	rs78092914	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1410457_1410466delGATCAGCACA	uc002fsr.2	-						INPP5K_uc002fss.2_Intron|INPP5K_uc002fsq.2_Intron|INPP5K_uc010cjr.2_Intron|INPP5K_uc010vql.1_Intron|INPP5K_uc010vqm.1_Intron	NM_016532	NP_057616	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K isoform						actin cytoskeleton organization	cytosol|endoplasmic reticulum|membrane fraction|neuron projection|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol bisphosphate phosphatase activity|inositol bisphosphate phosphatase activity|inositol trisphosphate phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|lipid phosphatase activity|protein binding				0						CCATTCAAGGGATCAGCACATGCCGTCACA	0.552													20	24	---	---	---	---	
SLC43A2	124935	broad.mit.edu	37	17	1495029	1495029	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1495029delG	uc002fsv.2	-						SLC43A2_uc002fsu.2_Intron|SLC43A2_uc002fsw.2_Intron|SLC43A2_uc002fsx.2_Intron|SLC43A2_uc010vqo.1_Intron	NM_152346	NP_689559	Q8N370	LAT4_HUMAN	solute carrier family 43, member 2						cellular nitrogen compound metabolic process|ion transport	integral to membrane|plasma membrane					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		GGGGGGGGGAGGGGGCAGAGT	0.701													8	5	---	---	---	---	
SPATA22	84690	broad.mit.edu	37	17	3371151	3371151	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3371151delC	uc002fvm.2	-						SPATA22_uc010vrg.1_Intron|SPATA22_uc010vrf.1_Intron|SPATA22_uc002fvn.2_Intron|SPATA22_uc002fvo.2_Intron|SPATA22_uc002fvp.2_Intron|SPATA22_uc010ckf.2_Intron	NM_032598	NP_115987	Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22												0						TTTTCCTTATCCCCCTCCTGT	0.443													4	2	---	---	---	---	
ASGR2	433	broad.mit.edu	37	17	7016797	7016798	+	Intron	DEL	AC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7016797_7016798delAC	uc002gep.3	-						ASGR2_uc002gem.1_Intron|ASGR2_uc002gen.1_Intron|ASGR2_uc002geo.1_Intron|ASGR2_uc002ger.3_Intron|ASGR2_uc002geq.3_Intron|ASGR2_uc010clw.2_Intron|ASGR2_uc010vtl.1_Intron	NM_001181	NP_001172	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2 isoform a						cell surface receptor linked signaling pathway|endocytosis	focal adhesion|integral to membrane|nucleolus	asialoglycoprotein receptor activity|protein binding|sugar binding			ovary(1)	1					Antihemophilic Factor(DB00025)	ctcacacaatacacacacacaa	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	9652490	9652490	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9652490delT								USP43 (19489 upstream) : DHRS7C (22266 downstream)																							ggataatttcttatgacctgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	10506462	10506462	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10506462delA	uc002gml.1	+											Homo sapiens cDNA FLJ40181 fis, clone TESTI2018178.																		actcatgaataaaaaaggtag	0.050													4	2	---	---	---	---	
SHISA6	388336	broad.mit.edu	37	17	11154741	11154741	+	Intron	DEL	A	-	-	rs141844888		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11154741delA	uc002gna.3	+						SHISA6_uc002gnb.3_Intron	NM_207386	NP_997269	Q6ZSJ9	SHSA6_HUMAN	shisa homolog 6							integral to membrane				breast(1)	1						TTTAATTGAGAAAAAAAAAAA	0.398													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	18172039	18172040	+	IGR	DEL	AA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18172039_18172040delAA								SMCR7 (2946 upstream) : TOP3A (5195 downstream)																							AAGATTTTAGAAAAAAAAAAAG	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	18271876	18271877	+	IGR	INS	-	TTTG	TTTG	rs146916928	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18271876_18271877insTTTG								SHMT1 (5020 upstream) : EVPLL (9202 downstream)																							gcttttgtttctttgtattttt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21225026	21225027	+	IGR	INS	-	T	T	rs5819752		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21225026_21225027insT								MAP2K3 (6477 upstream) : KCNJ12 (54672 downstream)																							AGCGCTGGTGGTTCCCCACAGT	0.525													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21225031	21225032	+	IGR	INS	-	G	G	rs146208204		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21225031_21225032insG								MAP2K3 (6482 upstream) : KCNJ12 (54667 downstream)																							TGGTGGTTCCCCACAGTCTGAG	0.515													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21245238	21245239	+	IGR	INS	-	T	T	rs147043183		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21245238_21245239insT								MAP2K3 (26689 upstream) : KCNJ12 (34460 downstream)																							gattgcccagatcacacaatga	0.124													3	5	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21312637	21312638	+	Intron	INS	-	TGT	TGT	rs143247012		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21312637_21312638insTGT	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	aggagACTTGGTGTGGGGCATC	0.312										Prostate(3;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21518648	21518649	+	IGR	INS	-	A	A	rs148316050		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21518648_21518649insA								C17orf51 (40917 upstream) : FAM27L (306721 downstream)																							cgcaaaaattcaaaaattgcaa	0.109													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21536815	21536815	+	IGR	DEL	A	-	-	rs113534870		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21536815delA								C17orf51 (59084 upstream) : FAM27L (288555 downstream)																							gggcattcttaacgttgttcc	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21549031	21549032	+	IGR	INS	-	G	G	rs149320251		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21549031_21549032insG								C17orf51 (71300 upstream) : FAM27L (276338 downstream)																							CCCTGTGGCCAGGGGCACAGCT	0.114													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21549173	21549173	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21549173delA								C17orf51 (71442 upstream) : FAM27L (276197 downstream)																							taagtgagttaacagctgtaa	0.085													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	22216386	22216386	+	IGR	DEL	C	-	-	rs139395717	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22216386delC								FLJ36000 (303316 upstream) : None (None downstream)																							aaacaaaaaaCCAGCCTCCAG	0.318													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25398171	25398172	+	IGR	INS	-	T	T	rs139158731	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25398171_25398172insT								None (None upstream) : WSB1 (222934 downstream)																							aagtctctctgctcccttcctc	0.000													5	3	---	---	---	---	
TBC1D3	729873	broad.mit.edu	37	17	36351714	36351715	+	Intron	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36351714_36351715insA	uc002hpr.2	-						TBC1D3_uc010cvk.2_Intron|TBC1D3_uc010wdn.1_Intron	NM_001123391	NP_001116863	Q8IZP1	TBC3A_HUMAN	TBC1 domain family, member 3							intracellular	Rab GTPase activator activity				0	Breast(7;2.97e-12)	Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		gaactttaattaaaaaaaaaga	0.040													4	5	---	---	---	---	
TBC1D3	729873	broad.mit.edu	37	17	36358655	36358656	+	Intron	INS	-	G	G	rs10574123		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36358655_36358656insG	uc010wdn.1	-						TBC1D3_uc010cvk.2_5'Flank			Q8IZP1	TBC3A_HUMAN	Homo sapiens TBC1D3 mRNA for TBC1 domain family, member 3, complete cds.							intracellular	Rab GTPase activator activity				0	Breast(7;2.97e-12)	Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTTATATTCTCTTAATTATTAT	0.252													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	37213234	37213235	+	5'Flank	INS	-	T	T	rs148158521	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37213234_37213235insT	uc002hre.1	+											Homo sapiens cDNA FLJ37796 fis, clone BRSSN1000092.																		GCCTGCGCCTCTTTTTTTAAAA	0.673													5	3	---	---	---	---	
FAM134C	162427	broad.mit.edu	37	17	40734988	40734988	+	Intron	DEL	T	-	-	rs35747013		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40734988delT	uc002ial.2	-						FAM134C_uc010wgq.1_Intron|FAM134C_uc002iam.1_Intron|FAM134C_uc010cyk.1_Intron	NM_178126	NP_835227	Q86VR2	F134C_HUMAN	hypothetical protein LOC162427							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.134)		CTCCCCTTTATTTTTTTTTTA	0.363													9	4	---	---	---	---	
EFTUD2	9343	broad.mit.edu	37	17	42937009	42937010	+	Intron	INS	-	CA	CA	rs139421777	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42937009_42937010insCA	uc002ihn.2	-						EFTUD2_uc010wje.1_Intron|EFTUD2_uc010wjf.1_Intron	NM_004247	NP_004238	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain							Cajal body|catalytic step 2 spliceosome|cytoplasm|nuclear speck	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(33;0.109)				acacaaatacgcacacacacac	0.292													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	47279677	47279677	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47279677delC								B4GALNT2 (32326 upstream) : GNGT2 (3920 downstream)																							TCCATTCTTACCCTTCCTCCC	0.448													4	2	---	---	---	---	
UTP18	51096	broad.mit.edu	37	17	49361746	49361746	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49361746delT	uc002its.2	+							NM_016001	NP_057085	Q9Y5J1	UTP18_HUMAN	UTP18, small subunit processome component						rRNA processing	nucleolus					0			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)			GTGTTTAGCCTTTTTTTTTTA	0.313													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	55864760	55864761	+	IGR	DEL	GA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55864760_55864761delGA								MSI2 (107461 upstream) : MRPS23 (52083 downstream)																							GGATAAGAGGGAGAGGGGCAAG	0.525													4	2	---	---	---	---	
SKA2	348235	broad.mit.edu	37	17	57228294	57228294	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57228294delA	uc002ixd.2	-						SKA2_uc010dde.1_Intron|SKA2_uc002ixe.2_Intron	NM_182620	NP_872426	Q8WVK7	SKA2_HUMAN	spindle and KT associated 2 isoform 1						cell division|chromosome segregation|mitotic anaphase|mitotic prometaphase|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytosol|spindle microtubule	microtubule binding				0						ACTTAGATATAAAAAATATTC	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	61673450	61673450	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61673450delT								DCAF7 (1811 upstream) : TACO1 (4793 downstream)																							GAGAATTTAAttttttttttt	0.239													3	3	---	---	---	---	
SMURF2	64750	broad.mit.edu	37	17	62547477	62547477	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62547477delA	uc002jep.1	-						SMURF2_uc002jeq.1_Intron|SMURF2_uc002jer.1_Intron	NM_022739	NP_073576	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2						BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			cctgtctcagaaaaaaaaaaa	0.169													3	3	---	---	---	---	
AXIN2	8313	broad.mit.edu	37	17	63552538	63552538	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63552538delC	uc002jfi.2	-						AXIN2_uc010den.1_Intron|AXIN2_uc002jfh.2_Intron	NM_004655	NP_004646	Q9Y2T1	AXIN2_HUMAN	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						AGAGGCCAGACCCAGGATCTT	0.567									Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome		OREG0024671	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64498940	64498940	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64498940delT	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)	acctggctaattttttttttt	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	71853829	71853829	+	IGR	DEL	C	-	-	rs112346711		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71853829delC								C17orf54 (29153 upstream) : RPL38 (345966 downstream)																							ACATACCCCACCCCCCCCCAA	0.537													3	3	---	---	---	---	
KCTD2	23510	broad.mit.edu	37	17	73057959	73057959	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73057959delG	uc002jmp.2	+						KCTD2_uc010dfz.2_Intron|KCTD2_uc002jmq.2_Intron	NM_015353	NP_056168	Q14681	KCTD2_HUMAN	potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity				0	all_lung(278;0.226)					TGCCGCTGACGGGGGGGGACT	0.567													4	2	---	---	---	---	
SEPT9	10801	broad.mit.edu	37	17	75372128	75372128	+	Intron	DEL	G	-	-	rs76223580		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75372128delG	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_5'Flank	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			TTCCGAATCAGGGTAGAGAAA	0.552													5	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75800656	75800657	+	IGR	DEL	CA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75800656_75800657delCA								SEPT9 (303980 upstream) : FLJ45079 (74452 downstream)																							CACCGCCACCCACACACACACA	0.540													4	3	---	---	---	---	
ASPSCR1	79058	broad.mit.edu	37	17	79953982	79953982	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79953982delA	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	Q9BZE9	ASPC1_HUMAN	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)			CTATTTAGCTAAAAAAAAAAG	0.607			T	TFE3	alveolar soft part sarcoma								5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	1997481	1997482	+	IGR	INS	-	A	A	rs143971870	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1997481_1997482insA								C18orf2 (590300 upstream) : METTL4 (540043 downstream)																							ATTTTTTTCGTAAAAAAAGCAA	0.317													8	5	---	---	---	---	
NDC80	10403	broad.mit.edu	37	18	2594606	2594609	+	Intron	DEL	AGTC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2594606_2594609delAGTC	uc002kli.2	+							NM_006101	NP_006092	O14777	NDC80_HUMAN	kinetochore associated 2						attachment of spindle microtubules to kinetochore|cell division|establishment of mitotic spindle orientation|mitotic prometaphase|mitotic sister chromatid segregation|mitotic spindle organization|phosphatidylinositol-mediated signaling	condensed nuclear chromosome outer kinetochore|cytosol|Ndc80 complex	protein binding			ovary(1)	1						AGCCTGCACAAGTCAGTTCATTTT	0.387													5	3	---	---	---	---	
MYOM1	8736	broad.mit.edu	37	18	3195846	3195846	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3195846delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						CAGGCGCTGCTTTTTTTTTTC	0.308													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	4642899	4642900	+	IGR	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4642899_4642900insA								DLGAP1 (187633 upstream) : LOC642597 (500772 downstream)																							ACTGGCTGATTAAAAAAAAAAG	0.248													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10432281	10432281	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10432281delT								VAPA (472264 upstream) : APCDD1 (22344 downstream)																							TCACACACACTTTTCAAGGCT	0.517													4	2	---	---	---	---	
AFG3L2	10939	broad.mit.edu	37	18	12359741	12359741	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12359741delA	uc002kqz.1	-							NM_006796	NP_006787	Q9Y4W6	AFG32_HUMAN	AFG3 ATPase family gene 3-like 2						cell death|protein catabolic process|proteolysis	integral to membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0					Adenosine triphosphate(DB00171)	accccacctcaaaaaaaaaag	0.129													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	20161352	20161353	+	IGR	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20161352_20161353insT								CTAGE1 (163474 upstream) : RBBP8 (351942 downstream)																							ttttacaccaattgtcctctct	0.000													4	2	---	---	---	---	
ANKRD29	147463	broad.mit.edu	37	18	21191836	21191836	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21191836delA	uc002kun.2	-						ANKRD29_uc002kuo.2_Intron	NM_173505	NP_775776	Q8N6D5	ANR29_HUMAN	ankyrin repeat domain 29											ovary(3)|breast(1)	4	all_cancers(21;5.07e-05)|all_epithelial(16;2.49e-07)|Lung NSC(20;0.00211)|all_lung(20;0.00676)|Colorectal(14;0.0202)|Ovarian(20;0.127)					gtTAAAAAAGAAAAAAAAAAA	0.184													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	26326787	26326788	+	IGR	DEL	AC	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26326787_26326788delAC								CDH2 (569342 upstream) : None (None downstream)																							acacacacatacacacacacac	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	27664822	27664822	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27664822delT								None (None upstream) : MIR302F (214054 downstream)																							ATATACTAAATTTTTTTAAAT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	27927324	27927324	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27927324delG								MIR302F (48398 upstream) : DSC3 (642729 downstream)																							tgcaagaggtggattcccatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	27979078	27979079	+	IGR	DEL	AG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27979078_27979079delAG								MIR302F (100152 upstream) : DSC3 (590974 downstream)																							gtacttggaaagagagagagag	0.000													4	2	---	---	---	---	
ASXL3	80816	broad.mit.edu	37	18	31226008	31226008	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31226008delA	uc010dmg.1	+						ASXL3_uc002kxq.2_Intron	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						AAATTTATCCAAAAAAAAAAT	0.254													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38559106	38559106	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38559106delT								None (None upstream) : KC6 (501132 downstream)																							aaccacttgctttAGTTTGAG	0.199													4	2	---	---	---	---	
ST8SIA5	29906	broad.mit.edu	37	18	44292791	44292792	+	Intron	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44292791_44292792insA	uc002lcj.1	-						ST8SIA5_uc002lci.1_Intron|ST8SIA5_uc010xcy.1_Intron|ST8SIA5_uc010xcz.1_Intron|ST8SIA5_uc010dno.1_Intron	NM_013305	NP_037437	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3						ataactcttccaaaaaaaaagc	0.000													4	2	---	---	---	---	
HDHD2	84064	broad.mit.edu	37	18	44663014	44663014	+	Intron	DEL	T	-	-	rs144963110		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44663014delT	uc002lcs.2	-						HDHD2_uc002lct.2_Intron	NM_032124	NP_115500	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain								hydrolase activity				0						AATACTTAGGtttttttttaa	0.284													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	48368290	48368290	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48368290delA								MRO (16536 upstream) : ME2 (37145 downstream)																							gggttgtcctaaggattaaaA	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	49381445	49381445	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49381445delG								MEX3C (657755 upstream) : DCC (485126 downstream)																							CTGAAGCACTGGGGGGTCAGG	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53326093	53326094	+	IGR	DEL	TG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53326093_53326094delTG								TCF4 (22908 upstream) : TXNL1 (943961 downstream)																							CCAAGGTGTATGTGTGTGTGTT	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	54885054	54885054	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54885054delT								WDR7 (188018 upstream) : ST8SIA3 (134667 downstream)																							ctttaaggggttagcccactg	0.050													4	2	---	---	---	---	
CCBE1	147372	broad.mit.edu	37	18	57103522	57103523	+	Intron	INS	-	G	G	rs138297937	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57103522_57103523insG	uc002lib.2	-						CCBE1_uc010dpq.2_Intron|CCBE1_uc002lia.2_Intron	NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	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)				TACAGGAGCCTGGGGGTCCTCC	0.490													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65532330	65532331	+	IGR	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65532330_65532331insT								DSEL (348363 upstream) : TMX3 (808596 downstream)																							cttccctcttgtttttttttat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68087459	68087460	+	IGR	INS	-	AT	AT			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68087459_68087460insAT								SOCS6 (90025 upstream) : None (None downstream)																							agttgcattccatatatttctt	0.119													4	2	---	---	---	---	
ZNF407	55628	broad.mit.edu	37	18	72408749	72408749	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72408749delG	uc002llw.2	+						ZNF407_uc010xfc.1_Intron|ZNF407_uc010dqu.1_Intron	NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CTTGCTTCCTGGTAATGATGA	0.408													4	2	---	---	---	---	
ATP9B	374868	broad.mit.edu	37	18	76954175	76954175	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76954175delT	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmy.1_Intron|ATP9B_uc002lmz.1_Intron	NM_198531	NP_940933	O43861	ATP9B_HUMAN	ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		AACTCACATCTTTTTTTTTTA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	4144346	4144347	+	IGR	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4144346_4144347insT								MAP2K2 (20220 upstream) : CREB3L3 (9282 downstream)																							ttctttctttctttttttttct	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	5367196	5367196	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5367196delG								PTPRS (26382 upstream) : ZNRF4 (88230 downstream)																							GTTGGCAGTAGGGGGAAGGAG	0.562													4	2	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7153066	7153066	+	Intron	DEL	A	-	-	rs113402674		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7153066delA	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199	P06213	INSR_HUMAN	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)	acacccccccacacacacaca	0.050													6	4	---	---	---	---	
ARHGEF18	23370	broad.mit.edu	37	19	7494015	7494017	+	Intron	DEL	CCC	-	-	rs67217673		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7494015_7494017delCCC	uc010xjm.1	+						ARHGEF18_uc002mgh.2_Intron	NM_015318	NP_056133	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)				CTCTGAGGCTCCCCCCTGGTATG	0.631													4	5	---	---	---	---	
CDC37	11140	broad.mit.edu	37	19	10516196	10516197	+	5'Flank	INS	-	G	G	rs150485063	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10516196_10516197insG	uc002mof.1	-						CDC37_uc010dxf.1_5'Flank|CDC37_uc002mog.1_5'Flank|CDC37_uc002moh.2_5'Flank|MIR1181_hsa-mir-1181|MI0006274_5'Flank	NM_007065	NP_008996	Q16543	CDC37_HUMAN	cell division cycle 37 protein						protein targeting|regulation of cyclin-dependent protein kinase activity|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway		unfolded protein binding				0			OV - Ovarian serous cystadenocarcinoma(20;4.65e-10)|Epithelial(33;6.48e-07)|all cancers(31;2.31e-06)	GBM - Glioblastoma multiforme(1328;0.0318)		TGTGTGTGTGTGTGGGGGGGAG	0.589													4	4	---	---	---	---	
DNM2	1785	broad.mit.edu	37	19	10844690	10844691	+	Intron	INS	-	A	A	rs111312260		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10844690_10844691insA	uc002mps.1	+						DNM2_uc010dxk.2_Intron|DNM2_uc002mpt.1_Intron|DNM2_uc002mpv.1_Intron|DNM2_uc002mpu.1_Intron|DNM2_uc010dxl.1_Intron	NM_001005361	NP_001005361	P50570	DYN2_HUMAN	dynamin 2 isoform 2						G2/M transition of mitotic cell cycle|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|post-Golgi vesicle-mediated transport|receptor internalization|signal transduction|synaptic vesicle transport|transferrin transport	cell junction|cytosol|Golgi membrane|microtubule|postsynaptic density|postsynaptic membrane	GTP binding|GTPase activity|microtubule binding			central_nervous_system(2)|skin(2)|ovary(1)|breast(1)	6			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			tctcaaaaaataaaaaaaaaaa	0.074													4	2	---	---	---	---	
NOTCH3	4854	broad.mit.edu	37	19	15276831	15276831	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15276831delC	uc002nan.2	-	30	5510	c.5434delG	c.(5434-5436)GAGfs	p.E1812fs		NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3 precursor	1812	Cytoplasmic (Potential).				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)			TCATCTGCCTCATCCTCTTCA	0.587													47	28	---	---	---	---	
BRD4	23476	broad.mit.edu	37	19	15432834	15432835	+	Intron	INS	-	AC	AC	rs57941063	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15432834_15432835insAC	uc002nat.3	-						BRD4_uc002nau.3_Intron	NM_014299	NP_055114	O60885	BRD4_HUMAN	bromodomain-containing protein 4 isoform short						interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle	condensed nuclear chromosome|cytoplasm	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			GGCACATACATACACACACACA	0.396			T	NUT|C15orf55	lethal midline carcinoma of young people								4	2	---	---	---	---	
USHBP1	83878	broad.mit.edu	37	19	17374674	17374674	+	Intron	DEL	A	-	-	rs77430153		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17374674delA	uc002nfs.1	-						USHBP1_uc002nft.1_Intron|USHBP1_uc010xpk.1_Intron|USHBP1_uc010eam.1_5'UTR	NM_031941	NP_114147	Q8N6Y0	USBP1_HUMAN	Usher syndrome 1C binding protein 1								PDZ domain binding			ovary(1)	1						agcaagactcaaaaaaaaaag	0.234													6	3	---	---	---	---	
UPF1	5976	broad.mit.edu	37	19	18947041	18947041	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18947041delT	uc002nkg.2	+						UPF1_uc002nkf.2_Intron	NM_002911	NP_002902	Q92900	RENT1_HUMAN	regulator of nonsense transcripts 1						cell cycle|DNA repair|DNA replication|histone mRNA catabolic process|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational termination	chromatin|cytoplasmic mRNA processing body|exon-exon junction complex	ATP binding|ATP-dependent RNA helicase activity|chromatin binding|DNA binding|protein binding|protein binding|RNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2						TCAGAAGTCCTTTGCATAATA	0.488													4	2	---	---	---	---	
ZNF98	148198	broad.mit.edu	37	19	22603999	22603999	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22603999delT	uc002nqt.2	-							NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				TAATGCTTTGTCAAAAAATGA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	28694164	28694165	+	IGR	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28694164_28694165insA								LOC148189 (409316 upstream) : LOC148145 (761875 downstream)																							tatgggcacacagagatactag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29916880	29916880	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29916880delC	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		CACTTTGCAGCCCCACAACCA	0.517													4	2	---	---	---	---	
ZNF536	9745	broad.mit.edu	37	19	30873477	30873477	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30873477delT	uc002nsu.1	+						ZNF536_uc010edd.1_Intron	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					GGGCAGGGAATTTTTTTTTTT	0.353													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	32718266	32718266	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32718266delA								TSHZ3 (878076 upstream) : ZNF507 (118248 downstream)																							AAAAGTAAAGAAAAAAAAAGA	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	35023882	35023882	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35023882delG								WTIP (31798 upstream) : LOC643719 (43757 downstream)																							TTACATGGTTGGGGCCCTCCC	0.383													4	2	---	---	---	---	
ZNF181	339318	broad.mit.edu	37	19	35225746	35225754	+	5'UTR	DEL	GTTCCCAGG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35225746_35225754delGTTCCCAGG	uc002nvu.3	+	1					ZNF181_uc010xsa.1_Intron|ZNF181_uc010xsb.1_5'UTR|ZNF181_uc010xsc.1_5'UTR	NM_001029997	NP_001025168	Q2M3W8	ZN181_HUMAN	zinc finger protein 181 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			CACCCTGTTAGTTCCCAGGGAGAGATTGG	0.450													20	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	35950327	35950327	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35950327delT								FFAR2 (7660 upstream) : KRTDAP (27903 downstream)																							TTTGCCCCACTTTTTTTTTTC	0.453													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	41324352	41324353	+	IGR	INS	-	A	A	rs144591646	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41324352_41324353insA								EGLN2 (10016 upstream) : CYP2A6 (25091 downstream)																							GAATCTATTACAATGTACTAAG	0.455													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42256105	42256105	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42256105delG								CEACAM5 (21669 upstream) : CEACAM6 (3293 downstream)																							GCGTCAACTTGGTCCTAAAAT	0.493													4	2	---	---	---	---	
PSG6	5675	broad.mit.edu	37	19	43461720	43461720	+	Intron	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43461720delC	uc002ovh.1	-						PSG11_uc002ouw.2_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron			Q00889	PSG6_HUMAN	SubName: Full=Putative uncharacterized protein PSG6;						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)				CTTTAAATGACCATATGTTTA	0.274													4	2	---	---	---	---	
RSPH6A	81492	broad.mit.edu	37	19	46318680	46318681	+	5'Flank	INS	-	T	T	rs74596352		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46318680_46318681insT	uc002pdm.2	-							NM_030785	NP_110412	Q9H0K4	RSH6A_HUMAN	radial spokehead-like 1							intracellular				ovary(1)|central_nervous_system(1)	2						CCCGCCATCCCTTTTTTTTTTT	0.624													4	2	---	---	---	---	
PPP5C	5536	broad.mit.edu	37	19	46880834	46880834	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46880834delT	uc002pem.2	+						PPP5C_uc010xya.1_Intron|PPP5C_uc002pen.2_Intron	NM_006247	NP_006238	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit						mitosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein dephosphorylation|transcription, DNA-dependent	Golgi apparatus|nucleus	metal ion binding|protein binding|protein serine/threonine phosphatase activity|signal transducer activity			lung(1)|pancreas(1)	2		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		gtttttagagttttatgtgcc	0.065													4	2	---	---	---	---	
CCDC8	83987	broad.mit.edu	37	19	46916341	46916342	+	5'UTR	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46916341_46916342insA	uc002pep.2	-	1						NM_032040	NP_114429	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8							plasma membrane				ovary(3)	3				OV - Ovarian serous cystadenocarcinoma(262;4.66e-05)|all cancers(93;0.000582)|Epithelial(262;0.00428)|GBM - Glioblastoma multiforme(486;0.0421)		AGTCTTGAGGGAGGGACTGGAT	0.564													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53738115	53738116	+	IGR	INS	-	G	G	rs146965909		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53738115_53738116insG								ZNF665 (41496 upstream) : ZNF677 (522 downstream)																							TAAAAAAAAAATCCATTGCTTA	0.248													4	2	---	---	---	---	
TTYH1	57348	broad.mit.edu	37	19	54943038	54943038	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54943038delT	uc002qfq.2	+						TTYH1_uc010yey.1_Intron|TTYH1_uc002qfr.2_Intron|TTYH1_uc002qft.2_Intron|TTYH1_uc002qfu.1_3'UTR	NM_020659	NP_065710	Q9H313	TTYH1_HUMAN	tweety 1 isoform 1						cell adhesion	chloride channel complex|plasma membrane	chloride channel activity|iron ion transmembrane transporter activity				0	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		GAAGGACGAGTTTTTTTTGTT	0.443													4	2	---	---	---	---	
RDH13	112724	broad.mit.edu	37	19	55573586	55573587	+	Intron	INS	-	GGT	GGT	rs146463466	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55573586_55573587insGGT	uc002qio.3	-						RDH13_uc002qip.2_Intron|RDH13_uc010yfq.1_Intron	NM_001145971	NP_001139443	Q8NBN7	RDH13_HUMAN	retinol dehydrogenase 13 isoform 1								binding|oxidoreductase activity			large_intestine(1)|ovary(1)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(297;0.199)	GBM - Glioblastoma multiforme(193;0.0504)	Vitamin A(DB00162)	gacccctctacggagtcacgac	0.213													3	3	---	---	---	---	
AURKC	6795	broad.mit.edu	37	19	57742514	57742514	+	5'UTR	DEL	G	-	-	rs150998448		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57742514delG	uc002qoe.2	+	1					AURKC_uc002qoc.2_Intron|AURKC_uc002qod.2_Intron|AURKC_uc010etv.2_5'UTR	NM_001015878	NP_001015878	Q9UQB9	AURKC_HUMAN	aurora kinase C isoform 1						cell cycle|cytokinesis	condensed chromosome|cytoplasm|midbody|spindle midzone	ATP binding|protein serine/threonine kinase activity			lung(4)|ovary(2)	6		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)		GATTGGAAGCGCCCCGGCCAG	0.647													24	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	1924741	1924741	+	IGR	DEL	T	-	-	rs67919550		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1924741delT								SIRPA (4202 upstream) : PDYN (34662 downstream)																							tttggagatattttttttctg	0.000													4	2	---	---	---	---	
C20orf30	29058	broad.mit.edu	37	20	5080119	5080119	+	Intron	DEL	T	-	-	rs5840075		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5080119delT	uc010gbi.2	-							NM_014145	NP_054864	Q96A57	CT030_HUMAN	hypothetical protein LOC29058 isoform 2							integral to membrane					0						acttcctgagttttttttttt	0.209													8	5	---	---	---	---	
PAK7	57144	broad.mit.edu	37	20	9689586	9689587	+	Intron	INS	-	C	C	rs143875446	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9689586_9689587insC	uc002wnl.2	-						PAK7_uc002wnk.2_Intron|PAK7_uc002wnj.2_Intron|PAK7_uc010gby.1_Intron	NM_020341	NP_065074	Q9P286	PAK7_HUMAN	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)			tccttcctctgctcacatccac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	9941213	9941214	+	IGR	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9941213_9941214insT								PAK7 (121526 upstream) : ANKRD5 (74483 downstream)																							ggtcttactccttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	10717080	10717080	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10717080delA								JAG1 (62386 upstream) : None (None downstream)																							TGGTTTAAGGAAAAAAAAATG	0.443													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	14394448	14394449	+	Intron	INS	-	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14394448_14394449insC	uc002wou.2	+						MACROD2_uc002wot.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				TTTTTTTCCTGCTTTTTTTTTC	0.371													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15918375	15918376	+	Intron	DEL	TA	-	-	rs76061067		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15918375_15918376delTA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				ATAGAAAATTtatatatatata	0.243													5	3	---	---	---	---	
C20orf72	92667	broad.mit.edu	37	20	17970348	17970349	+	Intron	INS	-	T	T	rs138796036		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17970348_17970349insT	uc002wqh.2	+						C20orf72_uc010gco.2_Intron|C20orf72_uc010gcp.2_Intron	NM_052865	NP_443097	Q9BQP7	CT072_HUMAN	hypothetical protein LOC92667												0						CTTCTTGGGCCTTTTTTTTTTT	0.267													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	21278076	21278076	+	IGR	DEL	A	-	-	rs113644583		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21278076delA								PLK1S1 (50820 upstream) : XRN2 (5866 downstream)																							aaaaacacccagtgcggccct	0.234													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29582837	29582837	+	IGR	DEL	G	-	-	rs11696313	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29582837delG								None (None upstream) : FRG1B (29042 downstream)																							ACAAATGCACGTCCTGCTTCA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29600972	29600972	+	IGR	DEL	A	-	-	rs112429825		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29600972delA								None (None upstream) : FRG1B (10907 downstream)																							aaactatttcaaaaaaatgaa	0.000													3	5	---	---	---	---	
CHMP4B	128866	broad.mit.edu	37	20	32417252	32417252	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32417252delT	uc002xaa.2	+							NM_176812	NP_789782	Q9H444	CHM4B_HUMAN	chromatin modifying protein 4B						cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			ovary(1)|central_nervous_system(1)	2						CTTCCCTCCCTTTCTTTGGCC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	34664142	34664142	+	IGR	DEL	T	-	-	rs113482157		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34664142delT								LOC647979 (25260 upstream) : EPB41L1 (15284 downstream)																							TTCACCCAACTTTTTTTTTTC	0.418													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37304366	37304367	+	IGR	INS	-	ATGA	ATGA	rs141937149	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37304366_37304367insATGA								ADIG (87262 upstream) : SLC32A1 (48738 downstream)																							ctaaagaatgcatgaatgaatg	0.020													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37401668	37401669	+	IGR	INS	-	C	C	rs138108565	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37401668_37401669insC								ACTR5 (579 upstream) : PPP1R16B (32679 downstream)																							GCTCATACAGTCTACCAAGGGT	0.505													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	42375708	42375708	+	IGR	DEL	G	-	-	rs67675099		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42375708delG								GTSF1L (20066 upstream) : TOX2 (167784 downstream)																							CAGCACTTGTGGAGTGCCCGT	0.562													5	3	---	---	---	---	
SLC2A10	81031	broad.mit.edu	37	20	45360398	45360399	+	Intron	DEL	AG	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45360398_45360399delAG	uc002xsl.2	+							NM_030777	NP_110404	O95528	GTR10_HUMAN	solute carrier family 2 member 10							endomembrane system|integral to membrane|perinuclear region of cytoplasm|plasma membrane	D-glucose transmembrane transporter activity|sugar:hydrogen symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				CAGAGGCCACAGAGAGAGAGAG	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	47049849	47049849	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47049849delC								LOC284749 (50468 upstream) : PREX1 (190944 downstream)																							cagtgtccttcccttccttca	0.134													4	2	---	---	---	---	
SLC9A8	23315	broad.mit.edu	37	20	48472663	48472663	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48472663delG	uc002xuv.1	+						SLC9A8_uc010zym.1_Intron|SLC9A8_uc010zyj.1_Intron|SLC9A8_uc010zyk.1_Intron|SLC9A8_uc010zyl.1_Intron|SLC9A8_uc010gib.1_Intron	NM_015266	NP_056081	Q9Y2E8	SL9A8_HUMAN	sodium/hydrogen exchanger 8							Golgi membrane|integral to membrane	sodium:hydrogen antiporter activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			TTTTAGTagtggtttctgagc	0.070													4	2	---	---	---	---	
NFATC2	4773	broad.mit.edu	37	20	50125314	50125315	+	Intron	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50125314_50125315insA	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	Q13469	NFAC2_HUMAN	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)					CAGCCAGTCTCAAAAAAATCCA	0.574													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	50472569	50472569	+	IGR	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50472569delG								SALL4 (53521 upstream) : ZFP64 (227982 downstream)																							cagtgggggtggggtctgcaa	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	50914513	50914514	+	IGR	INS	-	A	A	rs112998768		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50914513_50914514insA								ZFP64 (105989 upstream) : TSHZ2 (674363 downstream)																							gcacagcgtggaaaaaaaaaaa	0.059													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52985630	52985631	+	IGR	DEL	TT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52985630_52985631delTT								PFDN4 (149139 upstream) : DOK5 (106626 downstream)																							TTTTGAGTAGTTAAGATAACAT	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56031577	56031578	+	IGR	INS	-	TTTTG	TTTTG	rs138213018	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56031577_56031578insTTTTG								RBM38 (47193 upstream) : CTCFL (32302 downstream)																							acttgactcctttttgttttgt	0.000													6	6	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62076856	62076857	+	Intron	INS	-	CCCCAAAGGG	CCCCAAAGGG	rs138698925	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62076856_62076857insCCCCAAAGGG	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	GCAAGCTGACCCCCCCACCCCT	0.678													11	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10773090	10773090	+	IGR	DEL	A	-	-	rs71326351		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10773090delA								None (None upstream) : TPTE (133653 downstream)																							actgctcaataaaaaaaaagg	0.000													4	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11050605	11050606	+	Intron	INS	-	A	A	rs150695624		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11050605_11050606insA	uc002yit.1	-							NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CCTTTGATAATATATATAAATA	0.213													1	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11076406	11076407	+	Intron	DEL	TT	-	-	rs142727884		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11076406_11076407delTT	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)		taatttactattttttttttct	0.000													9	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11079693	11079693	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11079693delT	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)		TTCAATGCCCtttttttaatt	0.169													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	24878846	24878847	+	IGR	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24878846_24878847insT								None (None upstream) : None (None downstream)																							TATTTTACCAATGTTTTTTTCA	0.302													4	2	---	---	---	---	
APP	351	broad.mit.edu	37	21	27487012	27487012	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27487012delT	uc002ylz.2	-						APP_uc010glk.2_Intron|APP_uc002yma.2_Intron|APP_uc011ach.1_Intron|APP_uc002ymb.2_Intron|APP_uc010glj.2_Intron|APP_uc011aci.1_Intron|APP_uc011acj.1_Intron	NM_000484	NP_000475	P05067	A4_HUMAN	amyloid beta A4 protein isoform a precursor						adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)				AAATGCTTCATTTTTTTTTCC	0.313													4	2	---	---	---	---	
KRTAP19-8	728299	broad.mit.edu	37	21	32413120	32413121	+	5'Flank	DEL	AA	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32413120_32413121delAA	uc010glt.2	-							NM_001099219	NP_001092689	Q3LI54	KR198_HUMAN	keratin associated protein 19-8							intermediate filament				upper_aerodigestive_tract(1)	1						actccatctcaaaaaaaaaaaa	0.000													4	3	---	---	---	---	
TIAM1	7074	broad.mit.edu	37	21	32904436	32904436	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32904436delA	uc002yow.1	-						TIAM1_uc002yox.1_Intron	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10						tctcaaaaagaaaaaaagaaa	0.214													4	2	---	---	---	---	
GCFC1	94104	broad.mit.edu	37	21	34107532	34107532	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34107532delA	uc002yqn.2	-						uc002yqk.2_Intron|GCFC1_uc002yql.2_Intron|GCFC1_uc002yqm.2_Intron|GCFC1_uc002yqo.2_Intron	NM_016631	NP_057715	Q9Y5B6	GCFC1_HUMAN	GC-rich sequence DNA-binding factor candidate							cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2						ACAGCATGTTAAAAAAAAAAA	0.313													9	5	---	---	---	---	
IL10RB	3588	broad.mit.edu	37	21	34660710	34660711	+	Intron	DEL	AG	-	-	rs66834406		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34660710_34660711delAG	uc002yrk.1	+						IL10RB_uc002yrl.1_Intron	NM_000628	NP_000619	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta precursor						immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0						acacacacacagacacGCCTCT	0.401													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	34759759	34759759	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34759759delT								IFNAR1 (27633 upstream) : IFNGR2 (15443 downstream)																							CTCTGGCCCCTTGGCTTATTC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	36027477	36027478	+	IGR	INS	-	A	A	rs140500761	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36027477_36027478insA								RCAN1 (40095 upstream) : CLIC6 (14210 downstream)																							AACTTTAAAGGAAAAAAAAAAC	0.342													1	5	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	42053997	42053997	+	Intron	DEL	T	-	-	rs77359915		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42053997delT	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				gttcatggtattttttttttg	0.114													5	3	---	---	---	---	
KLHL22	84861	broad.mit.edu	37	22	20820090	20820090	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20820090delT	uc002zsl.1	-						KLHL22_uc011ahr.1_Intron|KLHL22_uc002zsm.1_Intron	NM_032775	NP_116164	Q53GT1	KLH22_HUMAN	kelch-like						cell division	Cul3-RING ubiquitin ligase complex				lung(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			ATACAGCATGtttttttttgg	0.244													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	23247455	23247456	+	Intron	DEL	TG	-	-	rs138768797		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23247455_23247456delTG	uc011aim.1	+						uc002zws.2_Intron					Parts of antibodies, mostly variable regions.												0						tctgtctgtctgtctctctctc	0.416													15	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	23330961	23330961	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23330961delT								LOC96610 (65879 upstream) : RTDR1 (70633 downstream)																							tgcttttgggttttttttttt	0.100													4	3	---	---	---	---	
CABIN1	23523	broad.mit.edu	37	22	24417287	24417288	+	Intron	INS	-	G	G	rs144289253	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24417287_24417288insG	uc002zzi.1	+						CABIN1_uc002zzj.1_Intron|CABIN1_uc002zzl.1_Intron|CABIN1_uc010guk.1_Intron|CABIN1_uc002zzk.1_Intron	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1						cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						GAGCAGTTTTTTTGTGTGTGTG	0.193													2	4	---	---	---	---	
CABIN1	23523	broad.mit.edu	37	22	24417288	24417289	+	Intron	INS	-	G	G	rs5996662	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24417288_24417289insG	uc002zzi.1	+						CABIN1_uc002zzj.1_Intron|CABIN1_uc002zzl.1_Intron|CABIN1_uc010guk.1_Intron|CABIN1_uc002zzk.1_Intron	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1						cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						AGCAGTTTTTTTGTGTGTGTGT	0.188													2	4	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26174254	26174255	+	Intron	INS	-	A	A	rs143540045	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26174254_26174255insA	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						Aaagtgctggcagggcaggcta	0.183													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	28051416	28051416	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28051416delT								MIAT (936467 upstream) : MN1 (92850 downstream)																							TTTGGTGTGCTTTGGGTAACG	0.522													4	2	---	---	---	---	
HORMAD2	150280	broad.mit.edu	37	22	30544401	30544401	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30544401delT	uc003agy.2	+							NM_152510	NP_689723	Q8N7B1	HORM2_HUMAN	HORMA domain containing 2						meiosis|mitosis	chromosome|nucleus					0			Epithelial(10;0.125)			atagaggaactttttttaggg	0.000													4	2	---	---	---	---	
INPP5J	27124	broad.mit.edu	37	22	31511169	31511169	+	Intron	DEL	C	-	-	rs61038576		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31511169delC	uc010gwf.2	+						SELM_uc011alj.1_Intron			Q15735	PI5PA_HUMAN	RecName: Full=Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A;          EC=3.1.3.56; AltName: Full=Inositol polyphosphate 5-phosphatase J;							cytoplasm|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|SH3 domain binding			skin(1)	1						actctaaaaactttttttgac	0.050													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	32735511	32735511	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32735511delA								SLC5A4 (84193 upstream) : RFPL3 (15361 downstream)																							TGTTCGACGTAAACTCATGAA	0.383													4	2	---	---	---	---	
RBM9	23543	broad.mit.edu	37	22	36385806	36385806	+	Intron	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36385806delA	uc003aon.3	-						RBM9_uc003aoo.3_Intron	NM_001082578	NP_001076047	O43251	RFOX2_HUMAN	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						AAGGTAAAGGAGCTCCAATCT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	36446625	36446625	+	IGR	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36446625delA								RBM9 (22040 upstream) : APOL3 (89747 downstream)																							AAGAACTATTAAAAAAAAAAT	0.279													2	4	---	---	---	---	
CARD10	29775	broad.mit.edu	37	22	37902158	37902177	+	Intron	DEL	CAGCCTTCCTGCCAGGACCT	-	-	rs738304	by1000genomes	TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37902158_37902177delCAGCCTTCCTGCCAGGACCT	uc003asx.1	-						CARD10_uc003ast.1_Intron|CARD10_uc003asw.1_Intron|CARD10_uc003asy.1_Intron	NM_014550	NP_055365	Q9BWT7	CAR10_HUMAN	caspase recruitment domain protein 10						activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1)	6	Melanoma(58;0.0574)					GCCAGGACCCCAGCCTTCCTGCCAGGACCTCCACAATCTT	0.664													15	8	---	---	---	---	
FAM19A5	25817	broad.mit.edu	37	22	49090920	49090921	+	Intron	DEL	GT	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49090920_49090921delGT	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436	Q7Z5A7	F19A5_HUMAN	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)		AGGCCAGGTGgtgtgtgtgtct	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	685765	685766	+	IGR	INS	-	C	C			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:685765_685766insC								SHOX (65620 upstream) : CRLF2 (629121 downstream)																							GCAGGGACCCTCCCCACCTGAG	0.594													4	2	---	---	---	---	
UBA1	7317	broad.mit.edu	37	X	47066043	47066043	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47066043delT	uc004dhj.3	+						UBA1_uc004dhk.3_Intron|UBA1_uc004dhm.2_5'Flank	NM_153280	NP_695012	P22314	UBA1_HUMAN	ubiquitin-activating enzyme E1						cell death|protein modification process		ATP binding|ligase activity|protein binding|small protein activating enzyme activity			ovary(1)	1						tttattttgatttttttttca	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	56492621	56492621	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56492621delT								KLF8 (178301 upstream) : UBQLN2 (97439 downstream)																							ctctttcagatttttttatgt	0.000													4	2	---	---	---	---	
ATP7A	538	broad.mit.edu	37	X	77299156	77299156	+	Intron	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77299156delT	uc004ecx.3	+							NM_000052	NP_000043	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide						ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0						TCCCTCCAACttttttttttt	0.129													5	3	---	---	---	---	
NXF4	55999	broad.mit.edu	37	X	101821152	101821152	+	RNA	DEL	A	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101821152delA	uc004ejf.1	+	11		c.1352delA				NR_002216				Homo sapiens cDNA FLJ42710 fis, clone BRAMY3007609, moderately similar to Homo sapiens nuclear RNA export factor 2 (NXF2).												0						CTGAGATAATAAAACCTTGTA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	102365231	102365231	+	IGR	DEL	C	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102365231delC								NXF3 (17209 upstream) : BEX4 (104789 downstream)																							tgccatggctccagccagtcc	0.055													4	2	---	---	---	---	
ZNF280C	55609	broad.mit.edu	37	X	129360471	129360471	+	Intron	DEL	G	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129360471delG	uc004evm.2	-						ZNF280C_uc010nrf.1_Intron	NM_017666	NP_060136	Q8ND82	Z280C_HUMAN	zinc finger protein 280C						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)	3						CCTATTTCTAGCTATCTTTCA	0.353													4	2	---	---	---	---	
RBMX2	51634	broad.mit.edu	37	X	129546260	129546261	+	Intron	INS	-	T	T			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129546260_129546261insT	uc004evt.2	+							NM_016024	NP_057108	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2								nucleotide binding|RNA binding			breast(3)|ovary(1)	4						AAGAAAGGTGCTTTTTTTTTTT	0.218													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	133407790	133407791	+	IGR	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133407790_133407791insA								CCDC160 (27984 upstream) : PHF6 (99551 downstream)																							CCAAGAAGTTGAAAAAAAAAAT	0.252													9	4	---	---	---	---	
HSFX2	100130086	broad.mit.edu	37	X	148685933	148685948	+	Intron	DEL	CTGCTGCCTTGCCCCT	-	-	rs72102447		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148685933_148685948delCTGCTGCCTTGCCCCT	uc004fdl.2	-						HSFX1_uc004fdm.2_Intron|TMEM185A_uc011mxp.1_Intron|TMEM185A_uc004fdo.2_Intron|TMEM185A_uc011mxq.1_Intron|TMEM185A_uc004fdp.3_Intron	NM_016153	NP_057237	Q9UBD0	HSFX1_HUMAN	heat shock transcription factor family, X linked							cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GGGGCTCAGCCTGCTGCCTTGCCCCTCTGCTGCCTT	0.528													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10019366	10019367	+	IGR	INS	-	A	A			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10019366_10019367insA								TTTY22 (368512 upstream) : None (None downstream)																							tctgcacactgaacacccccgt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13524407	13524407	+	IGR	DEL	T	-	-			TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13524407delT								None (None upstream) : None (None downstream)																							TGGAATGAGCTTTCTATGGAG	0.313													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59032844	59032844	+	IGR	DEL	C	-	-	rs76127193		TCGA-CJ-5682-01A-11D-1534-10	TCGA-CJ-5682-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59032844delC								None (None upstream) : None (None downstream)																							acataacaggcactataaatg	0.199													4	2	---	---	---	---	
