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
CELA2A	63036	broad.mit.edu	37	1	15783663	15783663	+	Silent	SNP	C	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15783663C>A	uc001awk.2	+	2	149	c.123C>A	c.(121-123)CCC>CCA	p.P41P		NM_033440	NP_254275	P08217	CEL2A_HUMAN	elastase 2A preproprotein	41	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2						ACAGCTGGCCCTGGCAGGTGA	0.577													35	72	---	---	---	---	PASS
MYOM3	127294	broad.mit.edu	37	1	24383950	24383950	+	Silent	SNP	G	A	A	rs116002224	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24383950G>A	uc001bin.3	-	37	4381	c.4218C>T	c.(4216-4218)GGC>GGT	p.G1406G	MYOM3_uc001bil.3_Silent_p.G299G|MYOM3_uc001bim.3_Silent_p.G1063G	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3	1406	Ig-like C2-type 4.									skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		TGACGAAGACGCCGTAGCGGC	0.572													14	44	---	---	---	---	PASS
HOOK1	51361	broad.mit.edu	37	1	60330333	60330333	+	Silent	SNP	T	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60330333T>G	uc009wad.2	+	18	1758	c.1656T>G	c.(1654-1656)GCT>GCG	p.A552A	HOOK1_uc001czo.2_Silent_p.A552A|HOOK1_uc001czp.2_Intron|HOOK1_uc010oor.1_Silent_p.A510A	NM_015888	NP_056972	Q9UJC3	HOOK1_HUMAN	hook homolog 1	552	Sufficient for interaction with microtubules.|Potential.				early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|multicellular organismal development|protein transport	FHF complex|microtubule	identical protein binding			ovary(1)|breast(1)	2	all_cancers(7;0.000129)					AGTTGGAAGCTCATATGTAAG	0.323													8	39	---	---	---	---	PASS
TTLL7	79739	broad.mit.edu	37	1	84348787	84348787	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84348787G>A	uc001djc.2	-	20	2798	c.2402C>T	c.(2401-2403)CCG>CTG	p.P801L	TTLL7_uc001djb.2_RNA|TTLL7_uc001djd.2_RNA|TTLL7_uc001dje.2_RNA|TTLL7_uc001djf.2_RNA|TTLL7_uc001djg.2_RNA	NM_024686	NP_078962	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	801					cell differentiation|nervous system development|protein modification process	cilium|dendrite|microtubule basal body|perikaryon	tubulin-tyrosine ligase activity			ovary(1)	1				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		CACCACCTCCGGGCTTTTATT	0.438													5	16	---	---	---	---	PASS
CTBS	1486	broad.mit.edu	37	1	85020637	85020637	+	3'UTR	SNP	G	T	T	rs11801891	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85020637G>T	uc001dka.2	-	7					SPATA1_uc001djz.1_Intron|CTBS_uc001dkc.2_3'UTR|CTBS_uc001dkd.2_3'UTR|CTBS_uc001dkb.2_3'UTR	NM_004388	NP_004379	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl- precursor							lysosome	cation binding				0				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		TAGATCTGTTGATACAGATCA	0.284													7	36	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94487493	94487493	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94487493G>T	uc001dqh.2	-	33	4786	c.4682C>A	c.(4681-4683)TCC>TAC	p.S1561Y		NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	1561	Extracellular.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TCCTCCAATGGAAATTCCTCC	0.507													12	40	---	---	---	---	PASS
TBX19	9095	broad.mit.edu	37	1	168215575	168215575	+	Intron	SNP	G	A	A	rs2205697	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168215575G>A	uc001gfj.3	+						ANKRD36BP1_uc010plo.1_RNA|uc001gfk.1_5'Flank	NM_005149	NP_005140	O60806	TBX19_HUMAN	T-box 19						anatomical structure morphogenesis	nucleus	DNA binding				0	all_hematologic(923;0.215)					AACATATTTTGTCTTCGTAGT	0.358													4	13	---	---	---	---	PASS
TSEN15	116461	broad.mit.edu	37	1	184042058	184042058	+	3'UTR	SNP	T	C	C	rs11549003	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184042058T>C	uc001gqt.3	+	5					TSEN15_uc009wyg.2_RNA|TSEN15_uc001gqu.3_3'UTR	NM_052965	NP_443197	Q8WW01	SEN15_HUMAN	tRNA splicing endonuclease 15 isoform 1						mRNA processing|tRNA processing	nucleolus	protein binding				0						ATCTTTTATCTCAGAAATAGG	0.383													16	51	---	---	---	---	PASS
PLA2G4A	5321	broad.mit.edu	37	1	186908179	186908179	+	Silent	SNP	G	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186908179G>A	uc001gsc.2	+	9	940	c.735G>A	c.(733-735)GAG>GAA	p.E245E	PLA2G4A_uc010pos.1_Silent_p.E185E	NM_024420	NP_077734	P47712	PA24A_HUMAN	cytosolic phospholipase A2, group IVA	245	PLA2c.				phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			lung(2)|breast(1)	3					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)	ATTTTCCAGAGAAAGGGCCAG	0.358													40	162	---	---	---	---	PASS
PLA2G4A	5321	broad.mit.edu	37	1	186908180	186908180	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186908180A>C	uc001gsc.2	+	9	941	c.736A>C	c.(736-738)AAA>CAA	p.K246Q	PLA2G4A_uc010pos.1_Missense_Mutation_p.K186Q	NM_024420	NP_077734	P47712	PA24A_HUMAN	cytosolic phospholipase A2, group IVA	246	PLA2c.				phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			lung(2)|breast(1)	3					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)	TTTTCCAGAGAAAGGGCCAGA	0.353													40	159	---	---	---	---	PASS
DNAH14	127602	broad.mit.edu	37	1	225155259	225155259	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225155259G>T	uc001how.2	+	6	840	c.625G>T	c.(625-627)GTT>TTT	p.V209F	DNAH14_uc001hou.3_Missense_Mutation_p.V209F|DNAH14_uc001hot.3_Intron|DNAH14_uc001hov.3_Missense_Mutation_p.V209F	NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform	336					microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						AGAATTTTGGGTTATTACTGC	0.313													19	63	---	---	---	---	PASS
TAF1B	9014	broad.mit.edu	37	2	10053412	10053412	+	Intron	SNP	C	T	T	rs12467598	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10053412C>T	uc002qzz.2	+						TAF1B_uc010exc.2_Silent_p.A435A|TAF1B_uc002qzy.3_Intron|TAF1B_uc010yja.1_Intron|TAF1B_uc010exd.2_Intron	NM_005680	NP_005671	Q53T94	TAF1B_HUMAN	TBP-associated factor 1B						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ATGCACCTGCCTTACTTCTGT	0.368													12	75	---	---	---	---	PASS
YIPF4	84272	broad.mit.edu	37	2	32530799	32530799	+	3'UTR	SNP	T	C	C	rs35368935	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32530799T>C	uc002rok.2	+	6						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)					AAATTTTACATGTTCCAGATG	0.323													7	31	---	---	---	---	PASS
FLJ40330	645784	broad.mit.edu	37	2	89084327	89084327	+	RNA	SNP	G	C	C	rs335121	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89084327G>C	uc010fhf.2	+	6		c.589G>C			FLJ40330_uc010fhg.2_RNA|FLJ40330_uc010fhh.2_RNA					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						TTGCAAAGCAGATTTAATGTC	0.294													5	16	---	---	---	---	PASS
GGT8P	645367	broad.mit.edu	37	2	91969071	91969071	+	RNA	SNP	T	C	C	rs115299304	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91969071T>C	uc010fho.1	+	2		c.1402T>C				NR_003503				Homo sapiens cDNA FLJ31276 fis, clone KIDNE2006376, weakly similar to GAMMA-GLUTAMYLTRANSPEPTIDASE 1 PRECURSOR (EC 2.3.2.2).												0						GAGAGACTGATCCTGCTGCGG	0.602													4	14	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	96548068	96548068	+	RNA	SNP	C	T	T	rs11695514	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96548068C>T	uc002sva.1	-	37		c.1853G>A			uc002suz.1_Missense_Mutation_p.G144S|uc002svb.1_Missense_Mutation_p.G144S					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		GATTTCCAACCGCCCGTTATT	0.303													22	109	---	---	---	---	PASS
MGAT4A	11320	broad.mit.edu	37	2	99272802	99272802	+	Intron	SNP	G	A	A	rs11679648	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99272802G>A	uc002sze.2	-						MGAT4A_uc010yvm.1_Intron|MGAT4A_uc010fil.2_Intron|MGAT4A_uc010fim.1_3'UTR	NM_012214	NP_036346	Q9UM21	MGT4A_HUMAN	alpha-1,3-mannosyl-glycoprotein						N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1						GATTTTAAACGGCACATGCTC	0.353													14	75	---	---	---	---	PASS
RGPD3	653489	broad.mit.edu	37	2	107040564	107040564	+	Missense_Mutation	SNP	C	T	T	rs55993306	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107040564C>T	uc010ywi.1	-	20	3916	c.3859G>A	c.(3859-3861)GAG>AAG	p.E1287K		NM_001144013	NP_001137485	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	1287					intracellular transport		binding			ovary(1)	1						GTTGTTGACTCATCAAAGTGG	0.408													15	80	---	---	---	---	PASS
RGPD4	285190	broad.mit.edu	37	2	108487330	108487330	+	Missense_Mutation	SNP	A	G	G	rs148409227		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108487330A>G	uc010ywk.1	+	20	2952	c.2870A>G	c.(2869-2871)AAT>AGT	p.N957S	RGPD4_uc002tdu.2_Missense_Mutation_p.N144S|RGPD4_uc010ywl.1_RNA	NM_182588	NP_872394	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	957					intracellular transport		binding			skin(2)	2						GGCCAGAAGAATGGCCGTGGT	0.403													13	58	---	---	---	---	PASS
HNMT	3176	broad.mit.edu	37	2	138724738	138724738	+	Intron	SNP	C	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138724738C>T	uc002tvc.2	+						HNMT_uc002tvd.2_3'UTR|HNMT_uc002tve.2_Intron|HNMT_uc002tvf.2_Intron	NM_006895	NP_008826	P50135	HNMT_HUMAN	histamine N-methyltransferase isoform 1						respiratory gaseous exchange	cytoplasm	histamine N-methyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.125)	Amodiaquine(DB00613)|Histamine Phosphate(DB00667)|Quinacrine(DB01103)	cctagcacttcgggaggctga	0.000													8	42	---	---	---	---	PASS
BAZ2B	29994	broad.mit.edu	37	2	160295297	160295297	+	Intron	SNP	C	A	A	rs2302923	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160295297C>A	uc002uao.2	-						BAZ2B_uc002uap.2_Intron|BAZ2B_uc002uas.1_Intron|BAZ2B_uc002uau.1_Intron|BAZ2B_uc002uaq.1_Intron|BAZ2B_uc002uat.3_3'UTR|BAZ2B_uc010fop.1_Intron	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						CGGGTACTTTCAAAGTGTTCT	0.294													9	46	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166866332	166866332	+	Missense_Mutation	SNP	G	A	A	rs146878122		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166866332G>A	uc010zcz.1	-	20	3884	c.3866C>T	c.(3865-3867)ACA>ATA	p.T1289I	SCN1A_uc002udo.3_Missense_Mutation_p.T1169I|SCN1A_uc010fpk.2_Missense_Mutation_p.T1141I	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1300	Helical; Name=S3 of repeat III; (By similarity).|III.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	GGCATTTGCTGTTAAACTGAC	0.363													5	21	---	---	---	---	PASS
MDH1B	130752	broad.mit.edu	37	2	207605882	207605882	+	Intron	SNP	A	G	G	rs10173707	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207605882A>G	uc002vbs.2	-						MDH1B_uc010ziw.1_Intron|MDH1B_uc010fui.2_Intron|MDH1B_uc010fuj.2_Intron|MDH1B_uc002vbt.2_RNA	NM_001039845	NP_001034934	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)						carbohydrate metabolic process|malate metabolic process|tricarboxylic acid cycle		binding|malate dehydrogenase activity			ovary(3)|kidney(1)	4				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		CCAACAACCTAACTAGGTCAT	0.204													12	76	---	---	---	---	PASS
UGT1A7	54577	broad.mit.edu	37	2	234591030	234591030	+	Silent	SNP	T	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234591030T>C	uc002vut.2	+	1	447	c.447T>C	c.(445-447)CCT>CCC	p.P149P	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Silent_p.P149P	NM_019077	NP_061950	Q9HAW7	UD17_HUMAN	UDP glycosyltransferase 1 family, polypeptide A7	149					drug metabolic process|negative regulation of fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	drug binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|retinoic acid binding			ovary(1)	1		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TTCTCGATCCTTTTGATGCCT	0.383													158	355	---	---	---	---	PASS
TTC21A	199223	broad.mit.edu	37	3	39178460	39178460	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39178460A>G	uc003cjc.2	+	24	3364	c.3187A>G	c.(3187-3189)AGC>GGC	p.S1063G	TTC21A_uc003cje.2_Missense_Mutation_p.S1064G|TTC21A_uc003cjd.2_RNA|TTC21A_uc011ayx.1_Missense_Mutation_p.S1015G|TTC21A_uc003cjf.2_Missense_Mutation_p.S184G	NM_145755	NP_665698	Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A isoform 2	1063							binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TTGGGGCCAGAGCGCCATCTA	0.547													11	47	---	---	---	---	PASS
TMPRSS7	344805	broad.mit.edu	37	3	111760771	111760771	+	5'UTR	SNP	A	G	G	rs774774	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111760771A>G	uc010hqb.2	+	2					TMPRSS7_uc011bhr.1_5'UTR	NM_001042575	NP_001036040	Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7						proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2						TTACAGGTAAAACAGAAAGCA	0.403													10	28	---	---	---	---	PASS
PLSCR4	57088	broad.mit.edu	37	3	145912177	145912177	+	3'UTR	SNP	T	G	G	rs9815240	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145912177T>G	uc010huy.2	-	9					PLSCR4_uc010huz.2_3'UTR|PLSCR4_uc003evt.3_3'UTR|PLSCR4_uc010hva.2_3'UTR|PLSCR4_uc003evu.3_3'UTR	NM_001128305	NP_001121777	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4 isoform a						blood coagulation|phospholipid scrambling	integral to membrane	calcium ion binding|phospholipid scramblase activity|SH3 domain binding				0						TTAACCATAGTTGATGGCTTG	0.328													22	117	---	---	---	---	PASS
C3orf16	389161	broad.mit.edu	37	3	149479301	149479301	+	Silent	SNP	C	T	T	rs954714	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149479301C>T	uc003exl.2	-	6	2062	c.1605G>A	c.(1603-1605)GCG>GCA	p.A535A	C3orf16_uc011bnt.1_Silent_p.A389A	NM_001144960	NP_001138432	E9PHT4	E9PHT4_HUMAN	hypothetical protein LOC389161	535											0						AGTTTTCACACGCTGTCAGAC	0.408													21	51	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164739060	164739060	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164739060G>C	uc003fei.2	-	27	3273	c.3211C>G	c.(3211-3213)CCT>GCT	p.P1071A		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	1071	Sucrase.|Lumenal.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	ATGCCAAAAGGATTTTCCTTG	0.353										HNSCC(35;0.089)			22	28	---	---	---	---	PASS
KCNMB3	27094	broad.mit.edu	37	3	178957783	178957783	+	3'UTR	SNP	C	T	T	rs3976507	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178957783C>T	uc011bqc.1	-	4					KCNMB3_uc003fjl.3_RNA	NM_001163677	NP_001157149	Q9NPA1	KCMB3_HUMAN	calcium-activated potassium channel beta 3						detection of calcium ion|platelet activation|regulation of action potential in neuron	voltage-gated potassium channel complex	calcium-activated potassium channel activity|potassium channel regulator activity				0	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)			TGTGACTGCACTTACTGTTTA	0.333													40	58	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506303	195506303	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506303G>T	uc011bto.1	-	3	12224	c.11764C>A	c.(11764-11766)CCT>ACT	p.P3922T	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|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)		TTGGTGACAGGAAGAGGGGTG	0.572													9	8	---	---	---	---	PASS
ZNF718	255403	broad.mit.edu	37	4	155905	155905	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155905A>T	uc003fzt.3	+	8	1563	c.1430A>T	c.(1429-1431)AAA>ATA	p.K477I	ZNF595_uc003fzu.1_Intron|ZNF718_uc010iaz.2_RNA|ZNF718_uc003fzw.3_3'UTR	NM_001039127	NP_001034216	Q3SXZ3	ZN718_HUMAN	zinc finger protein 718	477					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0681)|Epithelial(2;0.0838)|all cancers(2;0.135)|LUSC - Lung squamous cell carcinoma(95;0.18)		ACTGGAGGAAAATTTTAGAAA	0.358													13	23	---	---	---	---	PASS
DTHD1	401124	broad.mit.edu	37	4	36340753	36340753	+	Missense_Mutation	SNP	G	A	A	rs9654132	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36340753G>A	uc011bxy.1	+	8	1881	c.1490G>A	c.(1489-1491)CGT>CAT	p.R497H	DTHD1_uc003gsv.2_Intron	NM_001136536	NP_001130008	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	662					signal transduction						0						TTAATCAACCGTCCACAGAGT	0.348													26	129	---	---	---	---	PASS
GABRG1	2565	broad.mit.edu	37	4	46042945	46042945	+	3'UTR	SNP	C	T	T	rs6447493	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46042945C>T	uc003gxb.2	-	9						NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)		GTTACTGAAGCACAAAAGATT	0.289													4	7	---	---	---	---	PASS
UGT2B10	7365	broad.mit.edu	37	4	69696638	69696638	+	3'UTR	SNP	A	G	G	rs114612625	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69696638A>G	uc003hee.2	+	6					UGT2B10_uc011cam.1_3'UTR	NM_001075	NP_001066	P36537	UDB10_HUMAN	UDP glucuronosyltransferase 2B10 isoform 1						lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(3)|ovary(2)	5						GATAGATAGGAATACTTCAGT	0.333													32	117	---	---	---	---	PASS
MOBKL1A	92597	broad.mit.edu	37	4	71847860	71847860	+	3'UTR	SNP	A	T	T	rs58137770	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71847860A>T	uc003hfw.2	+	6					MOBKL1A_uc011cba.1_3'UTR	NM_173468	NP_775739	Q7L9L4	MOL1A_HUMAN	MOB1, Mps One Binder kinase activator-like 1A						hippo signaling cascade|protein autophosphorylation	cytoplasm|nucleus	kinase activator activity|kinase binding|metal ion binding				0		all_hematologic(202;0.21)	Lung(101;0.235)			TTTTATCTGGATTGTTTTTGT	0.388													4	11	---	---	---	---	PASS
FAM190A	401145	broad.mit.edu	37	4	91701720	91701720	+	Intron	SNP	C	T	T	rs2271592	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91701720C>T	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_3'UTR|FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						AAGACTCTTTCCATCCAGTTC	0.343													8	38	---	---	---	---	PASS
ADH7	131	broad.mit.edu	37	4	100356466	100356466	+	5'UTR	SNP	A	G	G	rs17537595	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100356466A>G	uc003huv.1	-	1						NM_000673	NP_000664	P40394	ADH7_HUMAN	class IV alcohol dehydrogenase, mu or sigma						ethanol oxidation|fatty acid omega-oxidation|response to bacterium|response to ethanol|xenobiotic metabolic process	cytosol|soluble fraction	alcohol dehydrogenase activity, zinc-dependent|aldehyde oxidase activity|ethanol binding|receptor antagonist activity|retinol binding|retinol dehydrogenase activity			lung(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)	NADH(DB00157)	TCTGTTGTATATAACAGCAGC	0.443													12	67	---	---	---	---	PASS
TNIP3	79931	broad.mit.edu	37	4	122085399	122085399	+	5'UTR	SNP	A	G	G	rs41278073	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122085399A>G	uc010ing.2	-	1					TNIP3_uc010inh.2_Intron|TNIP3_uc011cgj.1_Intron|TNIP3_uc010ini.2_5'UTR	NM_024873	NP_079149	Q96KP6	TNIP3_HUMAN	TNFAIP3 interacting protein 3											ovary(1)	1						ATCACCGTTAACTCATAATAG	0.328													3	7	---	---	---	---	PASS
PLCXD3	345557	broad.mit.edu	37	5	41313654	41313654	+	3'UTR	SNP	C	T	T	rs73075970	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41313654C>T	uc003jmm.1	-	3						NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						AGAGTGTTTACAGATAGTATG	0.408													4	9	---	---	---	---	PASS
FCHO2	115548	broad.mit.edu	37	5	72286668	72286668	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72286668G>T	uc003kcl.2	+	5	588	c.472G>T	c.(472-474)GCT>TCT	p.A158S	FCHO2_uc011csl.1_Missense_Mutation_p.A158S|FCHO2_uc011csk.1_Missense_Mutation_p.A158S|FCHO2_uc011csm.1_5'UTR	NM_138782	NP_620137	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2 isoform a	158										ovary(1)	1		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		AAAGGAAGGAGCTACACAAAG	0.289													42	139	---	---	---	---	PASS
ANKRD31	256006	broad.mit.edu	37	5	74443132	74443132	+	Missense_Mutation	SNP	C	T	T	rs1422698	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74443132C>T	uc003kdo.1	-	14	2296	c.2104G>A	c.(2104-2106)GAC>AAC	p.D702N				Q8N7Z5	ANR31_HUMAN	Homo sapiens cDNA FLJ40191 fis, clone TESTI2019280, weakly similar to Homo sapiens nasopharyngeal carcinoma susceptibility protein LZ16 mRNA.	702											0						TATATCTGGTCAAGAGTTGAT	0.333													39	31	---	---	---	---	PASS
ANKRD31	256006	broad.mit.edu	37	5	74506658	74506658	+	Silent	SNP	C	T	T	rs2219745	byFrequency	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74506658C>T	uc003kdo.1	-	4	513	c.321G>A	c.(319-321)CTG>CTA	p.L107L				Q8N7Z5	ANR31_HUMAN	Homo sapiens cDNA FLJ40191 fis, clone TESTI2019280, weakly similar to Homo sapiens nasopharyngeal carcinoma susceptibility protein LZ16 mRNA.	107											0						CTTACTGTAACAGAGCTTGAT	0.274													37	275	---	---	---	---	PASS
CKMT2	1160	broad.mit.edu	37	5	80562120	80562120	+	3'UTR	SNP	G	A	A	rs545	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80562120G>A	uc003khc.3	+	11					RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_3'UTR|CKMT2_uc003khd.3_3'UTR|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816	P17540	KCRS_HUMAN	sarcomeric mitochondrial creatine kinase						creatine metabolic process|muscle contraction	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	CTGCTGGTACGACAGACATAA	0.363													5	26	---	---	---	---	PASS
CAST	831	broad.mit.edu	37	5	96101850	96101850	+	Splice_Site	SNP	G	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96101850G>C	uc003klz.1	+	25	2043	c.1881_splice	c.e25+1	p.Q627_splice	CAST_uc003klt.2_Splice_Site_p.Q614_splice|CAST_uc003klu.2_Splice_Site_p.Q710_splice|CAST_uc003klv.2_Splice_Site_p.Q688_splice|CAST_uc003klw.2_Splice_Site_p.Q691_splice|CAST_uc003klx.2_Splice_Site_p.Q669_splice|CAST_uc003kly.2_Splice_Site_p.Q675_splice|CAST_uc011cuo.1_Splice_Site_p.Q673_splice|CAST_uc011cur.1_Splice_Site_p.Q613_splice|CAST_uc011cus.1_Splice_Site_p.Q614_splice|CAST_uc003kma.1_Splice_Site_p.Q585_splice|CAST_uc011cut.1_Splice_Site_p.Q555_splice|CAST_uc003kmb.2_Splice_Site_p.Q573_splice|CAST_uc003kmc.2_Splice_Site_p.Q627_splice|CAST_uc003kmd.2_Splice_Site_p.Q605_splice|CAST_uc003kme.2_Splice_Site_p.Q586_splice|CAST_uc003kmf.2_Splice_Site_p.Q592_splice|CAST_uc003kmh.2_Splice_Site_p.Q341_splice|CAST_uc010jbj.2_Splice_Site_p.Q342_splice|CAST_uc010jbk.2_Splice_Site_p.Q342_splice|CAST_uc010jbl.1_Splice_Site_p.Q350_splice|CAST_uc003kmi.2_Splice_Site|CAST_uc003kmj.2_Splice_Site_p.Q349_splice|CAST_uc003kmk.2_Splice_Site|ERAP1_uc003kml.2_Intron	NM_001042443	NP_001035908	P20810	ICAL_HUMAN	calpastatin isoform i								calcium-dependent cysteine-type endopeptidase inhibitor activity|protein binding			central_nervous_system(3)|ovary(1)|kidney(1)	5		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		TAATGGACAGGTAAACTGAGG	0.373													16	68	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12122035	12122035	+	Silent	SNP	A	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12122035A>C	uc003nac.2	+	4	2186	c.2007A>C	c.(2005-2007)GGA>GGC	p.G669G	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	669					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				GAAGTTTAGGAAGTACGGATT	0.502													25	62	---	---	---	---	PASS
EYS	346007	broad.mit.edu	37	6	66005857	66005857	+	Missense_Mutation	SNP	T	A	A	rs17411795	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66005857T>A	uc011dxu.1	-	12	2460	c.1922A>T	c.(1921-1923)GAG>GTG	p.E641V		NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	641			E -> V.		response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						AGTATCTATCTCACAGATGTT	0.438													15	13	---	---	---	---	PASS
TTK	7272	broad.mit.edu	37	6	80751942	80751942	+	3'UTR	SNP	G	A	A	rs17254634	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80751942G>A	uc003pjc.2	+	22					TTK_uc003pjb.3_3'UTR	NM_003318	NP_003309	P33981	TTK_HUMAN	TTK protein kinase						mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1)	11		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		CGTAATGTCAGATACCACCTA	0.323													8	28	---	---	---	---	PASS
CD164	8763	broad.mit.edu	37	6	109689431	109689431	+	3'UTR	SNP	A	G	G	rs974034	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109689431A>G	uc003pte.2	-	6					CD164_uc003ptd.2_3'UTR|CD164_uc003ptf.2_3'UTR|CD164_uc011eap.1_3'UTR|CD164_uc010kdn.2_3'UTR	NM_006016	NP_006007	Q04900	MUC24_HUMAN	CD164 molecule, sialomucin isoform 1						hemopoiesis|heterophilic cell-cell adhesion|immune response|muscle organ development|negative regulation of cell adhesion|negative regulation of cell proliferation|signal transduction	endosome membrane|extracellular region|integral to plasma membrane|lysosomal membrane	protein binding				0		all_cancers(87;4.65e-22)|all_epithelial(87;2.54e-20)|all_lung(197;1.6e-05)|Lung NSC(302;2.92e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.0175)		Epithelial(106;7.83e-46)|all cancers(137;1.15e-45)|OV - Ovarian serous cystadenocarcinoma(136;2.89e-26)|BRCA - Breast invasive adenocarcinoma(108;0.00128)|GBM - Glioblastoma multiforme(226;0.16)		ATGACATAAGATGCTTTACAA	0.323													12	54	---	---	---	---	PASS
CD164	8763	broad.mit.edu	37	6	109689907	109689907	+	3'UTR	SNP	G	T	T	rs11251	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109689907G>T	uc003pte.2	-	6					CD164_uc003ptd.2_Intron|CD164_uc003ptf.2_3'UTR|CD164_uc011eap.1_Intron|CD164_uc010kdn.2_3'UTR	NM_006016	NP_006007	Q04900	MUC24_HUMAN	CD164 molecule, sialomucin isoform 1						hemopoiesis|heterophilic cell-cell adhesion|immune response|muscle organ development|negative regulation of cell adhesion|negative regulation of cell proliferation|signal transduction	endosome membrane|extracellular region|integral to plasma membrane|lysosomal membrane	protein binding				0		all_cancers(87;4.65e-22)|all_epithelial(87;2.54e-20)|all_lung(197;1.6e-05)|Lung NSC(302;2.92e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.0175)		Epithelial(106;7.83e-46)|all cancers(137;1.15e-45)|OV - Ovarian serous cystadenocarcinoma(136;2.89e-26)|BRCA - Breast invasive adenocarcinoma(108;0.00128)|GBM - Glioblastoma multiforme(226;0.16)		CTTCACGGATGATGCTCCCAA	0.353													11	45	---	---	---	---	PASS
AKD1	221264	broad.mit.edu	37	6	109931580	109931580	+	Silent	SNP	T	C	C	rs56107923	byFrequency	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109931580T>C	uc003ptn.2	-	17	1907	c.1830A>G	c.(1828-1830)GAA>GAG	p.E610E		NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1	610					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1						CTCCAAGGACTTCCTGTAAGA	0.328													18	121	---	---	---	---	PASS
C6orf174	387104	broad.mit.edu	37	6	127775166	127775166	+	3'UTR	SNP	T	C	C	rs9375513	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127775166T>C	uc003qbd.2	-	8					C6orf174_uc003qbc.2_5'UTR|C6orf174_uc003qbb.2_5'Flank|KIAA0408_uc011ebs.1_5'UTR	NM_001012279	NP_001012279	Q5TF21	CF174_HUMAN	hypothetical protein LOC387104 precursor							integral to membrane				breast(3)|ovary(2)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)		GTTTCTGCTCTTCTCTGCCTC	0.388													8	20	---	---	---	---	PASS
C7orf28A	51622	broad.mit.edu	37	7	5965334	5965334	+	3'UTR	SNP	C	T	T	rs150333500	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5965334C>T	uc003spf.2	+	15						NM_015622	NP_056437	P86791	CCZ1_HUMAN	hypothetical protein LOC51622							lysosomal membrane					0		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)|OV - Ovarian serous cystadenocarcinoma(56;7.91e-15)		GACGGCTCACCGAGAGCATAT	0.443													25	177	---	---	---	---	PASS
C7orf72	100130988	broad.mit.edu	37	7	50173777	50173777	+	Missense_Mutation	SNP	A	G	G	rs998928	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50173777A>G	uc011kcj.1	+	4	802	c.802A>G	c.(802-804)ACC>GCC	p.T268A		NM_001161834	NP_001155306			hypothetical protein LOC100130988											ovary(1)	1						ATTGGAAAAAACCGCTGACCC	0.383													8	34	---	---	---	---	PASS
PION	54103	broad.mit.edu	37	7	76942805	76942805	+	Silent	SNP	C	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76942805C>T	uc003ugf.2	-	28	2350	c.2271G>A	c.(2269-2271)CCG>CCA	p.P757P	PION_uc011kgo.1_Silent_p.P78P|PION_uc003ugd.2_Silent_p.P151P	NM_017439	NP_059135	A4D1B5	GSAP_HUMAN	pigeon homolog	757					beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1						TCAGTATTACCGGAGGAAGCC	0.348													54	204	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82584788	82584788	+	Silent	SNP	A	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82584788A>C	uc003uhx.2	-	5	5770	c.5481T>G	c.(5479-5481)CCT>CCG	p.P1827P	PCLO_uc003uhv.2_Silent_p.P1827P	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1758					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						AGAGATTACTAGGTGGTGTCT	0.408													17	117	---	---	---	---	PASS
STEAP2	261729	broad.mit.edu	37	7	89854554	89854554	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89854554G>T	uc003ujz.2	+	2	551	c.158G>T	c.(157-159)GGC>GTC	p.G53V	STEAP2_uc003ujy.2_Missense_Mutation_p.G95V|STEAP2_uc010len.2_Missense_Mutation_p.G53V|STEAP2_uc003uka.2_Missense_Mutation_p.G53V|STEAP2_uc003ukb.2_Missense_Mutation_p.G53V|STEAP2_uc003ukc.2_Missense_Mutation_p.G53V|STEAP2_uc003ukd.2_Missense_Mutation_p.G53V	NM_152999	NP_694544	Q8NFT2	STEA2_HUMAN	six transmembrane epithelial antigen of the	53					electron transport chain|endocytosis|Golgi to plasma membrane transport|ion transport|iron ion homeostasis|regulated secretory pathway|response to hormone stimulus	cytosol|early endosome|endosome membrane|integral to Golgi membrane|plasma membrane|trans-Golgi network transport vesicle|vesicular fraction	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity|transporter activity			ovary(2)	2	all_hematologic(106;0.112)					ATTAGATGCGGCTATCATGTG	0.393													18	98	---	---	---	---	PASS
CCDC132	55610	broad.mit.edu	37	7	92987673	92987673	+	Silent	SNP	G	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92987673G>A	uc003umo.2	+	28	2948	c.2820G>A	c.(2818-2820)CTG>CTA	p.L940L	CCDC132_uc003umq.2_RNA|CCDC132_uc003ump.2_Silent_p.L910L|CCDC132_uc003umr.2_RNA|CCDC132_uc011khz.1_Silent_p.L660L	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a	940											0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			ATGTTTGCCTGGGATCCCATA	0.378													11	69	---	---	---	---	PASS
NAA38	51691	broad.mit.edu	37	7	117832138	117832138	+	3'UTR	SNP	G	A	A	rs1061731	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117832138G>A	uc003vjg.2	+	4						NM_016200	NP_057284	O95777	NAA38_HUMAN	U6 snRNA-associated Sm-like protein LSm8						nuclear mRNA splicing, via spliceosome	nucleus|ribonucleoprotein complex	protein binding|U6 snRNA binding				0						GTTTTTATGAGTGTGTCACTG	0.274													12	40	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	7808219	7808219	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7808219A>T	uc010lro.1	+	6	550	c.268A>T	c.(268-270)ATA>TTA	p.I90L		NM_001039615	NP_001034704			zinc finger protein 705D																		AAAACACATGATATCCATGCA	0.328													23	34	---	---	---	---	PASS
DEFB134	613211	broad.mit.edu	37	8	11853734	11853734	+	Silent	SNP	G	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11853734G>C	uc011kxn.1	-	1	27	c.27C>G	c.(25-27)GTC>GTG	p.V9V		NM_001033019	NP_001028191	Q4QY38	DB134_HUMAN	beta-defensin 134 precursor	9					defense response to bacterium	extracellular region					0			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.159)		GGAAAAGAAAGACAAACACAA	0.483													11	35	---	---	---	---	PASS
ADAM18	8749	broad.mit.edu	37	8	39581343	39581343	+	Silent	SNP	G	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39581343G>A	uc003xni.2	+	19	2094	c.2094G>A	c.(2092-2094)CCG>CCA	p.P698P	ADAM18_uc010lww.2_RNA|ADAM18_uc010lwx.2_Silent_p.P674P	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	a disintegrin and metalloprotease domain 18	698	Helical; (Potential).				cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			TTTTTCTGCCGTTTTTCATAG	0.303													28	60	---	---	---	---	PASS
POTEA	340441	broad.mit.edu	37	8	43147814	43147814	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43147814C>T	uc003xpz.1	+	1	230	c.187C>T	c.(187-189)CGA>TGA	p.R63*	POTEA_uc003xqa.1_Nonsense_Mutation_p.R63*	NM_001005365	NP_001005365	Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A isoform 2	63										ovary(1)	1						TCACGTCCGTCGAGAAGATCT	0.597													28	42	---	---	---	---	PASS
TRPA1	8989	broad.mit.edu	37	8	72935039	72935039	+	3'UTR	SNP	C	T	T	rs10085964	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72935039C>T	uc003xza.2	-	27					uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1							integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	TCACACGCAGCAAAATGAATC	0.383													4	13	---	---	---	---	PASS
TRPA1	8989	broad.mit.edu	37	8	72935045	72935045	+	3'UTR	SNP	G	C	C	rs10086177	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72935045G>C	uc003xza.2	-	27					uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1							integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	GCAGCAAAATGAATCATTCTG	0.393													5	14	---	---	---	---	PASS
CNGB3	54714	broad.mit.edu	37	8	87755891	87755891	+	5'UTR	SNP	A	C	C	rs7812496	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87755891A>C	uc003ydx.2	-	1						NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3						signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3						CTCTGTATTTATGACTGTGCC	0.363													13	83	---	---	---	---	PASS
MRPL13	28998	broad.mit.edu	37	8	121408195	121408195	+	3'UTR	SNP	T	C	C	rs6650	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121408195T>C	uc003ypa.2	-	7					MRPL13_uc010mdf.2_RNA	NM_014078	NP_054797	Q9BYD1	RM13_HUMAN	mitochondrial ribosomal protein L13						translation	mitochondrial large ribosomal subunit	protein binding|structural constituent of ribosome			central_nervous_system(1)	1	Lung NSC(37;1.69e-07)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			TGAAGGACTATACCTTCCTGA	0.318													10	43	---	---	---	---	PASS
CDC37L1	55664	broad.mit.edu	37	9	4706214	4706214	+	3'UTR	SNP	C	T	T	rs2181341	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4706214C>T	uc003zio.2	+	7						NM_017913	NP_060383	Q7L3B6	CD37L_HUMAN	cell division cycle 37 homolog (S.							cytoplasm					0	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)		TATTTTTGTTCGGTTTTTGAT	0.353													5	19	---	---	---	---	PASS
MUSK	4593	broad.mit.edu	37	9	113459655	113459655	+	Silent	SNP	C	T	T	rs41279051	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113459655C>T	uc004bey.2	+	5	635	c.537C>T	c.(535-537)AAC>AAT	p.N179N	MUSK_uc004bex.2_Silent_p.N179N	NM_005592	NP_005583	O15146	MUSK_HUMAN	skeletal muscle receptor tyrosine kinase	179	Ig-like 2.|Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity	p.N179N(1)		lung(3)|ovary(2)|central_nervous_system(1)	6						GGATTCATAACGTACAAAAGG	0.448													12	75	---	---	---	---	PASS
STAM	8027	broad.mit.edu	37	10	17737139	17737139	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17737139A>C	uc001ipj.1	+	7	843	c.627A>C	c.(625-627)CAA>CAC	p.Q209H	STAM_uc010qcf.1_Missense_Mutation_p.Q98H|STAM_uc009xjw.1_5'UTR	NM_003473	NP_003464	Q92783	STAM1_HUMAN	signal transducing adaptor molecule 1	209					cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	SH3/SH2 adaptor activity			large_intestine(1)|ovary(1)	2						CTAACCACCAACATGAAGGCC	0.403													12	66	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	30986364	30986364	+	5'UTR	SNP	G	A	A	rs7078530	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30986364G>A	uc010qdx.1	+	3										SubName: Full=cDNA FLJ59642, highly similar to Supervillin;																		CAATAGTGGGGACTGCTTCCT	0.537													9	45	---	---	---	---	PASS
OR51B2	79345	broad.mit.edu	37	11	5344552	5344552	+	3'UTR	SNP	C	T	T	rs7934105	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5344552C>T	uc001mao.1	-	1					HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron	NM_033180	NP_149420	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATTCTGGCTTCATTTTTATGT	0.368													6	16	---	---	---	---	PASS
OR51B2	79345	broad.mit.edu	37	11	5344561	5344561	+	3'UTR	SNP	G	A	A	rs7933257	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5344561G>A	uc001mao.1	-	1					HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron	NM_033180	NP_149420	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCATTTTTATGTCTGTGTCTG	0.373													7	18	---	---	---	---	PASS
LOC440040	440040	broad.mit.edu	37	11	49598257	49598257	+	Missense_Mutation	SNP	G	T	T	rs7101891	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49598257G>T	uc010rhy.1	+	2	848	c.370G>T	c.(370-372)GTA>TTA	p.V124L	LOC440040_uc009ymb.2_Missense_Mutation_p.V124L	NR_027044				SubName: Full=cDNA FLJ60249, highly similar to Metabotropic glutamate receptor 5;												0						TTCCAGTTCTGTAGCCATTCA	0.493													5	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	55064967	55064967	+	RNA	SNP	T	G	G	rs11821230	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55064967T>G	uc001nhl.1	-	2		c.456A>C								Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit20-11-30-F.																		TCCAGCATCTTGTTCTGGTGG	0.408													12	42	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	55065607	55065607	+	RNA	SNP	C	T	T	rs55900934	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55065607C>T	uc001nhl.1	-	1		c.102G>A								Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit20-11-30-F.																		GCAACAACTGCCATGTCTTGC	0.488													4	10	---	---	---	---	PASS
KIAA1731	85459	broad.mit.edu	37	11	93462607	93462607	+	Missense_Mutation	SNP	A	T	T	rs7131178	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93462607A>T	uc009ywb.1	+	26	7461	c.7310A>T	c.(7309-7311)GAG>GTG	p.E2437V	KIAA1731_uc001pdu.1_Missense_Mutation_p.E617V|KIAA1731_uc001pdw.1_Missense_Mutation_p.E449V|KIAA1731_uc001pdx.1_Missense_Mutation_p.E303V	NM_033395	NP_203753	Q9C0D2	K1731_HUMAN	hypothetical protein LOC85459	2437				E -> V (in Ref. 3; BAB71582/BAC04502/ BAC04638/BAC05264).		centrosome					0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TAGGTGAGTGAGTTTCTGCCT	0.318													17	49	---	---	---	---	PASS
CNTN5	53942	broad.mit.edu	37	11	100226962	100226962	+	3'UTR	SNP	C	T	T	rs1216182	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100226962C>T	uc001pga.2	+	25					CNTN5_uc001pgb.2_3'UTR|CNTN5_uc010ruk.1_3'UTR	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		AAACTGCTGACTTAATTTGCT	0.438													11	40	---	---	---	---	PASS
CASP1	834	broad.mit.edu	37	11	104905316	104905316	+	Intron	SNP	A	G	G	rs536909	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104905316A>G	uc010rve.1	-						CASP1_uc001pig.2_Intron|CASP1_uc001pik.2_5'UTR|CASP1_uc010rvf.1_Intron|CASP1_uc010rvg.1_Intron|CASP1_uc010rvh.1_Intron|CASP1_uc010rvi.1_Intron|CASP1_uc001pim.3_Intron|CASP1_uc009yxi.2_Intron|CASP1_uc010rvj.1_Intron|CASP1_uc009yxj.2_Intron|CASP1_uc010rvk.1_Intron|CASP1_uc010rvl.1_Intron	NM_033292	NP_150634	P29466	CASP1_HUMAN	caspase 1 isoform alpha precursor						cellular response to mechanical stimulus|cellular response to organic substance|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis|signal transduction	cytosol	caspase activator activity|cysteine-type endopeptidase activity|protein binding			ovary(2)	2		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)|Penicillamine(DB00859)	CCCTCCTCACAGTTGGGTAAT	0.413													8	11	---	---	---	---	PASS
SLCO1C1	53919	broad.mit.edu	37	12	20903757	20903757	+	Intron	SNP	T	C	C	rs10841611	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20903757T>C	uc001rej.3	+						SLCO1C1_uc010sii.1_Silent_p.H649H|SLCO1C1_uc010sij.1_Intron|SLCO1C1_uc009zip.2_Silent_p.H483H|SLCO1C1_uc001rei.2_Intron|SLCO1C1_uc010sik.1_Silent_p.H531H	NM_017435	NP_059131	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(5)|pancreas(1)|skin(1)	7	Esophageal squamous(101;0.149)					CCGCATCTCATTGCTACAGCA	0.378													17	66	---	---	---	---	PASS
FAR2	55711	broad.mit.edu	37	12	29486745	29486745	+	3'UTR	SNP	T	C	C	rs1052583	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29486745T>C	uc001ris.3	+	12					FAR2_uc001rit.2_3'UTR|FAR2_uc009zjm.2_3'UTR	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						TAGCCATCGCTTTTTATCTGG	0.393													8	32	---	---	---	---	PASS
SLC38A2	54407	broad.mit.edu	37	12	46759057	46759057	+	Intron	SNP	G	C	C	rs12307969	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46759057G>C	uc001rpg.2	-						SLC38A2_uc010sli.1_5'UTR|SLC38A2_uc001rph.2_Intron	NM_018976	NP_061849	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2						cellular nitrogen compound metabolic process|glutamate secretion|neurotransmitter secretion|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			urinary_tract(1)|skin(1)	2	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		CATTTCATAGGAATACCATGA	0.318													5	8	---	---	---	---	PASS
OR6C2	341416	broad.mit.edu	37	12	55846433	55846433	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55846433T>C	uc001sgz.1	+	1	436	c.436T>C	c.(436-438)TGT>CGT	p.C146R		NM_054105	NP_473446	Q9NZP2	OR6C2_HUMAN	olfactory receptor, family 6, subfamily C,	146	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2						AGTTCTCTGCTGTTGGGTGGC	0.473													9	33	---	---	---	---	PASS
NACA	4666	broad.mit.edu	37	12	57107434	57107434	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57107434C>A	uc001slz.2	-	5	617	c.268G>T	c.(268-270)GGA>TGA	p.G90*	NACA_uc001sly.2_Nonsense_Mutation_p.G90*|NACA_uc009zoy.1_Nonsense_Mutation_p.G1953*|NACA_uc001smc.2_Nonsense_Mutation_p.G90*|NACA_uc001sma.2_Nonsense_Mutation_p.G800*|NACA_uc001smb.2_Nonsense_Mutation_p.G90*|NACA_uc010squ.1_Intron	NM_001113201	NP_001106672	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha	90	NAC-A/B.				interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1						CTAGTAACTCCTGTAACCTGC	0.398			T	BCL6	NHL								51	124	---	---	---	---	PASS
LRIG3	121227	broad.mit.edu	37	12	59308052	59308052	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59308052C>T	uc001sqr.2	-	2	548	c.302G>A	c.(301-303)CGA>CAA	p.R101Q	LRIG3_uc009zqh.2_Missense_Mutation_p.R41Q|LRIG3_uc010ssh.1_RNA	NM_153377	NP_700356	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like	101	LRR 2.					integral to membrane				skin(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;1.17e-18)			TCACACTTCTCGAAGGCTTTG	0.323													27	93	---	---	---	---	PASS
DPY19L2	283417	broad.mit.edu	37	12	63963092	63963092	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63963092T>G	uc001srp.1	-	21	2219	c.2038A>C	c.(2038-2040)AAA>CAA	p.K680Q	DPY19L2_uc010sso.1_Missense_Mutation_p.K127Q	NM_173812	NP_776173	Q6NUT2	D19L2_HUMAN	dpy-19-like 2	680					multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		TTGGCAGATTTTCGACTATAT	0.254													15	48	---	---	---	---	PASS
MDM1	56890	broad.mit.edu	37	12	68719475	68719475	+	Intron	SNP	G	C	C	rs58306230	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68719475G>C	uc001stz.2	-						MDM1_uc010stc.1_Intron|MDM1_uc009zqv.1_Intron|MDM1_uc001sua.3_3'UTR|MDM1_uc010std.1_3'UTR	NM_017440	NP_059136	Q8TC05	MDM1_HUMAN	mouse Mdm1 nuclear protein homolog isoform 1							nucleus				ovary(3)|skin(2)	5			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		taaatctacagtgcaaaattg	0.090													3	4	---	---	---	---	PASS
CAPS2	84698	broad.mit.edu	37	12	75715330	75715330	+	Missense_Mutation	SNP	C	A	A	rs10879901	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75715330C>A	uc001sxk.3	-	6	572	c.375G>T	c.(373-375)TTG>TTT	p.L125F	CAPS2_uc001sxm.3_5'UTR|CAPS2_uc009zsa.2_5'UTR|CAPS2_uc001sxj.3_Missense_Mutation_p.L68F|CAPS2_uc001sxl.3_Missense_Mutation_p.L106F	NM_032606	NP_115995	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	125							calcium ion binding			ovary(2)	2						TTGGTGCTGGCAAATTTTCAG	0.299													27	175	---	---	---	---	PASS
GCN1L1	10985	broad.mit.edu	37	12	120622662	120622662	+	Silent	SNP	G	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120622662G>T	uc001txo.2	-	3	163	c.150C>A	c.(148-150)CTC>CTA	p.L50L		NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis	50					regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACAATTTGCAGAGCCCCTTCA	0.463													33	79	---	---	---	---	PASS
DDX55	57696	broad.mit.edu	37	12	124092409	124092409	+	Intron	SNP	A	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124092409A>G	uc001ufi.2	+						DDX55_uc001ufh.2_5'UTR|DDX55_uc001ufj.1_Intron|DDX55_uc001ufk.2_5'UTR	NM_020936	NP_065987	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		tcacaaactcaggttcttaca	0.244													4	15	---	---	---	---	PASS
ZNF268	10795	broad.mit.edu	37	12	133780309	133780309	+	Missense_Mutation	SNP	G	T	T	rs36127550	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133780309G>T	uc010tcf.1	+	6	2367	c.2037G>T	c.(2035-2037)TTG>TTT	p.L679F	ZNF268_uc010tbv.1_Missense_Mutation_p.L518F|ZNF268_uc010tbw.1_Missense_Mutation_p.L518F|ZNF268_uc010tbx.1_Missense_Mutation_p.L539F|ZNF268_uc010tby.1_Missense_Mutation_p.L518F|ZNF268_uc010tbz.1_Missense_Mutation_p.L518F|ZNF268_uc010tca.1_Missense_Mutation_p.L518F|ZNF268_uc010tcb.1_Missense_Mutation_p.L539F|ZNF268_uc010tcc.1_Missense_Mutation_p.L518F|ZNF268_uc010tcd.1_Missense_Mutation_p.L518F|ZNF268_uc010tce.1_Missense_Mutation_p.L518F|ZNF268_uc010tcg.1_Missense_Mutation_p.L518F|ZNF268_uc010tch.1_Missense_Mutation_p.L679F	NM_003415	NP_003406	Q14587	ZN268_HUMAN	zinc finger protein 268 isoform a	679	C2H2-type 15.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		CCTTTAGTTTGAAGTCCCAGC	0.418													10	12	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19442226	19442226	+	RNA	SNP	C	G	G	rs7321327	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19442226C>G	uc010tcj.1	-	1		c.3884G>C				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						CCTGGTTTGTCATTTTTAAGT	0.254													13	56	---	---	---	---	PASS
HMGB1	3146	broad.mit.edu	37	13	31036642	31036642	+	Intron	SNP	C	G	G	rs3742305	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31036642C>G	uc001usw.2	-						HMGB1_uc001usz.2_Intron|HMGB1_uc001usv.2_Intron|HMGB1_uc001usx.2_Intron|HMGB1_uc001usy.2_Intron|HMGB1_uc001uta.1_Missense_Mutation_p.M168I	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)		GCGTACTTGTCATCATTTTAC	0.383													59	211	---	---	---	---	PASS
RNASE12	493901	broad.mit.edu	37	14	21058902	21058902	+	5'UTR	SNP	G	A	A	rs41317318	byFrequency	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21058902G>A	uc001vxt.2	-	1					RNASE11_uc010ahx.2_5'Flank|RNASE11_uc010ahw.2_5'Flank|RNASE11_uc001vxs.2_5'Flank|uc001vxu.1_Intron	NM_001024822	NP_001019993	Q5GAN4	RNS12_HUMAN	ribonuclease, RNase A family, 12 (non-active)							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)		GAGTGACTTCGCATCTTTGGC	0.308													15	79	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22236756	22236756	+	Intron	SNP	G	C	C	rs766738	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22236756G>C	uc010tmf.1	+						uc001wbt.1_Missense_Mutation_p.R7S					SubName: Full=Putative uncharacterized protein ENSP00000374943;																		GGCTGAGAAGGCTGGGTCTAC	0.473													11	71	---	---	---	---	PASS
NID2	22795	broad.mit.edu	37	14	52473372	52473372	+	Missense_Mutation	SNP	T	C	C	rs147018937	byFrequency	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52473372T>C	uc001wzo.2	-	20	4121	c.3887A>G	c.(3886-3888)AAA>AGA	p.K1296R	NID2_uc010tqs.1_Missense_Mutation_p.K1248R|NID2_uc010tqt.1_Missense_Mutation_p.K1296R	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	1296	LDL-receptor class B 4.					basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)					CTCCAGTTTTTTGGTTCCTTT	0.428													13	65	---	---	---	---	PASS
ADAM20	8748	broad.mit.edu	37	14	70989121	70989121	+	3'UTR	SNP	A	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70989121A>G	uc001xme.2	-	2						NM_003814	NP_003805	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20 preproprotein						proteolysis|single fertilization	integral to membrane	metalloendopeptidase activity|zinc ion binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		CTGTAGAGTAAGTAAGAATAG	0.373													3	7	---	---	---	---	PASS
NUMB	8650	broad.mit.edu	37	14	73750819	73750819	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73750819T>A	uc001xny.1	-	10	1239	c.919A>T	c.(919-921)AGG>TGG	p.R307W	NUMB_uc010aro.1_Intron|NUMB_uc010arp.1_Intron|NUMB_uc010arq.1_Intron|NUMB_uc010arr.1_Intron|NUMB_uc001xoa.1_Missense_Mutation_p.R307W|NUMB_uc001xnz.1_Missense_Mutation_p.R296W|NUMB_uc001xob.1_Missense_Mutation_p.R296W|NUMB_uc001xod.1_Missense_Mutation_p.R307W|NUMB_uc001xoc.1_Missense_Mutation_p.R307W|NUMB_uc010ars.1_Missense_Mutation_p.R296W|NUMB_uc001xof.1_Missense_Mutation_p.R271W|NUMB_uc010ttz.1_Missense_Mutation_p.R53W	NM_001005743	NP_001005743	P49757	NUMB_HUMAN	numb homolog isoform 1	307					axon guidance|lateral ventricle development|neuroblast division in subventricular zone|positive regulation of neurogenesis	integral to plasma membrane				ovary(2)|central_nervous_system(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		TCAGTCTTCCTCTGCATAGTG	0.468													37	73	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	20588458	20588458	+	3'UTR	SNP	G	C	C	rs2291971	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20588458G>C	uc001ytg.2	-	27										RecName: Full=Putative HERC2-like protein 3;																		TGCTGGCCATGACTGCAGTGC	0.458													5	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	20588563	20588563	+	3'UTR	SNP	A	G	G	rs2291972	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20588563A>G	uc001ytg.2	-	27					uc010tyx.1_RNA					RecName: Full=Putative HERC2-like protein 3;																		GCGGTTGCAGAAGCCCAGTAG	0.463													12	55	---	---	---	---	PASS
OR4N3P	390539	broad.mit.edu	37	15	22414262	22414262	+	Silent	SNP	C	T	T	rs1429510	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22414262C>T	uc001yuf.2	+	1	561	c.561C>T	c.(559-561)GCC>GCT	p.A187A		NM_001080841	NP_001074310			RecName: Full=Olfactory receptor 4N2; AltName: Full=Olfactory receptor OR14-8; AltName: Full=Olfactory receptor OR14-13;												0						CTTTCCCAGCCGACAAGGTGG	0.453													15	36	---	---	---	---	PASS
NOX5	79400	broad.mit.edu	37	15	69315443	69315443	+	Intron	SNP	C	T	T	rs438866	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69315443C>T	uc002ars.1	+						NOX5_uc002arp.1_Intron|NOX5_uc002arq.1_Intron|NOX5_uc010bid.1_Intron|NOX5_uc002arr.1_Intron|NOX5_uc010bie.1_Intron|NOX5_uc002aro.2_RNA	NM_024505	NP_078781	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5						angiogenesis|angiogenesis|cytokine secretion|cytokinesis|electron transport chain|endothelial cell proliferation|induction of apoptosis|positive regulation of reactive oxygen species metabolic process|regulation of fusion of sperm to egg plasma membrane|regulation of proton transport|superoxide anion generation	endoplasmic reticulum|endoplasmic reticulum|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|hydrogen ion channel activity|NADP binding|superoxide-generating NADPH oxidase activity			breast(1)|pancreas(1)	2						AGACTTCTTCCTGGGTGTCAT	0.458													16	30	---	---	---	---	PASS
TARSL2	123283	broad.mit.edu	37	15	102215895	102215895	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102215895A>C	uc002bxm.2	-	13	1751	c.1696T>G	c.(1696-1698)TAC>GAC	p.Y566D	TARSL2_uc002bxl.2_Missense_Mutation_p.Y111D|TARSL2_uc010usi.1_RNA	NM_152334	NP_689547	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	566					threonyl-tRNA aminoacylation	cytoplasm	ATP binding|threonine-tRNA ligase activity			ovary(2)	2	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AATGTTGAGTAAACAGATTGC	0.353													89	278	---	---	---	---	PASS
CNTNAP4	85445	broad.mit.edu	37	16	76528976	76528976	+	Intron	SNP	T	C	C	rs4268783	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76528976T>C	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron|CNTNAP4_uc002few.2_3'UTR	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						GATTTCCATATGATTTCTTTA	0.323													9	45	---	---	---	---	PASS
MAP1LC3B	81631	broad.mit.edu	37	16	87436808	87436808	+	3'UTR	SNP	G	C	C	rs7865	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87436808G>C	uc002fjx.2	+	4					MAP1LC3B_uc010chs.2_RNA	NM_022818	NP_073729	Q9GZQ8	MLP3B_HUMAN	microtubule-associated proteins 1A/1B light						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule	protein binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0249)		CACAGATCATGAAACAGTAGT	0.388													7	21	---	---	---	---	PASS
DNAH2	146754	broad.mit.edu	37	17	7643076	7643076	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7643076C>T	uc002giu.1	+	8	1210	c.1196C>T	c.(1195-1197)GCC>GTC	p.A399V	DNAH2_uc002git.2_Missense_Mutation_p.A481V|DNAH2_uc010vuk.1_Missense_Mutation_p.A399V	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	399	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TATCACTTCGCCCGCTGGGAA	0.488													34	95	---	---	---	---	PASS
CDRT4	284040	broad.mit.edu	37	17	15341022	15341022	+	3'UTR	SNP	T	G	G	rs2954757		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15341022T>G	uc002gop.1	-	4					CDRT4_uc010vvw.1_3'UTR	NM_173622	NP_775893	Q8N9R6	CDRT4_HUMAN	CMT1A duplicated region transcript 4												0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0874)		GAGCTTAACTTTTGTACGTTC	0.458													5	18	---	---	---	---	PASS
CDRT4	284040	broad.mit.edu	37	17	15341023	15341023	+	3'UTR	SNP	T	C	C	rs76787574	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15341023T>C	uc002gop.1	-	4					CDRT4_uc010vvw.1_3'UTR	NM_173622	NP_775893	Q8N9R6	CDRT4_HUMAN	CMT1A duplicated region transcript 4												0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0874)		AGCTTAACTTTTGTACGTTCT	0.458													6	18	---	---	---	---	PASS
SLFN12L	342615	broad.mit.edu	37	17	33805150	33805150	+	Missense_Mutation	SNP	T	C	C	rs2304968	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33805150T>C	uc002hjn.2	-	4	2114	c.1235A>G	c.(1234-1236)TAT>TGT	p.Y412C		NM_001145027	NP_001138499			schlafen family member 12-like											ovary(1)	1						ACGAAGAGGATAACTCTGGGA	0.398													16	55	---	---	---	---	PASS
TOM1L1	10040	broad.mit.edu	37	17	53038783	53038783	+	3'UTR	SNP	G	A	A	rs1057980	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53038783G>A	uc002iud.2	+	16					TOM1L1_uc010dca.1_3'UTR|TOM1L1_uc010wnb.1_3'UTR|TOM1L1_uc010wnc.1_3'UTR|TOM1L1_uc010dbz.2_3'UTR|TOM1L1_uc010wnd.1_3'UTR|COX11_uc010wne.1_Intron|COX11_uc010wnf.1_Intron|COX11_uc002iue.2_RNA|COX11_uc010wng.1_3'UTR	NM_005486	NP_005477	O75674	TM1L1_HUMAN	target of myb1-like 1						intracellular protein transport|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	cytosol|endosome membrane|Golgi stack|lysosome	SH3 domain binding|ubiquitin binding			ovary(1)	1						TGACAACAGCGTGAGATTTCA	0.368													5	8	---	---	---	---	PASS
TTYH2	94015	broad.mit.edu	37	17	72256449	72256449	+	3'UTR	SNP	C	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72256449C>G	uc002jkc.2	+	14					TTYH2_uc010wqw.1_3'UTR|TTYH2_uc002jkd.2_3'UTR	NM_032646	NP_116035	Q9BSA4	TTYH2_HUMAN	tweety 2 isoform 1							chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4						ATCTGGAGCCCGAGAGGCCTC	0.547													14	19	---	---	---	---	PASS
ANKRD30B	374860	broad.mit.edu	37	18	14848820	14848820	+	Missense_Mutation	SNP	C	T	T	rs4090319	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14848820C>T	uc010dlo.2	+	34	3110	c.2930C>T	c.(2929-2931)ACG>ATG	p.T977M	ANKRD30B_uc010xal.1_Missense_Mutation_p.T119M	NM_001145029	NP_001138501	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	1062	Potential.			T -> M (in Ref. 3; AAK27326).						ovary(1)|skin(1)	2						ATGGAACAAACGAAAAATAAG	0.348													14	26	---	---	---	---	PASS
KLHL14	57565	broad.mit.edu	37	18	30254569	30254569	+	3'UTR	SNP	C	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30254569C>T	uc002kxm.1	-	9					KLHL14_uc010dmd.1_3'UTR	NM_020805	NP_065856	Q9P2G3	KLH14_HUMAN	kelch-like 14							cytosol|endoplasmic reticulum membrane				ovary(1)	1						GTGATGTCACCTGCCATTGCT	0.388													9	36	---	---	---	---	PASS
ZNF585A	199704	broad.mit.edu	37	19	37642434	37642434	+	3'UTR	SNP	G	A	A	rs141288430	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37642434G>A	uc002ofo.1	-	5					ZNF585A_uc002ofm.1_3'UTR|ZNF585A_uc002ofn.1_3'UTR	NM_199126	NP_954577	Q6P3V2	Z585A_HUMAN	zinc finger protein 585A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGCTGCATGCGTGCAACAGTG	0.463													5	11	---	---	---	---	PASS
ZNF585A	199704	broad.mit.edu	37	19	37642467	37642467	+	3'UTR	SNP	G	T	T	rs111776093	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37642467G>T	uc002ofo.1	-	5					ZNF585A_uc002ofm.1_3'UTR|ZNF585A_uc002ofn.1_3'UTR	NM_199126	NP_954577	Q6P3V2	Z585A_HUMAN	zinc finger protein 585A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CAACCCTCAGGGGGGTTTTCT	0.463													8	32	---	---	---	---	PASS
PSG6	5675	broad.mit.edu	37	19	43406432	43406432	+	3'UTR	SNP	C	T	T	rs62110886	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43406432C>T	uc002ovh.1	-	6					PSG3_uc002ouf.2_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovi.2_3'UTR|PSG6_uc010xwk.1_3'UTR|PSG6_uc002ove.1_3'UTR|PSG6_uc002ovf.1_3'UTR|PSG6_uc002ovg.1_3'UTR			Q00889	PSG6_HUMAN	SubName: Full=Putative uncharacterized protein PSG6;						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)				gcacattttccaataaaaaat	0.050													9	24	---	---	---	---	PASS
ZNF845	91664	broad.mit.edu	37	19	53854397	53854397	+	Missense_Mutation	SNP	G	C	C	rs10415799	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53854397G>C	uc010ydv.1	+	4	586	c.469G>C	c.(469-471)GAA>CAA	p.E157Q	ZNF845_uc010ydw.1_Missense_Mutation_p.E157Q	NM_138374	NP_612383	Q96IR2	ZN845_HUMAN	zinc finger protein 845	157					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GTTTCAGACCGAAGGGAAAAT	0.408													25	129	---	---	---	---	PASS
SAMSN1	64092	broad.mit.edu	37	21	15858207	15858207	+	3'UTR	SNP	G	A	A	rs80062901	byFrequency	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15858207G>A	uc002yju.1	-	8					SAMSN1_uc010gky.1_3'UTR|SAMSN1_uc002yjv.1_3'UTR	NM_022136	NP_071419	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization						negative regulation of adaptive immune response|negative regulation of B cell activation|negative regulation of peptidyl-tyrosine phosphorylation	cytoplasm|nucleus|ruffle	phosphotyrosine binding			ovary(3)|pancreas(1)	4				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		GAATGCATCTGTAGATATATA	0.333													9	19	---	---	---	---	PASS
GPR82	27197	broad.mit.edu	37	X	41586291	41586291	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41586291T>A	uc004dfs.1	+	3	252	c.12T>A	c.(10-12)AAT>AAA	p.N4K	CASK_uc004dfl.3_Intron|CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron|GPR82_uc004dft.2_Missense_Mutation_p.N4K|GPR82_uc004dfu.1_RNA	NM_080817	NP_543007	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	4	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2						TGAACAACAATACAACATGTA	0.303													25	32	---	---	---	---	PASS
ODZ1	10178	broad.mit.edu	37	X	123514605	123514605	+	Silent	SNP	G	A	A	rs139883667	byFrequency	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123514605G>A	uc004euj.2	-	31	8023	c.7959C>T	c.(7957-7959)CGC>CGT	p.R2653R	ODZ1_uc011muj.1_Silent_p.R2659R|ODZ1_uc010nqy.2_Silent_p.R2660R	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	2653	Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23						GGGCCACTGCGCGCTGTCTGG	0.537													15	79	---	---	---	---	PASS
LOC100128842	100128842	broad.mit.edu	37	1	1195951	1195952	+	3'UTR	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1195951_1195952delCA	uc010nyh.1	-	1					UBE2J2_uc001adm.2_Intron|UBE2J2_uc001adn.2_Intron|UBE2J2_uc001ado.2_Intron|UBE2J2_uc001adp.2_Intron|UBE2J2_uc001adq.2_Intron|UBE2J2_uc001adr.2_Intron|UBE2J2_uc001ads.2_Intron	NR_027361				Homo sapiens cDNA FLJ36836 fis, clone ASTRO2011149.												0						CACCAAGAGCCACACACACACA	0.589													4	2	---	---	---	---	
MXRA8	54587	broad.mit.edu	37	1	1296243	1296244	+	5'Flank	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1296243_1296244delCA	uc001aew.2	-						MXRA8_uc001aex.3_5'Flank|MXRA8_uc001aey.3_5'Flank|MXRA8_uc010nyl.1_5'Flank|MXRA8_uc001aez.2_5'Flank|MXRA8_uc001afa.2_Intron	NM_032348	NP_115724	Q9BRK3	MXRA8_HUMAN	matrix-remodelling associated 8 precursor							integral to membrane					0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		cagacacatgcacacacacaca	0.238													4	2	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7107657	7107658	+	Intron	DEL	GT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7107657_7107658delGT	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		GAGGCTCTGAGTGACCCTAGAA	0.327													4	2	---	---	---	---	
ENO1	2023	broad.mit.edu	37	1	8931076	8931077	+	Intron	DEL	TC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8931076_8931077delTC	uc001apj.1	-						ENO1_uc001api.1_5'UTR|ENO1_uc001apk.1_Intron|ENO1_uc001apl.1_Intron|ENO1_uc009vmi.1_Intron|ENO1_uc009vmj.1_Intron|ENO1_uc009vmk.1_Intron|ENO1_uc009vml.1_Intron|ENO1_uc009vmm.1_RNA	NM_001428	NP_001419	P06733	ENOA_HUMAN	enolase 1						gluconeogenesis|glycolysis|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|response to virus	phosphopyruvate hydratase complex|plasma membrane|sarcomere	DNA binding|magnesium ion binding|phosphopyruvate hydratase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|kidney(1)|central_nervous_system(1)	4	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;2.54e-20)|all_lung(118;2.99e-06)|Lung NSC(185;6.25e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.42e-07)|COAD - Colon adenocarcinoma(227;2.78e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		CGTTCAATCTTCCACAAATGCT	0.505													4	2	---	---	---	---	
CASP9	842	broad.mit.edu	37	1	15830968	15830968	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15830968delA	uc001awn.2	-						CASP9_uc001awm.1_Intron|CASP9_uc001awo.2_Intron|CASP9_uc001awp.2_Intron|CASP9_uc009voi.2_Intron|CASP9_uc010obm.1_Intron|CASP9_uc001awq.2_Intron	NM_001229	NP_001220	P55211	CASP9_HUMAN	caspase 9 isoform alpha preproprotein						activation of caspase activity by cytochrome c|induction of apoptosis by intracellular signals|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol	cysteine-type endopeptidase activity|enzyme activator activity|protein binding			central_nervous_system(1)|kidney(1)	2		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		AGGTGCTGCCAAAAAGGGACC	0.582													4	2	---	---	---	---	
PLEKHM2	23207	broad.mit.edu	37	1	16056542	16056556	+	Intron	DEL	GGGCGGGGCGGGGCG	-	-	rs12729712		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16056542_16056556delGGGCGGGGCGGGGCG	uc010obo.1	+							NM_015164	NP_055979	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M						Golgi organization	cytoplasm	kinesin binding			ovary(1)	1		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		TCGCCTACCTgggcggggcggggcggggcggggcg	0.465													5	3	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17200421	17200421	+	Intron	DEL	T	-	-	rs66859527		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17200421delT	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		TCCTTGTCTCTTTTTTTTTCT	0.398													4	2	---	---	---	---	
VWA5B1	127731	broad.mit.edu	37	1	20617601	20617601	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20617601delG	uc009vps.2	+						VWA5B1_uc001bdd.2_Intron|VWA5B1_uc010odc.1_Intron	NM_001039500	NP_001034589	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1							extracellular region					0						GGCCCCACTTGTGTCAGGAGG	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	22883571	22883572	+	IGR	DEL	GC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22883571_22883572delGC								ZBTB40 (25921 upstream) : EPHA8 (6432 downstream)																							cctgacttgtgcaactgggcgg	0.243													4	2	---	---	---	---	
RCAN3	11123	broad.mit.edu	37	1	24858081	24858082	+	Intron	INS	-	C	C	rs150693874	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24858081_24858082insC	uc001bjj.2	+						RCAN3_uc009vrd.2_Intron|RCAN3_uc009vre.2_Intron|RCAN3_uc009vrf.2_Intron|RCAN3_uc009vrg.2_Intron	NM_013441	NP_038469	Q9UKA8	RCAN3_HUMAN	Down syndrome critical region gene 1-like 2						anatomical structure morphogenesis|calcium-mediated signaling		nucleotide binding|RNA binding|troponin I binding				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		TTACCTCCTAAGTTGTTTTGCT	0.218													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	28921983	28921983	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28921983delA								RAB42 (897 upstream) : TAF12 (7628 downstream)																							gcctcctggtaacctaaccta	0.219													4	2	---	---	---	---	
SNRNP40	9410	broad.mit.edu	37	1	31744491	31744491	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31744491delT	uc001bso.2	-						SNRNP40_uc009vtt.2_5'Flank|SNRNP40_uc010oge.1_Intron	NM_004814	NP_004805	Q96DI7	SNR40_HUMAN	WD repeat domain 57 (U5 snRNP specific)							catalytic step 2 spliceosome|cytoplasm|nucleoplasm|small nucleolar ribonucleoprotein complex|U5 snRNP	protein binding				0						GAAAAACACCtttttttaatt	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	40798707	40798707	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40798707delT								COL9A2 (15647 upstream) : SMAP2 (41021 downstream)																							AAGAGAAACATTTTTACAGTC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	55931116	55931116	+	IGR	DEL	T	-	-	rs138182494		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55931116delT								USP24 (250354 upstream) : None (None downstream)																							TGGCCTTTTCTTTTTTTTTTC	0.363													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	62146433	62146434	+	IGR	INS	-	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62146433_62146434insT								NFIA (217974 upstream) : TM2D1 (285 downstream)																							AAAGCAAAAAAGGAAGAAGTTC	0.465													4	2	---	---	---	---	
INADL	10207	broad.mit.edu	37	1	62299093	62299093	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62299093delA	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron|INADL_uc001dac.2_Intron	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						TCACATTAATAAAAAAAACTG	0.323													4	2	---	---	---	---	
SLC35D1	23169	broad.mit.edu	37	1	67470293	67470294	+	Intron	INS	-	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67470293_67470294insG	uc001ddk.2	-							NM_015139	NP_055954	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-glucuronic						chondroitin sulfate biosynthetic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	integral to endoplasmic reticulum membrane	UDP-glucuronic acid transmembrane transporter activity|UDP-N-acetylgalactosamine transmembrane transporter activity				0					Lorazepam(DB00186)	AAAATGGTATAAAATATAAACA	0.243													4	3	---	---	---	---	
LPHN2	23266	broad.mit.edu	37	1	82187544	82187544	+	Intron	DEL	A	-	-	rs80152757	byFrequency	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82187544delA	uc001dit.3	+						LPHN2_uc001dis.2_Intron	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		TACCAAGGGGAAAAAAAAAAC	0.438													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	87903467	87903467	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87903467delC								LMO4 (88864 upstream) : None (None downstream)																							AATAATGCAGCCCCAGCAAGG	0.403													4	2	---	---	---	---	
ABCA4	24	broad.mit.edu	37	1	94481004	94481005	+	Intron	INS	-	A	A	rs148696094	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94481004_94481005insA	uc001dqh.2	-						ABCA4_uc009wdp.1_Intron	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4						phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GGGAATGGCTGCCCCCAGGCTT	0.554													3	3	---	---	---	---	
DPH5	51611	broad.mit.edu	37	1	101467286	101467287	+	Intron	DEL	GG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101467286_101467287delGG	uc001dts.2	-						DPH5_uc001dtr.2_Intron|DPH5_uc001dtq.2_Intron|DPH5_uc001dtt.2_Intron|DPH5_uc001dtu.2_Intron|DPH5_uc001dtv.2_Intron|DPH5_uc001dtw.2_Intron|DPH5_uc001dtx.2_Intron|DPH5_uc001dty.2_Intron|DPH5_uc001dtz.2_Intron	NM_015958	NP_057042	Q9H2P9	DPH5_HUMAN	diphthine synthase isoform a						peptidyl-diphthamide biosynthetic process from peptidyl-histidine		diphthine synthase activity				0		all_epithelial(167;3.1e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0385)|all cancers(265;0.043)|COAD - Colon adenocarcinoma(174;0.151)|Colorectal(144;0.173)|Lung(183;0.198)		CACCAAAAAAGGTAACAGGAAC	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	118865300	118865300	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118865300delC								SPAG17 (137452 upstream) : TBX15 (560366 downstream)																							aatgtcctcaccctcttctcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120428737	120428737	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120428737delT								NBPF7 (40958 upstream) : ADAM30 (7420 downstream)																							GAGTCTAGGGTTGCAGCTAGG	0.517											OREG0013732	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145555991	145555993	+	Intron	DEL	GAG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145555991_145555993delGAG	uc001emp.3	+						ANKRD35_uc010oyx.1_Intron|ANKRD35_uc001eob.1_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TACACAAAGTGAGGAAAGAAAAT	0.360													4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145596350	145596350	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145596350delA	uc001emp.3	+						POLR3C_uc001eog.2_Intron|POLR3C_uc001eoh.2_Intron|POLR3C_uc001eoi.2_Intron|POLR3C_uc009wix.2_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ATGAGAAGAGAAAAAAAGGCA	0.274													4	2	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	148306201	148306201	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148306201delG	uc001eqf.2	-						LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc009wkf.1_Intron|uc001erb.2_Intron|uc001erd.3_Intron|uc001erc.3_Intron|uc010paj.1_Intron|uc010pam.1_Intron|uc001erl.1_Intron|uc001erm.1_Intron|uc001erz.2_Intron|uc010pao.1_Intron|uc010paq.1_Intron|uc010par.1_Intron|uc010pas.1_Intron|uc010pat.1_Intron|uc010pau.1_Intron|uc010pav.1_Intron|uc010paw.1_Intron	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						TGCTGAGCCTGGAAAAGGAGG	0.458													4	2	---	---	---	---	
GBA	2629	broad.mit.edu	37	1	155208696	155208696	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155208696delG	uc001fjh.2	-						RAG1AP1_uc010pey.1_Intron|GBA_uc010pfw.1_Intron|GBA_uc010pfx.1_Intron|GBA_uc001fji.2_Intron|GBA_uc001fjj.2_Intron|GBA_uc001fjk.2_Intron|GBA_uc001fjl.2_Intron|GBA_uc010pfy.1_Intron|GBA_uc009wqk.1_Intron	NM_000157	NP_000148	P04062	GLCM_HUMAN	glucocerebrosidase precursor						carbohydrate metabolic process|cell death|cellular response to tumor necrosis factor|ceramide biosynthetic process|glucosylceramide catabolic process|lysosome organization|negative regulation of interleukin-6 production|negative regulation of MAP kinase activity|positive regulation of protein dephosphorylation|sphingosine biosynthetic process|termination of signal transduction	lysosomal lumen|lysosomal membrane	cation binding|glucosylceramidase activity|receptor binding			ovary(1)|skin(1)	2	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		Alglucerase(DB00088)|Imiglucerase(DB00053)	TGTCAGGGATGGGCAGAAGTC	0.338									Gaucher_disease_type_I				4	2	---	---	---	---	
VSIG8	391123	broad.mit.edu	37	1	159833699	159833700	+	5'Flank	DEL	AC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159833699_159833700delAC	uc001fuh.2	-							NM_001013661	NP_001013683	Q5VU13	VSIG8_HUMAN	V-set and immunoglobulin domain containing 8							integral to membrane				central_nervous_system(1)	1	all_hematologic(112;0.0597)					CATTAAGGAAACACAAGGAGTC	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	159836956	159836957	+	IGR	DEL	CT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159836956_159836957delCT								VSIG8 (4509 upstream) : CCDC19 (5199 downstream)																							attaaggagactcagtccctat	0.099													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165427039	165427040	+	IGR	DEL	TT	-	-	rs67696117		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165427039_165427040delTT								RXRG (12609 upstream) : LOC400794 (19039 downstream)																							gagctttgggTTTTTTTTTTAA	0.252													3	3	---	---	---	---	
RABGAP1L	9910	broad.mit.edu	37	1	174221447	174221447	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174221447delA	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjy.2_Intron	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						TAAAGTTTATAGTCAAATAAA	0.299													9	4	---	---	---	---	
XPR1	9213	broad.mit.edu	37	1	180783868	180783868	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180783868delG	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0						CAAGATAGAAGGTGTTAAATT	0.323													4	2	---	---	---	---	
NPL	80896	broad.mit.edu	37	1	182781558	182781558	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182781558delG	uc009wyb.2	+						NPL_uc010pnx.1_Intron|NPL_uc010pny.1_Intron|NPL_uc001gpo.1_Intron|NPL_uc009wyc.2_Intron|NPL_uc001gpp.3_Intron|NPL_uc001gpq.1_Intron	NM_030769	NP_110396	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase						carbohydrate metabolic process	cytoplasm	N-acetylneuraminate lyase activity			ovary(1)|central_nervous_system(1)|skin(1)	3						GATAGGAGATGGAAGCACCTT	0.433													4	2	---	---	---	---	
CNTN2	6900	broad.mit.edu	37	1	205016662	205016663	+	Intron	INS	-	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205016662_205016663insC	uc001hbr.2	+						CNTN2_uc001hbq.1_Intron	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor						axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TGGCCGCGTGACCCCCTGAGCA	0.550													4	2	---	---	---	---	
CNTN2	6900	broad.mit.edu	37	1	205020627	205020628	+	Intron	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205020627_205020628delCA	uc001hbr.2	+						CNTN2_uc001hbq.1_Intron	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor						axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CTGAGAGTGGCAAGGACAGGGA	0.559													4	2	---	---	---	---	
CR1L	1379	broad.mit.edu	37	1	207870600	207870600	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207870600delT	uc001hga.3	+						CR1L_uc001hfz.2_Intron|CR1L_uc001hgb.1_Intron	NM_175710	NP_783641	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like							cytoplasm|extracellular region|membrane					0						AGTTGCATACTTTAGATGTAA	0.393													4	2	---	---	---	---	
CAMK1G	57172	broad.mit.edu	37	1	209785647	209785648	+	Intron	DEL	CT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209785647_209785648delCT	uc001hhd.2	+						CAMK1G_uc001hhf.3_3'UTR|CAMK1G_uc001hhe.2_Intron	NM_020439	NP_065172	Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG							Golgi membrane|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			breast(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		ACACAAAGGCCTCTCCCACTCA	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	223965174	223965174	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223965174delT								CAPN2 (1456 upstream) : TP53BP2 (2422 downstream)																							ATTCCTTTGGTTTCCTTCAGG	0.488													4	2	---	---	---	---	
CEP170	9859	broad.mit.edu	37	1	243292425	243292425	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243292425delA	uc001hzs.2	-						CEP170_uc001hzt.2_Intron|CEP170_uc001hzu.2_Intron|CEP170_uc001hzr.2_Intron|CEP170_uc001hzv.1_Intron	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha							centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			TTTAATTATTACAAGAACAAT	0.299													3	3	---	---	---	---	
PXDN	7837	broad.mit.edu	37	2	1665309	1665321	+	Intron	DEL	GGATGCAGGTGGA	-	-	rs6146592		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1665309_1665321delGGATGCAGGTGGA	uc002qxa.2	-						PXDN_uc002qxb.1_Intron	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor						extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GGCAGTGCAGGGATGCAGGTGGAGGATGGGACC	0.596													4	2	---	---	---	---	
ADAM17	6868	broad.mit.edu	37	2	9634514	9634514	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9634514delT	uc002qzu.2	-						IAH1_uc010yiz.1_Intron|ADAM17_uc010ewy.2_Intron|ADAM17_uc010ewz.2_Intron	NM_003183	NP_003174	P78536	ADA17_HUMAN	a disintegrin and metalloprotease domain 17						B cell differentiation|cell adhesion mediated by integrin|epidermal growth factor receptor signaling pathway|epidermal growth factor receptor transactivation by G-protein coupled receptor signaling pathway|germinal center formation|membrane protein intracellular domain proteolysis|negative regulation of interleukin-8 production|nerve growth factor receptor signaling pathway|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of chemokine production|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of protein phosphorylation|positive regulation of T cell chemotaxis|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of mast cell apoptosis|response to drug|response to high density lipoprotein particle stimulus|response to hypoxia|response to lipopolysaccharide|spleen development|T cell differentiation in thymus|wound healing, spreading of epidermal cells	actin cytoskeleton|apical plasma membrane|cell surface|cytoplasm|integral to plasma membrane|membrane raft	integrin binding|interleukin-6 receptor binding|metalloendopeptidase activity|PDZ domain binding|SH3 domain binding|zinc ion binding			lung(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		ACCAACCAACTTTACCATAAA	0.453													4	2	---	---	---	---	
VSNL1	7447	broad.mit.edu	37	2	17794381	17794381	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17794381delG	uc002rcm.2	+							NM_003385	NP_003376	P62760	VISL1_HUMAN	visinin-like 1								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TCTTTTTTTTGGAGCTCAGAC	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20298081	20298082	+	IGR	INS	-	ACT	ACT	rs67746406		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20298081_20298082insACT								LAPTM4A (46292 upstream) : SDC1 (102476 downstream)																							TTGCATCCAGCACAAGAAACCT	0.465											OREG0014473	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	4	---	---	---	---	
KLHL29	114818	broad.mit.edu	37	2	23922454	23922454	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23922454delC	uc010ykg.1	+						KLHL29_uc010ykh.1_Intron			Q96CT2	KLH29_HUMAN	RecName: Full=Kelch-like protein 29; AltName: Full=Kelch repeat and BTB domain-containing protein 9;											ovary(1)|lung(1)	2						TGTCCTTTCTCCCCTGTCTTG	0.338													4	2	---	---	---	---	
CIB4	130106	broad.mit.edu	37	2	26817879	26817879	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26817879delT	uc002rhm.2	-							NM_001029881	NP_001025052	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATTCTCAATCTTTTTTTTTTA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	26873518	26873518	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26873518delA								CIB4 (9307 upstream) : KCNK3 (42063 downstream)																							cagcaggatgaagggaggaga	0.000													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	45884450	45884450	+	Intron	DEL	C	-	-	rs57098385		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45884450delC	uc002rut.2	+							NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			aatcccacttctaccatctac	0.134													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65388507	65388507	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65388507delT								RAB1A (31072 upstream) : ACTR2 (66322 downstream)																							ataagtgggctttggatatgt	0.010													4	2	---	---	---	---	
SPRED2	200734	broad.mit.edu	37	2	65645442	65645443	+	Intron	INS	-	C	C	rs147935920	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65645442_65645443insC	uc002sdr.3	-						SPRED2_uc010fcx.1_Intron	NM_181784	NP_861449	Q7Z698	SPRE2_HUMAN	sprouty-related protein with EVH-1 domain 2						inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			ovary(1)|lung(1)|central_nervous_system(1)	3						ATTTAGCCTCACCTGACTTGAC	0.470													3	6	---	---	---	---	
MIR1285-2	100302268	broad.mit.edu	37	2	70481272	70481272	+	5'Flank	DEL	T	-	-	rs112545635		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70481272delT	hsa-mir-1285-2|MI0006347	-																							0						TATAGACCCAttttttttttt	0.189													9	5	---	---	---	---	
NCAPH	23397	broad.mit.edu	37	2	97025685	97025685	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97025685delC	uc002svz.1	+						NCAPH_uc010fhv.1_Intron|NCAPH_uc010yum.1_Intron|NCAPH_uc010fhw.1_Intron|NCAPH_uc010yun.1_Intron|NCAPH_uc002swa.1_Intron	NM_015341	NP_056156	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|microtubule cytoskeleton|nucleus				urinary_tract(1)|skin(1)	2		Ovarian(717;0.0221)				GATGTGTTTTCTTAGCCAAAA	0.239													9	6	---	---	---	---	
INPP4A	3631	broad.mit.edu	37	2	99165096	99165096	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99165096delT	uc002syy.2	+						INPP4A_uc010yvj.1_Intron|INPP4A_uc010yvk.1_Intron|INPP4A_uc002syx.2_Intron|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696	Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type 1						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1						ATTTTTCAAATATATAAGTTT	0.353													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	101840786	101840786	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101840786delG								TBC1D8 (72940 upstream) : C2orf29 (28559 downstream)																							GGTGGCTCATGAAGATCCTAA	0.348													4	2	---	---	---	---	
RFX8	731220	broad.mit.edu	37	2	102022802	102022802	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102022802delT	uc010yvx.1	-						RFX8_uc002tbb.1_Intron	NM_001145664	NP_001139136	Q6ZV50	RFX8_HUMAN	regulatory factor X, 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0						AAAAAGCAAAttttttttttt	0.209													3	3	---	---	---	---	
MAP4K4	9448	broad.mit.edu	37	2	102311854	102311854	+	5'Flank	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102311854delG	uc002tbg.2	+						MAP4K4_uc002tbc.2_5'Flank|MAP4K4_uc002tbd.2_5'Flank|MAP4K4_uc002tbe.2_5'Flank|MAP4K4_uc002tbf.2_5'Flank|MAP4K4_uc010yvy.1_5'Flank|MAP4K4_uc002tbh.2_5'Flank|MAP4K4_uc002tbi.2_5'Flank	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4						TTGAATctgtggaaggaggct	0.214													4	2	---	---	---	---	
PAX8	7849	broad.mit.edu	37	2	113989122	113989123	+	Intron	INS	-	G	G	rs144547150	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113989122_113989123insG	uc010yxt.1	-						PAX8_uc010yxu.1_Intron|PAX8_uc010yxv.1_Intron|PAX8_uc002tjm.2_Intron|PAX8_uc002tjn.2_Intron	NM_003466	NP_003457	Q06710	PAX8_HUMAN	paired box 8 isoform PAX8A						branching involved in ureteric bud morphogenesis|cellular response to gonadotropin stimulus|central nervous system development|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric comma-shaped body morphogenesis|metanephric distal convoluted tubule development|metanephric nephron tubule formation|metanephric S-shaped body morphogenesis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|otic vesicle development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of thyroid-stimulating hormone secretion|thyroid gland development|transcription, DNA-dependent	nucleoplasm	protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity			ovary(1)|lung(1)	2						GCTATGAAGTAGTGAAGGAGTT	0.505			T	PPARG	follicular thyroid		Thyroid dysgenesis 						4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114518054	114518054	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114518054delG								SLC35F5 (3654 upstream) : ACTR3 (129483 downstream)																							catcctatgtggtcagttgag	0.000													4	2	---	---	---	---	
TFCP2L1	29842	broad.mit.edu	37	2	121989684	121989693	+	Intron	DEL	TTTTGTTTTG	-	-	rs3835787		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121989684_121989693delTTTTGTTTTG	uc002tmx.2	-						TFCP2L1_uc010flr.2_Intron|TFCP2L1_uc010flq.2_Intron	NM_014553	NP_055368	Q9NZI6	TF2L1_HUMAN	LBP-9						female pregnancy|steroid biosynthetic process	mitochondrion|nucleolus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			pancreas(2)|ovary(1)	3	Renal(3;0.01)					CTGCCACTCTttttgttttgttttgttttg	0.281													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129170412	129170412	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129170412delA								HS6ST1 (94241 upstream) : None (None downstream)																							AGTCACACATACTGAGCACAG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	145802949	145802950	+	Intron	DEL	CT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145802949_145802950delCT	uc002twc.2	+						uc002twd.2_Intron|uc002twe.2_Intron					Homo sapiens hypothetical gene supported by BC043549; BX648102, mRNA (cDNA clone IMAGE:5172341).																		CACAAACTCACTCTCTCTCTCA	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	151986075	151986076	+	IGR	INS	-	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151986075_151986076insA								RND3 (641895 upstream) : RBM43 (118653 downstream)																							agtgtggaaggtaaatatgcct	0.000													4	2	---	---	---	---	
NEB	4703	broad.mit.edu	37	2	152460714	152460715	+	Intron	DEL	TC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152460714_152460715delTC	uc010fnx.2	-							NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTGCCCCCCATCTCTCTCTCTT	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	170433856	170433856	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170433856delA								FASTKD1 (3432 upstream) : PPIG (6994 downstream)																							GCTGGGTCTTaaaaaaaaaag	0.303													9	5	---	---	---	---	
PPIG	9360	broad.mit.edu	37	2	170463838	170463839	+	Intron	INS	-	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170463838_170463839insA	uc002uez.2	+						PPIG_uc010fpx.2_Intron|PPIG_uc010fpy.2_Intron|PPIG_uc002ufa.2_Intron|PPIG_uc002ufb.2_Intron|PPIG_uc002ufc.1_Intron|PPIG_uc002ufd.2_Intron	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G						protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)	GGTATTTTTTCTTCTTAGGACA	0.292													16	7	---	---	---	---	
SLC25A12	8604	broad.mit.edu	37	2	172666977	172666977	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172666977delA	uc002uhh.2	-						SLC25A12_uc010fqh.2_Intron	NM_003705	NP_003696	O75746	CMC1_HUMAN	solute carrier family 25, member 12						gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	GTATAATGTCACGTTTTCTTG	0.328													4	2	---	---	---	---	
SLC25A12	8604	broad.mit.edu	37	2	172750395	172750396	+	Intron	DEL	CC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172750395_172750396delCC	uc002uhh.2	-						SLC25A12_uc010fqh.2_Intron|SLC25A12_uc010zdv.1_Intron	NM_003705	NP_003696	O75746	CMC1_HUMAN	solute carrier family 25, member 12						gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	GCCACTTCCTCCCACACCCTTT	0.530													4	2	---	---	---	---	
RAPGEF4	11069	broad.mit.edu	37	2	173666383	173666383	+	Intron	DEL	A	-	-	rs11324142		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173666383delA	uc002uhv.3	+						RAPGEF4_uc002uhu.2_Intron|RAPGEF4_uc010fqn.2_Intron	NM_007023	NP_008954	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4						blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)			ccaaggtcataaagctgctgg	0.199													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	200000851	200000851	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200000851delT								PLCL1 (986245 upstream) : SATB2 (133373 downstream)																							CAGAGGATAGTGGGAAGTTCT	0.388													3	3	---	---	---	---	
CFLAR	8837	broad.mit.edu	37	2	202028875	202028875	+	3'UTR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202028875delT	uc002uxb.3	+	10					CFLAR_uc002uxc.3_3'UTR|CFLAR_uc010zhl.1_3'UTR|CFLAR_uc010fsy.2_RNA|CFLAR_uc010fsx.2_3'UTR|CFLAR_uc002uxg.2_3'UTR	NM_003879	NP_003870	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator isoform						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis		cysteine-type endopeptidase activity|protein binding				0						gtattcccagttacttgggag	0.000													4	6	---	---	---	---	
CASP8	841	broad.mit.edu	37	2	202095893	202095894	+	5'Flank	INS	-	T	T	rs137889636	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202095893_202095894insT	uc002uxr.1	+						CASP8_uc010ftc.1_5'Flank|CASP8_uc002uxo.1_5'Flank|CASP8_uc002uxp.1_5'Flank|CASP8_uc002uxq.1_5'Flank|CASP8_uc002uxn.2_5'Flank	NM_033355	NP_203519	Q14790	CASP8_HUMAN	caspase 8 isoform B precursor						activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor	centrosome|cytosol|mitochondrial outer membrane	cysteine-type endopeptidase activity|protein binding|protein binding			upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1)	5						gcttaaagataaaatgttaaaa	0.000										HNSCC(4;0.00038)			0	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	207231956	207231956	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207231956delG								ZDBF2 (52808 upstream) : ADAM23 (76412 downstream)																							gtcagactctggggtgcaaat	0.144													4	2	---	---	---	---	
TRIP12	9320	broad.mit.edu	37	2	230634174	230634174	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230634174delA	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.1_Intron	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		ACCTCTTTCCaaaaaaaaaaa	0.333													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232580257	232580258	+	IGR	DEL	CC	-	-	rs838437	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232580257_232580258delCC								PTMA (2009 upstream) : PDE6D (16889 downstream)																							AGACCTTTCTCCCTCTCTGTTG	0.569											OREG0015277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	234482278	234482278	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234482278delC								USP40 (6850 upstream) : UGT1A8 (44013 downstream)																							agcttaaggaccccagggtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	235614969	235614970	+	IGR	INS	-	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235614969_235614970insC								ARL4C (209276 upstream) : SH3BP4 (245658 downstream)																							TCACCAAAGAGCCCCTATAGCA	0.535													4	2	---	---	---	---	
ASB1	51665	broad.mit.edu	37	2	239347943	239347943	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239347943delG	uc002vyg.2	+							NM_001040445	NP_001035535	Q9Y576	ASB1_HUMAN	ankyrin repeat and SOCS box-containing protein						intracellular signal transduction|negative regulation of cytokine biosynthetic process						0		all_epithelial(40;2.65e-14)|Breast(86;7.61e-05)|Renal(207;0.00183)|all_lung(227;0.0283)|Ovarian(221;0.0365)|Lung NSC(271;0.0941)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)		GGTGGTGTTTGTGTTTGTAGT	0.507													4	2	---	---	---	---	
ATG4B	23192	broad.mit.edu	37	2	242589936	242589936	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242589936delG	uc002wbv.2	+						ATG4B_uc002wbu.2_Intron|ATG4B_uc002wbw.2_Intron|ATG4B_uc010zox.1_Intron|ATG4B_uc010zoy.1_Intron|ATG4B_uc010fzp.2_Intron|ATG4B_uc010zoz.1_5'Flank	NM_013325	NP_037457	Q9Y4P1	ATG4B_HUMAN	APG4 autophagy 4 homolog B isoform a						autophagic vacuole assembly|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		GGATGGCCATGGAAAACGACT	0.463													4	2	---	---	---	---	
GAL3ST2	64090	broad.mit.edu	37	2	242742509	242742510	+	Intron	INS	-	AA	AA			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242742509_242742510insAA	uc002wcj.1	+							NM_022134	NP_071417	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2						biosynthetic process	Golgi cisterna membrane|integral to membrane	galactosylceramide sulfotransferase activity				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		TCCTCCTGAGGCCCCTTCCTGG	0.683													4	2	---	---	---	---	
GAL3ST2	64090	broad.mit.edu	37	2	242742513	242742514	+	Intron	INS	-	GTG	GTG			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242742513_242742514insGTG	uc002wcj.1	+							NM_022134	NP_071417	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2						biosynthetic process	Golgi cisterna membrane|integral to membrane	galactosylceramide sulfotransferase activity				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		CCTGAGGCCCCTTCCTGGCGTC	0.678													4	2	---	---	---	---	
ATP2B2	491	broad.mit.edu	37	3	10501318	10501319	+	Intron	DEL	CC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10501318_10501319delCC	uc003bvt.2	-						ATP2B2_uc003bvv.2_Intron|ATP2B2_uc003bvw.2_Intron|ATP2B2_uc010hdp.2_Intron	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6						CTGCCCTCATCCCCCTCATTCT	0.465													4	2	---	---	---	---	
KAT2B	8850	broad.mit.edu	37	3	20141236	20141237	+	Intron	DEL	TG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20141236_20141237delTG	uc003cbq.2	+							NM_003884	NP_003875	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B						cell cycle arrest|cellular response to insulin stimulus|chromatin remodeling|histone H3 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|negative regulation of cell proliferation|transcription initiation from RNA polymerase I promoter	Ada2/Gcn5/Ada3 transcription activator complex|chromatin remodeling complex|PCAF complex	cyclin-dependent protein kinase inhibitor activity|histone acetyltransferase activity|histone deacetylase binding|protein kinase binding|transcription coactivator activity|transcription factor binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						CTTTAAAGGCTGTGTGTGTGTG	0.218													4	3	---	---	---	---	
RFT1	91869	broad.mit.edu	37	3	53141118	53141119	+	Intron	INS	-	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53141118_53141119insA	uc003dgj.2	-						RFT1_uc003dgk.2_Intron	NM_052859	NP_443091	Q96AA3	RFT1_HUMAN	RFT1 homolog						carbohydrate transport|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane	lipid transporter activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		aaattacaaataaaaaaaaata	0.188													4	2	---	---	---	---	
ADAMTS9	56999	broad.mit.edu	37	3	64554386	64554386	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64554386delA	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc003dmh.1_Intron|ADAMTS9_uc011bfp.1_Intron|uc003dmi.1_Intron	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1						glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		GGTGGCATTGAAAAAAAAAAT	0.408													4	2	---	---	---	---	
FAM86D	692099	broad.mit.edu	37	3	75479780	75479783	+	Intron	DEL	GAGT	-	-	rs79261256		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75479780_75479783delGAGT	uc003dpp.3	-						FAM86D_uc003dpo.3_Intron|FAM86D_uc003dps.3_Intron|FAM86D_uc003dpq.3_Intron|FAM86D_uc003dpr.3_Intron	NR_024241				RecName: Full=Protein FAM86B1;												0						ccaggaggcagagtgagggagaga	0.054													6	3	---	---	---	---	
WDR52	55779	broad.mit.edu	37	3	113120684	113120685	+	Intron	INS	-	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113120684_113120685insC	uc003eae.1	-							NM_018338	NP_060808	Q96MT7	WDR52_HUMAN	WD repeat domain 52 isoform 2											central_nervous_system(1)	1						AAAAGTCATTTCTTTTTCTTTC	0.302													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	134101973	134101974	+	IGR	INS	-	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134101973_134101974insT								AMOTL2 (7714 upstream) : ANAPC13 (94573 downstream)																							AATTATTAGTAtttttttttct	0.257													4	2	---	---	---	---	
PLS1	5357	broad.mit.edu	37	3	142322700	142322700	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142322700delA	uc010huv.2	+							NM_001145319	NP_001138791	Q14651	PLSI_HUMAN	plastin 1							cytoplasm	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(1)	1						AGCTGACCACAAAAAAAAAGG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144096561	144096561	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144096561delT								C3orf58 (385352 upstream) : None (None downstream)																							cagacatcaatttttttttct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144483052	144483053	+	IGR	INS	-	TT	TT	rs138355154	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144483052_144483053insTT								C3orf58 (771843 upstream) : None (None downstream)																							tcccagtctccttgtgccactt	0.050													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152815979	152815979	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152815979delT								P2RY1 (260138 upstream) : RAP2B (64050 downstream)																							atgtctgctcttaccacgctg	0.025													4	2	---	---	---	---	
SGEF	26084	broad.mit.edu	37	3	153963907	153963907	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153963907delG	uc011bog.1	+						SGEF_uc011boh.1_Intron|SGEF_uc011boi.1_Intron	NM_015595	NP_056410	Q96DR7	ARHGQ_HUMAN	Src homology 3 domain-containing guanine						regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			agtgctaattggggggtggtg	0.025													4	2	---	---	---	---	
ZBBX	79740	broad.mit.edu	37	3	167083684	167083684	+	Frame_Shift_Del	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167083684delT	uc003fep.2	-	6	586	c.263delA	c.(262-264)AATfs	p.N88fs	ZBBX_uc011bpc.1_Frame_Shift_Del_p.N88fs|ZBBX_uc003feq.2_Frame_Shift_Del_p.N59fs	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	88						intracellular	zinc ion binding			ovary(2)	2						CTTAACAACATTTCCTTTATT	0.299													48	32	---	---	---	---	
ACTL6A	86	broad.mit.edu	37	3	179304140	179304140	+	Intron	DEL	A	-	-	rs111457157		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179304140delA	uc003fjw.2	+						ACTL6A_uc003fjx.2_Intron|ACTL6A_uc003fjy.2_Intron	NM_004301	NP_004292	O96019	ACL6A_HUMAN	actin-like 6A isoform 1						chromatin remodeling|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|nervous system development|regulation of growth|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	Ino80 complex|npBAF complex|NuA4 histone acetyltransferase complex|plasma membrane|SWI/SNF complex	ATP binding|chromatin binding			ovary(1)	1	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			ggctgggtgcaagtggctcat	0.149													4	2	---	---	---	---	
ECE2	9718	broad.mit.edu	37	3	183980085	183980086	+	Intron	INS	-	CA	CA	rs148290763	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183980085_183980086insCA	uc003fni.3	+						CAMK2N2_uc003fnj.1_5'Flank	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A						brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			tatctctgtgccagtgtctccg	0.262													3	6	---	---	---	---	
EHHADH	1962	broad.mit.edu	37	3	184934813	184934813	+	Intron	DEL	G	-	-	rs35922888		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184934813delG	uc003fpf.2	-						EHHADH_uc011brs.1_Intron	NM_001966	NP_001957	Q08426	ECHP_HUMAN	enoyl-Coenzyme A, hydratase/3-hydroxyacyl							peroxisome	3-hydroxyacyl-CoA dehydrogenase activity|coenzyme binding|dodecenoyl-CoA delta-isomerase activity|enoyl-CoA hydratase activity			ovary(3)	3	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)		NADH(DB00157)	TGCGGAGACAGAAGTTCTCAA	0.328													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197872249	197872249	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197872249delC								LOC348840 (64707 upstream) : FAM157A (6988 downstream)																							CACCACAGCTCCCCCCACACA	0.408													4	2	---	---	---	---	
ZNF718	255403	broad.mit.edu	37	4	145016	145016	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145016delA	uc003fzt.3	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc010iaz.2_Intron|ZNF718_uc003fzw.3_Intron	NM_001039127	NP_001034216	Q3SXZ3	ZN718_HUMAN	zinc finger protein 718						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0681)|Epithelial(2;0.0838)|all cancers(2;0.135)|LUSC - Lung squamous cell carcinoma(95;0.18)		cctcccaagtagctgggacta	0.000													8	4	---	---	---	---	
C4orf42	92070	broad.mit.edu	37	4	1248389	1248389	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1248389delA	uc003gcy.1	+											Homo sapiens cDNA FLJ31571 fis, clone NT2RI2001726.											ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0101)	Colorectal(103;0.188)		tgaatcaagcaaaaaagagaa	0.000													4	2	---	---	---	---	
WHSC1	7468	broad.mit.edu	37	4	1876335	1876335	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1876335delG	uc003gdz.3	+						WHSC1_uc003gdx.2_Intron|WHSC1_uc003gdy.1_Intron|WHSC1_uc010icd.1_Intron	NM_001042424	NP_001035889	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1 protein						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		TGGAGCATCTGGGAGAAGAAG	0.413			T	IGH@	MM								4	2	---	---	---	---	
HTT	3064	broad.mit.edu	37	4	3208003	3208004	+	Intron	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3208003_3208004delCA	uc011bvq.1	+							NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GGCCTAACTTCACACAGCCTCT	0.510													4	2	---	---	---	---	
LYAR	55646	broad.mit.edu	37	4	4275973	4275973	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4275973delA	uc011bvy.1	-						LYAR_uc011bvx.1_Intron|LYAR_uc003ght.2_Intron	NM_001145725	NP_001139197	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive homolog							nucleolus	metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		caaaaaaaacaaaaaaaaaaa	0.199													11	5	---	---	---	---	
PPP2R2C	5522	broad.mit.edu	37	4	6559108	6559108	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6559108delA	uc011bwe.1	-						PPP2R2C_uc011bwd.1_5'Flank	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						caaggtcagcaaaaaaaaaag	0.000													4	2	---	---	---	---	
ACOX3	8310	broad.mit.edu	37	4	8441899	8441900	+	Intron	INS	-	G	G	rs151015149		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8441899_8441900insG	uc003glc.3	-						ACOX3_uc003gld.3_Intron|C4orf23_uc003glf.1_Intron|C4orf23_uc003glg.1_5'Flank	NM_003501	NP_003492	O15254	ACOX3_HUMAN	acyl-Coenzyme A oxidase 3 isoform a						bile acid metabolic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|pristanoyl-CoA oxidase activity			central_nervous_system(1)	1						ttcacgtggacccttaaagtcg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	8947834	8947834	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8947834delC								HMX1 (74291 upstream) : LOC650293 (3643 downstream)																							tatggagcagccccatttgaa	0.000													3	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	11028081	11028082	+	IGR	INS	-	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11028081_11028082insG								CLNK (341695 upstream) : MIR572 (342369 downstream)																							GTAGGCTGTGAGGGGTGGAGAG	0.550													6	3	---	---	---	---	
GPR125	166647	broad.mit.edu	37	4	22514538	22514539	+	Intron	DEL	TG	-	-	rs151247616		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22514538_22514539delTG	uc003gqm.1	-						GPR125_uc003gqo.2_Intron	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor						neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)				CAACAAAAACTGTGCTCAACTA	0.153													5	4	---	---	---	---	
TBC1D1	23216	broad.mit.edu	37	4	38009399	38009399	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38009399delT	uc003gtb.2	+						TBC1D1_uc011byd.1_Intron|TBC1D1_uc010ifd.2_Intron|TBC1D1_uc011byf.1_Intron	NM_015173	NP_055988	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family,							nucleus	Rab GTPase activator activity			ovary(1)	1						TTGGCTGCCCTTCGTGCTGTT	0.498													4	2	---	---	---	---	
TEC	7006	broad.mit.edu	37	4	48249957	48249957	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48249957delA	uc003gxz.2	-							NM_003215	NP_003206	P42680	TEC_HUMAN	tec protein tyrosine kinase						intracellular protein kinase cascade	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)	9						AATTAAAACTAAAAGGAGGAG	0.154													4	2	---	---	---	---	
TECRL	253017	broad.mit.edu	37	4	65241026	65241026	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65241026delC	uc003hcv.2	-						TECRL_uc003hcw.2_Intron	NM_001010874	NP_001010874	Q5HYJ1	TECRL_HUMAN	steroid 5 alpha-reductase 2-like 2						lipid metabolic process	cytoplasm|integral to membrane	oxidoreductase activity, acting on the CH-CH group of donors				0						TTAAATATATCATAAAATTCT	0.219													9	4	---	---	---	---	
CEP170L	645455	broad.mit.edu	37	4	119462760	119462760	+	Intron	DEL	G	-	-	rs111397559		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119462760delG	uc003icb.2	+							NR_003135				RecName: Full=Cep170-like protein;												0						tagatacataggctttcttat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153191976	153191977	+	IGR	INS	-	G	G	rs141170242	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153191976_153191977insG								PET112L (509830 upstream) : FBXW7 (50434 downstream)																							AAGCAGCAGTTGGGGGTGTCCA	0.490													4	3	---	---	---	---	
TLL1	7092	broad.mit.edu	37	4	166910810	166910811	+	Intron	INS	-	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166910810_166910811insA	uc003irh.1	+						TLL1_uc011cjn.1_Intron|TLL1_uc011cjo.1_Intron	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		GTTTTCattttattaatttttt	0.163													3	3	---	---	---	---	
SPOCK3	50859	broad.mit.edu	37	4	168104364	168104368	+	Intron	DEL	CCAGC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168104364_168104368delCCAGC	uc003iri.1	-						SPOCK3_uc011cjp.1_Intron|SPOCK3_uc011cjq.1_Intron|SPOCK3_uc011cjr.1_Intron|SPOCK3_uc003irj.1_Intron|SPOCK3_uc011cjs.1_Intron|SPOCK3_uc011cjt.1_Intron|SPOCK3_uc011cju.1_Intron|SPOCK3_uc011cjv.1_Intron|SPOCK3_uc003irk.3_Intron|SPOCK3_uc011cjw.1_Intron	NM_016950	NP_058646	Q9BQ16	TICN3_HUMAN	testican 3 isoform 2						signal transduction	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase inhibitor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		ccagcccagtccagcccagcccagc	0.098													4	2	---	---	---	---	
CCDC110	256309	broad.mit.edu	37	4	186383381	186383382	+	Intron	DEL	GT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186383381_186383382delGT	uc003ixu.3	-						CCDC110_uc003ixv.3_Intron|CCDC110_uc011ckt.1_Intron	NM_152775	NP_689988	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110 isoform a							nucleus				central_nervous_system(1)	1		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		aggatacagagtgagacctatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190005408	190005408	+	IGR	DEL	A	-	-	rs71598616		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190005408delA								TRIML1 (936759 upstream) : FRG1 (856566 downstream)																							atgtaagatgaaaatttgggg	0.000													4	2	---	---	---	---	
SLC12A7	10723	broad.mit.edu	37	5	1076520	1076530	+	Intron	DEL	CAGGTTCCAGC	-	-	rs111668454		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1076520_1076530delCAGGTTCCAGC	uc003jbu.2	-							NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride						potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			skin(2)|large_intestine(1)|ovary(1)	4	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CAGGCCCCCTCAGGTTCCAGCCATCCTGTGA	0.630													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2132443	2132443	+	IGR	DEL	C	-	-	rs11365878		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2132443delC								IRX4 (249563 upstream) : IRX2 (613838 downstream)																							ATGGCGTCAGCCCCCTCTTGG	0.627													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3280642	3280643	+	IGR	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3280642_3280643delCA								C5orf38 (525130 upstream) : IRX1 (315525 downstream)																							acacacaatgcacacacacaca	0.327													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	14983823	14983823	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14983823delT								ANKH (111936 upstream) : FBXL7 (516482 downstream)																							agagttttgcttttttTTTTT	0.214													3	3	---	---	---	---	
MYO10	4651	broad.mit.edu	37	5	16870329	16870329	+	Intron	DEL	A	-	-	rs11343947		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16870329delA	uc003jft.3	-						MYO10_uc003jfu.2_Intron|MYO10_uc003jfv.2_Intron	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						GAAGTGCAAGAAAAAAACCTT	0.458													4	2	---	---	---	---	
RICTOR	253260	broad.mit.edu	37	5	39003489	39003490	+	Intron	INS	-	AG	AG			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39003489_39003490insAG	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_Intron|RICTOR_uc003jlq.1_Intron|RICTOR_uc011cpk.1_Intron	NM_152756	NP_689969	Q6R327	RICTR_HUMAN	rapamycin-insensitive companion of mTOR						actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding			ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1)	10	all_lung(31;0.000396)					TATCACAAAGACTCACAAAAAC	0.243													7	5	---	---	---	---	
RICTOR	253260	broad.mit.edu	37	5	39003490	39003491	+	Intron	INS	-	TG	TG			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39003490_39003491insTG	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_Intron|RICTOR_uc003jlq.1_Intron|RICTOR_uc011cpk.1_Intron	NM_152756	NP_689969	Q6R327	RICTR_HUMAN	rapamycin-insensitive companion of mTOR						actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding			ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1)	10	all_lung(31;0.000396)					ATCACAAAGACTCACAAAAACA	0.243													9	4	---	---	---	---	
OXCT1	5019	broad.mit.edu	37	5	41765481	41765481	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41765481delC	uc003jmn.2	-						OXCT1_uc011cpo.1_Intron|OXCT1_uc011cpp.1_Intron	NM_000436	NP_000427	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1 precursor						cellular lipid metabolic process|ketone body catabolic process	mitochondrial matrix	3-oxoacid CoA-transferase activity|protein homodimerization activity			ovary(2)|large_intestine(1)	3					Succinic acid(DB00139)	gagtttccttcagccttggtc	0.000													4	2	---	---	---	---	
ZSWIM6	57688	broad.mit.edu	37	5	60822417	60822418	+	Intron	INS	-	T	T	rs34246689		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60822417_60822418insT	uc003jsr.2	+							NM_020928	NP_065979	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6								zinc ion binding				0						GTAAGCAAAGATTTTTTTTTTT	0.277													5	3	---	---	---	---	
COL4A3BP	10087	broad.mit.edu	37	5	74675414	74675414	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74675414delT	uc011csu.1	-						COL4A3BP_uc003kds.2_Intron|COL4A3BP_uc003kdt.2_Intron|COL4A3BP_uc003kdu.2_Intron	NM_005713	NP_005704	Q9Y5P4	C43BP_HUMAN	alpha 3 type IV collagen binding protein isoform						ER to Golgi ceramide transport|immune response	cytosol|endoplasmic reticulum membrane|Golgi apparatus	ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity			skin(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		AATTAGCATCttttttttttc	0.139													9	4	---	---	---	---	
F2RL1	2150	broad.mit.edu	37	5	76114825	76114825	+	5'Flank	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76114825delA	uc003keo.2	+							NM_005242	NP_005233	P55085	PAR2_HUMAN	coagulation factor II (thrombin) receptor-like 1						blood coagulation|elevation of cytosolic calcium ion concentration|positive regulation of leukocyte chemotaxis|positive regulation of positive chemotaxis|regulation of blood coagulation	Golgi apparatus|integral to plasma membrane	receptor binding|thrombin receptor activity			central_nervous_system(1)	1		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;7.7e-51)|Epithelial(54;2.77e-45)|all cancers(79;3.47e-41)		GGCCTCCCGCAGGTGAGTACG	0.721													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87715987	87715988	+	Intron	DEL	TT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87715987_87715988delTT	uc003kjd.2	+						uc003kje.2_Intron					Homo sapiens cDNA clone IMAGE:4814828.																		GAGTCAGCTCTTTTTACAAGAT	0.411													4	2	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	89920694	89920695	+	Intron	INS	-	C	C	rs11744994	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89920694_89920695insC	uc003kju.2	+						GPR98_uc003kjt.2_Intron	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GTTTTTTTTTTCCCCTCAGGTT	0.327													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	108587950	108587950	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108587950delG								FER (64577 upstream) : PJA2 (82461 downstream)																							ACCGGTCCTTGTTTTCCTGCA	0.522													4	2	---	---	---	---	
MCC	4163	broad.mit.edu	37	5	112717796	112717796	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112717796delG	uc003kql.3	-						MCC_uc003kqk.3_Intron	NM_001085377	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		actgaagaaagggtcagagaa	0.214													4	2	---	---	---	---	
SLC27A6	28965	broad.mit.edu	37	5	128325809	128325810	+	Intron	INS	-	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128325809_128325810insG	uc003kuy.2	+						SLC27A6_uc003kuz.2_Intron	NM_014031	NP_054750	Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid						long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		TGTATTGCAAAAAGCATATTTT	0.287													24	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134922510	134922510	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134922510delC								CXCL14 (7541 upstream) : LOC340074 (61864 downstream)																							tgtgcagggtcctgggcagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139429603	139429606	+	IGR	DEL	TTTG	-	-	rs5871722		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139429603_139429606delTTTG								NRG2 (6724 upstream) : PURA (64102 downstream)																							ACTTCACttttttgtttgtttgtt	0.137													4	2	---	---	---	---	
GLRA1	2741	broad.mit.edu	37	5	151245574	151245574	+	Intron	DEL	G	-	-	rs77425912		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151245574delG	uc003lut.2	-						GLRA1_uc003lur.2_Intron|GLRA1_uc003lus.2_Intron	NM_001146040	NP_001139512	P23415	GLRA1_HUMAN	glycine receptor, alpha 1 isoform 1 precursor						muscle contraction|negative regulation of transmission of nerve impulse|neuropeptide signaling pathway|positive regulation of acrosome reaction|regulation of membrane potential|startle response	cell junction|chloride channel complex|integral to plasma membrane|intracellular membrane-bounded organelle|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|protein binding|receptor activity|taurine binding|transmitter-gated ion channel activity			ovary(1)|central_nervous_system(1)	2		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TTCGACATGCGGGGGGCCATG	0.478													4	2	---	---	---	---	
KCNIP1	30820	broad.mit.edu	37	5	170082234	170082235	+	Intron	DEL	TG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170082234_170082235delTG	uc003mas.2	+						KCNIP1_uc003map.2_Intron|KCNIP1_uc003mat.2_Intron|KCNIP1_uc010jjp.2_Intron|KCNIP1_uc010jjq.2_Intron	NM_001034837	NP_001030009	Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1 isoform 1						detection of calcium ion|signal transduction|synaptic transmission	plasma membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			tttctttagttgtgcattagat	0.000													4	2	---	---	---	---	
SH3PXD2B	285590	broad.mit.edu	37	5	171821317	171821317	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171821317delT	uc003mbr.2	-						SH3PXD2B_uc003mbs.1_Intron	NM_001017995	NP_001017995	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B						adipose tissue development|bone development|cell communication|cell differentiation|eye development|heart development|podosome assembly	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-5-phosphate binding|SH2 domain binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			agcaacaaaattacacataca	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172632847	172632848	+	IGR	DEL	GG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172632847_172632848delGG								BNIP1 (41458 upstream) : NKX2-5 (26290 downstream)																							ATTTTCAAAAGGGACCTTGACA	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173178539	173178539	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173178539delT								BOD1 (134873 upstream) : CPEB4 (136792 downstream)																							TTCCATGACGTTTCCAGCTTT	0.299													4	2	---	---	---	---	
SLC22A23	63027	broad.mit.edu	37	6	3272331	3272332	+	3'UTR	DEL	GT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3272331_3272332delGT	uc003mvm.3	-	10					uc003mvi.1_Intron|SLC22A23_uc003mvn.3_3'UTR|SLC22A23_uc003mvo.3_3'UTR|SLC22A23_uc003mvp.1_RNA	NM_015482	NP_056297	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23 isoform a						ion transport	integral to membrane	transmembrane transporter activity			ovary(1)	1	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				GGTGACGGGCGTGTGTGTGTGG	0.535													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	7706117	7706117	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7706117delT								SNRNP48 (93918 upstream) : BMP6 (20894 downstream)																							CCAATGGTTGTTTTTTTTCCC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	23656618	23656618	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23656618delT								None (None upstream) : NRSN1 (469796 downstream)																							TCCCAAAGCCTTTAAAAAAAT	0.438													4	2	---	---	---	---	
HLA-B	3106	broad.mit.edu	37	6	31256479	31256480	+	Intron	INS	-	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31256479_31256480insA	uc003ntf.2	-						HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron			P01889	1B07_HUMAN	SubName: Full=MHC class I antigen;						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0						CCTGTGGTGACACCTCTTCCAC	0.455									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				9	4	---	---	---	---	
HLA-DQB1	3119	broad.mit.edu	37	6	32628231	32628232	+	Intron	INS	-	G	G	rs149858742	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32628231_32628232insG	uc003obw.2	-						HLA-DQB1_uc010juc.1_Intron|HLA-DQB1_uc003obv.2_Intron|HLA-DQB1_uc011dqd.1_Intron	NM_002123	NP_002114	P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	GTGTGGGAGGTGGGGAACAGCT	0.475									Melanoma_Familial_Clustering_of|ACTH-independent_macronodular_adrenal_hyperplasia|T-cell_Lymphoma_(Cutaneous)__Familial_Clustering_of|Sj_gren_syndrome				7	6	---	---	---	---	
ITPR3	3710	broad.mit.edu	37	6	33630207	33630208	+	Intron	INS	-	CTG	CTG			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33630207_33630208insCTG	uc011drk.1	+							NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3						activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19						GCCCTGCCAGCAGCCAACCCTG	0.683													4	2	---	---	---	---	
CDKN1A	1026	broad.mit.edu	37	6	36648701	36648701	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36648701delG	uc003omm.3	+						CDKN1A_uc011dtq.1_Intron|CDKN1A_uc003oml.2_Intron|CDKN1A_uc003omn.2_Intron	NM_000389	NP_000380	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A						cell cycle arrest|cellular response to extracellular stimulus|cellular response to ionizing radiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of fibroblast proliferation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|S phase of mitotic cell cycle|stress-induced premature senescence	cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleoplasm|PCNA-p21 complex	cyclin-dependent protein kinase activating kinase activity|cyclin-dependent protein kinase inhibitor activity|metal ion binding			ovary(1)|breast(1)	2						AGATTTTGATGGGGGAGGAGA	0.458									Multiple_Endocrine_Neoplasia_type_1		OREG0017387	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
DAAM2	23500	broad.mit.edu	37	6	39780394	39780396	+	Intron	DEL	TTC	-	-	rs34070868		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39780394_39780396delTTC	uc003oow.2	+						DAAM2_uc010jxc.2_Intron|DAAM2_uc003oox.2_Intron|DAAM2_uc003oov.3_Intron	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					CAGCCTTCTATTCTTAGTGTGGA	0.493													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	48785190	48785191	+	IGR	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48785190_48785191delCA								C6orf138 (706247 upstream) : MUT (613803 downstream)																							GCCTGTTTATCACTGTGACTTT	0.406													4	2	---	---	---	---	
DST	667	broad.mit.edu	37	6	56498032	56498032	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56498032delT	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron|DST_uc003pdc.3_Intron|DST_uc003pdd.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AGTTTCACTCttttttttttt	0.134													5	3	---	---	---	---	
SMAP1	60682	broad.mit.edu	37	6	71546554	71546557	+	Intron	DEL	ACTT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71546554_71546557delACTT	uc003pfr.2	+						SMAP1_uc003pfs.2_Intron|SMAP1_uc010kao.2_Intron|SMAP1_uc010kap.2_Intron	NM_001044305	NP_001037770	Q8IYB5	SMAP1_HUMAN	stromal membrane-associated GTPase-activating						regulation of ARF GTPase activity	plasma membrane	ARF GTPase activator activity|zinc ion binding				0						TTTTACACTAACTTTATCAGAACC	0.255													15	7	---	---	---	---	
KHDC1	80759	broad.mit.edu	37	6	73933244	73933245	+	Intron	INS	-	AAGGA	AAGGA	rs144553753	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73933244_73933245insAAGGA	uc011dyl.1	-									Q4VXA5	KHDC1_HUMAN	Homo sapiens cDNA FLJ30329 fis, clone BRACE2007201.							integral to membrane	RNA binding			skin(1)	1						AATTTCATCCTAAGAGGACAGC	0.495													4	2	---	---	---	---	
REV3L	5980	broad.mit.edu	37	6	111713853	111713854	+	Intron	INS	-	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111713853_111713854insG	uc003puy.3	-						REV3L_uc003pux.3_Intron|REV3L_uc003puz.3_Intron	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta						DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		ATATCTACCTTGTATTCCTTTT	0.257								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					6	4	---	---	---	---	
LAMA4	3910	broad.mit.edu	37	6	112462354	112462354	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112462354delT	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TAGAAATGACTTTTTTTTTTC	0.313													4	3	---	---	---	---	
HS3ST5	222537	broad.mit.edu	37	6	114504893	114504894	+	Intron	DEL	AA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114504893_114504894delAA	uc003pwh.3	-						uc003pwf.2_Intron	NM_153612	NP_705840	Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		agggatttttaaaggagattct	0.000													4	2	---	---	---	---	
FAM26F	441168	broad.mit.edu	37	6	116784194	116784195	+	Intron	DEL	GG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116784194_116784195delGG	uc003pwv.2	+							NM_001010919	NP_001010919	Q5R3K3	FA26F_HUMAN	hypothetical protein LOC441168							integral to membrane					0				GBM - Glioblastoma multiforme(226;0.0402)|all cancers(137;0.0627)|OV - Ovarian serous cystadenocarcinoma(136;0.0655)|Epithelial(106;0.231)		TGAGTTCTAAGGGAATGGTATG	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	136525717	136525717	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136525717delC	uc003qgq.1	-											Homo sapiens cDNA clone IMAGE:5266948.																		agtagagcagcaaggcaaggg	0.000													4	2	---	---	---	---	
GPR126	57211	broad.mit.edu	37	6	142701832	142701832	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142701832delC	uc010khc.2	+						GPR126_uc010khd.2_Intron|GPR126_uc010khe.2_Intron|GPR126_uc010khf.2_Intron	NM_020455	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126 alpha 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		CATGGGCCTTCTTCTTTGAAA	0.468													4	2	---	---	---	---	
UTRN	7402	broad.mit.edu	37	6	144772824	144772824	+	Intron	DEL	T	-	-	rs113888539		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144772824delT	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TTGGAGGACGTTTTTTTTTTT	0.353													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	150379517	150379517	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150379517delA								RAET1L (32849 upstream) : ULBP3 (3824 downstream)																							ccagagcccgaaggccaaaga	0.124													4	2	---	---	---	---	
TIAM2	26230	broad.mit.edu	37	6	155566511	155566511	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155566511delG	uc003qqb.2	+						TIAM2_uc003qqe.2_Intron|TIAM2_uc010kjj.2_Intron|TIAM2_uc003qqf.2_Intron|TIAM2_uc011efl.1_Intron|TIAM2_uc003qqg.2_Intron|TIAM2_uc003qqh.2_Intron	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		AACTTTCTTTGTTTCTTGTCC	0.483													9	4	---	---	---	---	
ARID1B	57492	broad.mit.edu	37	6	157405583	157405584	+	Intron	DEL	AC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157405583_157405584delAC	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron|ARID1B_uc003qqq.1_Intron	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GTACAACTTTACTCATTTTTTA	0.376													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	157626642	157626642	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157626642delT								ARID1B (96241 upstream) : C6orf35 (83413 downstream)																							tgaagaaaaataaaagtattt	0.000													4	2	---	---	---	---	
TULP4	56995	broad.mit.edu	37	6	158916105	158916105	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158916105delT	uc003qrf.2	+						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)		atcttttaactttttttttga	0.144													4	2	---	---	---	---	
UNC93A	54346	broad.mit.edu	37	6	167707852	167707852	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167707852delA	uc003qvq.2	+						UNC93A_uc003qvr.2_Intron	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1							integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		TTCTCCCACCAGCTTCAGAGG	0.622													1	5	---	---	---	---	
UNC93A	54346	broad.mit.edu	37	6	167707855	167707856	+	Intron	INS	-	CC	CC			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167707855_167707856insCC	uc003qvq.2	+						UNC93A_uc003qvr.2_Intron	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1							integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		TCCCACCAGCTTCAGAGGAGGC	0.614													1	5	---	---	---	---	
UNC93A	54346	broad.mit.edu	37	6	167707858	167707859	+	Intron	INS	-	TC	TC			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167707858_167707859insTC	uc003qvq.2	+						UNC93A_uc003qvr.2_Intron	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1							integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CACCAGCTTCAGAGGAGGCTCC	0.614													1	5	---	---	---	---	
UNC93A	54346	broad.mit.edu	37	6	167707861	167707861	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167707861delG	uc003qvq.2	+						UNC93A_uc003qvr.2_Intron	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1							integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CAGCTTCAGAGGAGGCTCCCA	0.607													1	5	---	---	---	---	
RSPH10B2	728194	broad.mit.edu	37	7	6819606	6819608	+	Intron	DEL	TTT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6819606_6819608delTTT	uc003sqw.1	+						RSPH10B2_uc010ktk.1_Intron|RSPH10B2_uc011jxc.1_Intron|RSPH10B2_uc010ktl.1_Intron	NM_173565	NP_775836	B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B											ovary(1)|pancreas(1)|skin(1)	3						gcctggctaattttttttttttt	0.000													4	2	---	---	---	---	
OSBPL3	26031	broad.mit.edu	37	7	24840073	24840073	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24840073delT	uc003sxf.2	-						OSBPL3_uc003sxd.2_Intron|OSBPL3_uc003sxe.2_Intron|OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron	NM_015550	NP_056365	Q9H4L5	OSBL3_HUMAN	oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1						Attttgttacttttttttttt	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	45406316	45406317	+	IGR	DEL	AC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45406316_45406317delAC								RAMP3 (182469 upstream) : ADCY1 (207422 downstream)																							gtgtgtgtgtACACATGTGCAT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	51714263	51714263	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51714263delG								COBL (329748 upstream) : None (None downstream)																							TCTCTTTCCTGGGATGCATCA	0.453													4	2	---	---	---	---	
RFC2	5982	broad.mit.edu	37	7	73661306	73661306	+	Intron	DEL	T	-	-	rs10709323		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73661306delT	uc003uaj.2	-						RFC2_uc011kfa.1_Intron|RFC2_uc003uak.2_Intron|RFC2_uc010lbp.2_Intron|RFC2_uc003ual.2_Intron	NM_181471	NP_852136	P35250	RFC2_HUMAN	replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2						aaatatACACttttttttttt	0.010													6	3	---	---	---	---	
GTF2IRD2	84163	broad.mit.edu	37	7	74236742	74236742	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74236742delT	uc003ubd.1	-						GTF2IRD2_uc011kfi.1_Intron|uc003ube.1_5'Flank|GTF2IRD2_uc003ubf.1_Intron|GTF2IRD2_uc003ubg.1_3'UTR	NM_173537	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						gcccggctaatttttttttgt	0.000													4	2	---	---	---	---	
HIP1	3092	broad.mit.edu	37	7	75243042	75243042	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75243042delA	uc003uds.1	-							NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8						ACCTGTTGCCAACCAACGTCC	0.184			T	PDGFRB	CMML								4	2	---	---	---	---	
PMS2L11	441263	broad.mit.edu	37	7	76627136	76627137	+	Intron	DEL	GT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76627136_76627137delGT	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						tggacgtgtggtgtgtgtgtgg	0.109													4	2	---	---	---	---	
MGC72080	389538	broad.mit.edu	37	7	97527949	97527951	+	Intron	DEL	GCA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97527949_97527951delGCA	uc010lfp.1	-											Homo sapiens cDNA, FLJ99734.												0						TCTGGATTTGGCAGACTGATGGT	0.384													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	99176166	99176166	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99176166delT								ZNF655 (2092 upstream) : ZNF498 (38405 downstream)																							ttttttcttcttttttttcaa	0.194													4	2	---	---	---	---	
CYP3A5	1577	broad.mit.edu	37	7	99271917	99271918	+	Intron	DEL	GG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99271917_99271918delGG	uc003urq.2	-						ZNF498_uc003urn.2_Intron|CYP3A5_uc003urr.2_Intron|CYP3A5_uc011kiy.1_Intron|CYP3A5_uc003urs.2_Intron|CYP3A5_uc010lgg.2_Intron|CYP3A5_uc003urt.2_Intron	NM_000777	NP_000768	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A,						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)	tattttctatggagcatctttg	0.000													6	3	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101801142	101801142	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101801142delT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						TGCCTTCAGATTACTCAAGGA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101977386	101977386	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101977386delA								SH2B2 (15209 upstream) : SPDYE6 (8807 downstream)																							gcctATGGACAAAAAAAAAAA	0.154													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	102022901	102022902	+	Intron	INS	-	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102022901_102022902insA	uc003uzd.1	+						uc003uze.1_Intron|PRKRIP1_uc003uzf.2_Intron|PRKRIP1_uc003uzg.2_Intron|PRKRIP1_uc011kkq.1_Intron	NM_001003686	NP_001003686			SubName: Full=Putative uncharacterized protein PMS2L3;																		CTAGGACCACCAAAAAAAAAAC	0.307													3	3	---	---	---	---	
PUS7	54517	broad.mit.edu	37	7	105102889	105102889	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105102889delA	uc003vcx.2	-						PUS7_uc010lji.2_Intron|PUS7_uc003vcy.2_Intron|PUS7_uc003vcz.1_Intron	NM_019042	NP_061915	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 homolog						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1						aaaaaaaaccaaaaaaaaaac	0.000													5	3	---	---	---	---	
CDHR3	222256	broad.mit.edu	37	7	105674291	105674291	+	3'UTR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105674291delT	uc003vdl.3	+	19					CDHR3_uc003vdk.2_3'UTR|CDHR3_uc003vdm.3_3'UTR|CDHR3_uc011klt.1_3'UTR|CDHR3_uc003vdn.2_3'UTR	NM_152750	NP_689963	Q6ZTQ4	CDHR3_HUMAN	hypothetical protein LOC222256 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1						aagagtgggattgctggagca	0.000													4	2	---	---	---	---	
LAMB4	22798	broad.mit.edu	37	7	107690122	107690123	+	Intron	INS	-	GAGGT	GAGGT			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107690122_107690123insGAGGT	uc010ljo.1	-						LAMB4_uc003vey.2_Intron|LAMB4_uc010ljp.1_Intron	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor						cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						TTGAATTTGCAATTGATGGGGG	0.213													9	4	---	---	---	---	
C7orf68	29923	broad.mit.edu	37	7	128098269	128098269	+	3'UTR	DEL	T	-	-	rs5887381		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128098269delT	uc003vne.3	+	2					C7orf68_uc010lli.2_3'UTR|C7orf68_uc010llj.1_RNA	NM_013332	NP_037464	Q9Y5L2	HIG2_HUMAN	hypoxia-inducible protein 2						autocrine signaling|positive regulation of cell proliferation|response to stress	cell surface|extracellular space|integral to membrane|stored secretory granule	receptor binding				0						GTTGAAGAGGTTGTGTGGGTG	0.443													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	130009112	130009113	+	RNA	INS	-	TCA	TCA	rs144449169	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130009112_130009113insTCA	uc003vpv.1	-	2		c.204_205insTGA								Homo sapiens cDNA FLJ40591 fis, clone THYMU2010161.																		AGAAGAGCTTCTCATCATCATC	0.520													5	3	---	---	---	---	
NUP205	23165	broad.mit.edu	37	7	135330619	135330619	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135330619delA	uc003vsw.2	+						NUP205_uc003vsx.2_Intron	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						AGAATGGAGGAGGTCTGCTAT	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148747518	148747518	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148747518delA								PDIA4 (21736 upstream) : ZNF786 (19215 downstream)																							aaaaacaaagaaaaaaaaaaC	0.214													4	2	---	---	---	---	
SSPO	23145	broad.mit.edu	37	7	149501110	149501110	+	Frame_Shift_Del	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149501110delG	uc010lpk.2	+	57	8246	c.8246delG	c.(8245-8247)TGGfs	p.W2749fs		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	2749	TSP type-1 6.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCGGCAGCCTGGGGGGGTGCC	0.667													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150607934	150607934	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150607934delA								ABP1 (49555 upstream) : KCNH2 (34116 downstream)																							atttctgcagaaaaaagggca	0.045													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	156393606	156393607	+	IGR	INS	-	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156393606_156393607insA								C7orf4 (59811 upstream) : C7orf13 (37455 downstream)																							taCCATTTTTTAAAAAAAAAGA	0.069													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	18228677	18228677	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18228677delA								NAT1 (147480 upstream) : NAT2 (20078 downstream)																							AAGAAATAACAAAAAAAAATC	0.368													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	22433416	22433417	+	IGR	DEL	TG	-	-	rs71805929		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22433416_22433417delTG								SORBS3 (409 upstream) : PDLIM2 (3226 downstream)																							CCGAAGCCCTtgtgtgtgtgtg	0.431													4	2	---	---	---	---	
KIF13B	23303	broad.mit.edu	37	8	28931030	28931031	+	Intron	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28931030_28931031delCA	uc003xhh.3	-						KIF13B_uc011laz.1_Intron	NM_015254	NP_056069	Q9NQT8	KI13B_HUMAN	kinesin family member 13B						microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		TATTCCTATTCACAGTGACCGA	0.450													4	2	---	---	---	---	
IDO2	169355	broad.mit.edu	37	8	39857356	39857356	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39857356delC	uc010lwy.1	+						IDO2_uc003xno.1_Intron|IDO2_uc010lwz.1_Intron|IDO2_uc003xnp.1_Intron	NM_194294	NP_919270	Q6ZQW0	I23O2_HUMAN	indoleamine-pyrrole 2,3 dioxygenase-like 1						tryptophan catabolic process to kynurenine	cytosol	heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			ovary(2)	2						AGAAGTCTTGCCCAATAGCCA	0.348													4	2	---	---	---	---	
ANK1	286	broad.mit.edu	37	8	41725142	41725143	+	Intron	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41725142_41725143delCA	uc003xom.2	-							NM_001142446	NP_001135918	P16157	ANK1_HUMAN	ankyrin 1 isoform 9						axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GCACCCATGCCACACACACACC	0.550													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	75288902	75288906	+	IGR	DEL	TTATT	-	-	rs59272628		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75288902_75288906delTTATT								GDAP1 (9569 upstream) : MIR2052 (329022 downstream)																							tttcattatcttattttaagactta	0.000													5	3	---	---	---	---	
PMP2	5375	broad.mit.edu	37	8	82357449	82357449	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82357449delT	uc003ycb.1	-						PMP2_uc010lzv.1_Intron	NM_002677	NP_002668	P02689	MYP2_HUMAN	peripheral myelin protein 2							cytoplasm	cholesterol binding|fatty acid binding|transporter activity				0			Epithelial(68;0.186)			GCAGATTTTCttttttttttt	0.194													3	3	---	---	---	---	
EBAG9	9166	broad.mit.edu	37	8	110565870	110565870	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110565870delA	uc003ynf.2	+						EBAG9_uc010mcn.1_Intron|EBAG9_uc003yng.2_Intron	NM_198120	NP_936056	O00559	RCAS1_HUMAN	estrogen receptor binding site associated						apoptosis|regulation of cell growth	focal adhesion|Golgi membrane|integral to membrane|soluble fraction	apoptotic protease activator activity				0			OV - Ovarian serous cystadenocarcinoma(57;1.39e-14)			GTCCTAAGCCAAAAAGCAGTT	0.269													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	122609072	122609072	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122609072delT								SNTB1 (784763 upstream) : HAS2 (16199 downstream)																							tgaaatttccttaaaaatcca	0.010													4	2	---	---	---	---	
DERL1	79139	broad.mit.edu	37	8	124034724	124034725	+	Intron	INS	-	TGAA	TGAA	rs138295786	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124034724_124034725insTGAA	uc003ypl.2	-						DERL1_uc003ypm.2_Intron|DERL1_uc011lif.1_Intron|DERL1_uc003ypn.2_Intron	NM_024295	NP_077271	Q9BUN8	DERL1_HUMAN	Der1-like domain family, member 1 isoform a						endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|intracellular transport of viral proteins in host cell|retrograde protein transport, ER to cytosol	integral to endoplasmic reticulum membrane	MHC class I protein binding|receptor activity				0	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			TACAGAGGGAGTGAAGAAACAA	0.495											OREG0018957	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	4	---	---	---	---	
ZFAT	57623	broad.mit.edu	37	8	135723226	135723226	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135723226delA	uc003yup.2	-						ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			caaggtacctaagcggcacag	0.050													4	2	---	---	---	---	
PTK2	5747	broad.mit.edu	37	8	141756641	141756641	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141756641delG	uc003yvu.2	-						PTK2_uc003yvo.2_Intron|PTK2_uc011ljq.1_Intron|PTK2_uc003yvp.2_Intron|PTK2_uc003yvq.2_Intron|PTK2_uc003yvr.2_Intron|PTK2_uc003yvs.2_Intron|PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560	Q05397	FAK1_HUMAN	PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			GTACTTGGCTGGGGAAGATAT	0.398													4	2	---	---	---	---	
PTP4A3	11156	broad.mit.edu	37	8	142426548	142426550	+	Intron	DEL	AGA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142426548_142426550delAGA	uc010mes.2	+									O75365	TP4A3_HUMAN	Homo sapiens cDNA, FLJ18299.							early endosome|plasma membrane	identical protein binding|prenylated protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0	all_cancers(97;2.55e-15)|all_epithelial(106;1.39e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0474)			TGGTATCCTTAGAAAGTGGCTGA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142648296	142648297	+	IGR	DEL	TC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142648296_142648297delTC								FLJ43860 (130966 upstream) : MIR1302-7 (219306 downstream)																							TTTGTGTCTTTCAAGTCTGTTT	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	145930158	145930158	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145930158delC								ARHGAP39 (18964 upstream) : ZNF251 (16137 downstream)																							ACATGCCTCGCCCCCACAAGG	0.592													4	2	---	---	---	---	
UBE2R2	54926	broad.mit.edu	37	9	33911753	33911753	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33911753delT	uc003ztm.2	+							NM_017811	NP_060281	Q712K3	UB2R2_HUMAN	ubiquitin-conjugating enzyme UBC3B						protein K48-linked ubiquitination|protein monoubiquitination		ATP binding|ubiquitin-protein ligase activity				0			LUSC - Lung squamous cell carcinoma(29;0.0176)	GBM - Glioblastoma multiforme(74;0.188)		CTGaaaaaaatttttttttat	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69430348	69430348	+	Intron	DEL	T	-	-	rs148059994		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69430348delT	uc010mnx.1	+							NM_001098806	NP_001092276			coiled-coil domain containing 29																		ATTTGAATCATTTTTAGCAGT	0.284													4	2	---	---	---	---	
RASEF	158158	broad.mit.edu	37	9	85622155	85622156	+	Intron	INS	-	CC	CC			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85622155_85622156insCC	uc004amo.1	-							NM_152573	NP_689786	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing						protein transport|small GTPase mediated signal transduction	perinuclear region of cytoplasm	calcium ion binding|GTP binding			upper_aerodigestive_tract(1)|lung(1)|breast(1)	3						TATTCCCACATCTGAATAATTT	0.411													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	87020216	87020216	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87020216delC								SLC28A3 (36803 upstream) : NTRK2 (263250 downstream)																							GTTCAAGCATCAGAGAGGACT	0.438													4	2	---	---	---	---	
DAPK1	1612	broad.mit.edu	37	9	90209623	90209623	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90209623delC	uc004apc.2	+						DAPK1_uc004ape.2_Intron|DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_Intron|DAPK1_uc011lth.1_Intron	NM_004938	NP_004929	P53355	DAPK1_HUMAN	death-associated protein kinase 1						apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2						AAATACCCAGCCCCACTGCCT	0.493									Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				4	2	---	---	---	---	
HIATL1	84641	broad.mit.edu	37	9	97206570	97206571	+	Intron	DEL	TT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97206570_97206571delTT	uc004aur.2	+						HIATL1_uc011luh.1_Intron	NM_032558	NP_115947	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1						transmembrane transport	integral to membrane|plasma membrane	protein binding|transporter activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)				GTGGGTGTGCTTAGCTGGCTCT	0.470													4	2	---	---	---	---	
C9orf5	23731	broad.mit.edu	37	9	111813112	111813112	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111813112delA	uc004bdt.3	-						C9orf5_uc004bds.3_Intron|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)		AATGAAAATTAAAAAAAAAAA	0.269													6	4	---	---	---	---	
TXN	7295	broad.mit.edu	37	9	113007320	113007322	+	Intron	DEL	GAA	-	-	rs144802558		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									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													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	116075600	116075601	+	RNA	INS	-	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116075600_116075601insC	uc004bhb.2	-	2		c.2116_2117insG								Homo sapiens cDNA FLJ26358 fis, clone HRT05087.																		TGGCAGCCTGTCCCCCTTCCCT	0.485													4	2	---	---	---	---	
RGS3	5998	broad.mit.edu	37	9	116334545	116334545	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116334545delG	uc004bhq.2	+						RGS3_uc004bhs.2_Intron|RGS3_uc004bht.2_Intron|RGS3_uc010muy.2_Intron|RGS3_uc004bhv.2_Intron|RGS3_uc010muz.1_Intron|RGS3_uc004bhw.2_Intron|RGS3_uc011lxh.1_Intron	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6						inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3						AGTTGGTGCAGGGCCAAGGGA	0.443													4	2	---	---	---	---	
RABEPK	10244	broad.mit.edu	37	9	127968225	127968226	+	Intron	INS	-	TC	TC	rs35136218		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127968225_127968226insTC	uc004bpi.2	+						RABEPK_uc004bph.1_Intron|RABEPK_uc004bpj.2_Intron|RABEPK_uc004bpk.2_Intron|RABEPK_uc004bpl.1_Intron|RABEPK_uc004bpm.2_Intron	NM_005833	NP_005824	Q7Z6M1	RABEK_HUMAN	Rab9 effector protein with kelch motifs						receptor-mediated endocytosis|vesicle docking involved in exocytosis	endosome membrane|plasma membrane				ovary(1)	1						ggaaaagagaattgagaatgac	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132161820	132161821	+	IGR	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132161820_132161821delCA								C9orf106 (76938 upstream) : C9orf50 (212685 downstream)																							cacacacgtgcacacacacaca	0.401													4	2	---	---	---	---	
NCS1	23413	broad.mit.edu	37	9	132985664	132985665	+	Intron	DEL	TT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132985664_132985665delTT	uc004bzi.2	+						NCS1_uc010myz.1_Intron	NM_014286	NP_055101	P62166	NCS1_HUMAN	frequenin homolog isoform 1						negative regulation of calcium ion transport via voltage-gated calcium channel activity|regulation of neuron projection development	cell junction|Golgi cisterna membrane|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|protein binding				0						gtccttagccttttttttttgt	0.213													6	3	---	---	---	---	
BAT2L1	84726	broad.mit.edu	37	9	134270344	134270344	+	Intron	DEL	G	-	-	rs113188231		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134270344delG	uc004cam.1	+									Q5JSZ5	PRC2B_HUMAN	SubName: Full=BAT2L protein;								protein binding				0						CCTGCCAGATGGGGTTTTTTT	0.473													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137197834	137197834	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137197834delA								RNU6ATAC (168148 upstream) : RXRA (11110 downstream)																							gatgatgttgatggtgttggt	0.000													4	2	---	---	---	---	
PMPCA	23203	broad.mit.edu	37	9	139310963	139310964	+	Intron	INS	-	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139310963_139310964insT	uc004chl.2	+						PMPCA_uc011mdy.1_Frame_Shift_Ins_p.T251fs|PMPCA_uc010nbk.2_RNA|PMPCA_uc010nbl.2_Intron|PMPCA_uc011mdz.1_Intron|PMPCA_uc004chm.1_5'UTR|PMPCA_uc004chn.1_5'Flank	NM_015160	NP_055975	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha						proteolysis	mitochondrial inner membrane|mitochondrial matrix	metalloendopeptidase activity|zinc ion binding				0		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)		TATACAGAACatttttttgttt	0.282													4	2	---	---	---	---	
LOC254312	254312	broad.mit.edu	37	10	10978618	10978618	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10978618delC	uc009xiu.2	-						LOC254312_uc001ikh.3_Intron|LOC254312_uc009xiv.2_Intron	NR_015413				Homo sapiens cDNA clone IMAGE:4838916.												0						TAACTTGTATCCCCCATCCCT	0.458													4	2	---	---	---	---	
ECHDC3	79746	broad.mit.edu	37	10	11797323	11797324	+	Intron	DEL	AA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11797323_11797324delAA	uc001ikw.3	+						ECHDC3_uc009xix.2_Intron	NM_024693	NP_078969	Q96DC8	ECHD3_HUMAN	enoyl Coenzyme A hydratase domain containing 3							mitochondrion	catalytic activity				0						agactctgtcaaaaaaaaaaaa	0.218													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42391495	42391495	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42391495delG								None (None upstream) : LOC441666 (435820 downstream)																							gaatggaatcgaagagaatca	0.000													4	2	---	---	---	---	
FRMPD2	143162	broad.mit.edu	37	10	49382781	49382781	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49382781delA	uc001jgi.2	-						FRMPD2_uc001jgh.2_Intron|FRMPD2_uc001jgj.2_Intron|FRMPD2L1_uc001jgf.2_Intron|FRMPD2_uc001jgg.2_Intron|FRMPD2_uc001jgk.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)		AATGGAAGAGAAAAAAAAAAC	0.423													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	50220651	50220651	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50220651delG								WDFY4 (29651 upstream) : C10orf72 (1682 downstream)																							ATTCAGTATTGGGTGTATACT	0.577													4	2	---	---	---	---	
PARG	8505	broad.mit.edu	37	10	51485576	51485576	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51485576delC	uc001jih.2	-						uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|AGAP7_uc001jio.2_Intron	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		ATTGTGCTTGCCCTCTGGATT	0.358													9	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	61338201	61338201	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61338201delA								FAM13C (215540 upstream) : SLC16A9 (72321 downstream)																							CTCCTCTCTTAAAAAAATACC	0.348													4	2	---	---	---	---	
KCNMA1	3778	broad.mit.edu	37	10	78669545	78669545	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78669545delA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxk.1_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxl.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)	aggaatttataatcaaacatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	82881881	82881881	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82881881delC								SH2D4B (475565 upstream) : NRG3 (753189 downstream)																							GTGAAGAGTGCAATGCTTGGG	0.368													4	2	---	---	---	---	
OPN4	94233	broad.mit.edu	37	10	88423774	88423777	+	Intron	DEL	TGTG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88423774_88423777delTGTG	uc001kdq.2	+						LDB3_uc010qml.1_5'Flank|OPN4_uc001kdp.2_Intron|OPN4_uc010qmk.1_Intron|OPN4_uc009xsx.1_3'UTR	NM_033282	NP_150598	Q9UHM6	OPN4_HUMAN	opsin 4 isoform 1						phototransduction|protein-chromophore linkage|regulation of circadian rhythm|rhythmic process|visual perception	integral to membrane|plasma membrane	11-cis retinal binding|G-protein coupled photoreceptor activity			ovary(1)	1						GGTCTGCACATGTGTGTGTGTGTG	0.529													4	2	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95070677	95070677	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95070677delG	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						TGGTCTCCTTGTCTCCCCACA	0.423													4	2	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95070679	95070679	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95070679delC	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						GTCTCCTTGTCTCCCCACACA	0.428													4	2	---	---	---	---	
SLIT1	6585	broad.mit.edu	37	10	98832863	98832863	+	Intron	DEL	T	-	-	rs76361641		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98832863delT	uc001kmw.2	-						SLIT1_uc009xvh.1_Intron	NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor						axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		AGCTATTCTCTTTTTTTTTCT	0.453											OREG0020407	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
CRTAC1	55118	broad.mit.edu	37	10	99685551	99685552	+	Intron	DEL	GT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99685551_99685552delGT	uc001kou.1	-						CRTAC1_uc001kov.2_Intron|CRTAC1_uc001kot.1_Intron	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		GAACAGTCAAGTGTGTGTGTGG	0.431													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	100104301	100104301	+	IGR	DEL	C	-	-	rs111572432		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100104301delC								LOXL4 (76294 upstream) : PYROXD2 (39022 downstream)																							AACACTGCCTCCTCCTCCTCC	0.527													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	109074361	109074361	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109074361delA								SORCS1 (150069 upstream) : None (None downstream)																							CTGAAATGCTACAGTcagcgt	0.204													4	2	---	---	---	---	
NRAP	4892	broad.mit.edu	37	10	115391083	115391083	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115391083delA	uc001laj.2	-						NRAP_uc009xyb.2_5'Flank|NRAP_uc001lak.2_Intron|NRAP_uc001lal.3_Intron	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TTATCTATTTAAAAAAAAATA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	119686735	119686735	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119686735delT								EMX2 (377679 upstream) : RAB11FIP2 (77694 downstream)																							tcacaatgccttttcctcttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122935360	122935360	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122935360delC								WDR11 (266325 upstream) : FGFR2 (302485 downstream)																							ACTGTCACTTCCCACCTCCCA	0.532													4	2	---	---	---	---	
FGFR2	2263	broad.mit.edu	37	10	123309140	123309141	+	Intron	DEL	CT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123309140_123309141delCT	uc010qtk.1	-						FGFR2_uc010qtg.1_Intron|FGFR2_uc010qth.1_Intron|FGFR2_uc010qti.1_Intron|FGFR2_uc010qtj.1_Intron|FGFR2_uc010qtl.1_Intron|FGFR2_uc010qtm.1_Intron|FGFR2_uc001lfl.3_Intron|FGFR2_uc001lfm.2_Intron|FGFR2_uc001lfn.3_Intron|FGFR2_uc010qtn.1_Intron|FGFR2_uc010qto.1_Intron|FGFR2_uc001lfo.1_Intron|FGFR2_uc010qtp.1_Intron|FGFR2_uc010qtq.1_Intron	NM_000141	NP_000132	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2 isoform 1						angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)	tgcgatcctgctctctctctct	0.000		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				4	2	---	---	---	---	
GPR123	84435	broad.mit.edu	37	10	134932571	134932572	+	Intron	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134932571_134932572delCA	uc001llx.3	+						GPR123_uc001llw.2_Intron	NM_001083909	NP_001077378	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123							integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		ttgcacactgcacacacacacg	0.144													4	2	---	---	---	---	
LOC619207	619207	broad.mit.edu	37	10	135275436	135275436	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135275436delC	uc001lnh.1	+						LOC619207_uc001lng.2_Intron|LOC619207_uc001lni.1_5'Flank					Homo sapiens cDNA FLJ45320 fis, clone BRHIP3005944, weakly  similar to Antigen WC1.1 precursor.												0						ATTCTGGGGACCCCATCTGAG	0.338													4	2	---	---	---	---	
SCGB1C1	147199	broad.mit.edu	37	11	190870	190871	+	5'Flank	INS	-	CTT	CTT	rs147540508		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:190870_190871insCTT	uc001loa.1	+							NM_145651	NP_663626	Q8TD33	SG1C1_HUMAN	secretoglobin, family 1C, member 1 precursor							extracellular region	binding			skin(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		tcccctttggccttatcagcat	0.000													3	3	---	---	---	---	
ODF3	113746	broad.mit.edu	37	11	194728	194728	+	5'Flank	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:194728delG	uc001lob.2	+						ODF3_uc010qvk.1_5'Flank|ODF3_uc001loc.2_5'Flank	NM_053280	NP_444510	Q96PU9	ODF3A_HUMAN	outer dense fiber of sperm tails 3						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm				ovary(1)	1		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		ACACACAAATGGGGACATCAG	0.577													4	2	---	---	---	---	
PNPLA2	57104	broad.mit.edu	37	11	819800	819801	+	Frame_Shift_Ins	INS	-	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:819800_819801insC	uc001lrt.2	+	2	284_285	c.82_83insC	c.(82-84)TGCfs	p.C28fs		NM_020376	NP_065109	Q96AD5	PLPL2_HUMAN	patatin-like phospholipase domain containing 2	28	Patatin.|Helical; Signal-anchor for type II membrane protein; (Potential).				negative regulation of sequestering of triglyceride|positive regulation of triglyceride catabolic process	integral to membrane|lipid particle|plasma membrane	triglyceride lipase activity				0		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.63e-25)|Epithelial(43;1.28e-24)|OV - Ovarian serous cystadenocarcinoma(40;7.09e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGTGGCCTCCTGCCTCCGCGAG	0.639													4	2	---	---	---	---	
PARVA	55742	broad.mit.edu	37	11	12499892	12499893	+	Intron	INS	-	TG	TG			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12499892_12499893insTG	uc001mki.2	+						PARVA_uc001mkh.2_3'UTR|PARVA_uc010rck.1_Intron	NM_018222	NP_060692	Q9NVD7	PARVA_HUMAN	parvin, alpha						cell adhesion|cell junction assembly|cilium morphogenesis	actin cytoskeleton|cytosol|focal adhesion	actin binding			breast(3)	3				Epithelial(150;0.00624)		CTTCAGATGCATGTGTGTGTGT	0.485													4	2	---	---	---	---	
SERGEF	26297	broad.mit.edu	37	11	18022306	18022308	+	Intron	DEL	CAC	-	-	rs35804255		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18022306_18022308delCAC	uc001mnm.2	-						SERGEF_uc009yhd.2_Intron|SERGEF_uc001mnn.2_Intron|SERGEF_uc010rcz.1_Intron|SERGEF_uc001mno.1_Intron	NM_012139	NP_036271	Q9UGK8	SRGEF_HUMAN	deafness locus associated putative guanine						negative regulation of protein secretion|signal transduction	cytoplasm|nucleus	protein binding|Ran guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1						AATACCATATCACAATACCATAT	0.197													5	5	---	---	---	---	
METT5D1	196074	broad.mit.edu	37	11	28299413	28299414	+	Intron	DEL	GT	-	-	rs139787496	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28299413_28299414delGT	uc001msh.2	+						METT5D1_uc001msg.2_Intron|METT5D1_uc001mse.2_Intron	NM_001113528	NP_001107000	A6NJ78	MET15_HUMAN	methyltransferase 5 domain containing 1 isoform								methyltransferase activity				0						tggaggttgagtggaaagataa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	33400473	33400473	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33400473delG								HIPK3 (24534 upstream) : C11orf41 (163404 downstream)																							AGGGGTTTGTGGGAAGAAGTG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	55890920	55890920	+	IGR	DEL	C	-	-	rs145330583		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55890920delC								OR8H3 (133 upstream) : OR8J3 (13329 downstream)																							CTTTGCTTGACTAAACATGAT	0.289													4	4	---	---	---	---	
STX3	6809	broad.mit.edu	37	11	59548691	59548691	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59548691delA	uc001nog.2	+						STX3_uc010rkx.1_Intron|STX3_uc010rky.1_Intron	NM_004177	NP_004168	Q13277	STX3_HUMAN	syntaxin 3						cellular response to oxidative stress|intracellular protein transport|neuron projection development|neurotransmitter transport	apical plasma membrane|azurophil granule|cell-cell junction|growth cone|integral to membrane|plasma membrane enriched fraction|SNARE complex|specific granule	arachidonic acid binding|SNAP receptor activity			ovary(2)	2						CACAGTAATGAAAAAAAAAAG	0.294													6	3	---	---	---	---	
MS4A12	54860	broad.mit.edu	37	11	60258255	60258255	+	5'Flank	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60258255delT	uc001npr.2	+						MS4A12_uc009ynb.2_5'Flank	NM_017716	NP_060186	Q9NXJ0	M4A12_HUMAN	membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity				0						ttttctctcctttttttatta	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	64182965	64182965	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64182965delG								RPS6KA4 (43279 upstream) : SLC22A11 (140133 downstream)																							ccagctctgaggggagtgggg	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	67354291	67354291	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67354291delA								GSTP1 (168 upstream) : NDUFV1 (20032 downstream)																							GAAGAGGAAGAAAAAAAAAGA	0.453													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69796910	69796910	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69796910delA								FGF3 (162718 upstream) : ANO1 (127498 downstream)																							TCACCACAATAAAAAAAAGTG	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71614686	71614686	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71614686delT								DEFB108B (66079 upstream) : RNF121 (25082 downstream)																							GTTGTCCTTGttttttttttc	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	81541831	81541831	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81541831delC								None (None upstream) : FAM181B (901222 downstream)																							aactggtctgcccagcccact	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	102429751	102429751	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102429751delA								MMP7 (28273 upstream) : MMP20 (17816 downstream)																							agcagcacctaaaaatcctgt	0.104													4	2	---	---	---	---	
PDGFD	80310	broad.mit.edu	37	11	103870637	103870638	+	Intron	INS	-	TGA	TGA			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103870637_103870638insTGA	uc001phq.2	-						PDGFD_uc001php.2_Intron	NM_025208	NP_079484	Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D isoform 1						positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		TCTGTTAGGGTCTTTAGGCTTT	0.416													10	5	---	---	---	---	
PDGFD	80310	broad.mit.edu	37	11	103870638	103870639	+	Intron	INS	-	A	A	rs113541111		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103870638_103870639insA	uc001phq.2	-						PDGFD_uc001php.2_Intron	NM_025208	NP_079484	Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D isoform 1						positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		CTGTTAGGGTCTTTAGGCTTTT	0.411													9	6	---	---	---	---	
DDX10	1662	broad.mit.edu	37	11	108544462	108544463	+	Intron	INS	-	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108544462_108544463insT	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		AGTTTCCAGCATCCTCTGAATA	0.252			T	NUP98	AML*								16	7	---	---	---	---	
TTC12	54970	broad.mit.edu	37	11	113230432	113230433	+	Intron	INS	-	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113230432_113230433insC	uc001pnu.2	+						TTC12_uc001pnv.2_Intron|TTC12_uc001pnw.2_Intron|TTC12_uc001pnx.2_Intron	NM_017868	NP_060338	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12								binding			pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		agtatgaggtgctgcatttaca	0.114													6	3	---	---	---	---	
DSCAML1	57453	broad.mit.edu	37	11	117520624	117520624	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117520624delC	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		ACCATGGCCTCCCCAGGAGTT	0.602													4	2	---	---	---	---	
DSCAML1	57453	broad.mit.edu	37	11	117578900	117578901	+	Intron	DEL	CG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117578900_117578901delCG	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		caaggagactcgggctgaaggg	0.213													4	2	---	---	---	---	
TMPRSS13	84000	broad.mit.edu	37	11	117795508	117795508	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117795508delC	uc001prs.1	-						TMPRSS13_uc001pru.1_Intron	NM_001077263	NP_001070731	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13						proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			pancreas(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		CCCAGAGAAACCCCACAAATA	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124144175	124144175	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124144175delT								OR8G2 (47865 upstream) : OR8D1 (35562 downstream)																							CCATCATTCCTTTTTTTTTTT	0.413													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	5041547	5041550	+	IGR	DEL	AGAC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5041547_5041550delAGAC								KCNA1 (14127 upstream) : KCNA5 (111535 downstream)																							TGGTGCAGTGAGACAGACAGACAT	0.471													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	13073411	13073412	+	IGR	INS	-	TTTG	TTTG	rs140093581	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13073411_13073412insTTTG								MIR614 (4559 upstream) : GPRC5D (20299 downstream)																							gaagtgctttatttatttgttt	0.119													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	19959499	19959500	+	IGR	DEL	TG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19959499_19959500delTG								AEBP2 (284326 upstream) : PDE3A (562697 downstream)																							TTTGGAAATATGTAATCCAGAA	0.450													4	2	---	---	---	---	
TM7SF3	51768	broad.mit.edu	37	12	27133722	27133722	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27133722delA	uc010sjl.1	-							NM_016551	NP_057635	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3 precursor							integral to membrane|plasma membrane				upper_aerodigestive_tract(2)	2	Colorectal(261;0.0847)					CATTCAGAAGAAAAAAAAAAT	0.303													5	3	---	---	---	---	
SLC4A8	9498	broad.mit.edu	37	12	51843220	51843220	+	Intron	DEL	A	-	-	rs113172935		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51843220delA	uc001rys.1	+						SLC4A8_uc010sni.1_Intron|SLC4A8_uc001rym.2_Intron|SLC4A8_uc001ryn.2_Intron|SLC4A8_uc001ryo.2_Intron|SLC4A8_uc001ryp.1_Intron|SLC4A8_uc010snj.1_Intron|SLC4A8_uc001ryq.3_Intron|SLC4A8_uc001ryr.2_Intron|SLC4A8_uc010snk.1_Intron	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate						bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)		aaaagaaaggaaaaaaaaaaa	0.204													4	2	---	---	---	---	
KRT72	140807	broad.mit.edu	37	12	52995273	52995274	+	5'UTR	INS	-	A	A	rs150944118	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52995273_52995274insA	uc001sar.2	-	1					KRT72_uc001saq.2_5'UTR|KRT72_uc010sns.1_5'UTR|KRT72_uc010snt.1_5'UTR	NM_001146225	NP_001139697	Q14CN4	K2C72_HUMAN	keratin 72 isoform 1							keratin filament	structural molecule activity			ovary(5)|pancreas(1)	6				BRCA - Breast invasive adenocarcinoma(357;0.195)		GCGGGAGGCAGAAGGGGCGCAA	0.639													3	4	---	---	---	---	
KRT8	3856	broad.mit.edu	37	12	53291008	53291008	+	3'UTR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53291008delA	uc001sbd.2	-	8					KRT8_uc009zmj.2_3'UTR|KRT8_uc009zmk.1_3'UTR|KRT8_uc009zml.1_3'UTR|KRT8_uc009zmm.1_3'UTR	NM_002273	NP_002264	P05787	K2C8_HUMAN	keratin 8						cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	ATTTTGGACCAAAAAAAAAAA	0.532													2	5	---	---	---	---	
SMARCC2	6601	broad.mit.edu	37	12	56565988	56565989	+	Intron	INS	-	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56565988_56565989insA	uc001skb.2	-						SMARCC2_uc001skd.2_Intron|SMARCC2_uc001ska.2_Intron|SMARCC2_uc001skc.2_Intron|SMARCC2_uc010sqf.1_Intron	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)			acttagcctcctgagtagctgg	0.119													4	2	---	---	---	---	
RBMS2	5939	broad.mit.edu	37	12	56980357	56980359	+	Intron	DEL	TAA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56980357_56980359delTAA	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						ttttttttactaatttttttagt	0.025													6	4	---	---	---	---	
OS9	10956	broad.mit.edu	37	12	58089374	58089374	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58089374delT	uc001spj.2	+						OS9_uc010srx.1_Intron|OS9_uc001spk.2_Intron|OS9_uc001spl.2_Intron|OS9_uc001spm.2_Intron|OS9_uc001spn.2_Intron|OS9_uc010sry.1_Intron|OS9_uc010srz.1_Intron	NM_006812	NP_006803	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum						ER-associated protein catabolic process|protein retention in ER lumen|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to endoplasmic reticulum stress	endoplasmic reticulum lumen|Hrd1p ubiquitin ligase complex	glycoprotein binding|protein binding|sugar binding			ovary(1)	1	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			GAGATATCTCTCCAAGTCACA	0.388													4	2	---	---	---	---	
TRHDE	29953	broad.mit.edu	37	12	72763270	72763270	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72763270delA	uc001sxa.2	+							NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme						cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3						GTGTCAGGACAAAAAAAACCT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80648149	80648153	+	IGR	DEL	TTTAT	-	-	rs67189718		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80648149_80648153delTTTAT								PPP1R12A (318914 upstream) : PTPRQ (189973 downstream)																							attgattttatttattttattttat	0.249													5	4	---	---	---	---	
CEP290	80184	broad.mit.edu	37	12	88473719	88473722	+	Intron	DEL	CTTC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88473719_88473722delCTTC	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						TTTTTCCTAACTTCATATAGATAA	0.250													4	6	---	---	---	---	
CEP290	80184	broad.mit.edu	37	12	88482616	88482618	+	Intron	DEL	TTT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88482616_88482618delTTT	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						tacaaaaaaatttaaaaatttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	107633916	107633917	+	IGR	DEL	CC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107633916_107633917delCC								CRY1 (146318 upstream) : BTBD11 (78280 downstream)																							TCTCCCTGTTCCCAGAGGTCTG	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119745657	119745657	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119745657delA								LOC144742 (4472 upstream) : CCDC60 (26860 downstream)																							GGGTGACTCTAAAAAAAAAAA	0.393													9	5	---	---	---	---	
RNF10	9921	broad.mit.edu	37	12	120990203	120990203	+	Intron	DEL	A	-	-	rs112757664		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120990203delA	uc001typ.3	+						RNF10_uc010szk.1_Intron|RNF10_uc001tyq.3_Intron	NM_014868	NP_055683	Q8N5U6	RNF10_HUMAN	ring finger protein 10						negative regulation of Schwann cell proliferation|positive regulation of myelination|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription regulatory region DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					actccgtctcaaaaaaaaaaG	0.164													11	5	---	---	---	---	
P2RX7	5027	broad.mit.edu	37	12	121582627	121582627	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121582627delG	uc001tzm.2	+						P2RX7_uc001tzn.2_Intron|P2RX7_uc001tzo.2_Intron|P2RX7_uc001tzp.2_Intron|P2RX7_uc001tzq.2_Intron	NM_002562	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X7							integral to membrane	ATP binding|ion channel activity|receptor activity			large_intestine(2)|lung(1)|breast(1)|skin(1)	5	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					acgggtgagtggacaagaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132342612	132342612	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132342612delG								MMP17 (6296 upstream) : ULK1 (36667 downstream)																							TGGGTGCTCTGGGTCATGCTG	0.607													4	2	---	---	---	---	
ZMYM5	9205	broad.mit.edu	37	13	20425258	20425258	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20425258delA	uc010tcn.1	-						ZMYM5_uc001umm.1_Intron|ZMYM5_uc001umn.2_Intron|ZMYM5_uc001umo.2_Intron	NM_001142684	NP_001136156	Q9UJ78	ZMYM5_HUMAN	zinc finger protein 237 isoform 3							nucleus	zinc ion binding				0		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		ctcaggcaggaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	20686600	20686601	+	IGR	INS	-	TTT	TTT	rs36161692		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20686600_20686601insTTT								ZMYM2 (25662 upstream) : GJA3 (25794 downstream)																							gAAATTCTTGGTGgttgttgtt	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	25217048	25217048	+	IGR	DEL	A	-	-	rs35201734		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25217048delA								LOC374491 (45238 upstream) : ATP12A (37647 downstream)																							atttggtgggaagatacctca	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	28371329	28371329	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28371329delC								GSX1 (3240 upstream) : PDX1 (122839 downstream)																							CGCAGATCCACAGCTGTGAGC	0.632													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	50469789	50469789	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50469789delT								LOC220429 (2273 upstream) : C13orf1 (17053 downstream)																							CTCCTATTTGTTTTCTTGTCT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	55408486	55408487	+	IGR	INS	-	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55408486_55408487insT								MIR1297 (522303 upstream) : None (None downstream)																							Acagtcgtgcattgattaacaa	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75800292	75800292	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75800292delC								None (None upstream) : LOC647288 (11598 downstream)																							taaacatttaccagcccacta	0.154													4	2	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110834671	110834671	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110834671delG	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			TAAGAAGCCTGGGAGCCTGGA	0.557													4	2	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110883398	110883399	+	Intron	DEL	GA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110883398_110883399delGA	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CAAGAACCTGGAGACAGGGTGC	0.554													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	21067616	21067616	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21067616delT	uc001vxu.1	+											Homo sapiens cDNA FLJ35891 fis, clone TESTI2009217.																		tgcactccgcttttttagttc	0.010													4	2	---	---	---	---	
SALL2	6297	broad.mit.edu	37	14	22003097	22003097	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22003097delT	uc001wbe.2	-						SALL2_uc010tma.1_Intron|SALL2_uc001wbg.1_Intron	NM_005407	NP_005398	Q9Y467	SALL2_HUMAN	sal-like 2								DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|large_intestine(1)	3	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		CAAGTTTTTGTTTTTTAACAG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	24851074	24851075	+	IGR	DEL	CT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24851074_24851075delCT								NFATC4 (2266 upstream) : NYNRIN (16917 downstream)																							CCTGAGGGCACTAGTTAGGCCA	0.584													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	59994107	59994108	+	IGR	INS	-	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59994107_59994108insG								JKAMP (22027 upstream) : RTN1 (68586 downstream)																							tttagctcaattttctttaaaa	0.000													4	3	---	---	---	---	
TMEM63C	57156	broad.mit.edu	37	14	77709045	77709045	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77709045delT	uc001xtf.2	+						TMEM63C_uc010asq.1_Intron	NM_020431	NP_065164	Q9P1W3	TM63C_HUMAN	transmembrane protein 63C							integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		CTCAGGTCCATTTTTTTTTGG	0.517													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	90692876	90692876	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90692876delA								KCNK13 (40681 upstream) : PSMC1 (30018 downstream)																							GGATGAGAGGAAAGTCTTAAC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	103721001	103721001	+	IGR	DEL	C	-	-	rs8015184	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103721001delC								TNFAIP2 (117225 upstream) : EIF5 (79492 downstream)																							cagctggtggcgggtgcgtga	0.184													4	2	---	---	---	---	
ATP10A	57194	broad.mit.edu	37	15	25956661	25956661	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25956661delG	uc010ayu.2	-							NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GGAAACTGCTGGGGTCTCTGA	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26142018	26142018	+	IGR	DEL	A	-	-	rs34366224		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26142018delA								ATP10A (31701 upstream) : GABRB3 (646677 downstream)																							attgcagtggaaaaaaaaaaa	0.184													3	3	---	---	---	---	
BAHD1	22893	broad.mit.edu	37	15	40737162	40737163	+	Intron	DEL	AA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40737162_40737163delAA	uc001zlu.2	+						BAHD1_uc001zlt.2_Intron|BAHD1_uc010bbp.1_Intron	NM_014952	NP_055767	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1						heterochromatin formation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin silencing complex|chromosome	chromatin binding|DNA binding|protein binding				0		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		CCCGTCAATTAAAAAAAAAATC	0.500													4	2	---	---	---	---	
C15orf57	90416	broad.mit.edu	37	15	40825442	40825442	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40825442delG	uc001zly.2	-						uc001zlx.1_Intron|MRPL42P5_uc010bbq.1_Intron|MRPL42P5_uc001zlz.1_5'Flank	NM_052849	NP_443081	Q9BV29	CO057_HUMAN	coiled-coil domain containing 32 isoform a											ovary(1)	1						TGTCAGGGTCGGGGGCAGATG	0.199													4	2	---	---	---	---	
INO80	54617	broad.mit.edu	37	15	41291963	41291963	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41291963delC	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						GGCAGGGTATCTCACAGGCCC	0.343													4	2	---	---	---	---	
RTF1	23168	broad.mit.edu	37	15	41773181	41773182	+	3'UTR	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41773181_41773182delCA	uc001zny.2	+	18						NM_015138	NP_055953	Q92541	RTF1_HUMAN	Paf1/RNA polymerase II complex component						histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		CCGCGCAGTTCATTGGCCACTC	0.550													4	2	---	---	---	---	
SPPL2A	84888	broad.mit.edu	37	15	51029111	51029112	+	Intron	INS	-	T	T	rs66555012		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51029111_51029112insT	uc001zyv.2	-							NM_032802	NP_116191	Q8TCT8	PSL2_HUMAN	signal peptide peptidase-like 2A							integral to membrane	aspartic-type endopeptidase activity				0				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		GAGGttttttgtttttttttct	0.144													6	3	---	---	---	---	
MYO5A	4644	broad.mit.edu	37	15	52720402	52720403	+	Intron	INS	-	C	C			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52720402_52720403insC	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010uge.1_Intron	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		ATTTTTAGCAAAATTATGTAAG	0.337													5	3	---	---	---	---	
MYO5A	4644	broad.mit.edu	37	15	52787593	52787593	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52787593delG	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010uge.1_Intron	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		cagaggctgagggccaggaac	0.000													4	2	---	---	---	---	
TLN2	83660	broad.mit.edu	37	15	63048757	63048757	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63048757delA	uc002alb.3	+						TLN2_uc002alc.3_Intron|TLN2_uc002ald.2_5'Flank	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2						cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						GTTCTGTGTTAAACCCTGGAC	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	63183304	63183304	+	IGR	DEL	G	-	-	rs34466641		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63183304delG								TLN2 (46477 upstream) : TPM1 (151534 downstream)																							TGGAAGGCATGGGGGGGTGGT	0.522													3	5	---	---	---	---	
ZWILCH	55055	broad.mit.edu	37	15	66808185	66808186	+	Intron	DEL	TC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66808185_66808186delTC	uc002aqb.2	+						RPL4_uc002apx.2_Intron|ZWILCH_uc010bhu.1_Intron|ZWILCH_uc002aqa.2_Intron|ZWILCH_uc010bhv.2_Intron	NM_017975	NP_060445	Q9H900	ZWILC_HUMAN	Zwilch						cell division|mitotic cell cycle checkpoint|mitotic prometaphase	condensed chromosome kinetochore|cytosol	protein binding			ovary(1)	1						gcacttatcttccctttctcta	0.015													5	4	---	---	---	---	
CYP1A2	1544	broad.mit.edu	37	15	75039237	75039238	+	5'Flank	DEL	TA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75039237_75039238delTA	uc002ayr.1	+							NM_000761	NP_000752	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A,						alkaloid metabolic process|exogenous drug catabolic process|methylation|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative deethylation|oxidative demethylation|steroid catabolic process|toxin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|caffeine oxidase activity|demethylase activity|electron carrier activity|enzyme binding|heme binding|oxygen binding			ovary(3)|breast(1)	4					Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Aciclovir(DB00787)|Alosetron(DB00969)|Aminophenazone(DB01424)|Amitriptyline(DB00321)|Anagrelide(DB00261)|Azelastine(DB00972)|Bortezomib(DB00188)|Caffeine(DB00201)|Carmustine(DB00262)|Chlordiazepoxide(DB00475)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Clomipramine(DB01242)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Desloratadine(DB00967)|Diazepam(DB00829)|Dibucaine(DB00527)|Diclofenac(DB00586)|Duloxetine(DB00476)|Enoxacin(DB00467)|Esomeprazole(DB00736)|Estradiol(DB00783)|Estrone(DB00655)|Fluorouracil(DB00544)|Flutamide(DB00499)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Grepafloxacin(DB00365)|Haloperidol(DB00502)|Hesperetin(DB01094)|Imipramine(DB00458)|Ketoconazole(DB01026)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Melatonin(DB01065)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mirtazapine(DB00370)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pefloxacin(DB00487)|Pimozide(DB01100)|Propafenone(DB01182)|Propranolol(DB00571)|Quinidine(DB00908)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifampin(DB01045)|Riluzole(DB00740)|Rofecoxib(DB00533)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Tacrine(DB00382)|Telithromycin(DB00976)|Terfenadine(DB00342)|Theophylline(DB00277)|Thiabendazole(DB00730)|Tizanidine(DB00697)|Tolbutamide(DB01124)|Verapamil(DB00661)|Warfarin(DB00682)|Zileuton(DB00744)|Zolmitriptan(DB00315)	tctgtttctctattggattccc	0.015													4	2	---	---	---	---	
IREB2	3658	broad.mit.edu	37	15	78738945	78738947	+	Intron	DEL	TTG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78738945_78738947delTTG	uc002bdr.2	+						IREB2_uc010unb.1_Intron|IREB2_uc002bdq.2_Intron	NM_004136	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2								4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		CCTGCTCACTTTGTACATGGCCT	0.448													4	2	---	---	---	---	
HOMER2	9455	broad.mit.edu	37	15	83523351	83523352	+	Intron	INS	-	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83523351_83523352insT	uc002bjg.2	-						HOMER2_uc002bjh.2_Intron|HOMER2_uc002bjj.2_Intron|HOMER2_uc002bji.2_Intron	NM_199330	NP_955362	Q9NSB8	HOME2_HUMAN	homer 2 isoform 2						metabotropic glutamate receptor signaling pathway	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane					0						TCTCCCACTGCCCACACCAGCT	0.604													9	4	---	---	---	---	
ADAMTSL3	57188	broad.mit.edu	37	15	84363866	84363866	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84363866delG	uc002bjz.3	+						ADAMTSL3_uc002bjy.1_Intron|ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)			gtgcatgtgtggtgtgtgtgt	0.159													4	2	---	---	---	---	
IQGAP1	8826	broad.mit.edu	37	15	91018049	91018049	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91018049delT	uc002bpl.1	+							NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1						energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			CCATAAGAGCttttttttttt	0.274													5	4	---	---	---	---	
IGF1R	3480	broad.mit.edu	37	15	99309920	99309922	+	Intron	DEL	GCC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99309920_99309922delGCC	uc002bul.2	+						IGF1R_uc010urq.1_Intron|IGF1R_uc010bon.2_Intron	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor						anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)	GTTAACCTCTGCCAAAGTTGATG	0.419													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	100450163	100450164	+	IGR	INS	-	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100450163_100450164insT								C15orf51 (103031 upstream) : ADAMTS17 (61479 downstream)																							TGGGGTTGAGGTTTTTTTTTAC	0.401													8	4	---	---	---	---	
RAB11FIP3	9727	broad.mit.edu	37	16	534674	534674	+	Intron	DEL	C	-	-	rs143123332	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:534674delC	uc002chf.2	+						RAB11FIP3_uc010uuf.1_Intron|RAB11FIP3_uc010uug.1_Intron	NM_014700	NP_055515	O75154	RFIP3_HUMAN	rab11-family interacting protein 3 isoform 1						cell cycle|cytokinesis|endocytic recycling|protein transport	centrosome|cleavage furrow|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		Hepatocellular(16;0.0218)				TATTTTTGTGCATTGCTGTAA	0.289													4	2	---	---	---	---	
C16orf89	146556	broad.mit.edu	37	16	5106373	5106374	+	Intron	DEL	TG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5106373_5106374delTG	uc010bud.2	-						ALG1_uc002cyj.2_Intron|C16orf89_uc002cyk.3_Intron	NM_152459	NP_689672	Q6UX73	CP089_HUMAN	hypothetical protein LOC146556 isoform 1							extracellular region				ovary(1)|skin(1)	2						Cccagcctgctgggttcgagat	0.208													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	15463308	15463308	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15463308delA	uc010bvf.1	-						uc010uzu.1_Intron					RecName: Full=NPIP-like protein 1;																		ccgtctcaggaaaaaaaaaaa	0.159													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	27045200	27045200	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27045200delA								HS3ST4 (896192 upstream) : C16orf82 (33019 downstream)																							CCACCTCTCCAAAAAAAAAAT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29233581	29233581	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29233581delC	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		gacaactcctcctttccttcc	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32266623	32266623	+	RNA	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32266623delA	uc002ecy.2	+	4		c.1262delA			uc010cav.1_RNA					Homo sapiens mRNA for TP53TG3b, complete cds.																		TCTTTAGATTAAAAAAAAAAA	0.348													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46406708	46406708	+	IGR	DEL	C	-	-	rs143473824		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46406708delC								None (None upstream) : ANKRD26P1 (96541 downstream)																							tcattcaattccattcgataa	0.000													4	2	---	---	---	---	
ABCC11	85320	broad.mit.edu	37	16	48232440	48232441	+	Intron	INS	-	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48232440_48232441insA	uc002eff.1	-						ABCC11_uc002efg.1_Intron|ABCC11_uc002efh.1_Intron|ABCC11_uc010vgk.1_Intron	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11							integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)				cagtaacatggaagatttttga	0.000									Cerumen_Type				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	50897825	50897826	+	IGR	DEL	GT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50897825_50897826delGT								CYLD (61979 upstream) : SALL1 (272060 downstream)																							gcctgagtgcgtgtgtgtgtgt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	56570422	56570422	+	IGR	DEL	G	-	-	rs112378908		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56570422delG								BBS2 (16414 upstream) : MT4 (28539 downstream)																							CCCACTTGGAGGGGGGCGTCG	0.443													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	65668298	65668298	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65668298delG								LOC283867 (58095 upstream) : CDH5 (732227 downstream)																							ATGCTGCTGTGGGCACAAAAG	0.532													4	2	---	---	---	---	
CA7	766	broad.mit.edu	37	16	66887054	66887054	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66887054delG	uc002eqi.2	+						uc002eqh.2_Intron|CA7_uc002eqj.2_Intron	NM_005182	NP_005173	P43166	CAH7_HUMAN	carbonic anhydrase VII isoform 1						one-carbon metabolic process	cytoplasm	carbonate dehydratase activity|zinc ion binding				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)		TTAGCTAGATGGGCTTGGAAC	0.507													4	2	---	---	---	---	
LRRC29	26231	broad.mit.edu	37	16	67250617	67250617	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67250617delT	uc002ese.2	-						LRRC29_uc002esf.2_Intron|LRRC29_uc002esg.2_Intron|LRRC29_uc010vjg.1_Intron	NM_012163	NP_036295	Q8WV35	LRC29_HUMAN	F-box and leucine-rich repeat protein 9												0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		gccaactgcattttgccccat	0.000													4	2	---	---	---	---	
DDX19A	55308	broad.mit.edu	37	16	70366640	70366640	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70366640delC	uc002eys.2	+						DDX19B_uc010vly.1_Intron|DDX19B_uc010vlv.1_Intron|DDX19B_uc010vlw.1_Intron|DDX19B_uc002eyo.2_Intron|DDX19B_uc002eyp.2_Intron|DDX19B_uc002eyq.2_Intron|DDX19B_uc002eyr.2_Intron|DDX19B_uc010vlx.1_Intron|uc002eyt.2_Intron	NM_007242	NP_009173	Q9NUU7	DD19A_HUMAN	DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform						mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)				ctgcaccccaccccctgaccc	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	72258536	72258538	+	IGR	DEL	TCT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72258536_72258538delTCT								PMFBP1 (52187 upstream) : ZFHX3 (558250 downstream)																							aattttaacctcttcttcaaaca	0.118													4	2	---	---	---	---	
ZFHX3	463	broad.mit.edu	37	16	72868590	72868590	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72868590delC	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)				GAAAGCAGCACCAGGCAGAAG	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	82372011	82372011	+	IGR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82372011delA								MPHOSPH6 (168182 upstream) : CDH13 (288567 downstream)																							TCTTCTCAGTAAACTCATGGC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88381985	88381985	+	IGR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88381985delC								BANP (271062 upstream) : ZNF469 (111894 downstream)																							cagggccccaccccactcctg	0.010													4	2	---	---	---	---	
ITGAE	3682	broad.mit.edu	37	17	3654762	3654763	+	Intron	INS	-	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3654762_3654763insG	uc002fwo.3	-							NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor						cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		CTGAAGGGGCTGAGGTGAGGCC	0.619													4	3	---	---	---	---	
USP6	9098	broad.mit.edu	37	17	5038289	5038289	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5038289delA	uc002gau.1	+						USP6_uc002gav.1_Intron|USP6_uc010ckz.1_Intron|uc002gay.1_5'Flank|uc002gba.2_5'Flank|uc002gbb.2_5'Flank	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6						protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5						tgtgcaaaagaaaaaaaaaat	0.169			T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								10	5	---	---	---	---	
NUP88	4927	broad.mit.edu	37	17	5320152	5320153	+	Intron	INS	-	T	T	rs11391160		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5320152_5320153insT	uc002gbo.1	-						NUP88_uc010vsx.1_Intron|NUP88_uc010cle.1_Intron|NUP88_uc010vsy.1_Intron|RPAIN_uc010vsz.1_5'Flank|RPAIN_uc002gbp.1_5'Flank|RPAIN_uc010vta.1_5'Flank|RPAIN_uc002gbq.2_5'Flank|RPAIN_uc010vtb.1_5'Flank|RPAIN_uc002gbs.2_5'Flank|RPAIN_uc002gbt.2_5'Flank|RPAIN_uc002gbu.2_5'Flank|RPAIN_uc002gbv.2_5'Flank|RPAIN_uc002gbr.2_5'Flank|RPAIN_uc002gbw.2_5'Flank	NM_002532	NP_002523	Q99567	NUP88_HUMAN	nucleoporin 88kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	transporter activity			kidney(1)	1						TAACTCACAAAttttttttttt	0.158													3	3	---	---	---	---	
ZBTB4	57659	broad.mit.edu	37	17	7363126	7363126	+	3'UTR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7363126delA	uc002ghc.3	-	5					ZBTB4_uc002ghd.3_3'UTR	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		CAATTCTCCCAAAAAAAAATG	0.393													7	5	---	---	---	---	
COX10	1352	broad.mit.edu	37	17	14021300	14021300	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14021300delC	uc002gof.3	+						COX10_uc010vvs.1_Intron|COX10_uc010vvt.1_Intron	NM_001303	NP_001294	Q12887	COX10_HUMAN	heme A:farnesyltransferase precursor						heme a biosynthetic process|heme O biosynthetic process|respiratory chain complex IV assembly	integral to membrane|mitochondrial membrane	protoheme IX farnesyltransferase activity				0		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		agtcaggccgcccacctagct	0.000													4	2	---	---	---	---	
ZNF286A	57335	broad.mit.edu	37	17	15610053	15610053	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15610053delA	uc010cot.2	+						ZNF286A_uc002goz.3_Intron|ZNF286A_uc010vwa.1_Intron|ZNF286A_uc002gpa.2_Intron	NM_001130842	NP_001124314	Q9HBT8	Z286A_HUMAN	zinc finger protein 286						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		cttaaaggggaaaaaaATTTT	0.144													4	2	---	---	---	---	
TOP3A	7156	broad.mit.edu	37	17	18211985	18211985	+	Intron	DEL	T	-	-	rs68169135		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18211985delT	uc002gsx.1	-						TOP3A_uc002gsw.1_5'Flank|TOP3A_uc010vxs.1_Intron|TOP3A_uc010cqa.1_Intron	NM_004618	NP_004609	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha						DNA topological change|meiosis	chromosome|PML body	ATP binding|DNA topoisomerase type I activity|protein binding|zinc ion binding			skin(3)	3						GTATATTAGCTTTTTTTTTTT	0.328													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21556565	21556565	+	IGR	DEL	G	-	-	rs112544946		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21556565delG								C17orf51 (78834 upstream) : FAM27L (268805 downstream)																							GTGGGGTCCTGGCCCATCTGC	0.318													3	3	---	---	---	---	
SLC6A4	6532	broad.mit.edu	37	17	28562144	28562144	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28562144delC	uc002hey.3	-							NM_001045	NP_001036	P31645	SC6A4_HUMAN	solute carrier family 6 member 4						response to toxin|serotonin uptake|thalamus development	cytosol|endomembrane system|endosome membrane|membrane raft	actin filament binding|Rab GTPase binding|serotonin transmembrane transporter activity|serotonin:sodium symporter activity			skin(3)|ovary(1)	4					Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Doxepin(DB01142)|Duloxetine(DB00476)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Minaprine(DB00805)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phentermine(DB00191)|Protriptyline(DB00344)|Sertraline(DB01104)|Sibutramine(DB01105)|Tegaserod(DB01079)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Zimelidine(DB04832)	CACTTAGGCGCCACTCAGAGA	0.512													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	32202381	32202381	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32202381delC	uc002hhu.2	-							NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	ATCCCAGCATCCTCTTGCTGC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33332963	33332963	+	5'Flank	DEL	T	-	-	rs71364691		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33332963delT	uc002hil.2	+											Homo sapiens cDNA FLJ34173 fis, clone FCBBF3015809.																		TATCACAGTATTTTTTTTTTT	0.323													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33548252	33548253	+	IGR	INS	-	AAC	AAC	rs151025413	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33548252_33548253insAAC								AMAC1 (26840 upstream) : SLFN5 (21833 downstream)																							atcttgccttaaacaacaacaa	0.134													5	3	---	---	---	---	
SOCS7	30837	broad.mit.edu	37	17	36517892	36517892	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36517892delG	uc002hqa.2	+						SOCS7_uc010cvl.2_Intron|SOCS7_uc002hqb.2_Intron	NM_014598	NP_055413	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7						intracellular signal transduction|negative regulation of signal transduction|regulation of growth	cytoplasm|nucleus|plasma membrane	protein binding|SH3 domain binding			skin(1)	1	Breast(7;3.47e-17)					TAGGTGGCCTGGGTGGCCCTA	0.398													4	2	---	---	---	---	
MEOX1	4222	broad.mit.edu	37	17	41728920	41728921	+	Intron	INS	-	A	A	rs148392997	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41728920_41728921insA	uc002idz.2	-						MEOX1_uc002iea.2_Intron|MEOX1_uc002ieb.2_Intron	NM_004527	NP_004518	P50221	MEOX1_HUMAN	mesenchyme homeobox 1 isoform 1							nucleus	sequence-specific DNA binding				0		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)		AAACAAGGGGGAAAAAAAAAGA	0.535													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	43430753	43430753	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43430753delT								MAP3K14 (36339 upstream) : ARHGAP27 (40516 downstream)																							ccaacaagcatttacttagaa	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	43430964	43430964	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43430964delG								MAP3K14 (36550 upstream) : ARHGAP27 (40305 downstream)																							aggtagtcctgggctggttct	0.005													4	2	---	---	---	---	
HOXB6	3216	broad.mit.edu	37	17	46684030	46684030	+	5'Flank	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46684030delA	uc002ins.1	-						HOXB6_uc010dbh.1_5'Flank	NM_018952	NP_061825	P17509	HXB6_HUMAN	homeobox B6						anterior/posterior axis specification, embryo	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GGCCTGAATGAGGACGCGGGT	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	47319436	47319436	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47319436delG								PHOSPHO1 (11308 upstream) : ZNF652 (47133 downstream)																							accatctaatgggttcgcctt	0.124													4	2	---	---	---	---	
ZNF652	22834	broad.mit.edu	37	17	47368296	47368296	+	3'UTR	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47368296delC	uc002iov.3	-	6					ZNF652_uc002iow.2_3'UTR|ZNF652_uc002iou.3_RNA	NM_001145365	NP_001138837	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			GCCAGAACTGCTGATGGAAAA	0.373													4	2	---	---	---	---	
ACSF2	80221	broad.mit.edu	37	17	48537883	48537883	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48537883delG	uc002iqu.2	+						ACSF2_uc010wml.1_Intron|ACSF2_uc010wmm.1_Intron|ACSF2_uc010wmn.1_Intron|ACSF2_uc010wmo.1_Intron	NM_025149	NP_079425	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2 precursor						fatty acid metabolic process	mitochondrion	ATP binding|ligase activity				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			AAAAGGGTCTGGGGGATTTTA	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	70425749	70425749	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70425749delG	uc002jix.2	-						uc002jiz.1_Intron					Homo sapiens cDNA FLJ20470 fis, clone KAT06815.																		TCCAACCCCCGCATCTGGAAC	0.488													4	2	---	---	---	---	
LGALS3BP	3959	broad.mit.edu	37	17	76969759	76969759	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76969759delG	uc002jwh.2	-						LGALS3BP_uc002jwi.2_Intron|LGALS3BP_uc010dhr.2_Intron	NM_005567	NP_005558	Q08380	LG3BP_HUMAN	galectin 3 binding protein						cell adhesion|cellular defense response	extracellular space|membrane|proteinaceous extracellular matrix	protein binding|scavenger receptor activity			central_nervous_system(3)|ovary(1)	4			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			GCTTCCTGTCGGGGAGAAGGC	0.567													4	2	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78891788	78891788	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78891788delC	uc002jyt.1	+						RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						TGTCTTAGTTCCTGCACCTCC	0.577													4	2	---	---	---	---	
DUS1L	64118	broad.mit.edu	37	17	80019400	80019401	+	Intron	INS	-	G	G			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80019400_80019401insG	uc002kdq.2	-						DUS1L_uc002kdp.2_Intron|DUS1L_uc002kdr.2_Intron|DUS1L_uc002kds.2_Intron|DUS1L_uc002kdt.2_Intron|DUS1L_uc010wvi.1_Intron	NM_022156	NP_071439	Q6P1R4	DUS1L_HUMAN	PP3111 protein						tRNA processing		flavin adenine dinucleotide binding|tRNA dihydrouridine synthase activity			skin(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			AACAGCACCATGGGGAGGGCAG	0.639													4	2	---	---	---	---	
ARHGAP28	79822	broad.mit.edu	37	18	6890641	6890641	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6890641delA	uc010wzi.1	+						ARHGAP28_uc002knc.2_Intron|ARHGAP28_uc002knd.2_Intron|ARHGAP28_uc002kne.2_Intron|ARHGAP28_uc002knf.2_Intron			B4DXL2	B4DXL2_HUMAN	SubName: Full=Putative uncharacterized protein ARHGAP28;						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)				CAAGCATTTTATATTCTCAAG	0.433													19	9	---	---	---	---	
ANKRD12	23253	broad.mit.edu	37	18	9256640	9256642	+	In_Frame_Del	DEL	AAC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9256640_9256642delAAC	uc002knv.2	+	9	3632_3634	c.3375_3377delAAC	c.(3373-3378)AAAACA>AAA	p.T1126del	ANKRD12_uc002knw.2_In_Frame_Del_p.T1103del|ANKRD12_uc002knx.2_In_Frame_Del_p.T1103del|ANKRD12_uc010dkx.1_In_Frame_Del_p.T833del	NM_015208	NP_056023	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12 isoform 1	1126						nucleus				ovary(2)|central_nervous_system(1)	3						ATAAAGAAAAAACAAAGCATACA	0.320													33	18	---	---	---	---	
CEP192	55125	broad.mit.edu	37	18	13004298	13004299	+	Intron	INS	-	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13004298_13004299insT	uc010xac.1	+						CEP192_uc002krs.1_Intron	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa											ovary(4)|pancreas(1)	5						agaagtttcacttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	28262001	28262002	+	IGR	INS	-	A	A	rs142745875	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28262001_28262002insA								MIR302F (383075 upstream) : DSC3 (308051 downstream)																							CTACCTCCTTCAGCAGTCATTC	0.376													4	2	---	---	---	---	
DTNA	1837	broad.mit.edu	37	18	32457470	32457471	+	Intron	INS	-	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32457470_32457471insA	uc010dmn.1	+						DTNA_uc002kxw.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010xby.1_Intron|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						CCATCATTAGCCATGTCTTCTT	0.238													4	2	---	---	---	---	
KIAA0427	9811	broad.mit.edu	37	18	46194891	46194891	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46194891delG	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron	NM_014772	NP_055587	O43310	CTIF_HUMAN	hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0						GGGGACAGCCGGGGGCCGGGG	0.567											OREG0024971	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	51431586	51431587	+	IGR	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51431586_51431587delCA								DCC (373804 upstream) : MBD2 (248988 downstream)																							GAGGAATCTTCACTCTGCCTCT	0.535													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	54832029	54832029	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54832029delT								WDR7 (134993 upstream) : ST8SIA3 (187692 downstream)																							CATCTTTCTATTTTTTTTTCC	0.388													4	2	---	---	---	---	
RAX	30062	broad.mit.edu	37	18	56937125	56937125	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56937125delA	uc002lhx.2	-						RAX_uc010dpp.2_Intron	NM_013435	NP_038463	Q9Y2V3	RX_HUMAN	retina and anterior neural fold homeobox						visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1		Lung NSC(161;0.0804)|Colorectal(73;0.0946)		STAD - Stomach adenocarcinoma(84;0.18)		AGAAGCTCAGAAAAAAAAAGT	0.458													4	2	---	---	---	---	
KDM4B	23030	broad.mit.edu	37	19	5011451	5011452	+	Intron	DEL	GA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5011451_5011452delGA	uc002mbq.3	+						KDM4B_uc010xil.1_Intron	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1						GGGCCCATCTGAGGCTTTGGGT	0.411													4	2	---	---	---	---	
ACER1	125981	broad.mit.edu	37	19	6313929	6313929	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6313929delA	uc002mel.2	-							NM_133492	NP_597999	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1							endoplasmic reticulum membrane|integral to membrane	ceramidase activity				0						atgccagaggagggccagtgg	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	33023598	33023598	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33023598delG								DPY19L3 (48362 upstream) : PDCD5 (48506 downstream)																							ctatctctctgtttctttctc	0.000													4	2	---	---	---	---	
SCGBL	284402	broad.mit.edu	37	19	35084750	35084751	+	Intron	DEL	AA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35084750_35084751delAA	uc002nvn.2	-							NM_001025591	NP_001020762	Q4G0G5	SCGBL_HUMAN	secretoglobin-like precursor							extracellular region	binding				0						TGTTGCTGTTAACAGCGTCCTG	0.540													4	2	---	---	---	---	
UPK1A	11045	broad.mit.edu	37	19	36157489	36157490	+	5'Flank	INS	-	A	A			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36157489_36157490insA	uc002oaw.2	+						UPK1A_uc010eeh.2_5'Flank	NM_007000	NP_008931	O00322	UPK1A_HUMAN	uroplakin 1A						epithelial cell differentiation|protein oligomerization	endoplasmic reticulum|integral to membrane	monosaccharide binding|protein homodimerization activity				0	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGGTCTGAGGCTCAGGGAGGGG	0.644													4	2	---	---	---	---	
CCDC9	26093	broad.mit.edu	37	19	47771849	47771850	+	Intron	DEL	CC	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47771849_47771850delCC	uc010xym.1	+							NM_015603	NP_056418	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9												0		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		TCTTATGTGTCCTAAAAGCAGT	0.282													4	2	---	---	---	---	
ZNF320	162967	broad.mit.edu	37	19	53376866	53376866	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53376866delC	uc010eqh.1	-						ZNF320_uc010eqi.1_Intron			A2RRD8	ZN320_HUMAN	Homo sapiens full length insert cDNA clone ZD42C02.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0534)		ctcttttattcccccacaACG	0.219													4	2	---	---	---	---	
ZNF264	9422	broad.mit.edu	37	19	57716531	57716534	+	Intron	DEL	ATAC	-	-	rs66638148		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57716531_57716534delATAC	uc002qob.2	+							NM_003417	NP_003408	O43296	ZN264_HUMAN	zinc finger protein 264						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)		TAATATTTAAATACATCAGTTTTT	0.289													4	2	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17410527	17410527	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17410527delA	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	ttttaacagcaaaaaaaaaat	0.040													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	17859987	17859988	+	IGR	INS	-	A	A	rs143268090	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17859987_17859988insA								BANF2 (143470 upstream) : SNX5 (62258 downstream)																							gatgaagagatacagtaaaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19804033	19804034	+	IGR	INS	-	TC	TC	rs57730958		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19804033_19804034insTC								SLC24A3 (100493 upstream) : RIN2 (66176 downstream)																							CTCTGCCTGCTTTTTTTTTTTT	0.386													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22977819	22977819	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22977819delT								FOXA2 (411718 upstream) : SSTR4 (38238 downstream)																							TGTTTGTCCATTTCTCTGGCA	0.388													4	2	---	---	---	---	
BLCAP	10904	broad.mit.edu	37	20	36150600	36150601	+	5'Flank	INS	-	A	A	rs10601050		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36150600_36150601insA	uc002xha.2	-						BLCAP_uc002xhb.2_Intron|BLCAP_uc002xhc.2_Intron|NNAT_uc002xhd.2_Intron|NNAT_uc002xhe.2_Intron	NM_006698	NP_006689	P62952	BLCAP_HUMAN	bladder cancer associated protein						apoptosis|cell cycle	integral to membrane					0		Myeloproliferative disorder(115;0.00878)				aaaataataataaaaaaaataa	0.297													4	8	---	---	---	---	
GDAP1L1	78997	broad.mit.edu	37	20	42908525	42908525	+	3'UTR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42908525delA	uc002xlq.2	+	6					GDAP1L1_uc010zwl.1_3'UTR|GDAP1L1_uc010zwm.1_3'UTR|GDAP1L1_uc010zwn.1_3'UTR	NM_024034	NP_076939	Q96MZ0	GD1L1_HUMAN	ganglioside-induced differentiation-associated											large_intestine(1)	1		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			AGTGGCACCCAAAAACCAGGC	0.542													4	2	---	---	---	---	
SPATA2	9825	broad.mit.edu	37	20	48520902	48520902	+	3'UTR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48520902delA	uc010gie.2	-	3					SPATA2_uc002xuw.2_3'UTR|SPATA2_uc010zyn.1_3'UTR	NM_001135773	NP_001129245	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm|nucleus				central_nervous_system(1)|skin(1)	2	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			AAAAGATTGCAAATGTTGCAG	0.488													4	2	---	---	---	---	
ZBP1	81030	broad.mit.edu	37	20	56195624	56195624	+	5'UTR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56195624delA	uc002xyo.2	-	1					ZBP1_uc010gjm.2_5'UTR|ZBP1_uc002xyp.2_5'UTR|ZBP1_uc010zzn.1_5'UTR	NM_030776	NP_110403	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1 isoform a							cytoplasm|nucleus	double-stranded RNA adenosine deaminase activity|left-handed Z-DNA binding|RNA binding			ovary(2)	2	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			CTTTTGAAAGAAAAAAAAAGT	0.483													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	57364218	57364218	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57364218delT								NPEPL1 (72851 upstream) : MIR296 (28452 downstream)																							CAGCTTCCCCTCCAAGCCCCG	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	60537341	60537341	+	IGR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60537341delG								MIR1257 (8623 upstream) : TAF4 (12514 downstream)																							GAAGGCGGATGGGCCTGGGGA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	61399621	61399622	+	IGR	INS	-	CCAT	CCAT	rs144216191	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61399621_61399622insCCAT								NTSR1 (5499 upstream) : C20orf20 (28183 downstream)																							CCTATACCTTCccatccatcca	0.238													4	2	---	---	---	---	
OPRL1	4987	broad.mit.edu	37	20	62728836	62728836	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62728836delG	uc002yic.2	+						OPRL1_uc002yid.2_Intron|OPRL1_uc002yif.3_Intron	NM_182647	NP_872588	P41146	OPRX_HUMAN	opiate receptor-like 1						elevation of cytosolic calcium ion concentration|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception	integral to plasma membrane	protein binding|X-opioid receptor activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)					TGCAGAATCCGGGGTGTGTTC	0.428													4	2	---	---	---	---	
C21orf99	149992	broad.mit.edu	37	21	14425970	14425972	+	Intron	DEL	CTC	-	-	rs113465228		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14425970_14425972delCTC	uc002yja.3	+							NR_026916				Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						cacgctgttactcctccttacaa	0.000													3	3	---	---	---	---	
CHODL	140578	broad.mit.edu	37	21	19407243	19407243	+	Intron	DEL	C	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19407243delC	uc002ykt.2	+						CHODL_uc002ykr.2_Intron|CHODL_uc002yks.2_Intron|CHODL_uc002yku.2_Intron			Q9H9P2	CHODL_HUMAN	RecName: Full=Chondrolectin; AltName: Full=Transmembrane protein MT75; Flags: Precursor;						muscle organ development	integral to membrane|perinuclear region of cytoplasm	sugar binding			upper_aerodigestive_tract(1)	1		all_epithelial(11;0.21)		Epithelial(23;0.000191)|all cancers(11;0.000827)|LUSC - Lung squamous cell carcinoma(23;0.00646)|Lung(58;0.0129)|OV - Ovarian serous cystadenocarcinoma(11;0.017)|COAD - Colon adenocarcinoma(22;0.03)|Colorectal(24;0.0917)		GGTTGCTGTACCACAgtaggt	0.229													4	2	---	---	---	---	
GRIK1	2897	broad.mit.edu	37	21	31045145	31045146	+	Intron	INS	-	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31045145_31045146insT	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron	NM_000830	NP_000821	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)	TCTCTGAGCCCCTTGCCTGTTT	0.406													4	2	---	---	---	---	
MORC3	23515	broad.mit.edu	37	21	37710947	37710947	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37710947delA	uc002yvi.2	+							NM_015358	NP_056173	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3						cell aging|maintenance of protein location in nucleus|negative regulation of fibroblast proliferation|peptidyl-serine phosphorylation|protein stabilization	aggresome|intermediate filament cytoskeleton|PML body	ATP binding|zinc ion binding			ovary(2)	2						cctatctcacaaaaaaaaaaa	0.085													10	7	---	---	---	---	
KCNJ6	3763	broad.mit.edu	37	21	39260934	39260934	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39260934delG	uc011aej.1	-						KCNJ6_uc002ywo.2_Intron	NM_002240	NP_002231	P48051	IRK6_HUMAN	potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)	aaggatgtatggggcccatgc	0.000													4	2	---	---	---	---	
ERG	2078	broad.mit.edu	37	21	40018711	40018713	+	Intron	DEL	TTG	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40018711_40018713delTTG	uc010gnw.2	-						ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc002yxc.3_Intron|ERG_uc010gnz.2_Intron	NM_001136155	NP_001129627	P11308	ERG_HUMAN	ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)				CTCAGCATCTTTGTTGTTGTTGT	0.438													4	2	---	---	---	---	
SLC19A1	6573	broad.mit.edu	37	21	46935514	46935514	+	3'UTR	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46935514delG	uc002zhl.1	-	6					SLC19A1_uc010gpy.1_Intron|SLC19A1_uc011aft.1_3'UTR|SLC19A1_uc002zhm.1_Intron|SLC19A1_uc010gpz.1_3'UTR	NM_194255	NP_919231	P41440	S19A1_HUMAN	solute carrier family 19 member 1						folic acid metabolic process	integral to plasma membrane|membrane fraction	folic acid binding|folic acid transporter activity|methotrexate transporter activity|reduced folate carrier activity				0				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)		CCTCGAGGCAGGGGTCGTGGG	0.652													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	22000621	22000621	+	IGR	DEL	C	-	-	rs138337151		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22000621delC								SDF2L1 (2034 upstream) : MIR301B (6649 downstream)																							CCCTGGGCATCCCCCTGTCCA	0.463													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	23338837	23338838	+	IGR	DEL	CT	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23338837_23338838delCT								LOC96610 (73755 upstream) : RTDR1 (62756 downstream)																							cagggctcccctgccaccatca	0.030													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27858647	27858647	+	IGR	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27858647delT								MIAT (743698 upstream) : MN1 (285619 downstream)																							ctttcttttcttttttttttA	0.383													6	3	---	---	---	---	
TTC28	23331	broad.mit.edu	37	22	28510905	28510906	+	Intron	DEL	AA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28510905_28510906delAA	uc003adp.3	-							NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28								binding				0						AGGTAATTCCAAAAATATGTAT	0.248													4	2	---	---	---	---	
MICALL1	85377	broad.mit.edu	37	22	38332899	38332899	+	Intron	DEL	A	-	-	rs75570183		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38332899delA	uc003aui.2	+							NM_033386	NP_203744	Q8N3F8	MILK1_HUMAN	molecule interacting with Rab13							cytoplasm|cytoskeleton	protein binding|zinc ion binding			breast(1)	1	Melanoma(58;0.045)					actccgtctcaaaaaaaaaaa	0.204													2	4	---	---	---	---	
RANGAP1	5905	broad.mit.edu	37	22	41658604	41658605	+	Intron	INS	-	T	T	rs148801486	by1000genomes	TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41658604_41658605insT	uc003azs.2	-						RANGAP1_uc003azt.2_Intron|RANGAP1_uc003azu.2_Intron|RANGAP1_uc011aoz.1_Intron	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1						mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0						CACAGCCATCCTTGAGGAACAG	0.347													4	2	---	---	---	---	
C22orf46	79640	broad.mit.edu	37	22	42092313	42092313	+	3'UTR	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42092313delA	uc003bax.1	+	2						NM_001142964	NP_001136436	C9J442	CV046_HUMAN	hypothetical protein LOC79640							extracellular region					0						GAAGCCAGAGAAAGTGCACAG	0.502											OREG0026594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
EFCAB6	64800	broad.mit.edu	37	22	44158927	44158928	+	Intron	INS	-	T	T			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44158927_44158928insT	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Intron|EFCAB6_uc003beb.3_Intron	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				GCACTCATTCAtttttttttaa	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45048823	45048824	+	IGR	DEL	TG	-	-	rs68121032		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45048823_45048824delTG								NCRNA00207 (80494 upstream) : PRR5 (15769 downstream)																							agatgtagactgtgaagaaggt	0.000													3	3	---	---	---	---	
GRAMD4	23151	broad.mit.edu	37	22	47024026	47024026	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47024026delG	uc003bhx.2	+							NM_015124	NP_055939	Q6IC98	GRAM4_HUMAN	death-inducing-protein						apoptosis	integral to membrane|mitochondrial membrane				ovary(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)		TGGGTGTCTCGGGAACAAAAA	0.602													4	2	---	---	---	---	
MED14	9282	broad.mit.edu	37	X	40540270	40540270	+	Intron	DEL	T	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40540270delT	uc004dex.3	-							NM_004229	NP_004220	O60244	MED14_HUMAN	mediator complex subunit 14						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(2)|kidney(1)|skin(1)	4						CTAAATGGAATTTTTTTTTGG	0.318													6	3	---	---	---	---	
POF1B	79983	broad.mit.edu	37	X	84634529	84634529	+	Intron	DEL	A	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84634529delA	uc004eer.2	-						POF1B_uc004ees.2_Intron	NM_024921	NP_079197	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B								actin binding				0						AATATAATGGAAAAAAAagac	0.383													6	3	---	---	---	---	
ZCCHC16	340595	broad.mit.edu	37	X	111477746	111477746	+	Intron	DEL	G	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111477746delG	uc004epo.1	+							NM_001004308	NP_001004308	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16								nucleic acid binding|zinc ion binding			ovary(1)	1						AGGAGCCCCTGGCTTTGGGAT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9903942	9903943	+	IGR	DEL	CA	-	-			TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9903942_9903943delCA								TTTY22 (253088 upstream) : None (None downstream)																							TGAacatacccacacacacaga	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59013319	59013319	+	IGR	DEL	C	-	-	rs56037744		TCGA-A3-3351-01A-02D-1386-10	TCGA-A3-3351-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59013319delC								None (None upstream) : None (None downstream)																							AAACACTGTACTTTTGTTTCT	0.373													6	3	---	---	---	---	
