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
UTS2	10911	broad.mit.edu	37	1	7913390	7913390	+	5'Flank	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7913390A>G	uc001aor.2	-						UTS2_uc001aoq.2_5'UTR|UTS2_uc001aos.2_Silent_p.L34L	NM_006786	NP_006777	O95399	UTS2_HUMAN	urotensin 2 isoform b preproprotein						muscle contraction|regulation of blood pressure|synaptic transmission	extracellular space	hormone activity				0	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)		GAATTAAAGGAAGGCTTGGAT	0.383													5	326	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16918543	16918543	+	5'UTR	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918543A>G	uc009vos.1	-	7					NBPF1_uc010oce.1_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		GAAGAGGTGGAGCCAGGGACT	0.458													11	172	---	---	---	---	PASS
SCP2	6342	broad.mit.edu	37	1	53427254	53427254	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53427254C>T	uc001cur.1	+	6	597	c.476C>T	c.(475-477)GCT>GTT	p.A159V	SCP2_uc001cus.1_RNA|SCP2_uc010ono.1_Missense_Mutation_p.A78V|SCP2_uc010onp.1_Missense_Mutation_p.A135V|SCP2_uc009vzi.1_Missense_Mutation_p.A115V|SCP2_uc001cuq.1_Missense_Mutation_p.A115V	NM_002979	NP_002970	P22307	NLTP_HUMAN	sterol carrier protein 2 isoform 1 proprotein	159					bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|lipid transport	mitochondrion|nucleus|peroxisomal matrix	propanoyl-CoA C-acyltransferase activity|propionyl-CoA C2-trimethyltridecanoyltransferase activity|protein binding|sterol binding			breast(1)	1						CACCCAGTTGCTCCTCAGATG	0.373													14	388	---	---	---	---	PASS
HOOK1	51361	broad.mit.edu	37	1	60325915	60325915	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60325915G>C	uc009wad.2	+	16	1549	c.1447G>C	c.(1447-1449)GGC>CGC	p.G483R	HOOK1_uc001czo.2_Missense_Mutation_p.G483R|HOOK1_uc001czp.2_RNA|HOOK1_uc010oor.1_Missense_Mutation_p.G441R	NM_015888	NP_056972	Q9UJC3	HOOK1_HUMAN	hook homolog 1	483	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)					ACAGCAAGAAGGCTCTGAGAA	0.373													39	246	---	---	---	---	PASS
AGL	178	broad.mit.edu	37	1	100346345	100346345	+	Silent	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100346345T>C	uc001dsi.1	+	14	2293	c.1893T>C	c.(1891-1893)CCT>CCC	p.P631P	AGL_uc001dsj.1_Silent_p.P631P|AGL_uc001dsk.1_Silent_p.P631P|AGL_uc001dsl.1_Silent_p.P631P|AGL_uc001dsm.1_Silent_p.P615P|AGL_uc001dsn.1_Silent_p.P614P	NM_000642	NP_000633	P35573	GDE_HUMAN	amylo-1,6-glucosidase,	631	4-alpha-glucanotransferase.				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		ATGAGTGTCCTATTGTGGTAA	0.383													6	657	---	---	---	---	PASS
LOC648740	648740	broad.mit.edu	37	1	104114048	104114048	+	5'UTR	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104114048A>G	uc001dur.2	+	1					AMY2B_uc010ouo.1_Intron|AMY2B_uc001duq.2_Intron	NM_020978	NP_066188			amylase, pancreatic, alpha-2B precursor												0						GATGATTTCCATGAGAGACTT	0.308													7	43	---	---	---	---	PASS
UBE2Q1	55585	broad.mit.edu	37	1	154527220	154527220	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154527220C>A	uc001fff.1	-	4	670	c.579G>T	c.(577-579)GAG>GAT	p.E193D		NM_017582	NP_060052	Q7Z7E8	UB2Q1_HUMAN	ubiquitin-conjugating enzyme E2Q	193							ATP binding|protein binding|ubiquitin-protein ligase activity				0	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			CCTCAGGCATCTCCTCATCTT	0.527													7	55	---	---	---	---	PASS
GBAP1	2630	broad.mit.edu	37	1	155188758	155188758	+	5'UTR	SNP	A	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155188758A>C	uc001fjd.2	-	1					RAG1AP1_uc010pey.1_Intron|GBAP1_uc001fjf.3_Intron|GBAP1_uc001fje.3_Intron					SubName: Full=cDNA FLJ56170, highly similar to Glucosylceramidase (EC 3.2.1.45);												0						GGATGCAGGTACCTGCCATAG	0.478													8	16	---	---	---	---	PASS
ARHGEF11	9826	broad.mit.edu	37	1	156909401	156909401	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156909401C>A	uc001fqo.2	-	36	4955	c.3915G>T	c.(3913-3915)AGG>AGT	p.R1305S	ARHGEF11_uc010phu.1_Missense_Mutation_p.R721S|ARHGEF11_uc001fqn.2_Missense_Mutation_p.R1345S	NM_014784	NP_055599	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1305					actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CAGCCAGATTCCTGTCCAGTT	0.512													12	69	---	---	---	---	PASS
FCRL2	79368	broad.mit.edu	37	1	157716433	157716433	+	3'UTR	SNP	T	G	G	rs75480906		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157716433T>G	uc001fre.2	-	12					FCRL2_uc001frd.2_3'UTR|FCRL2_uc010phz.1_3'UTR|FCRL2_uc009wsp.2_3'UTR	NM_030764	NP_110391	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2 precursor						cell-cell signaling	integral to membrane|plasma membrane|soluble fraction	receptor activity|SH3/SH2 adaptor activity			ovary(1)|pancreas(1)	2	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CTGTGGCAGGTGATAAGCCTC	0.413													13	88	---	---	---	---	PASS
POU2F1	5451	broad.mit.edu	37	1	167365627	167365627	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167365627G>T	uc001gec.2	+	11	1185	c.1023G>T	c.(1021-1023)AAG>AAT	p.K341N	POU2F1_uc010plg.1_RNA|POU2F1_uc001ged.2_Missense_Mutation_p.K339N|POU2F1_uc001gee.2_Missense_Mutation_p.K341N|POU2F1_uc010plh.1_Missense_Mutation_p.K278N|POU2F1_uc001gef.2_Missense_Mutation_p.K353N|POU2F1_uc001geg.2_Missense_Mutation_p.K239N|POU2F1_uc009wvg.1_5'Flank	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1	341	POU-specific.				negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5						ACATGTGCAAGTTGAAGCCAC	0.388													67	223	---	---	---	---	PASS
SELL	6402	broad.mit.edu	37	1	169665687	169665687	+	Silent	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169665687T>C	uc001ggk.2	-	8	1287	c.1089A>G	c.(1087-1089)AAA>AAG	p.K363K	C1orf112_uc001ggj.2_Intron|SELL_uc010pls.1_Silent_p.K316K	NM_000655	NP_000646	P14151	LYAM1_HUMAN	selectin L precursor	363	Cytoplasmic (Potential).				blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	integral to plasma membrane	glycosphingolipid binding|heparin binding|protease binding|sugar binding				0	all_hematologic(923;0.208)					TTCTCTTGGATTTCTTGCCTG	0.274													6	378	---	---	---	---	PASS
DHX9	1660	broad.mit.edu	37	1	182852294	182852294	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182852294T>C	uc001gpr.2	+	25	3098	c.2935T>C	c.(2935-2937)TTT>CTT	p.F979L	DHX9_uc001gps.2_Missense_Mutation_p.F765L|DHX9_uc001gpt.2_Missense_Mutation_p.F258L|DHX9_uc009wyd.2_5'UTR	NM_001357	NP_001348	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 9	979					CRD-mediated mRNA stabilization|nuclear mRNA splicing, via spliceosome	centrosome|CRD-mediated mRNA stability complex|nucleolus|nucleoplasm|ribonucleoprotein complex	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|double-stranded RNA binding|protein binding			ovary(2)	2						GACACAAGTGTTTACTAACAC	0.363													7	383	---	---	---	---	PASS
CACNA1S	779	broad.mit.edu	37	1	201041938	201041938	+	Silent	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201041938C>T	uc001gvv.2	-	16	2399	c.2172G>A	c.(2170-2172)GAG>GAA	p.E724E		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	724	Cytoplasmic (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	TAGATTCAAACTCATCGATTT	0.488													41	204	---	---	---	---	PASS
ADAM17	6868	broad.mit.edu	37	2	9634938	9634938	+	Intron	SNP	A	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9634938A>C	uc002qzu.2	-						IAH1_uc010yiz.1_RNA|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)		TTGTTCTGAGACCTGCCTCTC	0.468													7	29	---	---	---	---	PASS
YPEL5	51646	broad.mit.edu	37	2	30379606	30379606	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30379606T>C	uc002rna.3	+	4	650	c.89T>C	c.(88-90)CTC>CCC	p.L30P	YPEL5_uc002rnb.3_Missense_Mutation_p.L30P|YPEL5_uc002rnc.3_Missense_Mutation_p.L30P|YPEL5_uc002rmz.3_Missense_Mutation_p.L30P|YPEL5_uc010ezn.2_Intron|YPEL5_uc002rnd.2_Missense_Mutation_p.L30P	NM_001127401	NP_001120873	P62699	YPEL5_HUMAN	yippee-like 5	30							peptide-methionine-(S)-S-oxide reductase activity				0	Acute lymphoblastic leukemia(172;0.155)					CGCTCAGAACTCATCTCCACT	0.433													5	198	---	---	---	---	PASS
CAPN13	92291	broad.mit.edu	37	2	30964652	30964652	+	Intron	SNP	T	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30964652T>G	uc002rnn.2	-						CAPN13_uc002rnm.2_Intron|CAPN13_uc002rno.2_3'UTR	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					GAGAGGCAGGTAAAATAGTCC	0.582													10	22	---	---	---	---	PASS
STON1	11037	broad.mit.edu	37	2	48822492	48822492	+	3'UTR	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48822492C>A	uc002rwo.3	+	5					STON1_uc010fbm.2_3'UTR|STON1-GTF2A1L_uc002rwp.1_Intron|STON1-GTF2A1L_uc010yol.1_Intron|STON1_uc002rwr.2_RNA|STON1_uc002rwq.2_3'UTR	NM_006873	NP_006864	Q9Y6Q2	STON1_HUMAN	stonin 1						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex				skin(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGTAATTCACCGAAACCACAC	0.413													4	223	---	---	---	---	PASS
GMCL1	64395	broad.mit.edu	37	2	70057234	70057234	+	Silent	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70057234G>A	uc002sfu.2	+	1	417	c.210G>A	c.(208-210)GAG>GAA	p.E70E		NM_178439	NP_848526	Q96IK5	GMCL1_HUMAN	germ cell-less	70					cell differentiation|multicellular organismal development|spermatogenesis	nuclear matrix				ovary(3)	3						AGACGGACGAGGATGAGGAGG	0.682													3	20	---	---	---	---	PASS
C2orf3	6936	broad.mit.edu	37	2	75907426	75907426	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75907426G>T	uc002sno.2	-	12	1835	c.1705C>A	c.(1705-1707)CTT>ATT	p.L569I	C2orf3_uc010ffs.2_Missense_Mutation_p.L131I|C2orf3_uc002snn.2_Missense_Mutation_p.L400I|C2orf3_uc010fft.2_Missense_Mutation_p.L244I	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936	569					negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						GGATCCCAAAGGAATTCTACA	0.313													75	441	---	---	---	---	PASS
TMEM182	130827	broad.mit.edu	37	2	103414319	103414319	+	Intron	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103414319C>A	uc010fjb.2	+						TMEM182_uc002tcc.3_Intron|TMEM182_uc002tcd.3_Intron|TMEM182_uc010ywe.1_RNA	NM_144632	NP_653233	Q6ZP80	TM182_HUMAN	transmembrane protein 182 precursor							integral to membrane					0						CTGGGGTCTCCAGTTTACCGT	0.453													60	297	---	---	---	---	PASS
TTC21B	79809	broad.mit.edu	37	2	166731270	166731270	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166731270G>T	uc002udk.2	-	29	4079	c.3946C>A	c.(3946-3948)CCT>ACT	p.P1316T	TTC21B_uc002udj.1_RNA	NM_024753	NP_079029	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	1316						cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5						TATTTTCAAGGTCTTAAAGAC	0.348													54	261	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179441843	179441843	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179441843C>G	uc010zfg.1	-	273	61739	c.61515G>C	c.(61513-61515)AAG>AAC	p.K20505N	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.K14200N|TTN_uc010zfi.1_Missense_Mutation_p.K14133N|TTN_uc010zfj.1_Missense_Mutation_p.K14008N|uc002umv.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	21432							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTATATAGGACTTAATTGGTG	0.448													9	155	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179656858	179656858	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179656858G>T	uc010zfg.1	-	10	1827	c.1603C>A	c.(1603-1605)CAA>AAA	p.Q535K	TTN_uc010zfh.1_Missense_Mutation_p.Q535K|TTN_uc010zfi.1_Missense_Mutation_p.Q535K|TTN_uc010zfj.1_Missense_Mutation_p.Q535K|TTN_uc002unb.2_Missense_Mutation_p.Q535K|TTN_uc010frg.1_Missense_Mutation_p.Q209K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	535							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTAGTTTCTTGTTCTTTGGCT	0.284													7	614	---	---	---	---	PASS
WDR75	84128	broad.mit.edu	37	2	190324065	190324065	+	Silent	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190324065G>A	uc002uql.1	+	8	753	c.693G>A	c.(691-693)AGG>AGA	p.R231R	WDR75_uc002uqm.1_Silent_p.R167R|WDR75_uc002uqn.1_Silent_p.R9R|WDR75_uc002uqo.1_Silent_p.R9R	NM_032168	NP_115544	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	231	WD 3.					nucleolus				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)			CCAATAGGAGGAATTTTTATG	0.318													58	387	---	---	---	---	PASS
NAB1	4664	broad.mit.edu	37	2	191555228	191555228	+	3'UTR	SNP	A	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191555228A>C	uc002usb.2	+	10					NAB1_uc010fsc.2_3'UTR|NAB1_uc010fsd.2_3'UTR|NAB1_uc002usc.2_3'UTR|NAB1_uc010zgh.1_3'UTR	NM_005966	NP_005957	Q13506	NAB1_HUMAN	NGFI-A binding protein 1						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0405)|all cancers(119;0.109)			AGATAAAACAACAGCCACAAA	0.368													6	6	---	---	---	---	PASS
SAG	6295	broad.mit.edu	37	2	234235795	234235795	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234235795C>T	uc002vuh.2	+	7	852	c.464C>T	c.(463-465)GCA>GTA	p.A155V	SAG_uc010zmq.1_Missense_Mutation_p.A21V	NM_000541	NP_000532	P10523	ARRS_HUMAN	S-arrestin	155					rhodopsin mediated phototransduction|rhodopsin mediated signaling pathway		protein phosphatase inhibitor activity			ovary(1)	1		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		GAGGTCAAAGCATTCGCCACA	0.592													13	64	---	---	---	---	PASS
TSEN2	80746	broad.mit.edu	37	3	12545142	12545142	+	Silent	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12545142C>T	uc003bxc.2	+	5	1077	c.690C>T	c.(688-690)CTC>CTT	p.L230L	TSEN2_uc003bwy.2_Silent_p.L230L|TSEN2_uc003bwz.2_Intron|TSEN2_uc003bxa.2_Silent_p.L230L|TSEN2_uc011auq.1_Silent_p.L230L|TSEN2_uc003bxb.2_Silent_p.L230L|TSEN2_uc011aur.1_Silent_p.L139L	NM_025265	NP_079541	Q8NCE0	SEN2_HUMAN	tRNA-intron nuclease 2 isoform 1	230					mRNA processing|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|nucleolus|tRNA-intron endonuclease complex	nucleic acid binding|tRNA-intron endonuclease activity			central_nervous_system(1)	1						CTCTCATCCTCCAGCGTGGCC	0.587													11	36	---	---	---	---	PASS
BSN	8927	broad.mit.edu	37	3	49662433	49662433	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49662433G>A	uc003cxe.3	+	2	364	c.250G>A	c.(250-252)GAA>AAA	p.E84K		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	84					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GGACCCCAAGGAACCCCTGGG	0.557													5	8	---	---	---	---	PASS
WDR52	55779	broad.mit.edu	37	3	113049451	113049451	+	Missense_Mutation	SNP	A	C	C	rs79365690		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113049451A>C	uc003ead.1	-	8	1236	c.1223T>G	c.(1222-1224)GTT>GGT	p.V408G	WDR52_uc010hqk.1_5'Flank			Q96MT7	WDR52_HUMAN	RecName: Full=WD repeat protein 52.; Flags: Fragment;	Error:Variant_position_missing_in_Q96MT7_after_alignment										central_nervous_system(1)	1						TTCCTCAACAACAGCCACTTT	0.408													31	243	---	---	---	---	PASS
C3orf15	89876	broad.mit.edu	37	3	119449158	119449158	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119449158C>T	uc003ede.3	+	8	1029	c.952C>T	c.(952-954)CGG>TGG	p.R318W	C3orf15_uc010hqy.1_Missense_Mutation_p.R318W|C3orf15_uc010hqz.2_Missense_Mutation_p.R256W|C3orf15_uc011bjd.1_Missense_Mutation_p.R192W|C3orf15_uc011bje.1_Missense_Mutation_p.R298W|C3orf15_uc010hra.1_Missense_Mutation_p.R79W	NM_033364	NP_203528	Q7Z4T9	AAT1_HUMAN	AAT1-alpha	318						mitochondrion	protein binding			ovary(2)|pancreas(1)	3				GBM - Glioblastoma multiforme(114;0.186)		CTTGAATGCCCGGTGGTCTAA	0.438													6	492	---	---	---	---	PASS
C3orf33	285315	broad.mit.edu	37	3	155493591	155493591	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155493591C>A	uc003fal.1	-	4	362	c.92G>T	c.(91-93)AGA>ATA	p.R31I	C3orf33_uc003fam.1_Missense_Mutation_p.R74I	NM_173657	NP_775928	Q96NB5	Q96NB5_HUMAN	hypothetical protein LOC285315	31							hydrolase activity, acting on ester bonds|nucleic acid binding				0			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			AACATTTCTTCTTATAAATTC	0.299													62	351	---	---	---	---	PASS
CNOT6L	246175	broad.mit.edu	37	4	78666018	78666018	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78666018C>A	uc011ccd.1	-	7	702	c.571G>T	c.(571-573)GTT>TTT	p.V191F	CNOT6L_uc003hks.2_Missense_Mutation_p.V191F|CNOT6L_uc003hkt.1_Missense_Mutation_p.V34F|CNOT6L_uc011cce.1_Intron	NM_144571	NP_653172	Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	191					nuclear-transcribed mRNA poly(A) tail shortening	cytosol	exonuclease activity|protein binding			large_intestine(1)	1						TAACACATAACCGTGAATGAT	0.403													8	263	---	---	---	---	PASS
SEC31A	22872	broad.mit.edu	37	4	83748633	83748633	+	Silent	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83748633G>A	uc003hnf.2	-	24	3344	c.3180C>T	c.(3178-3180)GGC>GGT	p.G1060G	SEC31A_uc003hnd.2_Silent_p.G229G|SEC31A_uc003hne.2_Silent_p.G809G|SEC31A_uc011ccl.1_Silent_p.G1006G|SEC31A_uc003hnl.2_Silent_p.G907G|SEC31A_uc003hng.2_Silent_p.G1045G|SEC31A_uc003hnh.2_Silent_p.G1060G|SEC31A_uc003hni.2_Silent_p.G946G|SEC31A_uc003hnj.2_Silent_p.G1021G|SEC31A_uc011ccm.1_Silent_p.G1040G|SEC31A_uc011ccn.1_Silent_p.G1045G|SEC31A_uc003hnk.2_Silent_p.G1021G|SEC31A_uc003hnm.2_Silent_p.G1060G	NM_001077207	NP_001070675	O94979	SC31A_HUMAN	SEC31 homolog A isoform 1	1060	Interaction with PDCD6.|Pro-rich.				COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)				GGAAGGGCTGGCCACCTGGAA	0.542													4	178	---	---	---	---	PASS
FAM13A	10144	broad.mit.edu	37	4	89649724	89649724	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89649724A>T	uc003hse.1	-	24	3240	c.3032T>A	c.(3031-3033)GTG>GAG	p.V1011E	FAM13A_uc011cdp.1_Missense_Mutation_p.V113E|FAM13A_uc003hsa.1_Missense_Mutation_p.V454E|FAM13A_uc003hsb.1_Missense_Mutation_p.V685E|FAM13A_uc003hsd.1_Missense_Mutation_p.V657E|FAM13A_uc003hsc.1_Missense_Mutation_p.V671E|FAM13A_uc011cdq.1_Missense_Mutation_p.V657E|FAM13A_uc003hsf.1_Missense_Mutation_p.V597E|FAM13AOS_uc003hry.1_RNA|FAM13AOS_uc003hrz.1_RNA	NM_014883	NP_055698	O94988	FA13A_HUMAN	family with sequence similarity 13, member A1	1011					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2						GCTGATGAGCACCTCCAGGAG	0.498													5	329	---	---	---	---	PASS
FAM13A	10144	broad.mit.edu	37	4	89649725	89649725	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89649725C>T	uc003hse.1	-	24	3239	c.3031G>A	c.(3031-3033)GTG>ATG	p.V1011M	FAM13A_uc011cdp.1_Missense_Mutation_p.V113M|FAM13A_uc003hsa.1_Missense_Mutation_p.V454M|FAM13A_uc003hsb.1_Missense_Mutation_p.V685M|FAM13A_uc003hsd.1_Missense_Mutation_p.V657M|FAM13A_uc003hsc.1_Missense_Mutation_p.V671M|FAM13A_uc011cdq.1_Missense_Mutation_p.V657M|FAM13A_uc003hsf.1_Missense_Mutation_p.V597M|FAM13AOS_uc003hry.1_RNA|FAM13AOS_uc003hrz.1_RNA	NM_014883	NP_055698	O94988	FA13A_HUMAN	family with sequence similarity 13, member A1	1011					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2						CTGATGAGCACCTCCAGGAGC	0.502													6	355	---	---	---	---	PASS
WWC2	80014	broad.mit.edu	37	4	184203759	184203759	+	Intron	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184203759G>T	uc010irx.2	+						WWC2_uc003ivk.3_Intron|WWC2_uc003ivl.3_Intron|WWC2_uc010iry.2_Intron|WWC2_uc003ivn.3_Intron|WWC2_uc010irz.2_Intron|WWC2_uc003ivo.3_5'Flank	NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2											ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		GGCTCATTGTGTGAGTCTGTT	0.403													5	25	---	---	---	---	PASS
KIAA1430	57587	broad.mit.edu	37	4	186097083	186097083	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186097083T>C	uc003ixf.3	-	3	1324	c.1177A>G	c.(1177-1179)AGG>GGG	p.R393G	KIAA1430_uc003ixg.2_Missense_Mutation_p.R393G	NM_020827	NP_065878	Q9P2B7	K1430_HUMAN	hypothetical protein LOC57587	393	Potential.										0		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)		TTCAAAAGCCTCTGATTTTCC	0.453													7	510	---	---	---	---	PASS
FAM105B	90268	broad.mit.edu	37	5	14693052	14693052	+	Silent	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14693052C>T	uc003jfk.2	+	7	1106	c.954C>T	c.(952-954)GTC>GTT	p.V318V		NM_138348	NP_612357	Q96BN8	F105B_HUMAN	hypothetical protein LOC90268	318										ovary(2)	2	Lung NSC(4;0.00696)					TCATCACAGTCTACCCCACCG	0.542													18	107	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19473346	19473346	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19473346T>C	uc003jgc.2	-	12	2739	c.2362A>G	c.(2362-2364)AGA>GGA	p.R788G	CDH18_uc003jgd.2_Missense_Mutation_p.R788G|CDH18_uc011cnm.1_3'UTR	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	788	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TAAGTTGTTCTTTCAGATTCT	0.428													6	108	---	---	---	---	PASS
ZSWIM6	57688	broad.mit.edu	37	5	60827477	60827477	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60827477T>A	uc003jsr.2	+	9	2170	c.2170T>A	c.(2170-2172)TCT>ACT	p.S724T		NM_020928	NP_065979	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	724							zinc ion binding				0						GCAGCTCATTTCTAAGCTTCA	0.463													31	140	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	90281200	90281200	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90281200C>A	uc003kju.2	+	85	18109	c.18013C>A	c.(18013-18015)CAC>AAC	p.H6005N	GPR98_uc003kjt.2_Missense_Mutation_p.H3711N|GPR98_uc003kjw.2_Missense_Mutation_p.H1666N|GPR98_uc003kjx.2_Missense_Mutation_p.H33N	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	6005	Cytoplasmic (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GAATGATGAGCACACAGAGAG	0.403													137	707	---	---	---	---	PASS
NCRNA00219	114915	broad.mit.edu	37	5	111496807	111496807	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111496807A>G	uc003kpq.1	+	1	582	c.329A>G	c.(328-330)TAC>TGC	p.Y110C	EPB41L4A_uc003kpp.1_Intron|NCRNA00219_uc003kps.2_RNA|SNORA13_uc003kpt.1_5'Flank					RecName: Full=Putative uncharacterized protein TIGA1;												0						ATTTGTGTTTACATCATCGAC	0.542													6	23	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12121984	12121984	+	Silent	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12121984C>A	uc003nac.2	+	4	2135	c.1956C>A	c.(1954-1956)ACC>ACA	p.T652T	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	652					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)				AGCAGGCTACCGATTACTCCC	0.493													3	47	---	---	---	---	PASS
ZNF184	7738	broad.mit.edu	37	6	27425183	27425183	+	Silent	SNP	C	A	A	rs61736959	byFrequency	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27425183C>A	uc003njj.2	-	3	892	c.81G>T	c.(79-81)GCG>GCT	p.A27A	ZNF184_uc010jqv.2_Silent_p.A27A|ZNF184_uc003nji.2_Silent_p.A27A	NM_007149	NP_009080	Q99676	ZN184_HUMAN	zinc finger protein 184	27					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						TGAAAGTCACCGCTTCCTGAA	0.418													4	262	---	---	---	---	PASS
ZKSCAN3	80317	broad.mit.edu	37	6	28329175	28329175	+	Silent	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28329175A>G	uc003nle.3	+	3	693	c.477A>G	c.(475-477)CAA>CAG	p.Q159Q	ZKSCAN3_uc010jrc.2_Silent_p.Q159Q|ZKSCAN3_uc003nlf.3_Silent_p.Q11Q	NM_024493	NP_077819	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	159					positive regulation of transcription, DNA-dependent|viral reproduction	nucleus	chromatin binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						CAGGGTCACAAAGTAGCCAAT	0.433													26	192	---	---	---	---	PASS
OR2B3	442184	broad.mit.edu	37	6	29054173	29054173	+	Silent	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29054173A>G	uc003nlx.2	-	1	918	c.853T>C	c.(853-855)TTG>CTG	p.L285L		NM_001005226	NP_001005226			olfactory receptor, family 2, subfamily B,											skin(1)	1						AGGGAGTTCAACATGGATGTG	0.403													31	159	---	---	---	---	PASS
NCR2	9436	broad.mit.edu	37	6	41309823	41309823	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41309823G>C	uc003oqh.2	+	4	667	c.580G>C	c.(580-582)GTG>CTG	p.V194L	NCR2_uc003oqi.2_Missense_Mutation_p.V206L|NCR2_uc003oqj.2_Missense_Mutation_p.V194L	NM_004828	NP_004819	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	194	Helical; (Potential).				cellular defense response	integral to plasma membrane	transmembrane receptor activity			ovary(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)					CATTGCCCTGGTGCCTGTGTT	0.637													5	182	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70878567	70878567	+	Silent	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70878567C>T	uc003pfc.1	+	40	2679	c.2562C>T	c.(2560-2562)GGC>GGT	p.G854G		NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	854	Triple-helical region 5 (COL5).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						GCGATCCTGGCCCAGTGGTAT	0.388													80	422	---	---	---	---	PASS
DOPEY1	23033	broad.mit.edu	37	6	83865677	83865677	+	Silent	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83865677A>G	uc003pjs.1	+	34	6719	c.6459A>G	c.(6457-6459)GTA>GTG	p.V2153V	DOPEY1_uc011dyy.1_Silent_p.V2144V|DOPEY1_uc010kbl.1_Silent_p.V2144V|DOPEY1_uc003pjt.2_RNA	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	2153					protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CAGCTCGTGTAGCAGTGGCTC	0.373													6	469	---	---	---	---	PASS
OSTM1	28962	broad.mit.edu	37	6	108365951	108365951	+	3'UTR	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108365951T>C	uc003psd.2	-	6					OSTM1_uc003pse.1_5'Flank	NM_014028	NP_054747	Q86WC4	OSTM1_HUMAN	osteopetrosis associated transmembrane protein 1							integral to membrane				central_nervous_system(1)	1		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0131)|Epithelial(106;0.0438)|OV - Ovarian serous cystadenocarcinoma(136;0.0571)|all cancers(137;0.0581)		CTTCCACCATTCATTCACGTG	0.348													6	561	---	---	---	---	PASS
RSPH4A	345895	broad.mit.edu	37	6	116948791	116948791	+	Splice_Site	SNP	G	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116948791G>C	uc003pxe.2	+	3	1067	c.922_splice	c.e3-1	p.A308_splice	RSPH4A_uc010kee.2_Splice_Site_p.A308_splice	NM_001010892	NP_001010892	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A isoform 1						cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton|radial spoke					0						TGTTTCCCCAGGCAGAAAACG	0.398									Kartagener_syndrome				7	288	---	---	---	---	PASS
RSPO3	84870	broad.mit.edu	37	6	127517220	127517220	+	3'UTR	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127517220C>T	uc003qar.2	+	5					RSPO3_uc003qas.1_Intron	NM_032784	NP_116173	Q9BXY4	RSPO3_HUMAN	R-spondin 3 precursor							extracellular region	heparin binding				0				GBM - Glioblastoma multiforme(226;0.0555)		GACAGGTGCTCTAGCCATTAG	0.418													25	138	---	---	---	---	PASS
TXLNB	167838	broad.mit.edu	37	6	139565732	139565732	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139565732C>A	uc011eds.1	-	9	1431	c.1266G>T	c.(1264-1266)GAG>GAT	p.E422D		NM_153235	NP_694967	Q8N3L3	TXLNB_HUMAN	taxilin beta	422	Potential.					cytoplasm				large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		ACTTCCTCACCTCTTCAATCA	0.388													7	697	---	---	---	---	PASS
STXBP5	134957	broad.mit.edu	37	6	147588238	147588238	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147588238T>C	uc003qlz.2	+	7	810	c.649T>C	c.(649-651)TCT>CCT	p.S217P	STXBP5_uc010khz.1_Missense_Mutation_p.S217P|STXBP5_uc003qlx.2_RNA|STXBP5_uc003qly.2_5'UTR	NM_001127715	NP_001121187	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn) isoform b	217	WD 4.				exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		TGGCTTTGAATCTGGAACAGT	0.313													104	654	---	---	---	---	PASS
IGF2R	3482	broad.mit.edu	37	6	160509177	160509177	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160509177G>T	uc003qta.2	+	42	6466	c.6318G>T	c.(6316-6318)AAG>AAT	p.K2106N		NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor	2106	14.|Lumenal (Potential).				receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)		CTGCATTCAAGAGGTCAGGAG	0.522											OREG0017769	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	91	---	---	---	---	PASS
MLLT4	4301	broad.mit.edu	37	6	168289959	168289959	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168289959A>G	uc003qwd.2	+	7	1101	c.959A>G	c.(958-960)GAT>GGT	p.D320G	MLLT4_uc003qwb.1_Missense_Mutation_p.D320G|MLLT4_uc003qwc.1_Missense_Mutation_p.D321G|MLLT4_uc003qwf.2_Missense_Mutation_p.D21G	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	321	Ras-associating 2.				adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		ATTCTTGATGATGATGAGTGT	0.363			T	MLL	AL								6	486	---	---	---	---	PASS
MLLT4	4301	broad.mit.edu	37	6	168343847	168343847	+	Silent	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168343847G>T	uc003qwd.2	+	23	3256	c.3114G>T	c.(3112-3114)TCG>TCT	p.S1038S	MLLT4_uc003qwb.1_Silent_p.S1023S|MLLT4_uc003qwc.1_Silent_p.S1039S|MLLT4_uc003qwg.1_Silent_p.S348S	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	1039	PDZ.				adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		ATGTGAAGTCGGTTGTGAAAG	0.383			T	MLL	AL								6	615	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	39894557	39894557	+	RNA	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39894557T>C	uc003thg.2	-	1		c.303A>G								full-length cDNA clone CS0DF025YB16 of Fetal brain of Homo sapiens (human).																		TCACCCTATGTTGAAAAGAAA	0.413													6	444	---	---	---	---	PASS
WBSCR16	81554	broad.mit.edu	37	7	74470047	74470047	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74470047G>A	uc003ubr.2	-	9	1318	c.1192C>T	c.(1192-1194)CGC>TGC	p.R398C	WBSCR16_uc010lca.2_Missense_Mutation_p.R201C|WBSCR16_uc010lcb.1_Missense_Mutation_p.R398C	NM_030798	NP_110425	Q96I51	WBS16_HUMAN	Williams-Beuren syndrome chromosome region 16	398	RCC1 5.										0						CATCGGATGCGGGAAACCTGG	0.542													8	108	---	---	---	---	PASS
SEMA3E	9723	broad.mit.edu	37	7	82997339	82997339	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82997339T>A	uc003uhy.1	-	17	2357	c.1891A>T	c.(1891-1893)AGA>TGA	p.R631*		NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor	631	Ig-like C2-type.				axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)				TTAACCACTCTGTCATCTGTC	0.403													44	224	---	---	---	---	PASS
PPP1R9A	55607	broad.mit.edu	37	7	94540664	94540664	+	Silent	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94540664C>T	uc003unp.2	+	2	1521	c.1239C>T	c.(1237-1239)GAC>GAT	p.D413D	PPP1R9A_uc010lfj.2_Silent_p.D413D|PPP1R9A_uc011kif.1_Silent_p.D413D|PPP1R9A_uc003unq.2_Silent_p.D413D|PPP1R9A_uc011kig.1_Silent_p.D413D	NM_017650	NP_060120	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	413						cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			ATAATTCAGACTGGGGAGAGA	0.423										HNSCC(28;0.073)			28	147	---	---	---	---	PASS
SLC26A4	5172	broad.mit.edu	37	7	107312680	107312680	+	Silent	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107312680A>G	uc003vep.2	+	4	626	c.402A>G	c.(400-402)AGA>AGG	p.R134R		NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin	134	Cytoplasmic (Potential).				regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7						GAACATCAAGACATATCTCAG	0.338									Pendred_syndrome				6	392	---	---	---	---	PASS
SLC26A4	5172	broad.mit.edu	37	7	107334908	107334908	+	Silent	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107334908C>T	uc003vep.2	+	11	1548	c.1324C>T	c.(1324-1326)CTG>TTG	p.L442L	SLC26A4_uc011kmb.1_Silent_p.L29L|SLC26A4_uc011kmc.1_Intron|SLC26A4_uc011kmd.1_Silent_p.L11L	NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin	442	Helical; (Potential).				regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7						GGGGAAGCTTCTGGAACCCTT	0.463									Pendred_syndrome				24	296	---	---	---	---	PASS
WASL	8976	broad.mit.edu	37	7	123332841	123332841	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123332841G>C	uc003vkz.2	-	9	1235	c.907C>G	c.(907-909)CCT>GCT	p.P303A		NM_003941	NP_003932	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome gene-like protein	303	Pro-rich.				actin polymerization or depolymerization|axon guidance|cellular component movement|nitric oxide metabolic process|protein complex assembly|regulation of nitric-oxide synthase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|cytosol|nucleolus|plasma membrane	actin binding|small GTPase regulator activity				0						CCCCTagcaggaggaggagga	0.443													3	29	---	---	---	---	PASS
OR2A2	442361	broad.mit.edu	37	7	143807113	143807113	+	Silent	SNP	G	A	A	rs141248378	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143807113G>A	uc011ktz.1	+	1	438	c.438G>A	c.(436-438)ACG>ACA	p.T146T		NM_001005480	NP_001005480	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A,	146	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	Melanoma(164;0.0783)					TGGTTCTCACGTCCTGGTCAT	0.517													7	243	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	3245041	3245041	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3245041C>T	uc011kwk.1	-	18	3150	c.2760G>A	c.(2758-2760)TGG>TGA	p.W920*	CSMD1_uc011kwj.1_Nonsense_Mutation_p.W312*|CSMD1_uc003wqe.2_Nonsense_Mutation_p.W76*	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	920	Extracellular (Potential).|Sushi 5.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		AGGCGTGGTTCCACTGGTGGT	0.587													3	32	---	---	---	---	PASS
JPH1	56704	broad.mit.edu	37	8	75227397	75227397	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75227397T>C	uc003yae.2	-	2	878	c.838A>G	c.(838-840)ACC>GCC	p.T280A	JPH1_uc003yaf.2_Missense_Mutation_p.T280A|JPH1_uc003yag.1_Missense_Mutation_p.T144A	NM_020647	NP_065698	Q9HDC5	JPH1_HUMAN	junctophilin 1	280	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			CCCATGTAGGTTTCCGTGGTG	0.537													8	101	---	---	---	---	PASS
KLF10	7071	broad.mit.edu	37	8	103664082	103664082	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103664082C>A	uc011lhk.1	-	3	632	c.478G>T	c.(478-480)GCT>TCT	p.A160S	KLF10_uc011lhj.1_Missense_Mutation_p.A149S	NM_005655	NP_005646	Q13118	KLF10_HUMAN	Kruppel-like factor 10 isoform a	160					cell proliferation|cell-cell signaling|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|skeletal system development|transforming growth factor beta receptor signaling pathway	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			TGGGCATCAGCTGTATGACGA	0.473											OREG0018913	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	71	---	---	---	---	PASS
MED30	90390	broad.mit.edu	37	8	118552346	118552346	+	3'UTR	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118552346C>A	uc003yoj.2	+	4					MED30_uc011lib.1_3'UTR	NM_080651	NP_542382	Q96HR3	MED30_HUMAN	TRAP/Mediator complex component TRAP25						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding				0	all_cancers(13;3.41e-25)|Lung NSC(37;3.02e-05)|Ovarian(258;0.00163)		STAD - Stomach adenocarcinoma(47;0.0266)			TTTATTTTTACATTGTGATTT	0.224													4	37	---	---	---	---	PASS
PTENP1	11191	broad.mit.edu	37	9	33675379	33675379	+	3'UTR	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33675379C>A	uc003zth.3	-	1						NR_023917				SubName: Full=Phosphatase and tensin homolog 2; Flags: Fragment;												0						AAAAAGGTCCCTTTTCAGTTT	0.318													3	45	---	---	---	---	PASS
OR13C8	138802	broad.mit.edu	37	9	107332046	107332046	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107332046A>G	uc011lvo.1	+	1	598	c.598A>G	c.(598-600)ACA>GCA	p.T200A		NM_001004483	NP_001004483	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C,	200	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						GATTAGTATGACAGGGTCGAA	0.358													7	570	---	---	---	---	PASS
PSMD5	5711	broad.mit.edu	37	9	123580304	123580304	+	Silent	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123580304A>G	uc004bko.2	-	10	1414	c.1395T>C	c.(1393-1395)AAT>AAC	p.N465N	PSMD5_uc011lye.1_Silent_p.N422N	NM_005047	NP_005038	Q16401	PSMD5_HUMAN	proteasome 26S non-ATPase subunit 5	465					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|proteasome regulatory particle assembly|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	protein binding				0						TTGTCTTGGAATTGGCAAGTG	0.428													5	277	---	---	---	---	PASS
PSMB7	5695	broad.mit.edu	37	9	127177673	127177673	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127177673A>T	uc004boj.2	-	1	49	c.32T>A	c.(31-33)GTT>GAT	p.V11D	PSMB7_uc010mwm.2_Missense_Mutation_p.V11D	NM_002799	NP_002790	Q99436	PSB7_HUMAN	proteasome beta 7 subunit proprotein	11					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0						GAAGCCTCCAACTGGTGGAGC	0.612											OREG0019476	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	54	---	---	---	---	PASS
TOR1B	27348	broad.mit.edu	37	9	132571289	132571289	+	Silent	SNP	C	A	A	rs112230862		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132571289C>A	uc004byk.1	+	4	807	c.747C>A	c.(745-747)GTC>GTA	p.V249V		NM_014506	NP_055321	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B) precursor	249					chaperone mediated protein folding requiring cofactor|response to unfolded protein	endoplasmic reticulum lumen	ATP binding|nucleoside-triphosphatase activity|unfolded protein binding				0		Ovarian(14;0.0586)				TACTGTCTGTCGGAGTCTTCA	0.502													4	191	---	---	---	---	PASS
LOC441666	441666	broad.mit.edu	37	10	42833154	42833154	+	RNA	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42833154T>C	uc010qey.1	-	3		c.821A>G				NR_024380				Homo sapiens noncoding mRNA sequence.												0						TTGTAGGTTGTATCTCCAGTA	0.338													3	15	---	---	---	---	PASS
C10orf4	118924	broad.mit.edu	37	10	95459948	95459948	+	Intron	SNP	A	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95459948A>C	uc001kiz.1	-						C10orf4_uc001kiv.1_Intron|C10orf4_uc001kja.1_Intron|C10orf4_uc001kjb.1_5'UTR|C10orf4_uc009xuh.1_Intron	NM_145246	NP_660289	Q70Z53	F10C1_HUMAN	FRA10AC1 protein							nucleus	protein binding				0		Colorectal(252;0.122)				gttatcttaaacagccacaat	0.149													30	61	---	---	---	---	PASS
JAKMIP3	282973	broad.mit.edu	37	10	133961488	133961488	+	Silent	SNP	C	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133961488C>G	uc001lkx.3	+	13	1782	c.1782C>G	c.(1780-1782)CTC>CTG	p.L594L	JAKMIP3_uc009yba.1_Silent_p.L31L	NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		AGGCTCGGCTCAGACACGAGG	0.552													12	86	---	---	---	---	PASS
SLC5A12	159963	broad.mit.edu	37	11	26702712	26702712	+	Silent	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26702712C>T	uc001mra.2	-	12	1678	c.1365G>A	c.(1363-1365)GGG>GGA	p.G455G	SLC5A12_uc001mrb.2_RNA	NM_178498	NP_848593	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/glucose	455	Helical; (Potential).				sodium ion transport	apical plasma membrane|integral to membrane	symporter activity			ovary(1)|skin(1)	2						AAATGAAGGCCCCAATGGCCA	0.473													4	179	---	---	---	---	PASS
MIR129-2	406918	broad.mit.edu	37	11	43602946	43602946	+	RNA	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43602946C>A	hsa-mir-129-2|MI0000473	+			c.3C>A			uc001mxo.1_RNA																	0						GCATATTCTGCCCTTCGCGAA	0.592													7	109	---	---	---	---	PASS
KBTBD4	55709	broad.mit.edu	37	11	47599123	47599123	+	Silent	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47599123T>C	uc001nfx.2	-	2	600	c.429A>G	c.(427-429)CAA>CAG	p.Q143Q	NDUFS3_uc001nft.3_Intron|KBTBD4_uc001nfw.1_Silent_p.Q168Q|KBTBD4_uc001nfz.2_Silent_p.Q159Q|KBTBD4_uc001nfy.2_Silent_p.Q143Q|NDUFS3_uc010rhn.1_5'Flank|NDUFS3_uc001nga.2_5'Flank	NM_016506	NP_057590	Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	143										ovary(1)|central_nervous_system(1)	2						AGTTTCCCACTTGCACTGTGC	0.537													20	133	---	---	---	---	PASS
MPEG1	219972	broad.mit.edu	37	11	58978936	58978936	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58978936C>T	uc001nnu.3	-	1	1559	c.1403G>A	c.(1402-1404)AGC>AAC	p.S468N		NM_001039396	NP_001034485	Q2M385	MPEG1_HUMAN	macrophage expressed gene 1 precursor	468	Extracellular (Potential).					integral to membrane				ovary(1)|skin(1)	2		all_epithelial(135;0.125)				TACTTGGCTGCTGGCCACACA	0.512													5	155	---	---	---	---	PASS
MS4A14	84689	broad.mit.edu	37	11	60183100	60183100	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60183100A>C	uc001npj.2	+	5	1224	c.659A>C	c.(658-660)CAA>CCA	p.Q220P	MS4A14_uc001npi.2_Missense_Mutation_p.Q108P|MS4A14_uc001npn.2_5'UTR|MS4A14_uc001npk.2_Missense_Mutation_p.Q203P|MS4A14_uc001npl.2_5'UTR|MS4A14_uc001npm.2_5'UTR	NM_032597	NP_115986	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member	220						integral to membrane	receptor activity			breast(1)	1						TTAGTCTCCCAACCAGGTAAT	0.398													37	331	---	---	---	---	PASS
KIAA1731	85459	broad.mit.edu	37	11	93460149	93460149	+	Silent	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93460149A>G	uc009ywb.1	+	24	6658	c.6507A>G	c.(6505-6507)GAA>GAG	p.E2169E	KIAA1731_uc001pdu.1_Silent_p.E349E|KIAA1731_uc001pdw.1_Silent_p.E181E|KIAA1731_uc001pdx.1_Silent_p.E35E	NM_033395	NP_203753	Q9C0D2	K1731_HUMAN	hypothetical protein LOC85459	2169						centrosome					0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CAGGATCTGAACAATGTTTTG	0.363													5	231	---	---	---	---	PASS
MMP10	4319	broad.mit.edu	37	11	102647343	102647343	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102647343C>A	uc001phg.1	-	5	809	c.787G>T	c.(787-789)GGA>TGA	p.G263*		NM_002425	NP_002416	P09238	MMP10_HUMAN	matrix metalloproteinase 10 preproprotein	263					collagen catabolic process|proteolysis	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			kidney(1)|lung(1)|breast(1)|central_nervous_system(1)	4	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)		CATCACTCACCGTAGAGAGAC	0.458													4	170	---	---	---	---	PASS
STT3A	3703	broad.mit.edu	37	11	125479362	125479362	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125479362C>A	uc001qcd.2	+	10	1105	c.995C>A	c.(994-996)TCG>TAG	p.S332*	STT3A_uc009zbm.2_Nonsense_Mutation_p.S332*|STT3A_uc001qce.2_Nonsense_Mutation_p.S332*|STT3A_uc010sbg.1_Nonsense_Mutation_p.S240*|STT3A_uc009zbn.2_Intron	NM_152713	NP_689926	P46977	STT3A_HUMAN	integral membrane protein 1	332	Cytoplasmic (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity				0	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		CGTTTCTACTCGCTGCTGGAT	0.453													65	294	---	---	---	---	PASS
RAD52	5893	broad.mit.edu	37	12	1025464	1025464	+	Intron	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1025464C>A	uc001qis.1	-						RAD52_uc001qit.1_Intron|RAD52_uc010sdt.1_Intron|RAD52_uc001qiu.1_Intron|RAD52_uc001qiv.1_Intron|RAD52_uc001qiw.1_Intron|RAD52_uc010sdu.1_3'UTR	NM_134424	NP_602296	P43351	RAD52_HUMAN	RAD52 homolog						DNA recombinase assembly|mitotic recombination|reciprocal meiotic recombination	nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)			GGCTACACTTCCTCCTGCAGA	0.572								Homologous_recombination					8	16	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2721135	2721135	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2721135T>C	uc009zdu.1	+	30	4157	c.3844T>C	c.(3844-3846)TTC>CTC	p.F1282L	CACNA1C_uc009zdv.1_Missense_Mutation_p.F1259L|CACNA1C_uc001qkb.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qkc.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qke.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qkf.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qjz.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qkd.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qkg.2_Missense_Mutation_p.F1262L|CACNA1C_uc009zdw.1_Missense_Mutation_p.F1262L|CACNA1C_uc001qkh.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qkl.2_Missense_Mutation_p.F1282L|CACNA1C_uc001qkn.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qko.2_Missense_Mutation_p.F1282L|CACNA1C_uc001qkp.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qkr.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qku.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qkq.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qks.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qkt.2_Missense_Mutation_p.F1262L|CACNA1C_uc001qka.1_Missense_Mutation_p.F797L|CACNA1C_uc001qki.1_Missense_Mutation_p.F998L|CACNA1C_uc001qkj.1_Missense_Mutation_p.F998L|CACNA1C_uc001qkk.1_Missense_Mutation_p.F998L|CACNA1C_uc001qkm.1_Missense_Mutation_p.F998L	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	1282	Helical; Name=S2 of repeat IV; (Potential).|IV.				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	CACTGGCCTCTTCACCGTGGA	0.547													5	206	---	---	---	---	PASS
CD27	939	broad.mit.edu	37	12	6554632	6554632	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6554632C>A	uc001qod.2	+	2	390	c.179C>A	c.(178-180)GCT>GAT	p.A60D	LOC678655_uc001qob.2_Intron|LOC678655_uc001qoc.2_Intron|LOC678655_uc009zel.1_Intron|CD27_uc001qoe.2_5'UTR	NM_001242	NP_001233	P26842	CD27_HUMAN	tumor necrosis factor receptor superfamily,	60	Extracellular (Potential).|TNFR-Cys 1.				anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway|immunoglobulin mediated immune response|induction of apoptosis|positive regulation of B cell differentiation|positive regulation of JNK cascade|release of cytoplasmic sequestered NF-kappaB	extracellular region|integral to plasma membrane	caspase inhibitor activity|protein binding|transmembrane receptor activity				0						AGAAAGGCTGCTCAGTGTGAT	0.582													14	86	---	---	---	---	PASS
VAMP1	6843	broad.mit.edu	37	12	6572035	6572035	+	3'UTR	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6572035A>G	uc001qok.2	-	5					TAPBPL_uc001qoi.1_Intron|VAMP1_uc001qoj.2_Intron|VAMP1_uc001qol.2_3'UTR	NM_014231	NP_055046	P23763	VAMP1_HUMAN	vesicle-associated membrane protein 1 isoform 1						neurotransmitter secretion|vesicle-mediated transport	cell junction|endocytic vesicle membrane|integral to plasma membrane|mitochondrial outer membrane|synaptic vesicle membrane|synaptosome	protein binding				0					Botulinum Toxin Type B(DB00042)	GGAATGTGGGAAACAAGGGCG	0.572													5	250	---	---	---	---	PASS
GPRC5D	55507	broad.mit.edu	37	12	13102515	13102515	+	Silent	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13102515C>T	uc010shp.1	-	1	804	c.804G>A	c.(802-804)TCG>TCA	p.S268S		NM_018654	NP_061124	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, family C, group 5,	268	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		CCTGTCTACACGATCTGTAGA	0.562													4	121	---	---	---	---	PASS
SLCO1A2	6579	broad.mit.edu	37	12	21471799	21471799	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21471799A>G	uc001rer.2	-	2	370	c.119T>C	c.(118-120)ATG>ACG	p.M40T	SLCO1A2_uc001res.2_Missense_Mutation_p.M40T|SLCO1A2_uc010siq.1_5'UTR|SLCO1A2_uc010sio.1_5'UTR|SLCO1A2_uc010sip.1_Intron|SLCO1A2_uc001ret.2_Missense_Mutation_p.M38T|SLCO1A2_uc001reu.2_Missense_Mutation_p.M20T	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A	40	Helical; Name=1; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						CATGGAATTCATATAAGATCC	0.303													6	449	---	---	---	---	PASS
SOX5	6660	broad.mit.edu	37	12	23998950	23998950	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23998950T>A	uc001rfw.2	-	3	550	c.448A>T	c.(448-450)AAA>TAA	p.K150*	SOX5_uc001rfx.2_Nonsense_Mutation_p.K137*|SOX5_uc001rfy.2_Nonsense_Mutation_p.K137*|SOX5_uc010siv.1_Nonsense_Mutation_p.K137*|SOX5_uc010siw.1_RNA|SOX5_uc001rfz.1_Nonsense_Mutation_p.K102*|SOX5_uc001rga.2_Nonsense_Mutation_p.K115*	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	150					transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						TCTTCCATTTTCCTCTGCTTC	0.458													42	267	---	---	---	---	PASS
ZNF641	121274	broad.mit.edu	37	12	48737208	48737208	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48737208C>T	uc001rrn.1	-	6	1030	c.865G>A	c.(865-867)GAG>AAG	p.E289K	ZNF641_uc001rro.1_Missense_Mutation_p.E275K|ZNF641_uc010sls.1_Missense_Mutation_p.E266K	NM_152320	NP_689533	Q96N77	ZN641_HUMAN	zinc finger protein 641	289					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2						TAGGGTCTCTCCCCAGTGTGT	0.532													13	177	---	---	---	---	PASS
KRT5	3852	broad.mit.edu	37	12	52910988	52910988	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52910988C>T	uc001san.2	-	6	1284	c.1121G>A	c.(1120-1122)CGG>CAG	p.R374Q	KRT5_uc009zmh.2_Missense_Mutation_p.R374Q	NM_000424	NP_000415	P13647	K2C5_HUMAN	keratin 5	374	Rod.|Coil 2.				epidermis development|hemidesmosome assembly	cytosol|keratin filament	protein binding|structural constituent of cytoskeleton				0				BRCA - Breast invasive adenocarcinoma(357;0.189)		ATCGCCATGCCGGCCAGCTGT	0.498													10	113	---	---	---	---	PASS
HNRNPA1	3178	broad.mit.edu	37	12	54675316	54675316	+	Intron	SNP	A	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54675316A>C	uc001sfl.2	+						CBX5_uc001sfk.3_5'Flank|CBX5_uc001sfi.3_5'Flank|HNRNPA1_uc001sfm.2_Intron|HNRNPA1_uc009zng.2_Intron|HNRNPA1_uc009znh.2_Intron|HNRNPA1_uc009zni.2_Intron|HNRNPA1_uc001sfn.2_Intron|HNRNPA1_uc001sfo.3_Intron|HNRNPA1_uc001sfp.1_5'UTR|HNRNPA1_uc009znj.1_5'Flank	NM_031157	NP_112420	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1						interspecies interaction between organisms|mRNA transport|nuclear import	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	nucleotide binding|protein binding|single-stranded DNA binding			skin(2)|ovary(1)	3						AAGCAGTAAAACAGCCGATTT	0.443													12	25	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88465604	88465604	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88465604A>G	uc001tar.2	-	42	6153	c.5809T>C	c.(5809-5811)TTT>CTT	p.F1937L	CEP290_uc001taq.2_Missense_Mutation_p.F997L	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	1937	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						GTTAAAGTAAAGACTTCCCCC	0.318													7	684	---	---	---	---	PASS
TMTC3	160418	broad.mit.edu	37	12	88554473	88554473	+	Silent	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88554473A>G	uc001tau.2	+	6	862	c.642A>G	c.(640-642)CTA>CTG	p.L214L	TMTC3_uc009zsm.2_RNA	NM_181783	NP_861448	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat	214	Helical; (Potential).					integral to membrane	binding			skin(1)	1						TGCCATTACTATGTACTACTG	0.338													5	393	---	---	---	---	PASS
KIAA1033	23325	broad.mit.edu	37	12	105551085	105551085	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105551085C>T	uc001tld.2	+	28	2984	c.2897C>T	c.(2896-2898)ACA>ATA	p.T966I	KIAA1033_uc010swr.1_Missense_Mutation_p.T967I|KIAA1033_uc010sws.1_Missense_Mutation_p.T778I	NM_015275	NP_056090	Q2M389	WAHS7_HUMAN	hypothetical protein LOC23325	966					endosome transport	WASH complex				kidney(1)|central_nervous_system(1)	2						GCAGAAGAAACATTAAAAGCA	0.284													6	347	---	---	---	---	PASS
BRAP	8315	broad.mit.edu	37	12	112119468	112119468	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112119468T>C	uc001tsn.3	-	3	610	c.416A>G	c.(415-417)CAT>CGT	p.H139R	BRAP_uc010syh.1_5'UTR|BRAP_uc009zvv.2_Missense_Mutation_p.H109R	NM_006768	NP_006759	Q7Z569	BRAP_HUMAN	BRCA1 associated protein	139					MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1						CATAATACCATGAACTATTTC	0.368													5	311	---	---	---	---	PASS
ACAD10	80724	broad.mit.edu	37	12	112147524	112147524	+	Intron	SNP	A	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112147524A>C	uc001tsq.2	+						ACAD10_uc009zvw.2_3'UTR|ACAD10_uc001tso.3_Intron|ACAD10_uc001tsp.2_Intron|ACAD10_uc009zvx.2_Intron|ACAD10_uc001tsr.2_5'Flank	NM_025247	NP_079523	Q6JQN1	ACD10_HUMAN	acyl-Coenzyme A dehydrogenase family, member 10								acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2						CCTCCCATGCACCAGCCACTA	0.388													5	30	---	---	---	---	PASS
ACADS	35	broad.mit.edu	37	12	121176678	121176678	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121176678G>A	uc001tza.3	+	8	1107	c.989G>A	c.(988-990)CGC>CAC	p.R330H	ACADS_uc010szl.1_Missense_Mutation_p.R326H|ACADS_uc001tzb.3_Missense_Mutation_p.R211H	NM_000017	NP_000008	P16219	ACADS_HUMAN	short-chain acyl-CoA dehydrogenase precursor	330						mitochondrial matrix	butyryl-CoA dehydrogenase activity			central_nervous_system(2)	2	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)	Lung NSC(355;0.163)			NADH(DB00157)	CTGACCTGGCGCGCTGCCATG	0.642													3	11	---	---	---	---	PASS
TPTE2	93492	broad.mit.edu	37	13	20006705	20006705	+	Missense_Mutation	SNP	C	G	G	rs138094641	byFrequency	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20006705C>G	uc001umd.2	-	17	1341	c.1130G>C	c.(1129-1131)GGA>GCA	p.G377A	TPTE2_uc009zzk.2_RNA|TPTE2_uc009zzl.2_Missense_Mutation_p.G266A|TPTE2_uc001ume.2_Missense_Mutation_p.G300A|TPTE2_uc009zzm.2_Missense_Mutation_p.G48A|TPTE2_uc010tcm.1_RNA|TPTE2_uc010tcl.1_Missense_Mutation_p.G48A	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	377	Phosphatase tensin-type.					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TGCAAAATATCCAACATATCT	0.323													5	147	---	---	---	---	PASS
TPTE2	93492	broad.mit.edu	37	13	20006716	20006716	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20006716A>C	uc001umd.2	-	17	1330	c.1119T>G	c.(1117-1119)AAT>AAG	p.N373K	TPTE2_uc009zzk.2_RNA|TPTE2_uc009zzl.2_Missense_Mutation_p.N262K|TPTE2_uc001ume.2_Missense_Mutation_p.N296K|TPTE2_uc009zzm.2_Missense_Mutation_p.N44K|TPTE2_uc010tcm.1_RNA|TPTE2_uc010tcl.1_Missense_Mutation_p.N44K	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	373	Phosphatase tensin-type.					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		CAACATATCTATTCTGAAAAG	0.318													7	133	---	---	---	---	PASS
SACS	26278	broad.mit.edu	37	13	23907922	23907922	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23907922G>C	uc001uon.2	-	10	10682	c.10093C>G	c.(10093-10095)CTA>GTA	p.L3365V	SACS_uc001uoo.2_Missense_Mutation_p.L3218V|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	3365					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		ATATAATGTAGAGCCTTCAAG	0.353													48	198	---	---	---	---	PASS
SLC25A30	253512	broad.mit.edu	37	13	45976461	45976461	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45976461T>C	uc001vag.2	-	6	575	c.438A>G	c.(436-438)ATA>ATG	p.I146M	SLC25A30_uc010tfs.1_Missense_Mutation_p.I71M|SLC25A30_uc001vah.2_Missense_Mutation_p.I71M|SLC25A30_uc010tft.1_Missense_Mutation_p.I95M|SLC25A30_uc001vaf.2_Missense_Mutation_p.I2M	NM_001010875	NP_001010875	Q5SVS4	KMCP1_HUMAN	solute carrier family 25, member 30	146	Solcar 2.				mitochondrial transport	integral to membrane|mitochondrial inner membrane	binding			breast(1)	1		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.95e-05)		TGAAGTTGCCTATCATTCCTC	0.413													5	559	---	---	---	---	PASS
MYCBP2	23077	broad.mit.edu	37	13	77629761	77629761	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77629761A>G	uc001vkf.2	-	81	13556	c.13465T>C	c.(13465-13467)TTT>CTT	p.F4489L	MYCBP2_uc010aev.2_Missense_Mutation_p.F3893L|MYCBP2_uc001vke.2_Missense_Mutation_p.F1106L	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	4489					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TCATTATAAAACCTCACACCA	0.348													41	255	---	---	---	---	PASS
CHD8	57680	broad.mit.edu	37	14	21883992	21883992	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21883992T>A	uc001was.1	-	6	1048	c.954A>T	c.(952-954)GAA>GAT	p.E318D	CHD8_uc001war.1_Missense_Mutation_p.E214D	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	597					ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		CTTCTTCTTCTTCATCATCTG	0.438													6	478	---	---	---	---	PASS
HEATR5A	25938	broad.mit.edu	37	14	31774139	31774139	+	Silent	SNP	G	T	T	rs61754159		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31774139G>T	uc001wrf.3	-	26	4409	c.4332C>A	c.(4330-4332)TCC>TCA	p.S1444S	HEATR5A_uc010ami.2_Silent_p.S1342S	NM_015473	NP_056288	Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	1731							binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		CAGGAAGTTCGGAAAGGATAA	0.418													4	290	---	---	---	---	PASS
C14orf37	145407	broad.mit.edu	37	14	58471373	58471373	+	3'UTR	SNP	T	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58471373T>G	uc001xdc.2	-	8					C14orf37_uc010tro.1_3'UTR	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor							integral to membrane	binding				0						ATGTGGCAGGTTGTTCTTTTT	0.383													12	37	---	---	---	---	PASS
UPF0639	400224	broad.mit.edu	37	14	69992827	69992827	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69992827T>C	uc010ttf.1	+	9	1123	c.911T>C	c.(910-912)CTG>CCG	p.L304P		NM_001161498	NP_001154970	B9EJC2	B9EJC2_HUMAN	similar to pleckstrin homology domain protein	304											0						GAGAAGCTCCTGGCAGAGAAG	0.592													8	29	---	---	---	---	PASS
BTBD7	55727	broad.mit.edu	37	14	93723595	93723595	+	Silent	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93723595A>G	uc001ybo.2	-	6	1880	c.1554T>C	c.(1552-1554)CCT>CCC	p.P518P	BTBD7_uc010aur.2_Silent_p.P43P|BTBD7_uc010two.1_Silent_p.P338P|BTBD7_uc001ybp.2_Silent_p.P167P|BTBD7_uc001ybq.3_Silent_p.P433P	NM_001002860	NP_001002860	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7 isoform 1	518										pancreas(1)	1		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		TTCGCACAAAAGGTAAGAGAG	0.403													7	385	---	---	---	---	PASS
C14orf153	84334	broad.mit.edu	37	14	104056602	104056602	+	Silent	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104056602A>G	uc010tyc.1	+	5	601	c.600A>G	c.(598-600)AAA>AAG	p.K200K	KLC1_uc010tyd.1_Intron|C14orf153_uc001ynl.3_RNA	NM_032374	NP_115750	Q96IL0	CN153_HUMAN	chromosome 14 open reading frame 153	187											0		Melanoma(154;0.226)				TTAAACAGAAACAAAAGAAGA	0.473													5	145	---	---	---	---	PASS
SPRED1	161742	broad.mit.edu	37	15	38591742	38591742	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38591742C>G	uc001zka.3	+	2	536	c.201C>G	c.(199-201)GAC>GAG	p.D67E		NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain	67	WH1.				inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		GACTCAGGGACAAAATGGTAA	0.368									Legius_syndrome				13	105	---	---	---	---	PASS
SLC24A5	283652	broad.mit.edu	37	15	48428782	48428782	+	Intron	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48428782C>A	uc001zwe.2	+						SLC24A5_uc010bel.2_Intron|uc001zwf.1_RNA	NM_205850	NP_995322	Q71RS6	NCKX5_HUMAN	solute carrier family 24, member 5 precursor						response to stimulus	integral to membrane|melanosome|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity				0		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		TCTATGGCTACTTTTGTTAGA	0.279													13	83	---	---	---	---	PASS
DMXL2	23312	broad.mit.edu	37	15	51778458	51778458	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51778458G>T	uc002abf.2	-	23	5519	c.5294C>A	c.(5293-5295)TCA>TAA	p.S1765*	DMXL2_uc010ufy.1_Nonsense_Mutation_p.S1765*|DMXL2_uc010bfa.2_Nonsense_Mutation_p.S1129*	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1765						cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)		ATAAGTGGATGAAGTCTCAAA	0.353													38	209	---	---	---	---	PASS
DMXL2	23312	broad.mit.edu	37	15	51778460	51778460	+	Silent	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51778460A>G	uc002abf.2	-	23	5517	c.5292T>C	c.(5290-5292)ACT>ACC	p.T1764T	DMXL2_uc010ufy.1_Silent_p.T1764T|DMXL2_uc010bfa.2_Silent_p.T1128T	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1764						cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)		AAGTGGATGAAGTCTCAAATT	0.348													36	209	---	---	---	---	PASS
TCF12	6938	broad.mit.edu	37	15	57489997	57489997	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57489997A>G	uc002aec.2	+	8	837	c.553A>G	c.(553-555)AAG>GAG	p.K185E	TCF12_uc010ugm.1_Missense_Mutation_p.K237E|TCF12_uc010ugn.1_Missense_Mutation_p.K181E|TCF12_uc002aea.2_Missense_Mutation_p.K185E|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Missense_Mutation_p.K185E|TCF12_uc002aed.2_Missense_Mutation_p.K185E	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b	185					immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		AAAAGTCAGAAAGGTGCCTCC	0.348			T	TEC	extraskeletal myxoid chondrosarcoma								63	331	---	---	---	---	PASS
TCF12	6938	broad.mit.edu	37	15	57489998	57489998	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57489998A>G	uc002aec.2	+	8	838	c.554A>G	c.(553-555)AAG>AGG	p.K185R	TCF12_uc010ugm.1_Missense_Mutation_p.K237R|TCF12_uc010ugn.1_Missense_Mutation_p.K181R|TCF12_uc002aea.2_Missense_Mutation_p.K185R|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Missense_Mutation_p.K185R|TCF12_uc002aed.2_Missense_Mutation_p.K185R	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b	185					immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		AAAGTCAGAAAGGTGCCTCCT	0.353			T	TEC	extraskeletal myxoid chondrosarcoma								65	330	---	---	---	---	PASS
LACTB	114294	broad.mit.edu	37	15	63421946	63421946	+	Intron	SNP	A	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63421946A>C	uc002alw.2	+						LACTB_uc002alv.2_3'UTR	NM_032857	NP_116246	P83111	LACTB_HUMAN	lactamase, beta isoform a							mitochondrion	hydrolase activity				0						TCCAAAATCAACCTGCCACAT	0.323													7	9	---	---	---	---	PASS
PIAS1	8554	broad.mit.edu	37	15	68480214	68480214	+	3'UTR	SNP	T	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68480214T>G	uc002aqz.2	+	14					PIAS1_uc002ara.2_3'UTR	NM_016166	NP_057250	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1						androgen receptor signaling pathway|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|positive regulation of protein sumoylation|positive regulation of transcription, DNA-dependent|regulation of interferon-gamma-mediated signaling pathway|transcription, DNA-dependent	nuclear speck	androgen receptor binding|DNA binding|enzyme binding|SUMO ligase activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)	2						CCAGATCGAATGAACTTGGCA	0.428													4	20	---	---	---	---	PASS
FEM1B	10116	broad.mit.edu	37	15	68582835	68582835	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68582835A>T	uc002arg.2	+	2	1754	c.1139A>T	c.(1138-1140)AAC>ATC	p.N380I	FEM1B_uc002arh.2_Missense_Mutation_p.N300I	NM_015322	NP_056137	Q9UK73	FEM1B_HUMAN	fem-1 homolog b	380					apoptosis|induction of apoptosis|regulation of DNA damage checkpoint|regulation of ubiquitin-protein ligase activity	cytoplasm|nucleus	death receptor binding|ubiquitin-protein ligase activity				0						GGTAACAGGAACACCCACAAG	0.408													34	201	---	---	---	---	PASS
ARIH1	25820	broad.mit.edu	37	15	72873082	72873082	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72873082C>A	uc002aut.3	+	12	1540	c.1226C>A	c.(1225-1227)GCA>GAA	p.A409E		NM_005744	NP_005735	Q9Y4X5	ARI1_HUMAN	ariadne ubiquitin-conjugating enzyme E2 binding	409					ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding				0						CGATCTAGGGCAGCCCTGCAG	0.353													8	131	---	---	---	---	PASS
TSC2	7249	broad.mit.edu	37	16	2131631	2131631	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2131631C>A	uc002con.2	+	31	3752	c.3646C>A	c.(3646-3648)CTC>ATC	p.L1216I	TSC2_uc010bsd.2_Missense_Mutation_p.L1216I|TSC2_uc002coo.2_Missense_Mutation_p.L1172I|TSC2_uc010uvv.1_Missense_Mutation_p.L1136I|TSC2_uc010uvw.1_Missense_Mutation_p.L1124I|TSC2_uc002cop.2_Missense_Mutation_p.L972I|TSC2_uc002coq.2_5'Flank|TSC2_uc002cor.2_5'Flank	NM_000548	NP_000539	P49815	TSC2_HUMAN	tuberous sclerosis 2 isoform 1	1216					cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)				GGAGAACCCGCTCAGCCCTTT	0.637			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				4	20	---	---	---	---	PASS
CP110	9738	broad.mit.edu	37	16	19557792	19557792	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19557792A>G	uc002dgl.3	+	12	3083	c.2836A>G	c.(2836-2838)ACA>GCA	p.T946A	CP110_uc002dgk.3_Missense_Mutation_p.T946A			O43303	CP110_HUMAN	RecName: Full=Centrosomal protein of 110 kDa;          Short=Cep110;	946					centriole replication|G2/M transition of mitotic cell cycle|regulation of cytokinesis	centriole|cytosol	protein binding				0						TCCTTCTGAAACAAGGTGAGA	0.229													6	452	---	---	---	---	PASS
LOC81691	81691	broad.mit.edu	37	16	20824600	20824600	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20824600G>A	uc002dhv.2	+	3	490	c.227G>A	c.(226-228)GGC>GAC	p.G76D	ERI2_uc002dht.3_Intron|LOC81691_uc002dhx.2_Missense_Mutation_p.G76D|LOC81691_uc002dhw.2_5'UTR|LOC81691_uc002dhy.3_Missense_Mutation_p.G76D	NM_030941	NP_112203	Q96IC2	REXON_HUMAN	exonuclease NEF-sp isoform 1	76						nucleolus	exonuclease activity|nucleotide binding|RNA binding			ovary(1)|kidney(1)	2						GCAGTTCTGGGCAAATCCAAT	0.378													42	215	---	---	---	---	PASS
ITGAX	3687	broad.mit.edu	37	16	31388553	31388553	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31388553C>T	uc002ebu.1	+	23	2823	c.2756C>T	c.(2755-2757)CCG>CTG	p.P919L	ITGAX_uc002ebt.2_Missense_Mutation_p.P919L	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	919	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						CTGGAGCTCCCGGTGAAGTAT	0.502													29	107	---	---	---	---	PASS
EDC4	23644	broad.mit.edu	37	16	67917881	67917881	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67917881C>A	uc002eur.2	+	29	4202	c.4036C>A	c.(4036-4038)CAC>AAC	p.H1346N	EDC4_uc010cer.2_Missense_Mutation_p.H965N|EDC4_uc002eus.2_Missense_Mutation_p.H1076N|EDC4_uc002eut.1_3'UTR|NRN1L_uc002euu.2_5'Flank	NM_014329	NP_055144	Q6P2E9	EDC4_HUMAN	autoantigen RCD8	1346					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|central_nervous_system(2)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		GGCCGTGATGCACCTGGACCA	0.637											OREG0023890	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	47	---	---	---	---	PASS
TCF25	22980	broad.mit.edu	37	16	89970484	89970484	+	Intron	SNP	T	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89970484T>G	uc002fpb.2	+						TCF25_uc002fpc.2_Intron|TCF25_uc002fpd.1_5'UTR	NM_014972	NP_055787	Q9BQ70	TCF25_HUMAN	NULP1						heart development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		GTGGCTGGGGTGTGTGCTGAG	0.637													5	13	---	---	---	---	PASS
ABR	29	broad.mit.edu	37	17	915255	915255	+	Intron	SNP	G	C	C	rs113364180		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:915255G>C	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc010vqf.1_Intron|ABR_uc010vqg.1_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron|ABR_uc002fsf.2_Missense_Mutation_p.C181W	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		TGGGTGGAGGGCAGCCCCCAC	0.662													10	40	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11648186	11648186	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11648186C>T	uc002gne.2	+	31	6252	c.6184C>T	c.(6184-6186)CCT>TCT	p.P2062S	DNAH9_uc010coo.2_Missense_Mutation_p.P1356S	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	2062					cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GAGAGGAGACCCTGACCGGCC	0.572													6	44	---	---	---	---	PASS
NOS2	4843	broad.mit.edu	37	17	26091141	26091141	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26091141G>C	uc002gzu.2	-	21	2722	c.2458C>G	c.(2458-2460)CCC>GCC	p.P820A		NM_000625	NP_000616	P35228	NOS2_HUMAN	nitric oxide synthase 2A	820	FAD-binding FR-type.				arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding			skin(2)|ovary(1)|breast(1)	4					Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)	GAGCAGGGGGGCAGCCTCTTG	0.607													8	89	---	---	---	---	PASS
PSME3	10197	broad.mit.edu	37	17	40986168	40986168	+	Intron	SNP	T	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40986168T>G	uc002ibr.2	+						PSME3_uc002ibp.2_Intron|PSME3_uc002ibq.2_Intron|PSME3_uc002ibs.2_5'UTR|PSME3_uc010whd.1_Intron	NM_005789	NP_005780	P61289	PSME3_HUMAN	proteasome activator subunit 3 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome activator complex	endopeptidase activator activity|identical protein binding|MDM2 binding|p53 binding				0		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		GACAGGCAGGTGCTGTCCTCA	0.468													11	16	---	---	---	---	PASS
C17orf53	78995	broad.mit.edu	37	17	42222584	42222584	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42222584A>G	uc002ifi.1	+	2	202	c.17A>G	c.(16-18)CAG>CGG	p.Q6R	C17orf53_uc010czq.1_Missense_Mutation_p.Q6R|C17orf53_uc002ifj.1_Missense_Mutation_p.Q6R|C17orf53_uc002ifk.1_5'Flank	NM_024032	NP_076937	Q8N3J3	CQ053_HUMAN	hypothetical protein LOC78995	6											0		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TGCAGTTTGCAGAAGCTGTTT	0.443													55	747	---	---	---	---	PASS
HOXB13	10481	broad.mit.edu	37	17	46805408	46805408	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46805408C>A	uc002ioa.2	-	1	704	c.548G>T	c.(547-549)TGT>TTT	p.C183F		NM_006361	NP_006352	Q92826	HXB13_HUMAN	homeobox B13	183					angiogenesis|epidermis development|response to wounding		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TCCCTGGCAACACATCTGGCT	0.577													19	76	---	---	---	---	PASS
CA10	56934	broad.mit.edu	37	17	49825236	49825236	+	Intron	SNP	A	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49825236A>T	uc002itw.3	-						CA10_uc002itu.3_Silent_p.G3G|CA10_uc002itv.3_Intron|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			GCCTCCCCAAACCCAGCATGG	0.532													9	69	---	---	---	---	PASS
SLC38A10	124565	broad.mit.edu	37	17	79257250	79257250	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79257250C>A	uc002jzz.1	-	4	691	c.316G>T	c.(316-318)GAC>TAC	p.D106Y	SLC38A10_uc002jzy.1_Missense_Mutation_p.D24Y|SLC38A10_uc002kab.2_Missense_Mutation_p.D106Y	NM_001037984	NP_001033073	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10 isoform a	106					amino acid transport|sodium ion transport	integral to membrane				pancreas(1)|skin(1)	2	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GACCCCAAGTCGCCGATCACG	0.597													5	61	---	---	---	---	PASS
MYOM1	8736	broad.mit.edu	37	18	3135721	3135721	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3135721G>A	uc002klp.2	-	15	2367	c.2033C>T	c.(2032-2034)GCA>GTA	p.A678V	MYOM1_uc002klq.2_Missense_Mutation_p.A678V	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a	678	Fibronectin type-III 2.					striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						TTCTGTTCCTGCCTCACACTG	0.512													10	30	---	---	---	---	PASS
CIRBP	1153	broad.mit.edu	37	19	1271824	1271824	+	Intron	SNP	T	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1271824T>G	uc002lrr.3	+						C19orf23_uc010xgk.1_5'Flank|CIRBP_uc010dsg.1_3'UTR|CIRBP_uc002lrt.2_Intron|CIRBP_uc010xgl.1_Intron|CIRBP_uc002lrv.3_Intron|CIRBP_uc002lru.2_Intron	NM_001280	NP_001271	Q14011	CIRBP_HUMAN	cold inducible RNA binding protein						mRNA stabilization|positive regulation of translation|response to cold|response to UV|stress granule assembly	nucleoplasm|stress granule	mRNA 3'-UTR binding|nucleotide binding|protein binding|SSU rRNA binding|translation repressor activity				0		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GACAGGCTGGTGGAGATTTTG	0.627													7	11	---	---	---	---	PASS
DNMT1	1786	broad.mit.edu	37	19	10283839	10283839	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10283839G>T	uc002mng.2	-	8	827	c.647C>A	c.(646-648)CCG>CAG	p.P216Q	DNMT1_uc010xlc.1_Missense_Mutation_p.P232Q|DNMT1_uc002mnh.2_Missense_Mutation_p.P111Q|DNMT1_uc010xld.1_Missense_Mutation_p.P216Q	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b	216	Interaction with DNMT3B.|Interaction with the PRC2/EED-EZH2 complex (By similarity).				chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)	TGCAGGAAGCGGTCTAGCAAC	0.443													6	388	---	---	---	---	PASS
C19orf62	29086	broad.mit.edu	37	19	17387524	17387524	+	Intron	SNP	T	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17387524T>G	uc002nfu.2	+						C19orf62_uc010xpl.1_3'UTR|C19orf62_uc002nfv.2_Intron|C19orf62_uc010ean.2_Intron|C19orf62_uc002nfw.2_Intron	NM_014173	NP_054892	Q9NWV8	BABA1_HUMAN	mediator of Rap80 interactions and targeting 40						chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of DNA repair|protein K63-linked deubiquitination|response to ionizing radiation	BRCA1-A complex|BRISC complex|cytoplasm	protein binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2						GAGGCTGGGGTGCCTAGAGGT	0.602													15	107	---	---	---	---	PASS
DMKN	93099	broad.mit.edu	37	19	35991482	35991482	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35991482C>T	uc002nzm.3	-	12	1423	c.1240G>A	c.(1240-1242)GGT>AGT	p.G414S	DMKN_uc002nzi.3_Missense_Mutation_p.G28S|DMKN_uc002nzj.2_Missense_Mutation_p.G88S|DMKN_uc002nzk.3_Missense_Mutation_p.G61S|DMKN_uc002nzl.3_Missense_Mutation_p.G127S|DMKN_uc002nzo.3_Missense_Mutation_p.G403S|DMKN_uc002nzn.3_Missense_Mutation_p.G373S|DMKN_uc002nzw.2_Missense_Mutation_p.G70S|DMKN_uc002nzr.2_Missense_Mutation_p.G70S|DMKN_uc002nzp.2_Missense_Mutation_p.G108S|DMKN_uc002nzq.2_Missense_Mutation_p.G90S|DMKN_uc002nzt.2_Missense_Mutation_p.G61S|DMKN_uc002nzs.2_Missense_Mutation_p.G61S|DMKN_uc002nzu.2_Missense_Mutation_p.G61S|DMKN_uc002nzv.2_Missense_Mutation_p.G61S|DMKN_uc010xsv.1_Missense_Mutation_p.G61S|DMKN_uc010xsw.1_Missense_Mutation_p.G110S	NM_033317	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine isoform 2 precursor	414						extracellular region				large_intestine(1)|ovary(1)|skin(1)	3	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GCGTCCGCACCCTGAAAGGAA	0.617													3	28	---	---	---	---	PASS
IL28A	282616	broad.mit.edu	37	19	39759207	39759207	+	5'UTR	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39759207G>T	uc002oku.1	+	1						NM_172138	NP_742150	Q8IZJ0	IL28A_HUMAN	interleukin 28A precursor						response to virus	extracellular space	cytokine activity			ovary(1)|skin(1)	2	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;5.39e-26)|all cancers(26;4.1e-23)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			CAGAGATCAGGAATGAAACTA	0.547													12	58	---	---	---	---	PASS
STRN4	29888	broad.mit.edu	37	19	47228597	47228597	+	Silent	SNP	C	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47228597C>G	uc002pfl.2	-	11	1497	c.1464G>C	c.(1462-1464)CGG>CGC	p.R488R	STRN4_uc002pfm.2_Silent_p.R495R|STRN4_uc010xyf.1_RNA|STRN4_uc010xyg.1_RNA	NM_013403	NP_037535	Q9NRL3	STRN4_HUMAN	zinedin isoform 1	488						cytoplasm|membrane	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding				0		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		ACCTGTGAGCCCGGAAAGCAT	0.607													16	108	---	---	---	---	PASS
ZNF577	84765	broad.mit.edu	37	19	52375740	52375740	+	3'UTR	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52375740A>G	uc010yde.1	-	7					ZNF577_uc010ydd.1_Intron|ZNF577_uc002pxx.3_3'UTR|ZNF577_uc002pxv.2_3'UTR|ZNF577_uc002pxw.2_3'UTR	NM_032679	NP_116068	Q9BSK1	ZN577_HUMAN	zinc finger protein 577 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TAATGGCTGGAGGATTCCTAC	0.398													9	61	---	---	---	---	PASS
ZNF765	91661	broad.mit.edu	37	19	53910951	53910951	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53910951A>T	uc010ydx.1	+	6	470	c.143A>T	c.(142-144)GAT>GTT	p.D48V	ZNF765_uc002qbm.2_Missense_Mutation_p.D48V|ZNF765_uc002qbn.2_Intron	NM_001040185	NP_001035275	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	48	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00379)		TACTTTTTAGATATCTCTTCC	0.338													16	118	---	---	---	---	PASS
LILRA1	11024	broad.mit.edu	37	19	55106239	55106239	+	Silent	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55106239G>A	uc002qgh.1	+	4	362	c.180G>A	c.(178-180)CTG>CTA	p.L60L	LILRA2_uc010yfg.1_Intron|LILRA1_uc010yfh.1_Silent_p.L60L	NM_006863	NP_006854	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor,	60	Ig-like C2-type 1.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response|regulation of immune response	integral to membrane|plasma membrane	antigen binding|transmembrane receptor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(193;0.0348)		AGTACCGTCTGTATAGAGAAA	0.572													7	213	---	---	---	---	PASS
ZNF256	10172	broad.mit.edu	37	19	58453407	58453407	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58453407G>C	uc002qqu.2	-	3	1004	c.769C>G	c.(769-771)CAT>GAT	p.H257D	ZNF256_uc010euj.2_Missense_Mutation_p.H104D	NM_005773	NP_005764	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	257	C2H2-type 2.				multicellular organismal development|negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		ACTCTCAAATGATCACTGAGG	0.433													13	165	---	---	---	---	PASS
SLC23A2	9962	broad.mit.edu	37	20	4855319	4855319	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4855319A>G	uc002wlg.1	-	10	1223	c.848T>C	c.(847-849)TTT>TCT	p.F283S	SLC23A2_uc010zqr.1_Missense_Mutation_p.F168S|SLC23A2_uc002wlh.1_Missense_Mutation_p.F283S|SLC23A2_uc002wli.2_Missense_Mutation_p.F282S	NM_005116	NP_005107	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (nucleobase	283	Helical; (Potential).				L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2						GTATTGAGAAAACAGTAATAC	0.368													5	309	---	---	---	---	PASS
PLCB4	5332	broad.mit.edu	37	20	9388624	9388624	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9388624A>G	uc002wnf.2	+	20	1808	c.1672A>G	c.(1672-1674)ACC>GCC	p.T558A	PLCB4_uc010gbw.1_Missense_Mutation_p.T558A|PLCB4_uc010gbx.2_Missense_Mutation_p.T570A|PLCB4_uc002wne.2_Missense_Mutation_p.T558A|PLCB4_uc002wnh.2_Missense_Mutation_p.T405A	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b	558					intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						TGTAGGTGCTACCACTAATAT	0.418													4	255	---	---	---	---	PASS
RIN2	54453	broad.mit.edu	37	20	19977395	19977395	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19977395G>A	uc002wro.1	+	10	2309	c.2273G>A	c.(2272-2274)CGA>CAA	p.R758Q	RIN2_uc010gcu.1_Missense_Mutation_p.R325Q|RIN2_uc010gcv.1_Missense_Mutation_p.R552Q	NM_018993	NP_061866	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	758					endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5						CAAGCAGCGCGACTGCTCAGC	0.522													23	141	---	---	---	---	PASS
C20orf26	26074	broad.mit.edu	37	20	20079377	20079377	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20079377G>T	uc002wru.2	+	8	854	c.778G>T	c.(778-780)GGC>TGC	p.G260C	C20orf26_uc010gcw.1_Missense_Mutation_p.G214C|C20orf26_uc010zse.1_Missense_Mutation_p.G260C|C20orf26_uc010zsf.1_Missense_Mutation_p.G260C	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074	260										ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		CTTTGACTTGGGCCCTTTCCA	0.493													6	281	---	---	---	---	PASS
C20orf26	26074	broad.mit.edu	37	20	20152553	20152553	+	Intron	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20152553G>T	uc002wru.2	+						C20orf26_uc010zse.1_Intron|C20orf26_uc010zsf.1_3'UTR	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		TCGGAGCACCGTAGccacatt	0.154													4	56	---	---	---	---	PASS
DHX35	60625	broad.mit.edu	37	20	37650496	37650496	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37650496G>T	uc002xjh.2	+	16	1522	c.1511G>T	c.(1510-1512)TGT>TTT	p.C504F	DHX35_uc010zwa.1_Missense_Mutation_p.C349F|DHX35_uc010zwb.1_Missense_Mutation_p.C349F|DHX35_uc010zwc.1_Missense_Mutation_p.C473F	NM_021931	NP_068750	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	504						catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|nucleic acid binding			lung(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)				AACTTCGGCTGTTCTCAGGAA	0.433													22	204	---	---	---	---	PASS
URB1	9875	broad.mit.edu	37	21	33697561	33697561	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33697561G>A	uc002ypn.2	-	31	5192	c.5099C>T	c.(5098-5100)GCA>GTA	p.A1700V		NM_014825	NP_055640	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog	1700						nucleolus	protein binding				0						TTGGAACCGTGCGCCCTCCAA	0.612													7	69	---	---	---	---	PASS
ITSN1	6453	broad.mit.edu	37	21	35144369	35144369	+	Silent	SNP	G	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35144369G>C	uc002yta.1	+	12	1315	c.1047G>C	c.(1045-1047)ACG>ACC	p.T349T	DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_RNA|ITSN1_uc002ysz.2_Silent_p.T349T|ITSN1_uc010gmg.2_Silent_p.T312T|ITSN1_uc010gmh.2_RNA|ITSN1_uc002ysw.2_Silent_p.T349T|ITSN1_uc010gmi.2_Silent_p.T312T|ITSN1_uc010gmj.2_Silent_p.T233T|ITSN1_uc002ysy.2_Silent_p.T349T|ITSN1_uc002ysx.2_Silent_p.T312T|ITSN1_uc002ytb.1_Silent_p.T349T|ITSN1_uc002ytc.1_Silent_p.T349T|ITSN1_uc002ytd.2_RNA|ITSN1_uc010gmk.2_Silent_p.T312T|ITSN1_uc010gml.2_RNA|ITSN1_uc002ytj.2_Silent_p.T349T|ITSN1_uc010gmm.1_RNA|ITSN1_uc002yte.2_Silent_p.T283T	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l	349	KLERQ.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4						CTGAAGTAACGTTTGAAGATA	0.443													33	169	---	---	---	---	PASS
DSCR4	10281	broad.mit.edu	37	21	39426752	39426752	+	3'UTR	SNP	T	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39426752T>G	uc002ywp.2	-	3						NM_005867	NP_005858	P56555	DSCR4_HUMAN	Down syndrome critical region protein 4											ovary(1)	1						ATTATGGCTGTTGTTTTTCCA	0.398													8	15	---	---	---	---	PASS
C21orf128	150147	broad.mit.edu	37	21	43522449	43522449	+	3'UTR	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43522449C>A	uc002zak.2	-	2					UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zaf.1_Intron|UMODL1_uc002zag.1_Intron|UMODL1_uc010gow.1_Intron|UMODL1_uc002zai.1_Intron|UMODL1_uc010gox.1_Intron|UMODL1_uc010goy.1_Intron|UMODL1_uc002zaj.1_Intron|UMODL1_uc010goz.1_Intron	NR_027243				RecName: Full=Uncharacterized protein C21orf128;												0						ACATCAAACACAAGCCGTTAA	0.468													7	14	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47981523	47981523	+	Intron	SNP	T	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47981523T>G	uc002zjo.2	+						DIP2A_uc011afz.1_Intron|DIP2A_uc002zjs.2_5'UTR|DIP2A_uc002zjt.2_5'Flank	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a						multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TCATGGCAGGTGTGCTGTGGA	0.557													12	25	---	---	---	---	PASS
LOC646851	646851	broad.mit.edu	37	22	39003432	39003432	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39003432T>C	uc011anx.1	-	12	1732	c.809A>G	c.(808-810)AAC>AGC	p.N270S	LOC646851_uc011anw.1_Missense_Mutation_p.N363S			B7Z7C6	B7Z7C6_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000348086;	270											0						TTTTTCTGAGTTCTGCTTGGC	0.328													8	764	---	---	---	---	PASS
RBX1	9978	broad.mit.edu	37	22	41368620	41368620	+	3'UTR	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41368620G>T	uc003azk.2	+	5						NM_014248	NP_055063	P62877	RBX1_HUMAN	ring-box 1						DNA repair|interspecies interaction between organisms|protein neddylation|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|viral reproduction	Cul3-RING ubiquitin ligase complex|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytosol|nucleus|SCF ubiquitin ligase complex	NEDD8 ligase activity|protein binding|zinc ion binding			skin(1)	1						TGCTGTTTCTGTAGCCATATT	0.348													38	196	---	---	---	---	PASS
TUBGCP6	85378	broad.mit.edu	37	22	50664330	50664330	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50664330C>T	uc003bkb.1	-	10	2388	c.1876G>A	c.(1876-1878)GTG>ATG	p.V626M	TUBGCP6_uc010har.1_Missense_Mutation_p.V626M|TUBGCP6_uc010has.1_RNA|TUBGCP6_uc010hat.1_5'Flank|TUBGCP6_uc003bkd.1_Translation_Start_Site	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	626					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GAGAAAATCACCGAGATCCGG	0.592													4	73	---	---	---	---	PASS
MID1	4281	broad.mit.edu	37	X	10442837	10442837	+	Intron	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10442837C>A	uc004cte.3	-						MID1_uc004ctd.3_Intron|MID1_uc004ctg.3_Intron|MID1_uc004cth.3_Intron|MID1_uc004ctk.3_Intron|MID1_uc004cti.3_Intron|MID1_uc004ctj.3_Intron|MID1_uc011mie.1_Intron|MID1_uc004ctm.1_Intron|MID1_uc004ctn.1_Intron|MID1_uc004cto.1_Intron|MID1_uc010ndw.1_Intron|MID1_uc004cts.1_Intron|MID1_uc004csz.3_Intron|MID1_uc004cta.3_Nonsense_Mutation_p.E79*|MID1_uc004ctb.3_Intron|MID1_uc004ctc.3_Intron|MID1_uc004ctl.1_Nonsense_Mutation_p.E79*|MID1_uc004ctp.1_Intron|MID1_uc004ctq.1_Intron|MID1_uc004ctr.1_Intron|MID1_uc010ndu.1_Intron|MID1_uc010ndv.1_Intron	NM_033290	NP_150632	O15344	TRI18_HUMAN	midline 1						microtubule cytoskeleton organization|pattern specification process|positive regulation of stress-activated MAPK cascade	cytoplasm|microtubule|microtubule associated complex|spindle	ligase activity|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|pancreas(1)	3						AGATGACTTTCAACATCACTG	0.338													11	180	---	---	---	---	PASS
GLRA2	2742	broad.mit.edu	37	X	14599498	14599498	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14599498C>T	uc010nep.2	+	5	796	c.464C>T	c.(463-465)TCG>TTG	p.S155L	GLRA2_uc010neq.2_Missense_Mutation_p.S155L|GLRA2_uc004cwe.3_Missense_Mutation_p.S155L|GLRA2_uc011mio.1_Missense_Mutation_p.S66L|GLRA2_uc011mip.1_Missense_Mutation_p.S133L	NM_001118885	NP_001112357	P23416	GLRA2_HUMAN	glycine receptor, alpha 2 isoform A	155	Extracellular (Probable).				neuropeptide signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity			ovary(1)|lung(1)	2	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)	CTACGGATTTCGAAAAATGGC	0.453													5	162	---	---	---	---	PASS
ACE2	59272	broad.mit.edu	37	X	15591566	15591566	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15591566C>A	uc004cxa.1	-	11	1633	c.1465G>T	c.(1465-1467)GAA>TAA	p.E489*	ACE2_uc004cxb.2_Nonsense_Mutation_p.E489*	NM_021804	NP_068576	Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2 precursor	489	Extracellular (Potential).				angiotensin-mediated drinking behavior|proteolysis|receptor biosynthetic process|regulation of cell proliferation|virion attachment, binding of host cell surface receptor	cell surface|extracellular space|integral to membrane|membrane raft|plasma membrane	carboxypeptidase activity|glycoprotein binding|metallopeptidase activity|peptidyl-dipeptidase activity|viral receptor activity|zinc ion binding			ovary(3)	3	Hepatocellular(33;0.183)				Moexipril(DB00691)	GGCACAGGTTCCACCACCCCA	0.433													45	220	---	---	---	---	PASS
SCML1	6322	broad.mit.edu	37	X	17770014	17770014	+	Silent	SNP	A	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17770014A>G	uc004cyb.2	+	7	1108	c.783A>G	c.(781-783)GAA>GAG	p.E261E	SCML1_uc004cyc.2_Silent_p.E234E|SCML1_uc004cyd.2_Silent_p.E140E|SCML1_uc004cye.2_Silent_p.E140E	NM_001037540	NP_001032629	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 isoform a	261	SAM.				anatomical structure morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)	3	Hepatocellular(33;0.183)					GGTCGGTGGAAGCAGTGGTCC	0.438													7	481	---	---	---	---	PASS
DDX3X	1654	broad.mit.edu	37	X	41202084	41202084	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41202084G>C	uc004dfe.2	+	6	1393	c.538G>C	c.(538-540)GAA>CAA	p.E180Q	DDX3X_uc010nhf.1_Missense_Mutation_p.E164Q|DDX3X_uc004dff.2_Missense_Mutation_p.E180Q|DDX3X_uc011mkq.1_Missense_Mutation_p.E164Q|DDX3X_uc011mkr.1_Missense_Mutation_p.E180Q|DDX3X_uc011mks.1_Intron|DDX3X_uc004dfg.2_RNA|DDX3X_uc011mkt.1_RNA	NM_001356	NP_001347	O00571	DDX3X_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3	180	Q motif.				interspecies interaction between organisms	cytoplasm|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding|RNA binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6						TCCACATATTGAAAGTGTGAG	0.378										HNSCC(61;0.18)			43	248	---	---	---	---	PASS
CASK	8573	broad.mit.edu	37	X	41401993	41401993	+	Silent	SNP	G	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41401993G>T	uc004dfl.3	-	22	2152	c.2106C>A	c.(2104-2106)GGC>GGA	p.G702G	CASK_uc004dfj.3_Silent_p.G242G|CASK_uc004dfk.3_Silent_p.G517G|CASK_uc004dfm.3_Silent_p.G679G|CASK_uc004dfn.3_Silent_p.G673G	NM_003688	NP_003679	O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein	702					cell adhesion	actin cytoskeleton|cytoplasm|nucleus|plasma membrane	ATP binding|calmodulin binding|guanylate kinase activity|protein serine/threonine kinase activity			ovary(3)|lung(2)|stomach(1)	6						TCTTTTTCTTGCCAAACCAAG	0.418													33	632	---	---	---	---	PASS
ATRX	546	broad.mit.edu	37	X	76972613	76972613	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76972613T>C	uc004ecp.3	-	2	360	c.128A>G	c.(127-129)AAC>AGC	p.N43S	ATRX_uc004ecq.3_Missense_Mutation_p.N43S|ATRX_uc004eco.3_5'UTR|ATRX_uc004ecr.2_Missense_Mutation_p.N43S|ATRX_uc010nlx.1_Missense_Mutation_p.N43S|ATRX_uc010nly.1_Intron	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	43					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	TTTACCTGTGTTTTGATTCAT	0.348			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						7	740	---	---	---	---	PASS
DACH2	117154	broad.mit.edu	37	X	85906058	85906058	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85906058G>C	uc004eew.2	+	4	830	c.660G>C	c.(658-660)ATG>ATC	p.M220I	DACH2_uc004eex.2_Missense_Mutation_p.M207I|DACH2_uc010nmq.2_Missense_Mutation_p.M86I|DACH2_uc011mra.1_Missense_Mutation_p.M53I|DACH2_uc010nmr.2_Missense_Mutation_p.M1I	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a	220					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5						CTGCAGCGATGGCTGAGGCGA	0.313													25	160	---	---	---	---	PASS
IL1RAPL2	26280	broad.mit.edu	37	X	104961379	104961379	+	Silent	SNP	C	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104961379C>G	uc004elz.1	+	7	1548	c.792C>G	c.(790-792)CCC>CCG	p.P264P		NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	264	Ig-like C2-type 3.|Extracellular (Potential).				central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3						TGAACATCCCCTGCAAAGCAT	0.433													73	452	---	---	---	---	PASS
COL4A5	1287	broad.mit.edu	37	X	107938641	107938641	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107938641G>A	uc004enz.1	+	51	5168	c.4966G>A	c.(4966-4968)GCA>ACA	p.A1656T	COL4A5_uc011mso.1_Missense_Mutation_p.A1653T|COL4A5_uc011msp.1_Missense_Mutation_p.A332T	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor	1650	Collagen IV NC1.		Missing (in APSX).		axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4						CTTTTGGCTGGCAACTGTAGA	0.453									Alport_syndrome_with_Diffuse_Leiomyomatosis				38	189	---	---	---	---	PASS
STAG2	10735	broad.mit.edu	37	X	123197875	123197875	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123197875C>T	uc004etz.3	+	19	2338	c.1999C>T	c.(1999-2001)CGG>TGG	p.R667W	STAG2_uc004eua.2_Missense_Mutation_p.R667W|STAG2_uc004eub.2_Missense_Mutation_p.R667W|STAG2_uc004euc.2_Missense_Mutation_p.R667W|STAG2_uc004eud.2_Missense_Mutation_p.R667W|STAG2_uc004eue.2_Missense_Mutation_p.R667W	NM_006603	NP_006594	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform b	667					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5						TAAATTTAACCGGCTTCTTGA	0.348													33	172	---	---	---	---	PASS
TFDP3	51270	broad.mit.edu	37	X	132351937	132351937	+	Silent	SNP	C	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132351937C>T	uc004exb.1	-	1	440	c.351G>A	c.(349-351)AAG>AAA	p.K117K		NM_016521	NP_057605	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	117	Potential.					transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					TCTCCCAGACCTTCATGGAAA	0.592													11	86	---	---	---	---	PASS
SPANXE	171489	broad.mit.edu	37	X	140785800	140785800	+	Missense_Mutation	SNP	G	A	A	rs145377089		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140785800G>A	uc004fbq.2	-	2	209	c.116C>T	c.(115-117)CCG>CTG	p.P39L		NM_145665	NP_663698	Q8TAD1	SPNXE_HUMAN	SPANX family, member E	39	Nuclear localization signal (Potential).					cytoplasm|nucleus					0	Acute lymphoblastic leukemia(192;7.65e-05)					TAGTTTTTTCGGAGCAGGTTG	0.488													22	402	---	---	---	---	PASS
MAMLD1	10046	broad.mit.edu	37	X	149639327	149639327	+	Silent	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149639327G>A	uc004fee.1	+	3	1558	c.1482G>A	c.(1480-1482)CAG>CAA	p.Q494Q	MAMLD1_uc011mxt.1_Silent_p.Q456Q|MAMLD1_uc011mxu.1_Silent_p.Q469Q|MAMLD1_uc011mxv.1_Silent_p.Q469Q|MAMLD1_uc011mxw.1_Silent_p.Q421Q	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	494	Poly-Gln.				male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)					GCcagcaacagcagcagcagc	0.433													3	32	---	---	---	---	PASS
HMGB3	3149	broad.mit.edu	37	X	150156447	150156447	+	3'UTR	SNP	C	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150156447C>G	uc004fep.2	+	5					HMGB3_uc004feq.2_3'UTR|HMGB3_uc004fer.2_3'UTR	NM_005342	NP_005333	O15347	HMGB3_HUMAN	high-mobility group box 3						DNA recombination|multicellular organismal development	chromosome|nucleus	DNA bending activity|double-stranded DNA binding				0	Acute lymphoblastic leukemia(192;6.56e-05)					GTAATTGACACATCTCTTATT	0.303													5	16	---	---	---	---	PASS
CSAG1	158511	broad.mit.edu	37	X	151909357	151909357	+	3'UTR	SNP	G	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151909357G>C	uc004fge.2	+	5					CSAG1_uc004fgf.2_3'UTR|CSAG1_uc004fgd.2_RNA	NM_153478	NP_705611	Q6PB30	CSAG1_HUMAN	chondrosarcoma associated gene 1 precursor											ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					GCTTCCTTGGGCAGCCAGTAA	0.527													10	99	---	---	---	---	PASS
MPP1	4354	broad.mit.edu	37	X	154010064	154010064	+	Silent	SNP	C	A	A	rs147268060		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154010064C>A	uc004fmp.1	-	10	1075	c.960G>T	c.(958-960)CCG>CCT	p.P320P	MPP1_uc010nvg.1_Silent_p.P300P|MPP1_uc011mzv.1_Silent_p.P290P|MPP1_uc004fmq.1_Silent_p.P274P|MPP1_uc011mzw.1_Silent_p.P303P	NM_002436	NP_002427	Q00013	EM55_HUMAN	palmitoylated membrane protein 1	320	Guanylate kinase-like.|Interaction with MPP5.				regulation of neutrophil chemotaxis|signal transduction	integral to plasma membrane|membrane fraction|stereocilium	guanylate kinase activity|protein binding			ovary(2)|central_nervous_system(1)	3	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TCTTCCTTGGCGGCCGTGTTG	0.507													32	187	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	6517	6517	+	5'UTR	SNP	G	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:6517G>A	uc011mfh.1	+	1					uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		CCTAGCTGCTGGCATCACTAT	0.507													15	22	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	10147	10147	+	5'Flank	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10147delC	uc001aaa.3	+						uc010nxq.1_5'Flank|uc010nxr.1_5'Flank					Homo sapiens mRNA for DEAD/H box polypeptide 11 like 1 (DDX11L1 gene).																		ctaaccctaacccctaaccct	0.000													3	3	---	---	---	---	
FBXO42	54455	broad.mit.edu	37	1	16616139	16616140	+	Intron	INS	-	T	T	rs145648121	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16616139_16616140insT	uc001ayg.2	-						FBXO42_uc001ayf.2_Intron	NM_018994	NP_061867	Q6P3S6	FBX42_HUMAN	F-box protein 42											upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		TCCCTCCACTATCATTCTTTAG	0.351													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	37791947	37791947	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37791947delT								GRIK3 (292103 upstream) : ZC3H12A (148172 downstream)																							TTGCCTTCCCTTTTTCATCTT	0.463													4	2	---	---	---	---	
RIMS3	9783	broad.mit.edu	37	1	41114002	41114002	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41114002delG	uc001cfu.1	-						RIMS3_uc001cfv.1_Intron	NM_014747	NP_055562	Q9UJD0	RIMS3_HUMAN	regulating synaptic membrane exocytosis 3						neurotransmitter transport	cell junction|synapse					0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)			atcaccacctgggccctccct	0.000													4	2	---	---	---	---	
ELAVL4	1996	broad.mit.edu	37	1	50569107	50569107	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50569107delA	uc001cry.3	+						ELAVL4_uc001crz.3_5'Flank|ELAVL4_uc001csa.3_5'Flank	NM_001144777	NP_001138249	P26378	ELAV4_HUMAN	ELAV-like 4 isoform 5						mRNA processing		AU-rich element binding|mRNA 3'-UTR binding|nucleotide binding			ovary(1)|pancreas(1)	2						CATGATAAAGAAAAAAAAAAG	0.313													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58908111	58908112	+	Intron	INS	-	CACATCCAC	CACATCCAC	rs706435	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58908111_58908112insCACATCCAC	uc001cyt.1	-							NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						CTCTGCAAACACACATCCACAC	0.426													4	2	---	---	---	---	
KANK4	163782	broad.mit.edu	37	1	62766309	62766309	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62766309delG	uc001dah.3	-						KANK4_uc001dai.3_Intron	NM_181712	NP_859063	Q5T7N3	KANK4_HUMAN	ankyrin repeat domain 38											ovary(3)|skin(2)|lung(1)	6						gtacagggtcggggaagcgga	0.040													4	2	---	---	---	---	
ITGB3BP	23421	broad.mit.edu	37	1	63909711	63909711	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63909711delG	uc001dba.1	-						ITGB3BP_uc001dbb.1_Intron|ITGB3BP_uc001dbc.1_Intron|ITGB3BP_uc001dbd.1_Intron	NM_014288	NP_055103	Q13352	CENPR_HUMAN	integrin beta 3 binding protein						apoptosis|cell adhesion|CenH3-containing nucleosome assembly at centromere|induction of apoptosis by extracellular signals|mitotic prometaphase|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome, centromeric region|cytosol|membrane fraction|nucleoplasm	protein C-terminus binding|signal transducer activity				0						GCAGAACTGAGGGAAATGCCT	0.398													4	2	---	---	---	---	
ROR1	4919	broad.mit.edu	37	1	64483749	64483749	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64483749delT	uc001dbj.2	+						ROR1_uc001dbi.3_Intron	NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19						CAAAAATGGCTTTACAGTTTG	0.483													4	2	---	---	---	---	
UOX	391051	broad.mit.edu	37	1	84835152	84835155	+	Intron	DEL	AATG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84835152_84835155delAATG	uc009wcg.2	-							NR_003927				Homo sapiens urate oxidase (pseudogene) (UOX), non-coding RNA.												0						atcaccattcaatgaatgaatgaa	0.098													4	2	---	---	---	---	
LMO4	8543	broad.mit.edu	37	1	87804911	87804911	+	Intron	DEL	T	-	-	rs34448167		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87804911delT	uc001dmi.2	+						LMO4_uc001dmj.2_Intron	NM_006769	NP_006760	P61968	LMO4_HUMAN	LIM domain only 4						neural tube closure|transcription from RNA polymerase II promoter	transcription factor complex	sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding				0		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)		GAATTGTATCTTTTTTTTTTT	0.289													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	87925279	87925279	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87925279delA								LMO4 (110676 upstream) : None (None downstream)																							aactctcaagaaaaaggatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88152262	88152262	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88152262delG								LMO4 (337659 upstream) : PKN2 (997660 downstream)																							TCAGAATTTAGGTCCGTGAAA	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	89038801	89038801	+	5'Flank	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89038801delT	uc001dml.1	-											Homo sapiens cDNA FLJ41840 fis, clone NT2RI3002303.																		tttttgtttgtttttttttga	0.189													4	2	---	---	---	---	
FAM69A	388650	broad.mit.edu	37	1	93332318	93332318	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93332318delA	uc001dpg.2	-						FAM69A_uc001dpc.2_Intron|FAM69A_uc010otg.1_Intron	NM_001006605	NP_001006606	Q5T7M9	FA69A_HUMAN	family with sequence similarity 69, member A							endoplasmic reticulum membrane|integral to membrane					0		all_lung(203;0.00265)|Lung NSC(277;0.00562)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000563)|all cancers(265;0.000751)|Epithelial(280;0.127)		ttccttgatgaaaaaatgttg	0.000													4	2	---	---	---	---	
SLC44A3	126969	broad.mit.edu	37	1	95343817	95343817	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95343817delA	uc001dqv.3	+						SLC44A3_uc001dqx.3_Intron|SLC44A3_uc010otq.1_Intron|SLC44A3_uc010otr.1_Intron|SLC44A3_uc001dqw.3_Intron|SLC44A3_uc010ots.1_Intron|SLC44A3_uc009wds.2_Intron|SLC44A3_uc010ott.1_Intron|SLC44A3_uc010otu.1_Intron	NM_001114106	NP_001107578	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3 isoform 1							integral to membrane|plasma membrane	choline transmembrane transporter activity			kidney(1)	1		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	acaaacaaacaaaaAAAAAAC	0.274													3	3	---	---	---	---	
DPYD	1806	broad.mit.edu	37	1	98264574	98264574	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98264574delT	uc001drv.2	-						DPYD_uc010oub.1_Intron|DPYD_uc001drw.2_Intron	NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	ggggtagacattacgtctcta	0.139													4	2	---	---	---	---	
S1PR1	1901	broad.mit.edu	37	1	101702121	101702121	+	5'Flank	DEL	T	-	-	rs140820637		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101702121delT	uc001dud.2	+						S1PR1_uc009weg.2_5'Flank	NM_001400	NP_001391	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1						cell adhesion	integral to membrane	lysosphingolipid and lysophosphatidic acid receptor activity			ovary(2)|lung(1)	3						TCTCTCCACCTTTTTTTTTTT	0.552													4	2	---	---	---	---	
OLFM3	118427	broad.mit.edu	37	1	102340728	102340728	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102340728delG	uc001dug.2	-						OLFM3_uc001duh.2_Intron|OLFM3_uc001dui.2_Intron|OLFM3_uc001duj.2_Intron	NM_058170	NP_477518	Q96PB7	NOE3_HUMAN	olfactomedin 3							extracellular region				ovary(2)|skin(1)	3		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		CCTCTAGATTGGGAGGAAAAA	0.194													4	2	---	---	---	---	
KCND3	3752	broad.mit.edu	37	1	112479926	112479926	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112479926delG	uc001ebu.1	-						KCND3_uc001ebv.1_Intron	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related							sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)		CAGACACAGTGACCTCTCTGG	0.418													4	2	---	---	---	---	
RSBN1	54665	broad.mit.edu	37	1	114327987	114327987	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114327987delT	uc001edq.2	-						RSBN1_uc001edr.2_Intron	NM_018364	NP_060834	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1							nucleus				ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		tacagttaacttttttttaat	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142663441	142663442	+	Intron	INS	-	A	A	rs147458002		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142663441_142663442insA	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		TCACTACAGGTCATTTCCCCTG	0.307													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142784487	142784488	+	Intron	INS	-	C	C	rs142084929		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142784487_142784488insC	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		atcctcactctcccccccaccc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143504762	143504763	+	IGR	INS	-	G	G	rs150986294	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143504762_143504763insG								None (None upstream) : LOC100286793 (142876 downstream)																							taaaactaaaagaaaaaagcct	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143544117	143544118	+	IGR	INS	-	AA	AA	rs71293657		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143544117_143544118insAA								None (None upstream) : LOC100286793 (103521 downstream)																							AATAGCTTGACAAAAAAAAAAA	0.277													9	4	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145002425	145002426	+	Intron	INS	-	A	A	rs147987741		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145002425_145002426insA	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron|uc001emi.3_5'Flank	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		ATTATACAAATAAAAGTTTAAT	0.272			T	PDGFRB	MPD								2	5	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145688850	145688850	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145688850delT	uc001emp.3	+							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)		Attttttttgttttttttttt	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148859441	148859445	+	IGR	DEL	GAAAG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148859441_148859445delGAAAG								NBPF16 (101130 upstream) : LOC645166 (68841 downstream)																							atgaaggagagaaagaagaagagaa	0.146													4	2	---	---	---	---	
CTSS	1520	broad.mit.edu	37	1	150710309	150710309	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150710309delG	uc001evn.2	-						CTSS_uc010pcj.1_Intron	NM_004079	NP_004070	P25774	CATS_HUMAN	cathepsin S preproprotein						immune response|proteolysis	extracellular region|lysosome	cysteine-type endopeptidase activity				0	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)			aattttaggtggaatggtcgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163695311	163695311	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163695311delG								NUF2 (369758 upstream) : PBX1 (833491 downstream)																							TAGGTGATGTGGATAGCAGGA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177459249	177459250	+	IGR	DEL	AC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177459249_177459250delAC								FAM5B (207692 upstream) : SEC16B (438239 downstream)																							ACTTAAATGtacacacacacat	0.347													4	2	---	---	---	---	
LAMC1	3915	broad.mit.edu	37	1	183105897	183105898	+	Intron	INS	-	ATTG	ATTG	rs140331463	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183105897_183105898insATTG	uc001gpy.3	+							NM_002293	NP_002284	P11047	LAMC1_HUMAN	laminin, gamma 1 precursor						axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent			ovary(3)|large_intestine(1)|kidney(1)	5					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TAGGTATCCACATTGAGGAGGG	0.391													4	3	---	---	---	---	
C1orf26	54823	broad.mit.edu	37	1	185232417	185232417	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185232417delA	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988	Q5T5J6	SWT1_HUMAN	hypothetical protein LOC54823												0						ACCCAGTAACAAAAAAAAAAG	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	187129982	187129983	+	IGR	DEL	TG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187129982_187129983delTG								PLA2G4A (171877 upstream) : None (None downstream)																							tggataagtatgtgtgtgtggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	187351418	187351418	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187351418delA								PLA2G4A (393313 upstream) : None (None downstream)																							TTGCAACACCAAAAAAAAATC	0.403													4	2	---	---	---	---	
NR5A2	2494	broad.mit.edu	37	1	200084720	200084720	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200084720delA	uc001gvb.2	+						NR5A2_uc001gvc.2_Intron|NR5A2_uc009wzh.2_Intron|NR5A2_uc010pph.1_Intron	NM_205860	NP_995582	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2						embryo development|positive regulation of viral genome replication|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	lipid binding|protein binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Prostate(682;0.19)					TCAAAGATGTAAGGGGAAAAA	0.368													4	2	---	---	---	---	
CAMSAP1L1	23271	broad.mit.edu	37	1	200816155	200816155	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200816155delA	uc001gvl.2	+						CAMSAP1L1_uc001gvk.2_Intron|CAMSAP1L1_uc001gvm.2_Intron	NM_203459	NP_982284	Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein							cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4						TAAAAGACATAAAATATATAT	0.254													8	7	---	---	---	---	
CDK18	5129	broad.mit.edu	37	1	205494569	205494569	+	Intron	DEL	T	-	-	rs80154131		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205494569delT	uc001hcr.2	+						CDK18_uc010pri.1_Intron|CDK18_uc001hcp.2_Intron|CDK18_uc001hcq.2_Intron|CDK18_uc010prj.1_Intron|CDK18_uc001hcs.2_Intron|CDK18_uc009xbm.1_Intron	NM_212503	NP_997668	Q07002	CDK18_HUMAN	PCTAIRE protein kinase 3 isoform a								ATP binding|cyclin-dependent protein kinase activity|protein binding|signal transducer activity			stomach(2)	2						GAATCCAGTCTTTTTTTTTTC	0.328													5	3	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	216465939	216465939	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216465939delT	uc001hku.1	-						USH2A_uc001hkv.2_Intron	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		gaaaatgatctttttttttct	0.055										HNSCC(13;0.011)			5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	224947806	224947807	+	IGR	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224947806_224947807insT								CNIH3 (19557 upstream) : DNAH14 (169549 downstream)																							CTGCTCCAGGCTTTTTTTTTCC	0.426													4	2	---	---	---	---	
CDC42BPA	8476	broad.mit.edu	37	1	227259632	227259633	+	Intron	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227259632_227259633insA	uc001hqr.2	-						CDC42BPA_uc001hqq.2_Intron|CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron|CDC42BPA_uc001hqp.2_Intron|CDC42BPA_uc001hqu.1_Intron	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				CCACTGCACTGAAAAAAAACGT	0.257													4	2	---	---	---	---	
C1orf100	200159	broad.mit.edu	37	1	244520637	244520637	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244520637delG	uc001iah.2	+						C1orf100_uc001iai.2_Intron	NM_001012970	NP_001012988	Q5SVJ3	CA100_HUMAN	hypothetical protein LOC200159												0	all_cancers(71;3.94e-05)|all_epithelial(71;0.000138)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|all_lung(81;0.0736)|Ovarian(71;0.0761)|Lung NSC(105;0.103)		all cancers(7;8.19e-08)|GBM - Glioblastoma multiforme(7;2.05e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.000984)			gttcagaagtggggtggagtg	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244558219	244558219	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244558219delC								C1orf100 (5828 upstream) : ADSS (13578 downstream)																							ATGGAGGGGACCCAAACGGGA	0.537													4	2	---	---	---	---	
C1orf101	257044	broad.mit.edu	37	1	244620375	244620376	+	Intron	DEL	GT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244620375_244620376delGT	uc001iak.1	+									Q5SY80	CA101_HUMAN	Homo sapiens cDNA: FLJ23552 fis, clone LNG09069.							integral to membrane				ovary(1)|breast(1)	2	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			tttaagcaaagtgaaaaaggtt	0.000													4	2	---	---	---	---	
OR2T3	343173	broad.mit.edu	37	1	248635239	248635240	+	5'Flank	INS	-	T	T	rs149584629	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248635239_248635240insT	uc001iel.1	+							NM_001005495	NP_001005495	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AAGTCCCAGGgtttttttttgt	0.277													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	279385	279385	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:279385delA								ACP1 (1105 upstream) : FAM150B (178 downstream)																							CCTTTACTTTAAAAAAAATGC	0.328													4	2	---	---	---	---	
MYT1L	23040	broad.mit.edu	37	2	2228938	2228938	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2228938delC	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CTGTGAGTGGCCACAGCCCCA	0.502													4	2	---	---	---	---	
TSSC1	7260	broad.mit.edu	37	2	3287306	3287306	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3287306delC	uc002qxj.2	-						TSSC1_uc002qxi.2_Intron	NM_003310	NP_003301	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1								protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		GCACCACGTTCACACCCCGGC	0.612													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6789232	6789233	+	IGR	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6789232_6789233insA								LOC400940 (660868 upstream) : CMPK2 (191270 downstream)																							ATAAGAGTAACAAAAAAAATGG	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	11491676	11491677	+	IGR	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11491676_11491677insA								ROCK2 (6965 upstream) : E2F6 (92825 downstream)																							gactccatctcaaaaaaaaaga	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18293318	18293318	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18293318delG								KCNS3 (179094 upstream) : NT5C1B (442673 downstream)																							agtttgatgtggtgcaaaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	21223105	21223106	+	IGR	INS	-	G	G	rs139067373	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21223105_21223106insG								C2orf43 (200278 upstream) : APOB (1196 downstream)																							TGGATGTGGCAGGAGAAACCCT	0.406													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23570703	23570704	+	IGR	INS	-	AT	AT	rs138266640	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23570703_23570704insAT								None (None upstream) : KLHL29 (184751 downstream)																							GAGGAAGCAGGCGGTCCTCAGA	0.579													4	2	---	---	---	---	
CAPN14	440854	broad.mit.edu	37	2	31453187	31453187	+	Intron	DEL	A	-	-	rs112426105		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31453187delA	uc002rnt.1	-									A8MX76	CAN14_HUMAN	RecName: Full=Calpain-14;          EC=3.4.22.-;						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity				0						caacattcttaagacttatct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38453406	38453406	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38453406delA								C2orf58 (44415 upstream) : ATL2 (68625 downstream)																							tcaagtattgaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42218079	42218080	+	IGR	DEL	CA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42218079_42218080delCA								None (None upstream) : PKDCC (57081 downstream)																							atgcactcaccacacacacaca	0.139													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45190056	45190057	+	IGR	INS	-	C	C	rs144101943	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45190056_45190057insC								SIX3 (17666 upstream) : SIX2 (42268 downstream)																							AGCTGACCTGATTATGGATGGA	0.540													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	48333524	48333525	+	IGR	DEL	GT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48333524_48333525delGT								FBXO11 (200710 upstream) : FOXN2 (208270 downstream)																							GAGAGACCCAGTGTGATAAGGA	0.416											OREG0014613	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
CCDC88A	55704	broad.mit.edu	37	2	55536585	55536585	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55536585delT	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron|CCDC88A_uc010fbw.2_5'Flank|CCDC88A_uc002ryu.2_Intron|CCDC88A_uc002rys.2_Intron|CCDC88A_uc002ryw.2_Intron|CCDC88A_uc010fby.1_Intron	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1						activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						AAAATTTACATTTTTTTTTCC	0.244													6	3	---	---	---	---	
CCDC85A	114800	broad.mit.edu	37	2	56582488	56582488	+	Intron	DEL	T	-	-	rs76514284		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56582488delT	uc002rzn.2	+							NM_001080433	NP_001073902	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A											breast(3)|ovary(2)	5			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CTGTTCAGAATTTTTTTTTCC	0.408													4	2	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61436298	61436298	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61436298delA	uc002sbe.2	-							NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			AACTCTAACTAAAAAAAAGTC	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	63290906	63290906	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63290906delT								OTX1 (6603 upstream) : C2orf86 (57631 downstream)																							AACATTAAGGTTTTTTTTTCC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	68177239	68177240	+	IGR	DEL	CT	-	-	rs140915539		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68177239_68177240delCT								ETAA1 (539706 upstream) : C1D (92093 downstream)																							acagcatcccctgtcttttctc	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	72006197	72006198	+	IGR	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72006197_72006198insA								DYSF (92305 upstream) : CYP26B1 (350169 downstream)																							TCTCCACTGGCAAAAAATCCTG	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	76797269	76797270	+	IGR	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76797269_76797270insA								C2orf3 (859158 upstream) : LRRTM4 (177588 downstream)																							ccaggaacattaaaaaaaaggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	78207879	78207879	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78207879delA								SNAR-H (25727 upstream) : None (None downstream)																							aaacaagaacaaaaaaagccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	79126539	79126540	+	IGR	INS	-	AGA	AGA	rs149106114		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79126539_79126540insAGA								SNAR-H (944387 upstream) : REG3G (126286 downstream)																							gcagtggcaagaggttattacg	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	83496742	83496742	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83496742delT								None (None upstream) : None (None downstream)																							ggccctcctctttttggcttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91801333	91801334	+	IGR	INS	-	C	C	rs147402585		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91801333_91801334insC								None (None upstream) : LOC654342 (3858 downstream)																							gttcatgactaccattagctcc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91801453	91801454	+	IGR	INS	-	T	T	rs149695974		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91801453_91801454insT								None (None upstream) : LOC654342 (3738 downstream)																							tgatttcattcttttttaaggc	0.000													4	2	---	---	---	---	
CIAO1	9391	broad.mit.edu	37	2	96935380	96935380	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96935380delT	uc002svs.2	+							NM_004804	NP_004795	O76071	CIAO1_HUMAN	WD repeat domain 39						chromosome segregation|iron-sulfur cluster assembly|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter	MMXD complex	protein binding				0						TGGCTGAGGGtttttttttgt	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103170626	103170626	+	IGR	DEL	G	-	-	rs5833025		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103170626delG								SLC9A4 (20196 upstream) : SLC9A2 (65540 downstream)																							tcaggattttgatatccactc	0.104													2	4	---	---	---	---	
SLC9A2	6549	broad.mit.edu	37	2	103313537	103313537	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103313537delT	uc002tca.2	+							NM_003048	NP_003039	Q9UBY0	SL9A2_HUMAN	solute carrier family 9 (sodium/hydrogen							integral to membrane|plasma membrane	sodium:hydrogen antiporter activity			central_nervous_system(3)|skin(3)|breast(2)	8						CTATCCTCCCTTTCCCTAGCA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	111472335	111472336	+	IGR	DEL	AA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111472335_111472336delAA								BUB1 (36651 upstream) : ACOXL (17814 downstream)																							TGCAAGCTTTAAAAAGAGTTCA	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	127269003	127269003	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127269003delT								None (None upstream) : GYPC (144681 downstream)																							ACCTGACAACTTTTTTTTTAA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130004304	130004304	+	Intron	DEL	A	-	-	rs35278705		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130004304delA	uc002tpv.1	-											Homo sapiens cDNA FLJ32036 fis, clone NTONG2000492.																		CCTCCTGTACAAAAAAACAAa	0.219													4	2	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	134031874	134031874	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134031874delA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|NCKAP5_uc002ttt.1_Intron|NCKAP5_uc002tts.1_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						tagtaagaacaaaaaaaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	136913770	136913771	+	IGR	DEL	GT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136913770_136913771delGT								CXCR4 (38045 upstream) : THSD7B (609344 downstream)																							ctggagtggagtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	138526866	138526866	+	IGR	DEL	A	-	-	rs75799523		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138526866delA								THSD7B (91579 upstream) : HNMT (194724 downstream)																							ACTTTAAAGGAAAAAAAAAAA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	145365509	145365509	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145365509delA								ZEB2 (87578 upstream) : None (None downstream)																							CCAGCTTAGCAAAGCGTTGGC	0.428													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146106353	146106353	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146106353delT								ZEB2 (828422 upstream) : None (None downstream)																							CAAATGTCTATTTTTTTTTGC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	154350648	154350648	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154350648delA								RPRM (15326 upstream) : GALNT13 (377778 downstream)																							agaaaaatttaaaaggcctat	0.000													4	2	---	---	---	---	
ZAK	51776	broad.mit.edu	37	2	174123787	174123787	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174123787delT	uc002uhz.2	+						uc002uib.2_Intron	NM_016653	NP_057737	Q9NYL2	MLTK_HUMAN	MLK-related kinase isoform 1						activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			lung(3)|stomach(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.176)			ttttttttaatttttttGTCT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	185025119	185025119	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185025119delT								NUP35 (998712 upstream) : ZNF804A (437974 downstream)																							atcagagatattgccctgtag	0.000													4	2	---	---	---	---	
TRAK2	66008	broad.mit.edu	37	2	202265472	202265472	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202265472delT	uc002uyb.3	-						TRAK2_uc002uyc.2_Intron	NM_015049	NP_055864	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2							early endosome|plasma membrane	GABA receptor binding				0						ttTAAAATGATTTTTTTTTTA	0.134													4	2	---	---	---	---	
ADAM23	8745	broad.mit.edu	37	2	207395346	207395346	+	Intron	DEL	A	-	-	rs5838028		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207395346delA	uc002vbq.2	+						ADAM23_uc010ziv.1_Intron	NM_003812	NP_003803	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23 preproprotein						cell adhesion|central nervous system development|proteolysis	extracellular region|integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			skin(2)|ovary(1)	3				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		tctcaaaaagaaaaaaaaaaa	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	216439015	216439016	+	IGR	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216439015_216439016insT								FN1 (138224 upstream) : MREG (368299 downstream)																							cattcactcactttttttttta	0.213													4	2	---	---	---	---	
VIL1	7429	broad.mit.edu	37	2	219313728	219313729	+	Intron	INS	-	A	A	rs144334662		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219313728_219313729insA	uc002via.2	+						VIL1_uc010zke.1_Intron|VIL1_uc002vib.2_Intron	NM_007127	NP_009058	P09327	VILI_HUMAN	villin 1						actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		acatggtctggaaaaaaaaaaa	0.203													2	8	---	---	---	---	
DES	1674	broad.mit.edu	37	2	220286392	220286392	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220286392delT	uc002vll.2	+							NM_001927	NP_001918	P17661	DESM_HUMAN	desmin						cytoskeleton organization|muscle filament sliding|regulation of heart contraction	cytosol|Z disc	protein binding|structural constituent of cytoskeleton			central_nervous_system(2)	2		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		CTGGAAACAAttttttttttt	0.289													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	220986025	220986026	+	IGR	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220986025_220986026insT								SLC4A3 (479324 upstream) : None (None downstream)																							ttctttctttctttctttcttt	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	229721490	229721490	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229721490delA								SPHKAP (675129 upstream) : PID1 (167200 downstream)																							GTGCAACTTTAAAAAAAAATC	0.388													4	2	---	---	---	---	
SUMF1	285362	broad.mit.edu	37	3	3896906	3896907	+	Intron	DEL	TC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3896906_3896907delTC	uc003bps.1	-							NM_182760		Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1 isoform 1							endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		GTGGTAGACATCTCTCTCTCCC	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	18621025	18621026	+	IGR	INS	-	C	C	rs140865953	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18621025_18621026insC								SATB1 (140773 upstream) : KCNH8 (568991 downstream)																							cccctttttttccctcacatca	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	24066277	24066277	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24066277delT								NR1D2 (44168 upstream) : LOC152024 (71503 downstream)																							CTGCTCATTGTTTTTTTGCCA	0.502													4	2	---	---	---	---	
THRB	7068	broad.mit.edu	37	3	24270128	24270128	+	Intron	DEL	A	-	-	rs138385171		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24270128delA	uc003ccx.3	-						THRB_uc010hfe.2_Intron|THRB_uc003ccy.3_Intron|THRB_uc003ccz.3_Intron|THRB_uc003cdc.2_Intron|THRB_uc003cdd.2_Intron|THRB_uc003cde.1_Intron	NM_001128176	NP_001121648	P10828	THB_HUMAN	thyroid hormone receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(2)|pancreas(1)	3					Levothyroxine(DB00451)|Liothyronine(DB00279)	tgtctcaaagaaaaaaaaaaa	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	42698269	42698271	+	Intron	DEL	ACC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42698269_42698271delACC	uc003clt.1	+						ZBTB47_uc003clu.1_5'Flank					SubName: Full=cDNA FLJ45122 fis, clone BRAWH3036247, weakly similar to Zinc finger protein 228;																		GTGGAGCTCAACCACCACCACCC	0.650													4	2	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54605716	54605717	+	Intron	DEL	AC	-	-	rs10617736		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54605716_54605717delAC	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		CATGAAAATAACACACATCACA	0.198													7	4	---	---	---	---	
C3orf67	200844	broad.mit.edu	37	3	58954102	58954102	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58954102delT	uc003dkt.1	-						uc003dku.1_Intron|C3orf67_uc003dkv.1_Intron|C3orf67_uc003dkw.2_Intron|C3orf67_uc011bfg.1_Intron	NM_198463	NP_940865	Q6ZVT6	CC067_HUMAN	hypothetical protein LOC200844												0		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)		agcatgttactttttttactt	0.000													4	2	---	---	---	---	
PTPRG	5793	broad.mit.edu	37	3	62131214	62131216	+	Intron	DEL	GAT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62131214_62131216delGAT	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		aaatgatgaagatgatgatgatg	0.330													4	2	---	---	---	---	
FOXP1	27086	broad.mit.edu	37	3	71149883	71149883	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71149883delC	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003doj.2_Intron|FOXP1_uc003dok.2_Intron	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GAACTGTTATCAAATGGACTG	0.423			T	PAX5	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	71681447	71681448	+	IGR	INS	-	C	C	rs140214395	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71681447_71681448insC								FOXP1 (48307 upstream) : EIF4E3 (46994 downstream)																							TTGATTacacaaacacacacac	0.144													4	2	---	---	---	---	
CGGBP1	8545	broad.mit.edu	37	3	88151122	88151122	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88151122delT	uc003dqu.2	-							NM_003663	NP_003654	Q9UFW8	CGBP1_HUMAN	CGG triplet repeat binding protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding				0		Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00359)|Lung(72;0.00677)		atctatcaaatttttttgccc	0.000													4	2	---	---	---	---	
FILIP1L	11259	broad.mit.edu	37	3	99611450	99611450	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99611450delT	uc003dtm.2	-						C3orf26_uc003dtk.1_Intron|C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Intron	NM_182909	NP_878913	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like isoform 1							cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1						acctcagtagttccaggcatc	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	109825687	109825687	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109825687delC								FLJ25363 (611673 upstream) : PVRL3 (965178 downstream)																							tagttcatctccaggctacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	109965674	109965674	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109965674delA								FLJ25363 (751660 upstream) : PVRL3 (825191 downstream)																							CGAGTTCTTTAAAAAAAATGC	0.303													4	2	---	---	---	---	
MYLK	4638	broad.mit.edu	37	3	123563429	123563430	+	Intron	INS	-	G	G	rs72587455	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123563429_123563430insG	uc003ego.2	-						MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Intron	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1						aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		ttaactcatcttaagacaggag	0.163													1	5	---	---	---	---	
RAB43	339122	broad.mit.edu	37	3	128864920	128864921	+	Intron	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128864920_128864921insA	uc003elo.1	-						ISY1_uc010hsz.1_Intron|ISY1_uc003elp.1_Intron|ISY1_uc010hta.1_Intron	NM_020701	NP_065752	Q86YS6	RAB43_HUMAN	ISY1 splicing factor homolog						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			lung(1)	1						actagcgtaagaaaaaaaaaat	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	135485263	135485264	+	IGR	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135485263_135485264insA								EPHB1 (505958 upstream) : PPP2R3A (199303 downstream)																							CATGAACAAGGAAAAAATTGCC	0.470													4	2	---	---	---	---	
ATR	545	broad.mit.edu	37	3	142257695	142257695	+	Intron	DEL	A	-	-	rs138807786		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142257695delA	uc003eux.3	-							NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein						cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						AATTAATAATAAAAAAAAAGT	0.169								Other_conserved_DNA_damage_response_genes					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144153541	144153543	+	IGR	DEL	AGG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144153541_144153543delAGG								C3orf58 (442332 upstream) : None (None downstream)																							CACTTGGGACAGGAGGAGGAGGG	0.335													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	148307730	148307731	+	IGR	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148307730_148307731insT								None (None upstream) : AGTR1 (107927 downstream)																							AAAAATAAAACTTTTTTTTTAA	0.277													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	154048453	154048453	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154048453delT								DHX36 (6167 upstream) : GPR149 (7009 downstream)																							CTTCTTCATCTTTTTTTTTTA	0.393													3	4	---	---	---	---	
MFSD1	64747	broad.mit.edu	37	3	158544299	158544299	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158544299delT	uc003fcl.1	+						MFSD1_uc003fcm.1_Intron|MFSD1_uc003fcn.1_Intron|MFSD1_uc011bow.1_Intron|MFSD1_uc011box.1_Intron	NM_022736	NP_073573	Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing						transmembrane transport	integral to membrane					0			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CATTAGTGGATTTTTGTTGTT	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	158781792	158781792	+	IGR	DEL	G	-	-	rs75186004	byFrequency	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158781792delG								MFSD1 (234288 upstream) : SCHIP1 (5325 downstream)																							ATCTGTGCCTGGGAAACATCT	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165904144	165904145	+	IGR	DEL	AA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165904144_165904145delAA								BCHE (348891 upstream) : None (None downstream)																							AGCAAGTGAGAAAGAGGGAGAA	0.386													4	2	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173512764	173512765	+	Intron	INS	-	TG	TG			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173512764_173512765insTG	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TCTCCTTTTTTTGTGTGTGTGT	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	174199671	174199671	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174199671delG	uc003fiq.1	+						uc003fir.2_Intron|uc003fis.2_Intron|uc010hwx.1_Intron					Homo sapiens NAALADL2 gene, partial 5'UTR, variant 1.																		attgggggctggtcatgtcag	0.000													4	2	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	187896827	187896828	+	Intron	DEL	AG	-	-	rs140480887		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187896827_187896828delAG	uc011bsg.1	+						FLJ42393_uc011bsh.1_RNA	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		ggagagagacagagagagagag	0.124			T	HMGA2|MLL|C12orf9	lipoma|leukemia								7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189844516	189844516	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189844516delT								LEPREL1 (4290 upstream) : CLDN1 (178987 downstream)																							ACCAAATTTGTTTTATAAGCA	0.264													4	2	---	---	---	---	
ATP13A5	344905	broad.mit.edu	37	3	193019693	193019694	+	Intron	DEL	TC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193019693_193019694delTC	uc011bsq.1	-							NM_198505	NP_940907	Q4VNC0	AT135_HUMAN	ATPase type 13A5						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|skin(4)|large_intestine(2)	11	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		GATCAAGAGATCAAGACGACAG	0.361													4	2	---	---	---	---	
LRCH3	84859	broad.mit.edu	37	3	197533378	197533378	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197533378delA	uc011bul.1	+						LRCH3_uc003fyj.1_Intron|LRCH3_uc011bum.1_Intron|LRCH3_uc011bun.1_Intron	NM_032773	NP_116162	Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH)							extracellular region				ovary(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		aaaaacttccaaaaatctgga	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	47589	47591	+	IGR	DEL	GAG	-	-	rs147614254		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47589_47591delGAG								None (None upstream) : ZNF595 (5636 downstream)																							gaagaaagaagagaagaagaaga	0.108													3	7	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	57746	57746	+	Intron	DEL	A	-	-	rs111852468		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57746delA	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		CTGGAAAAACAAAAGGGTTTT	0.303													6	4	---	---	---	---	
SLC26A1	10861	broad.mit.edu	37	4	983003	983003	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:983003delT	uc003gcb.2	-	4	2102	c.1724delA	c.(1723-1725)GAGfs	p.E575fs	SLC26A1_uc003gbx.2_Intron|IDUA_uc003gby.2_Intron|IDUA_uc003gbz.2_Intron|IDUA_uc003gca.2_Intron|SLC26A1_uc003gcc.2_Frame_Shift_Del_p.E575fs	NM_213613	NP_998778	Q9H2B4	S26A1_HUMAN	solute carrier family 26, member 1 isoform a	575	STAS.					integral to membrane|plasma membrane	secondary active sulfate transmembrane transporter activity			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TGAGCCCCCCTCCTTCCTCCT	0.692													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	4893268	4893269	+	IGR	DEL	GT	-	-	rs141953709		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4893268_4893269delGT								MSX1 (27610 upstream) : CYTL1 (123047 downstream)																							TCTTCCTAGGgtgtgtgtgtgt	0.272													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	8696355	8696356	+	IGR	INS	-	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8696355_8696356insG								CPZ (74869 upstream) : HMX1 (172417 downstream)																							ggtggtgctttgggaaagggag	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12395566	12395567	+	IGR	INS	-	AA	AA	rs77391154		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12395566_12395567insAA								HS3ST1 (965029 upstream) : HSP90AB2P (939470 downstream)																							TGTAATAAGTCAAAAAAAAAAT	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	13088555	13088555	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13088555delT								None (None upstream) : HSP90AB2P (246482 downstream)																							CCCAACTTGATTAGAAATTCA	0.393													4	2	---	---	---	---	
SLIT2	9353	broad.mit.edu	37	4	20268469	20268469	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20268469delG	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						atcaggggaaggttcacagag	0.214													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	34070810	34070810	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34070810delG								None (None upstream) : None (None downstream)																							TAGTCAGTGTGGTGCTGTATT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	40406757	40406757	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40406757delG								CHRNA9 (49784 upstream) : RBM47 (18515 downstream)																							CTGATAAGCTGATCCATGTGA	0.502													4	2	---	---	---	---	
ATP10D	57205	broad.mit.edu	37	4	47550740	47550740	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47550740delA	uc003gxk.1	+						ATP10D_uc003gxl.1_Intron	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D						ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3						TGTGTTTTGCAAAACCATACC	0.328													4	2	---	---	---	---	
CORIN	10699	broad.mit.edu	37	4	47644240	47644240	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47644240delA	uc003gxm.2	-						CORIN_uc011bzf.1_Intron|CORIN_uc011bzg.1_Intron	NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin						peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2						ctagagggctaaaaaaaaaat	0.095													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49160129	49160129	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49160129delC								CWH43 (96036 upstream) : None (None downstream)																							ccttttcaatctctggtttta	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55903021	55903021	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55903021delT								KIT (296142 upstream) : KDR (41406 downstream)																							ccagcctttatttaaaaccta	0.070													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	60129575	60129576	+	IGR	INS	-	AC	AC	rs146990400		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60129575_60129576insAC								None (None upstream) : None (None downstream)																							ccttaacacttacacacacaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	61262501	61262501	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61262501delT								None (None upstream) : LPHN3 (804473 downstream)																							atagacactcttttttttttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	65870720	65870721	+	IGR	INS	-	TT	TT	rs143899027	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65870720_65870721insTT								TECRL (595542 upstream) : EPHA5 (314561 downstream)																							cacccctccactttaatctcca	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	67422968	67422968	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67422968delA								MIR1269 (280322 upstream) : CENPC1 (915021 downstream)																							tggatcctttaagggctgtga	0.000													4	2	---	---	---	---	
STAP1	26228	broad.mit.edu	37	4	68450407	68450409	+	Intron	DEL	AGA	-	-	rs142916997		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68450407_68450409delAGA	uc003hde.3	+						STAP1_uc003hdf.2_Intron	NM_012108	NP_036240	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1						cellular membrane fusion|intracellular protein transport	cytoplasm					0						gccttgagatagaagaatgcttg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	73775313	73775314	+	IGR	DEL	TG	-	-	rs141172734		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73775313_73775314delTG								ADAMTS3 (340797 upstream) : COX18 (145102 downstream)																							CATACTAAACTGTGCAATGAAG	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84112726	84112727	+	IGR	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84112726_84112727insT								PLAC8 (76815 upstream) : COQ2 (69962 downstream)																							AGGAGACATTATCCCTGTCCTG	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84557329	84557329	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84557329delA								AGPAT9 (30304 upstream) : NKX6-1 (857107 downstream)																							gactccatctaaaaaaagcag	0.000													4	2	---	---	---	---	
ABCG2	9429	broad.mit.edu	37	4	89054064	89054064	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89054064delA	uc003hrg.2	-						ABCG2_uc003hrh.2_Intron|ABCG2_uc003hrf.2_5'Flank|ABCG2_uc003hri.1_Intron|ABCG2_uc003hrj.1_Intron|ABCG2_uc003hrk.1_Intron	NM_004827	NP_004818	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G, member 2						cellular iron ion homeostasis|urate metabolic process	integral to membrane|plasma membrane	ATP binding|heme transporter activity|protein homodimerization activity|xenobiotic-transporting ATPase activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Imatinib(DB00619)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nitrendipine(DB01054)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Topotecan(DB01030)	ctacttaaagaaaaaaaaaaa	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	90331081	90331081	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90331081delG								GPRIN3 (101920 upstream) : SNCA (314170 downstream)																							gacagacataggagtcttatt	0.154													4	2	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	91820044	91820045	+	Intron	DEL	TG	-	-	rs139768445	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91820044_91820045delTG	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						tctctggttttgtttttaatgc	0.000													4	2	---	---	---	---	
PPA2	27068	broad.mit.edu	37	4	106347029	106347029	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106347029delA	uc003hxl.2	-						PPA2_uc003hxm.2_Intron|PPA2_uc003hxn.2_Intron|PPA2_uc003hxo.2_Intron|PPA2_uc003hxp.2_Intron|PPA2_uc003hxq.2_Intron|PPA2_uc003hxr.2_Intron|PPA2_uc011cfa.1_Intron	NM_176869	NP_789845	Q9H2U2	IPYR2_HUMAN	inorganic pyrophosphatase 2 isoform 1 precursor						diphosphate metabolic process|tRNA aminoacylation for protein translation	mitochondrial matrix	inorganic diphosphatase activity|magnesium ion binding			pancreas(1)	1		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		gatagaggggaaaaaaagatt	0.000													4	2	---	---	---	---	
SGMS2	166929	broad.mit.edu	37	4	108759044	108759044	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108759044delG	uc003hyl.3	+							NM_001136258	NP_001129730	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2						sphingomyelin biosynthetic process	integral to Golgi membrane|integral to plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			lung(1)	1				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)	Choline(DB00122)	ttttttttgtgggtaaagagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	127463033	127463033	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127463033delT								None (None upstream) : None (None downstream)																							tcggtttatattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	129529758	129529759	+	IGR	INS	-	A	A	rs5861861		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129529758_129529759insA								PGRMC2 (320810 upstream) : PHF17 (201020 downstream)																							TTAACTGATTTAAAAAAAAAAA	0.450													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	130486060	130486060	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130486060delG								C4orf33 (452218 upstream) : None (None downstream)																							tatgcaaccaggctctgaagt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	134890870	134890870	+	IGR	DEL	A	-	-	rs56201618	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134890870delA								PCDH10 (778139 upstream) : PABPC4L (226621 downstream)																							CCATATGAAGAAAAAAGGGCT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	139892675	139892675	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139892675delA								SLC7A11 (729172 upstream) : CCRN4L (44268 downstream)																							ctgaggtgtgaaggtggtttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	145346890	145346890	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145346890delG								GYPA (284986 upstream) : HHIP (220283 downstream)																							ggatgaccctgggggaatgag	0.090													4	2	---	---	---	---	
LRBA	987	broad.mit.edu	37	4	151870920	151870921	+	Intron	INS	-	TA	TA	rs10680252		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151870920_151870921insTA	uc010ipj.2	-						LRBA_uc003ilu.3_Intron|LRBA_uc010ipk.1_Intron	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					CAAGGAAACTCGTAAGTTCAAA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	152835195	152835195	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152835195delT								PET112L (153049 upstream) : FBXW7 (407216 downstream)																							aatggggttgtttggtttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	154364908	154364908	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154364908delG								MND1 (28665 upstream) : KIAA0922 (22590 downstream)																							GTGCTTGTCTGGGAGTTGACA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	184531412	184531412	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184531412delG								ING2 (99163 upstream) : RWDD4A (29377 downstream)																							catgtgcattggggaaagagg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189324750	189324751	+	Intron	INS	-	G	G	rs80338586		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189324750_189324751insG	uc003izo.1	+											Homo sapiens cDNA FLJ38649 fis, clone HHDPC2007302.																		tgttgtttttttttgtttgttt	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190540544	190540544	+	IGR	DEL	A	-	-	rs68148160		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190540544delA								None (None upstream) : FRG1 (321430 downstream)																							ATAGGAGGGGAAAAAAAATCT	0.358													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190635014	190635014	+	IGR	DEL	A	-	-	rs112391585		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190635014delA								None (None upstream) : FRG1 (226960 downstream)																							CAGTTTTAATAAAAGGGAGTA	0.318													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2620354	2620354	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2620354delG								IRX4 (737474 upstream) : IRX2 (125927 downstream)																							GAGCCCTGTTGATTTAAGCCA	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6269686	6269687	+	IGR	INS	-	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6269686_6269687insC								KIAA0947 (779349 upstream) : FLJ33360 (40867 downstream)																							ATTTCCTGTTACCCCCACCATC	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20521904	20521905	+	IGR	DEL	AC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20521904_20521905delAC								CDH18 (533597 upstream) : GUSBP1 (820037 downstream)																							agcacaagtTacacacacacac	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	29584535	29584538	+	IGR	DEL	AATT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29584535_29584538delAATT								None (None upstream) : None (None downstream)																							AAATAAAAACAATTAAGTAGATTA	0.230													4	2	---	---	---	---	
RAI14	26064	broad.mit.edu	37	5	34817024	34817024	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34817024delA	uc003jir.2	+						RAI14_uc010iur.2_Intron|RAI14_uc011coj.1_Intron|RAI14_uc010ius.1_Intron|RAI14_uc003jis.2_Intron|RAI14_uc003jit.2_Intron|RAI14_uc011cok.1_Intron	NM_015577	NP_056392	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14 isoform a							cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)					AAACAACAACAAAAAAAAACA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	35416886	35416886	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35416886delA								PRLR (186092 upstream) : SPEF2 (201103 downstream)																							CAGCCTAACCAAAACAAAGTA	0.418													4	2	---	---	---	---	
GHR	2690	broad.mit.edu	37	5	42425920	42425920	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42425920delT	uc003jmt.2	+						uc003jmu.2_Intron|uc003jmv.1_Intron	NM_000163	NP_000154	P10912	GHR_HUMAN	growth hormone receptor precursor						2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|JAK-STAT cascade|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(4)|kidney(1)|skin(1)	6		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	AACATTTAGCTTTTTTTTATT	0.358													4	2	---	---	---	---	
MGC42105	167359	broad.mit.edu	37	5	43230491	43230491	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43230491delT	uc003jno.2	+							NM_153361	NP_699192	Q8IY84	NIM1_HUMAN	serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9						gtcatgcttctttttttaaag	0.000													4	2	---	---	---	---	
GZMA	3001	broad.mit.edu	37	5	54398826	54398826	+	Intron	DEL	T	-	-	rs80101709		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54398826delT	uc003jpm.2	+							NM_006144	NP_006135	P12544	GRAA_HUMAN	granzyme A precursor						cleavage of lamin|cytolysis|immune response|negative regulation of DNA binding|negative regulation of endodeoxyribonuclease activity|negative regulation of oxidoreductase activity|positive regulation of apoptosis	extracellular region|immunological synapse|nucleus	protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|pancreas(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				cctgtctctaTTTTTTTTTTT	0.100													4	2	---	---	---	---	
KIF2A	3796	broad.mit.edu	37	5	61645654	61645654	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61645654delT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron|KIF2A_uc010iwq.2_Intron	NM_004520	NP_004511	O00139	KIF2A_HUMAN	kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		aagaaagtccttagatcagtg	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	63347965	63347965	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63347965delA								HTR1A (90419 upstream) : RNF180 (113706 downstream)																							GTTTATATAGAAAAAAAAATG	0.269													4	2	---	---	---	---	
CCNB1	891	broad.mit.edu	37	5	68470536	68470536	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68470536delA	uc003jvm.2	+						CCNB1_uc011crd.1_Intron|CCNB1_uc010ixb.2_Intron	NM_031966	NP_114172	P14635	CCNB1_HUMAN	cyclin B1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitotic cell cycle spindle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|mitotic spindle stabilization|positive regulation of attachment of spindle microtubules to kinetochore|positive regulation of mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of cyclin-dependent protein kinase activity	condensed nuclear chromosome outer kinetochore|cytosol|microtubule organizing center|nucleoplasm|spindle pole					0		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		agcgagactcaaaaaaaaaag	0.144													6	3	---	---	---	---	
GFM2	84340	broad.mit.edu	37	5	74043245	74043245	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74043245delA	uc003kdh.1	-						GFM2_uc003kdi.1_Intron|GFM2_uc010izj.1_Intron|GFM2_uc010izk.1_Intron|GFM2_uc003kdj.1_Intron|GFM2_uc010izl.1_Intron	NM_032380	NP_115756	Q969S9	RRF2M_HUMAN	mitochondrial elongation factor G2 isoform 1						mitochondrial translation|ribosome disassembly	mitochondrion	GTP binding|GTPase activity				0		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		AATCATCAAGAAGCCACTTTG	0.368													4	2	---	---	---	---	
SV2C	22987	broad.mit.edu	37	5	75396911	75396911	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75396911delA	uc003kei.1	+							NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		AGGATGTATGAGGAGAGGGAA	0.438													6	5	---	---	---	---	
IQGAP2	10788	broad.mit.edu	37	5	75948269	75948270	+	Intron	INS	-	TTA	TTA	rs144997135	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75948269_75948270insTTA	uc003kek.2	+						IQGAP2_uc010izv.2_Intron|IQGAP2_uc011csv.1_Intron|IQGAP2_uc003kel.2_Intron	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		GAAATTCCATTTTACTCCTTTT	0.371													1	5	---	---	---	---	
SSBP2	23635	broad.mit.edu	37	5	80733496	80733496	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80733496delT	uc003kho.2	-						RNU5E_uc011cto.1_Intron|SSBP2_uc010jar.2_Intron|SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)		TTCCCAATCGTTTTTTTTTTA	0.289													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	84157255	84157256	+	IGR	INS	-	A	A	rs148894104	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84157255_84157256insA								EDIL3 (476644 upstream) : None (None downstream)																							agaaacacagcaaaaaaaactg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87187216	87187217	+	IGR	DEL	AG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87187216_87187217delAG								CCNH (478380 upstream) : TMEM161B (303807 downstream)																							agaaaacaacagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	97445293	97445294	+	IGR	DEL	AG	-	-	rs5869791		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97445293_97445294delAG								RIOK2 (926288 upstream) : RGMB (659705 downstream)																							CCTTCAGAGCAGAGAGTACCAG	0.550													4	4	---	---	---	---	
FER	2241	broad.mit.edu	37	5	108162649	108162649	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108162649delT	uc003kop.1	+						FER_uc011cve.1_Intron|FER_uc011cvf.1_Intron|FER_uc003koq.2_Intron|FER_uc011cvg.1_Intron	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		TTTTAGAAACTTTTTTTTTAT	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	110402321	110402321	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110402321delT								SLC25A46 (303839 upstream) : TSLP (3457 downstream)																							ACTGTGCCACTTTTTTTTTCA	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	118088234	118088234	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118088234delA								None (None upstream) : DTWD2 (84337 downstream)																							ATTTCATAATAAAAAAAAAAT	0.328													4	2	---	---	---	---	
ACSL6	23305	broad.mit.edu	37	5	131339616	131339616	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131339616delT	uc010jdo.1	-						ACSL6_uc003kvx.1_Intron|ACSL6_uc003kvy.1_Intron|ACSL6_uc003kwb.2_Intron|ACSL6_uc003kvz.1_Intron|ACSL6_uc003kwa.1_Intron|ACSL6_uc003kwc.1_Intron|ACSL6_uc003kwd.1_Intron	NM_015256	NP_056071	Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6						fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane|plasma membrane	ATP binding|long-chain fatty acid-CoA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGTAGCACCCTTTTTTTGGAT	0.463													4	2	---	---	---	---	
SLC22A4	6583	broad.mit.edu	37	5	131648275	131648276	+	Intron	DEL	CA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131648275_131648276delCA	uc003kwq.2	+						SLC22A4_uc010jdq.1_Intron|uc003kwr.3_Intron	NM_003059	NP_003050	Q9H015	S22A4_HUMAN	solute carrier family 22 member 4						body fluid secretion|sodium ion transport	apical plasma membrane|integral to plasma membrane|mitochondrion	ATP binding|carnitine transporter activity|cation:cation antiporter activity|PDZ domain binding|secondary active organic cation transmembrane transporter activity|symporter activity				0		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Carnitine(DB00583)	CTGCCATCACCACTGCCCTCCC	0.589													5	4	---	---	---	---	
HSPA4	3308	broad.mit.edu	37	5	132426534	132426534	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132426534delT	uc003kyj.2	+							NM_002154	NP_002145	P34932	HSP74_HUMAN	heat shock 70kDa protein 4						cellular chaperone-mediated protein complex assembly|protein import into mitochondrial outer membrane|response to unfolded protein	cytoplasm|nucleus	ATP binding			lung(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGTGGAATCATTTTTTTTTTC	0.308													4	3	---	---	---	---	
NDFIP1	80762	broad.mit.edu	37	5	141507577	141507577	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141507577delA	uc003lmi.3	+						NDFIP1_uc003lmj.1_Intron	NM_030571	NP_085048	Q9BT67	NFIP1_HUMAN	Nedd4 family interacting protein 1						cellular iron ion homeostasis|negative regulation of gene expression|negative regulation of protein transport|negative regulation of transporter activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of protein ubiquitination	endosome membrane|extracellular region|Golgi membrane|integral to membrane|perinuclear region of cytoplasm	signal transducer activity				0		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATATGACAGGAAAAAAAATCC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	141659179	141659179	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141659179delT								NDFIP1 (125173 upstream) : SPRY4 (30813 downstream)																							TCTCATTTTATTttttttcat	0.264													4	2	---	---	---	---	
SPINK5	11005	broad.mit.edu	37	5	147472906	147472907	+	Intron	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147472906_147472907insT	uc003lox.2	+						SPINK5_uc010jgq.1_Intron|SPINK5_uc010jgs.1_Intron|SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5 isoform						anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTTTCTTGGATTTTTTTTGGT	0.371													4	2	---	---	---	---	
FBXO38	81545	broad.mit.edu	37	5	147772874	147772877	+	Intron	DEL	ACAC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147772874_147772877delACAC	uc003lpf.1	+						FBXO38_uc003lpg.1_Intron|FBXO38_uc003lph.2_Intron	NM_205836	NP_995308	Q6PIJ6	FBX38_HUMAN	F-box protein 38 isoform b							cytoplasm|nucleus				ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGACCAGAACACACACACACAG	0.221													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155348526	155348526	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155348526delG	uc003lwa.1	+							NM_172244	NP_758447	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 2						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			gaggggtagtgggctgagact	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165753539	165753539	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165753539delC								None (None upstream) : ODZ2 (958304 downstream)																							CAGAGAGTCACCCCAGGTCAT	0.478													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	166790339	166790340	+	Intron	DEL	TG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166790339_166790340delTG	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		GCACATTGCCTGTGTAGAATCA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	168852705	168852705	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168852705delA								SLIT3 (124572 upstream) : CCDC99 (157933 downstream)																							AGGATACATTAAAAAAAAAGA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173029692	173029692	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173029692delG								LOC285593 (17618 upstream) : BOD1 (4456 downstream)																							tgtggtttttgcagtcttgtg	0.000													4	2	---	---	---	---	
SFXN1	94081	broad.mit.edu	37	5	174906894	174906894	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174906894delT	uc003mda.2	+						SFXN1_uc003mdb.1_Intron	NM_022754	NP_073591	Q9H9B4	SFXN1_HUMAN	sideroflexin 1						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity|protein binding			ovary(1)	1	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TCCATCCCCCTTTTACTGATC	0.473													4	2	---	---	---	---	
RNF130	55819	broad.mit.edu	37	5	179422202	179422203	+	Intron	DEL	CT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179422202_179422203delCT	uc003mll.1	-						RNF130_uc003mlm.1_Intron	NM_018434	NP_060904	Q86XS8	GOLI_HUMAN	ring finger protein 130 precursor						apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGGGACCTGCCTCTCTCTCTCT	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	179520780	179520780	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179520780delC								RNF130 (21671 upstream) : RASGEF1C (7016 downstream)																							GGAGCCCTGTCCTCCCACTGG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180547272	180547272	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180547272delT								BTNL9 (58750 upstream) : OR2V2 (34671 downstream)																							ccaggtggactttttTTTTGA	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	9483767	9483767	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9483767delT								HULC (829690 upstream) : TFAP2A (913150 downstream)																							TTTTCTATAATTTTTTTGTGC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14139074	14139074	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14139074delA								CD83 (1928 upstream) : None (None downstream)																							TCGTATTTATAATAATACTTA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14807465	14807466	+	IGR	DEL	CA	-	-	rs68020140		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14807465_14807466delCA								CD83 (670319 upstream) : JARID2 (438268 downstream)																							AAacacacatcacacacacaca	0.426													4	3	---	---	---	---	
JARID2	3720	broad.mit.edu	37	6	15247655	15247655	+	Intron	DEL	T	-	-	rs112292016		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15247655delT	uc003nbj.2	+						JARID2_uc011diu.1_Intron|JARID2_uc011div.1_5'Flank	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein						central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				GTGTGGTGGCTTTTTTTTTTT	0.388													1	5	---	---	---	---	
MBOAT1	154141	broad.mit.edu	37	6	20122054	20122055	+	Intron	DEL	AC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20122054_20122055delAC	uc003ncx.1	-						MBOAT1_uc011dji.1_Intron	NM_001080480	NP_001073949	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain						phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			TCTGTCCCCTACACACACACAC	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	23657385	23657385	+	IGR	DEL	T	-	-	rs67978802		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23657385delT								None (None upstream) : NRSN1 (469029 downstream)																							ACAACAAAACTCGTGAGCTCA	0.423													2	7	---	---	---	---	
NUDT3	11165	broad.mit.edu	37	6	34349228	34349228	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34349228delA	uc003ojl.2	-							NM_006703	NP_006694	O95989	NUDT3_HUMAN	nudix-type motif 3						cell-cell signaling|diadenosine polyphosphate catabolic process|diphosphoinositol polyphosphate catabolic process	cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|magnesium ion binding				0						TTCCCTCTTGAAAAAAAAATG	0.294													4	2	---	---	---	---	
ANKS1A	23294	broad.mit.edu	37	6	34910461	34910462	+	Intron	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34910461_34910462insT	uc003ojx.3	+						ANKS1A_uc011dss.1_Intron|ANKS1A_uc011dst.1_Intron|ANKS1A_uc010jvp.1_Intron	NM_015245	NP_056060	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain							cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4						CCTGATACTGATTTTTTTTTTT	0.361													3	4	---	---	---	---	
FKBP5	2289	broad.mit.edu	37	6	35558593	35558593	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35558593delA	uc011dte.1	-						FKBP5_uc003okx.2_Intron|FKBP5_uc011dtf.1_Intron|FKBP5_uc003oky.2_Intron|FKBP5_uc003okz.2_Intron	NM_001145776	NP_001139248	Q13451	FKBP5_HUMAN	FK506 binding protein 5 isoform 1						protein folding	cytoplasm|membrane|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1						TCAACCCAGGAAAAAAAAAGT	0.418													4	2	---	---	---	---	
CLPS	1208	broad.mit.edu	37	6	35764724	35764725	+	Intron	INS	-	A	A	rs146242201	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35764724_35764725insA	uc003ole.1	-						CLPS_uc003olf.1_Intron	NM_001832	NP_001823	P04118	COL_HUMAN	colipase preproprotein						lipid catabolic process|lipid digestion|retinoid metabolic process|steroid metabolic process	extracellular region					0						agaaaaaaaagaaaaaaaaGGT	0.277													2	4	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38821399	38821400	+	Intron	DEL	GT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38821399_38821400delGT	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						ATATGTAAGCGtgtgtgtgtgt	0.208													3	4	---	---	---	---	
TJAP1	93643	broad.mit.edu	37	6	43458007	43458007	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43458007delC	uc003ovd.2	+						TJAP1_uc003ovf.2_Intron|TJAP1_uc003ove.2_Intron|TJAP1_uc003ovc.2_Intron|TJAP1_uc010jyp.2_Intron|TJAP1_uc011dvh.1_Intron|TJAP1_uc003ovg.2_Intron|TJAP1_uc010jyq.2_Intron|TJAP1_uc011dvi.1_Intron	NM_001146016	NP_001139488	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 isoform a							Golgi apparatus|tight junction	protein binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CCACTGACCACCCCCCACCGT	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	45530424	45530425	+	IGR	INS	-	GA	GA			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45530424_45530425insGA								RUNX2 (11606 upstream) : CLIC5 (335765 downstream)																							AGGGTGAAAATGAGAGAGAGTT	0.450													4	2	---	---	---	---	
CLIC5	53405	broad.mit.edu	37	6	45869505	45869505	+	3'UTR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45869505delT	uc003oxv.3	-	6					CLIC5_uc003oxu.3_3'UTR	NM_001114086	NP_001107558	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5 isoform a						female pregnancy	actin cytoskeleton|cell cortex|chloride channel complex|Golgi apparatus|Golgi apparatus|insoluble fraction|microtubule organizing center	protein binding|voltage-gated chloride channel activity			ovary(1)|skin(1)	2						AAATTTTTCCTTTTTTTTTTC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57535282	57535283	+	IGR	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57535282_57535283insA								PRIM2 (21907 upstream) : GUSBL2 (710876 downstream)																							accctcagaacaaAAAAATTGG	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	63149460	63149460	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63149460delT								KHDRBS2 (153360 upstream) : LGSN (836397 downstream)																							cctgaatacctttttttttcc	0.000													4	2	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65987336	65987338	+	Intron	DEL	GTT	-	-	rs151199701		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65987336_65987338delGTT	uc011dxu.1	-							NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						aaaaaaaaaagttaattaattaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	67830970	67830970	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67830970delC								None (None upstream) : None (None downstream)																							gccccataaacccaggtgacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	70277482	70277482	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70277482delT								BAI3 (178080 upstream) : LMBRD1 (108269 downstream)																							atcaagattgttttttttttt	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	75766514	75766514	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75766514delA								None (None upstream) : COL12A1 (27529 downstream)																							TTGATTTTACAAGAAAAAAAA	0.318													4	2	---	---	---	---	
PHIP	55023	broad.mit.edu	37	6	79694135	79694136	+	Intron	INS	-	GT	GT	rs145636809	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79694135_79694136insGT	uc003pir.2	-						PHIP_uc003piq.2_5'Flank|PHIP_uc011dyp.1_Intron	NM_017934	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein						insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		CACTCTCTGGAGTACTTGGCTC	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	80056383	80056383	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80056383delT								HMGN3 (111928 upstream) : LCA5 (138326 downstream)																							GGTCCTAGCCTTTTTTTCTGC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85228769	85228769	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85228769delT								KIAA1009 (291434 upstream) : TBX18 (168312 downstream)																							CTTTTGTCTGTTTTTTTTACT	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	87062961	87062961	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87062961delG								SNHG5 (674510 upstream) : HTR1E (584063 downstream)																							GGGCCCAGTTGGTGACTTCAG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	96392154	96392154	+	IGR	DEL	G	-	-	rs11301353		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96392154delG								MANEA (334828 upstream) : FUT9 (71691 downstream)																							acagaaaaatgtaatccagga	0.000													4	2	---	---	---	---	
C6orf167	253714	broad.mit.edu	37	6	97716066	97716067	+	Intron	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97716066_97716067insT	uc003ppb.2	-						C6orf167_uc011eaf.1_Intron|C6orf167_uc010kcn.1_Intron|C6orf167_uc010kco.1_Intron|C6orf167_uc003ppc.2_Intron	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714						double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)		TCAAAAGtttcttttttttttt	0.119													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	98446862	98446863	+	IGR	DEL	GT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98446862_98446863delGT								C6orf167 (715801 upstream) : MIR2113 (25544 downstream)																							GGAGGCCAGCgtgtgtgtgtat	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	98466418	98466418	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98466418delT								C6orf167 (735357 upstream) : MIR2113 (5989 downstream)																							TGTTCTTCCCTTTTTTTTCCC	0.353													4	2	---	---	---	---	
FIG4	9896	broad.mit.edu	37	6	110040592	110040592	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110040592delT	uc003ptt.2	+						FIG4_uc011eau.1_Intron	NM_014845	NP_055660	Q92562	FIG4_HUMAN	Sac domain-containing inositol phosphatase 3						cell death	endosome membrane	protein binding			ovary(1)	1		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		TGTGTGTGTGttttttttttc	0.164													4	2	---	---	---	---	
FYN	2534	broad.mit.edu	37	6	112025508	112025509	+	Intron	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112025508_112025509insA	uc003pvj.2	-						FYN_uc003pvi.2_Intron|FYN_uc003pvk.2_Intron|FYN_uc003pvh.2_Intron|FYN_uc010kdy.1_5'Flank	NM_002037	NP_002028	P06241	FYN_HUMAN	protein-tyrosine kinase fyn isoform a						axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	TTTCACTCTTTAAAAAAAATCA	0.361													4	2	---	---	---	---	
FAM184A	79632	broad.mit.edu	37	6	119434622	119434622	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119434622delT	uc003pyk.3	-						FAM184A_uc003pyl.3_Intron	NM_001100411	NP_001093881	Q8NB25	F184A_HUMAN	hypothetical protein LOC79632 isoform 2											ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7						gttttcttccttttttttcaa	0.000													4	2	---	---	---	---	
MAP3K5	4217	broad.mit.edu	37	6	136920614	136920615	+	Intron	DEL	TC	-	-	rs71737097		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136920614_136920615delTC	uc003qhc.2	-						MAP3K5_uc011edj.1_Intron|MAP3K5_uc011edk.1_Intron	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		ACTTAAAGGAtctctctctctc	0.203													3	3	---	---	---	---	
MAP3K5	4217	broad.mit.edu	37	6	137053940	137053940	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137053940delT	uc003qhc.2	-						MAP3K5_uc011edk.1_Intron|MAP3K5_uc010kgw.1_Intron	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		AAAAACACCATTTTTTGAACT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	137857614	137857614	+	IGR	DEL	T	-	-	rs77530872	byFrequency	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137857614delT								OLIG3 (42083 upstream) : TNFAIP3 (330967 downstream)																							cactctcagctttcttcactg	0.000													4	2	---	---	---	---	
TXLNB	167838	broad.mit.edu	37	6	139613224	139613225	+	5'Flank	DEL	CA	-	-	rs10457685		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139613224_139613225delCA	uc011eds.1	-							NM_153235	NP_694967	Q8N3L3	TXLNB_HUMAN	taxilin beta							cytoplasm				large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		cacgcgcgcgcacacacacaca	0.391													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	139787837	139787837	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139787837delT								CITED2 (92052 upstream) : None (None downstream)																							GTAGTCATCCtttttttttgt	0.040													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	150359851	150359851	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150359851delG								RAET1L (13183 upstream) : ULBP3 (23490 downstream)																							aaaggatggagatttattgta	0.000													2	4	---	---	---	---	
PLEKHG1	57480	broad.mit.edu	37	6	150980427	150980427	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150980427delT	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		CTCCAAGGCATTTTTTTTTTC	0.363													3	4	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162625741	162625742	+	Intron	INS	-	T	T	rs141650101	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162625741_162625742insT	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		TTATTCAGAAGTTTTGTTTTTT	0.347													4	2	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162820567	162820568	+	Intron	DEL	AC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162820567_162820568delAC	uc003qtx.3	-						PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		AATAACACATACACACACACAC	0.292													4	3	---	---	---	---	
MLLT4	4301	broad.mit.edu	37	6	168260456	168260458	+	Intron	DEL	TTG	-	-	rs67829921		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168260456_168260458delTTG	uc003qwd.2	+						MLLT4_uc003qwb.1_Intron|MLLT4_uc003qwc.1_Intron	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		GGTTTTGTTATTGTTGTTTTTTT	0.241			T	MLL	AL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169685572	169685573	+	IGR	INS	-	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169685572_169685573insC								THBS2 (31435 upstream) : WDR27 (171734 downstream)																							tatcctggagacccccccatat	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1425442	1425442	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1425442delG								UNCX (148830 upstream) : MICALL2 (48554 downstream)																							TGGCCGGGGTGGGTGACTCTT	0.622													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	10190400	10190400	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10190400delA								PER4 (514953 upstream) : NDUFA4 (782415 downstream)																							CTAAAAAAGTAAAAAAAAAAG	0.169													4	2	---	---	---	---	
CCDC126	90693	broad.mit.edu	37	7	23640106	23640106	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23640106delT	uc003swl.2	+						CCDC126_uc003swm.2_Intron|CCDC126_uc003swn.2_Intron	NM_138771	NP_620126	Q96EE4	CC126_HUMAN	coiled-coil domain containing 126 precursor							extracellular region				ovary(1)|skin(1)	2						TGTGGAGGACTTTTTTTTGGG	0.403													4	2	---	---	---	---	
TAX1BP1	8887	broad.mit.edu	37	7	27798016	27798016	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27798016delT	uc003szl.2	+						TAX1BP1_uc011jzo.1_Intron|TAX1BP1_uc003szk.2_Intron|TAX1BP1_uc011jzp.1_Intron	NM_006024	NP_006015	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I)						anti-apoptosis|apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production	cytosol	identical protein binding|kinase binding|zinc ion binding			breast(1)	1			GBM - Glioblastoma multiforme(3;0.0823)			TTTTTGGAGATTTTTTTTTTT	0.289													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41414300	41414300	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41414300delA								C7orf10 (513943 upstream) : INHBA (314303 downstream)																							CACAGAGAGGAAGCCACTCAT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	43060943	43060944	+	IGR	INS	-	T	T	rs147240041	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43060943_43060944insT								MRPL32 (83492 upstream) : HECW1 (91254 downstream)																							acagcaacacattcttgaaaat	0.010													4	4	---	---	---	---	
NUDCD3	23386	broad.mit.edu	37	7	44454933	44454934	+	Intron	DEL	AG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44454933_44454934delAG	uc003tkz.2	-						NUDCD3_uc010kye.2_Intron	NM_015332	NP_056147	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3												0						GGTACACTGAAGAGAGAGAGAG	0.401													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46169116	46169116	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46169116delC								IGFBP3 (208245 upstream) : None (None downstream)																							gtacctcatgcccctgtgcta	0.025													4	2	---	---	---	---	
ZNF713	349075	broad.mit.edu	37	7	55991602	55991602	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55991602delA	uc003trc.1	+						ZNF713_uc003tra.1_Intron|MRPS17_uc003trb.2_Intron	NM_182633	NP_872439	Q8N859	ZN713_HUMAN	zinc finger protein 713						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			ATATTGTTTTAAAAATGCACA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57924142	57924143	+	IGR	DEL	AG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57924142_57924143delAG								ZNF716 (390877 upstream) : None (None downstream)																							AAGAAGAATCAGAGGTAAATTA	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61078978	61078980	+	IGR	DEL	TAA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61078978_61078980delTAA								None (None upstream) : None (None downstream)																							CATTAATTCTTAATAATTATTTC	0.148													4	2	---	---	---	---	
RABGEF1	27342	broad.mit.edu	37	7	66183553	66183553	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66183553delA	uc003tvf.2	+						RABGEF1_uc003tvg.2_Intron	NM_014504	NP_055319	Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1						endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1						tttaatttataaaaaaaaaat	0.000													4	2	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	70182821	70182821	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70182821delT	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		TACACAGAGGTTTTTGAACCT	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	81232922	81232922	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81232922delT	uc003uhk.1	-											Homo sapiens mRNA sequence.																		gctcatgtgattttttttcca	0.000													4	2	---	---	---	---	
GRM3	2913	broad.mit.edu	37	7	86378354	86378354	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86378354delT	uc003uid.2	+						GRM3_uc010lef.2_Intron|GRM3_uc010leg.2_Intron|GRM3_uc010leh.2_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor						synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	TGAGGCAACATTAGTAATATT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	115081049	115081049	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115081049delA								MDFIC (421786 upstream) : TFEC (494153 downstream)																							TTAAGAAAGTAAgaaggaagt	0.199													4	2	---	---	---	---	
KCND2	3751	broad.mit.edu	37	7	119958304	119958305	+	Intron	INS	-	AT	AT			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119958304_119958305insAT	uc003vjj.1	+							NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)					GTTGGGTTGACTACAAATAGTA	0.252													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	127083177	127083178	+	IGR	DEL	AC	-	-	rs138699496		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127083177_127083178delAC								ZNF800 (50410 upstream) : GCC1 (137505 downstream)																							acacacacagacacacacacac	0.035													3	3	---	---	---	---	
MKRN1	23608	broad.mit.edu	37	7	140155913	140155914	+	Intron	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140155913_140155914insT	uc003vvt.2	-						MKRN1_uc003vvs.2_Intron|MKRN1_uc011krd.1_Intron	NM_013446	NP_038474	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1 isoform 1								ligase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.00956)					CTAGCCAGTTCTTTTTTTTTTT	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152954073	152954079	+	IGR	DEL	TGCTCAT	-	-	rs143189556		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152954073_152954079delTGCTCAT								ACTR3B (401610 upstream) : DPP6 (630340 downstream)																							aggtcgagtgtgctcattgctcatttt	0.164													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153381426	153381426	+	IGR	DEL	A	-	-	rs113088491		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153381426delA								ACTR3B (828963 upstream) : DPP6 (202993 downstream)																							GTTTACCCAGAAAaaaaaata	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155026167	155026167	+	5'Flank	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155026167delC	uc003wlv.1	-						uc003wlw.1_5'Flank					Homo sapiens cDNA FLJ33922 fis, clone CTONG2016953.																		GGAGGGCCTGCGGTGGTGTAG	0.448													4	2	---	---	---	---	
ERICH1	157697	broad.mit.edu	37	8	682888	682888	+	5'Flank	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:682888delG	uc003wph.2	-						ERICH1_uc011kwh.1_5'Flank|ERICH1_uc003wpe.1_5'Flank	NM_207332	NP_997215	Q86X53	ERIC1_HUMAN	glutamate-rich 1											large_intestine(2)	2		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)		ggttctgggtgggggggctag	0.000													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	2819002	2819002	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2819002delT	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ATTCTCTGGCTTTTTTTTCTA	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	15299556	15299556	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15299556delT								SGCZ (203764 upstream) : TUSC3 (98174 downstream)																							ctgggcttcctttttttaaat	0.100													4	2	---	---	---	---	
EPB49	2039	broad.mit.edu	37	8	21934565	21934565	+	Intron	DEL	G	-	-	rs66792631		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21934565delG	uc011kyt.1	+						EPB49_uc010ltl.2_Intron|EPB49_uc011kys.1_Intron|EPB49_uc010ltn.2_Intron|EPB49_uc011kyu.1_Intron|EPB49_uc011kyv.1_Intron|EPB49_uc010ltq.2_Intron	NM_001114136	NP_001107608	Q08495	DEMA_HUMAN	erythrocyte membrane protein band 4.9 isoform 1						actin filament bundle assembly|actin filament capping	actin cytoskeleton|nucleus	actin binding			central_nervous_system(1)	1				Colorectal(74;9.05e-05)|READ - Rectum adenocarcinoma(5;0.0276)|COAD - Colon adenocarcinoma(73;0.0631)		GTCCACAGCTGGGGGCAGGAT	0.557													3	3	---	---	---	---	
REEP4	80346	broad.mit.edu	37	8	22000020	22000021	+	5'Flank	INS	-	CTT	CTT	rs148158119	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22000020_22000021insCTT	uc003xau.1	-						REEP4_uc010ltt.1_5'Flank|REEP4_uc011kyz.1_5'Flank	NM_025232	NP_079508	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4							integral to membrane				skin(1)	1				Colorectal(74;0.00187)|COAD - Colon adenocarcinoma(73;0.061)|READ - Rectum adenocarcinoma(644;0.0993)		CTCCCACACTCCTTCAGCAGAA	0.495													7	4	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	25443102	25443102	+	Intron	DEL	T	-	-	rs111921011		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25443102delT	uc003xek.2	+							NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		ATGTAAAAGATTTTTTTTTTT	0.413													3	3	---	---	---	---	
HMBOX1	79618	broad.mit.edu	37	8	28816889	28816896	+	Intron	DEL	GCCCTGAA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28816889_28816896delGCCCTGAA	uc003xhd.3	+						HMBOX1_uc010lvd.2_Intron|HMBOX1_uc003xhc.3_Intron|HMBOX1_uc010lve.2_Intron|HMBOX1_uc003xhe.2_Intron	NM_001135726	NP_001129198	Q6NT76	HMBX1_HUMAN	homeobox containing 1						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)		cagtgtggatgccctgaaggaggagcat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	29826884	29826885	+	IGR	DEL	TT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29826884_29826885delTT								LOC286135 (15763 upstream) : TMEM66 (93747 downstream)																							Atttttcacatttttttttttg	0.158													4	2	---	---	---	---	
LEPROTL1	23484	broad.mit.edu	37	8	29959768	29959768	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29959768delA	uc003xhw.3	+						LEPROTL1_uc003xhx.2_Intron	NM_015344	NP_056159	O95214	LERL1_HUMAN	leptin receptor overlapping transcript-like 1							integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		CTCAGTTTTTAACATCTATTG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	34364455	34364455	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34364455delA								DUSP26 (907016 upstream) : UNC5D (728520 downstream)																							cacagtagccaaaaaaaatct	0.000													4	2	---	---	---	---	
UNC5D	137970	broad.mit.edu	37	8	35187177	35187177	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35187177delA	uc003xjr.1	+							NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor						apoptosis|axon guidance	integral to membrane	receptor activity			upper_aerodigestive_tract(2)|ovary(2)|pancreas(1)|skin(1)	6				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		AAACCAGTTTAAAAAAAATTA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	36094907	36094907	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36094907delT								UNC5D (442727 upstream) : KCNU1 (546935 downstream)																							ACGAATAGAGTTTTTTTTTCT	0.368													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49812849	49812849	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49812849delT								EFCAB1 (164979 upstream) : SNAI2 (17390 downstream)																							TACCCAAGAATTTTTTTTGCA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49817278	49817279	+	IGR	DEL	AC	-	-	rs36101498		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49817278_49817279delAC								EFCAB1 (169408 upstream) : SNAI2 (12960 downstream)																							Ccacaaacatacacacacacac	0.381													4	2	---	---	---	---	
PXDNL	137902	broad.mit.edu	37	8	52459922	52459923	+	Intron	DEL	CA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52459922_52459923delCA	uc003xqu.3	-							NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				gtgacagcttcaccactagcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55815665	55815665	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55815665delA								RP1 (133134 upstream) : XKR4 (199352 downstream)																							TGCCATATGTAAAAAACATCC	0.328													4	2	---	---	---	---	
NSMAF	8439	broad.mit.edu	37	8	59543849	59543849	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59543849delT	uc003xtt.2	-						NSMAF_uc011lee.1_Intron|NSMAF_uc003xtu.2_Intron	NM_003580	NP_003571	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation						ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)				TTTTAGGCACTTTTTTTTTTA	0.259													6	4	---	---	---	---	
CHD7	55636	broad.mit.edu	37	8	61609505	61609506	+	Intron	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61609505_61609506insT	uc003xue.2	+							NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			ACCTCCCCCACTTTTTTTTTAA	0.267													4	2	---	---	---	---	
CLVS1	157807	broad.mit.edu	37	8	62324035	62324036	+	Intron	DEL	AG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62324035_62324036delAG	uc003xuh.2	+						CLVS1_uc003xui.2_Intron|CLVS1_uc010lyp.2_Intron	NM_173519	NP_775790	Q8IUQ0	CLVS1_HUMAN	retinaldehyde binding protein 1-like 1						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5						ctgcaggagcagagagagagaa	0.238													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	95323026	95323027	+	IGR	DEL	AA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95323026_95323027delAA								GEM (48469 upstream) : RAD54B (61162 downstream)																							CTGGAACCTTAAAAAAAAAAAC	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	97149622	97149624	+	IGR	DEL	TCT	-	-	rs145841846		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97149622_97149624delTCT								C8orf37 (868185 upstream) : GDF6 (4936 downstream)																							CAACTCTAAATCTTCTACCATGA	0.340													3	3	---	---	---	---	
POP1	10940	broad.mit.edu	37	8	99168152	99168152	+	Intron	DEL	T	-	-	rs9785153		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99168152delT	uc003yij.3	+						POP1_uc011lgv.1_Intron|POP1_uc003yik.2_Intron	NM_001145860	NP_001139332	Q99575	POP1_HUMAN	processing of precursor 1						tRNA 5'-leader removal|tRNA catabolic process	nucleolar ribonuclease P complex|ribonuclease MRP complex	identical protein binding|ribonuclease MRP activity|ribonuclease P activity			ovary(1)|breast(1)	2	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			tgtgtgtgtgtgtgtgtgtgt	0.109													4	6	---	---	---	---	
POP1	10940	broad.mit.edu	37	8	99168154	99168156	+	Intron	DEL	TGT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99168154_99168156delTGT	uc003yij.3	+						POP1_uc011lgv.1_Intron|POP1_uc003yik.2_Intron	NM_001145860	NP_001139332	Q99575	POP1_HUMAN	processing of precursor 1						tRNA 5'-leader removal|tRNA catabolic process	nucleolar ribonuclease P complex|ribonuclease MRP complex	identical protein binding|ribonuclease MRP activity|ribonuclease P activity			ovary(1)|breast(1)	2	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			tgtgtgtgtgtgtgtgtgtgtgt	0.118													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	105943939	105943939	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105943939delT								LRP12 (342719 upstream) : ZFPM2 (387208 downstream)																							TTTGGGGCAGTTTCCTAAGAA	0.214													4	2	---	---	---	---	
SYBU	55638	broad.mit.edu	37	8	110602779	110602780	+	Intron	DEL	AC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110602779_110602780delAC	uc003ynj.3	-						SYBU_uc003yni.3_Intron|SYBU_uc003ynk.3_Intron|SYBU_uc010mco.2_Intron|SYBU_uc003ynl.3_Intron|SYBU_uc010mcp.2_Intron|SYBU_uc010mcq.2_Intron|SYBU_uc003yno.3_Intron|SYBU_uc010mcr.2_Intron|SYBU_uc003ynm.3_Intron|SYBU_uc003ynn.3_Intron|SYBU_uc010mcs.2_Intron|SYBU_uc010mct.2_Intron|SYBU_uc010mcu.2_Intron|SYBU_uc003ynp.3_Intron|SYBU_uc010mcv.2_Intron|SYBU_uc011lhw.1_Intron	NM_001099754	NP_001093224	Q9NX95	SYBU_HUMAN	Golgi-localized syntaphilin-related protein							cytoplasmic membrane-bounded vesicle|cytoskeleton|Golgi membrane|integral to membrane				ovary(1)	1						ACTTAAAATAACACACACACAC	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	114825098	114825098	+	IGR	DEL	A	-	-	rs34271891		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114825098delA								CSMD3 (375856 upstream) : None (None downstream)																							AAAGAGGGGGAAAAAAACATA	0.423													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116409771	116409771	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116409771delA								None (None upstream) : TRPS1 (10954 downstream)																							taaagaaaataaaaaaaaaag	0.124													3	3	---	---	---	---	
SNTB1	6641	broad.mit.edu	37	8	121668287	121668287	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121668287delT	uc010mdg.2	-						SNTB1_uc003ype.2_Intron	NM_021021	NP_066301	Q13884	SNTB1_HUMAN	basic beta 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			GTTGAGCCTGTTTTTTTTGAA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	121928060	121928060	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121928060delA								SNTB1 (103751 upstream) : HAS2 (697211 downstream)																							CAGATTGGAGAAAAAATGGAA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128680758	128680758	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128680758delA								LOC727677 (186374 upstream) : MYC (67007 downstream)																							AACCACTCTGAAGTCACTTAC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129896169	129896169	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129896169delA								MIR1208 (733735 upstream) : GSDMC (864274 downstream)																							TGGGAATCTGAAGGTGGGACC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136847855	136847855	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136847855delT								KHDRBS3 (188009 upstream) : None (None downstream)																							CCAGTTTTTCTtttttttttt	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	140010863	140010863	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140010863delC								COL22A1 (84627 upstream) : KCNK9 (602219 downstream)																							aagtgattttcccccaaagtc	0.055													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	140248680	140248680	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140248680delG								COL22A1 (322444 upstream) : KCNK9 (364402 downstream)																							CTACTGATGAGGCCAGAATGA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142977004	142977005	+	IGR	DEL	AG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142977004_142977005delAG								MIR1302-7 (109330 upstream) : NCRNA00051 (302712 downstream)																							ttttacagctagcattcatggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143668408	143668408	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143668408delG								BAI1 (42041 upstream) : ARC (24002 downstream)																							GGTGTCCTGTGGGGCACCTGT	0.622													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143728664	143728664	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143728664delA								ARC (32831 upstream) : JRK (10211 downstream)																							tttcTTAATGAAAAAAAATTT	0.080													4	2	---	---	---	---	
KANK1	23189	broad.mit.edu	37	9	559402	559402	+	Intron	DEL	A	-	-	rs143076580		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:559402delA	uc003zgl.1	+						KANK1_uc003zgm.2_Intron|KANK1_uc003zgn.1_Intron|KANK1_uc003zgo.1_Intron	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a						negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		TGGAGAGGTTAAAAAAAAAAA	0.358													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	1948076	1948076	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1948076delC								DMRT2 (890523 upstream) : SMARCA2 (67266 downstream)																							GTAACATGCTCCCAGGCGACT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	6323830	6323832	+	IGR	DEL	TGG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6323830_6323832delTGG								IL33 (65848 upstream) : TPD52L3 (4543 downstream)																							CTCCAGTCTCTGGAAAAAAATAC	0.379													4	2	---	---	---	---	
MLLT3	4300	broad.mit.edu	37	9	20376546	20376548	+	Intron	DEL	TAT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20376546_20376548delTAT	uc003zoe.2	-						MLLT3_uc011lne.1_Intron|MLLT3_uc011lnf.1_Intron|MLLT3_uc003zof.2_Intron	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		TTACCTTTACTATTATTATTAAA	0.281			T	MLL	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	22416060	22416060	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22416060delC								CDKN2BAS (294969 upstream) : DMRTA1 (30780 downstream)																							TTAGTGCCTTCCACAACTGAT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	28943680	28943681	+	IGR	INS	-	A	A	rs141992154	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28943680_28943681insA								MIR873 (54727 upstream) : None (None downstream)																							AAAACGAATTGAAAAAAGTAAC	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68405348	68405349	+	IGR	INS	-	T	T	rs140647636		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68405348_68405349insT								FAM27B (611159 upstream) : MIR1299 (596890 downstream)																							aaaattctcaataaatgaggta	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68407256	68407257	+	5'Flank	DEL	CT	-	-	rs150223552	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68407256_68407257delCT	uc004aew.1	+											Homo sapiens cDNA, FLJ98602.																		ttttttaaacctctcatatggt	0.000													4	2	---	---	---	---	
FXN	2395	broad.mit.edu	37	9	71668426	71668427	+	Intron	INS	-	GG	GG	rs58150402	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71668426_71668427insGG	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135	Q16595	FRDA_HUMAN	frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0						gatggatggatagatagataga	0.059													4	2	---	---	---	---	
FXN	2395	broad.mit.edu	37	9	71668427	71668428	+	Intron	INS	-	TG	TG	rs75408130	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71668427_71668428insTG	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135	Q16595	FRDA_HUMAN	frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0						atggatggatagatagatagat	0.059													4	2	---	---	---	---	
GDA	9615	broad.mit.edu	37	9	74840362	74840363	+	Intron	DEL	CA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74840362_74840363delCA	uc004aiq.2	+						GDA_uc011lse.1_Intron|GDA_uc011lsf.1_Intron|GDA_uc004air.2_Intron|GDA_uc010mow.1_Intron|GDA_uc004ais.2_Intron|GDA_uc004ait.1_Intron	NM_004293	NP_004284	Q9Y2T3	GUAD_HUMAN	guanine deaminase						nervous system development|purine base metabolic process|purine nucleotide catabolic process	cytosol	guanine deaminase activity|zinc ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		cacccacatccacacacacaca	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	80896640	80896640	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80896640delT								CEP78 (9841 upstream) : PSAT1 (15419 downstream)																							GAAAAATGCCTTTTTTTTTTA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	83615621	83615621	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83615621delA								None (None upstream) : TLE1 (582979 downstream)																							ggtctgagtcaccaccttgta	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	84446515	84446516	+	IGR	DEL	CA	-	-	rs71910292		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84446515_84446516delCA								TLE1 (142919 upstream) : FLJ43950 (81836 downstream)																							CTCCTGCAACCACACACACACA	0.490													6	4	---	---	---	---	
C9orf153	389766	broad.mit.edu	37	9	88863640	88863641	+	Intron	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88863640_88863641insA	uc004aoo.2	-						GOLM1_uc010mqd.1_Intron|C9orf153_uc004aon.2_Intron	NM_001010907	NP_001010907	Q5TBE3	CI153_HUMAN	hypothetical protein LOC389766												0						tttctctgtagaaaaaaaaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	91330088	91330089	+	IGR	INS	-	GC	GC			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91330088_91330089insGC								LOC286238 (63013 upstream) : C9orf47 (275689 downstream)																							tgtgtgtgtgtgtgATCACTTG	0.332													4	2	---	---	---	---	
CORO2A	7464	broad.mit.edu	37	9	100951987	100951988	+	Intron	INS	-	A	A	rs149207138	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100951987_100951988insA	uc004aym.2	-						CORO2A_uc004ayn.2_Intron	NM_052820	NP_438171	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A						actin cytoskeleton organization|intracellular signal transduction	actin cytoskeleton|transcriptional repressor complex	actin filament binding			skin(2)|ovary(1)|pancreas(1)	4		Acute lymphoblastic leukemia(62;0.0559)				cttcaatctggaatctatgtct	0.104													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102248373	102248373	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102248373delT								SEC61B (255473 upstream) : NR4A3 (335764 downstream)																							GGAACCACAATTTTTTTGTTT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102651713	102651713	+	Intron	DEL	A	-	-	rs80339979		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102651713delA	uc004baj.3	-											Homo sapiens hypothetical gene supported by BC030123, mRNA (cDNA clone IMAGE:4815474).																		GTCACAGGGGACATCCATGTC	0.383													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110416481	110416481	+	IGR	DEL	T	-	-	rs34170642		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110416481delT								KLF4 (164434 upstream) : None (None downstream)																							CTCTCTGCACttttttttgtt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111458049	111458050	+	IGR	DEL	CA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111458049_111458050delCA								None (None upstream) : ACTL7B (158821 downstream)																							tgcacatgtgcacacacacaca	0.252													4	2	---	---	---	---	
IKBKAP	8518	broad.mit.edu	37	9	111681850	111681850	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111681850delA	uc004bdm.3	-						IKBKAP_uc004bdl.2_5'Flank|IKBKAP_uc011lwc.1_Intron|IKBKAP_uc010mtq.2_Intron	NM_003640	NP_003631	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene						immune response|protein complex assembly|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding|signal transducer activity			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	7						TTTCGGCATTAAAAAAAAAAA	0.353													7	4	---	---	---	---	
C9orf4	23732	broad.mit.edu	37	9	111904238	111904238	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111904238delA	uc004bdw.1	-							NM_014334	NP_055149	Q9P0K9	CI004_HUMAN	hypothetical protein LOC23732							integral to membrane					0						ccaaaaaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	112133421	112133421	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112133421delC								EPB41L4B (50400 upstream) : PTPN3 (4553 downstream)																							GCCAAGACCACCACGCAGCAG	0.587													4	2	---	---	---	---	
C9orf84	158401	broad.mit.edu	37	9	114544995	114544995	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114544995delA	uc004bfr.2	-						C9orf84_uc011lwt.1_Intron|C9orf84_uc004bfs.1_Intron	NM_173521	NP_775792	Q5VXU9	CI084_HUMAN	hypothetical protein LOC158401 isoform 1											ovary(2)	2						gatgaggtctaaaaaaaaaac	0.000													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119367489	119367489	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119367489delG	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron|ASTN2_uc004bjp.1_Intron|ASTN2_uc004bjq.1_Intron|ASTN2_uc011lxr.1_Intron|ASTN2_uc011lxs.1_Intron|ASTN2_uc011lxt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						GATACTGATCGGGGGGGAGAG	0.403													4	2	---	---	---	---	
ASS1	445	broad.mit.edu	37	9	133346618	133346619	+	Intron	INS	-	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133346618_133346619insC	uc004bzm.2	+						ASS1_uc004bzn.2_Intron|ASS1_uc010mza.2_Intron|ASS1_uc004bzo.2_Intron|ASS1_uc010mzb.2_Intron|ASS1_uc004bzp.2_Intron|ASS1_uc010mzc.2_Intron	NM_000050	NP_000041	P00966	ASSY_HUMAN	argininosuccinate synthetase 1						arginine biosynthetic process|urea cycle	cytosol	argininosuccinate synthase activity|ATP binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	agaggcagaggcccccccaacc	0.193													4	2	---	---	---	---	
ABL1	25	broad.mit.edu	37	9	133642780	133642781	+	Intron	INS	-	AC	AC			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133642780_133642781insAC	uc004bzv.2	+							NM_007313	NP_009297	P00519	ABL1_HUMAN	c-abl oncogene 1, receptor tyrosine kinase						actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)	ggactgcagtgacaatctctgc	0.109			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								4	2	---	---	---	---	
C9orf171	389799	broad.mit.edu	37	9	135344178	135344179	+	Intron	INS	-	CA	CA	rs137960607	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135344178_135344179insCA	uc004cbn.2	+						C9orf171_uc004cbo.2_Intron	NM_207417	NP_997300	Q6ZQR2	CI171_HUMAN	hypothetical protein LOC389799											ovary(4)|large_intestine(1)	5						acacacacacgcacacacacac	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	135449728	135449728	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135449728delT								C9orf171 (1054 upstream) : BARHL1 (8265 downstream)																							gacacttgactttttttctgc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	5862951	5862951	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5862951delT								GDI2 (7439 upstream) : ANKRD16 (40740 downstream)																							attattcatcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10167582	10167583	+	IGR	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10167582_10167583insA								None (None upstream) : SFTA1P (658819 downstream)																							ttgttgcaaaGAAAAATCAGCC	0.054													4	2	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11107663	11107664	+	Intron	INS	-	C	C	rs145741845	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11107663_11107664insC	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						gacaaaccccaccccccgccat	0.099													6	4	---	---	---	---	
OPTN	10133	broad.mit.edu	37	10	13168284	13168284	+	Intron	DEL	T	-	-	rs115582280		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13168284delT	uc001ilu.1	+						OPTN_uc001ilv.1_Intron|OPTN_uc001ilw.1_Intron|OPTN_uc001ilx.1_Intron|OPTN_uc001ily.1_Intron|OPTN_uc010qbr.1_Intron|OPTN_uc001ilz.1_Intron	NM_001008213	NP_001008214	Q96CV9	OPTN_HUMAN	optineurin						cell death|Golgi ribbon formation|Golgi to plasma membrane protein transport|protein targeting to Golgi|signal transduction	perinuclear region of cytoplasm|trans-Golgi network	protein C-terminus binding			ovary(2)	2						TTCGTAtttcttttttttttt	0.184													6	4	---	---	---	---	
PHYH	5264	broad.mit.edu	37	10	13323332	13323333	+	Intron	DEL	TG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13323332_13323333delTG	uc001imf.2	-						PHYH_uc001ime.2_Intron|PHYH_uc001img.2_Intron	NM_006214	NP_006205	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase isoform a precursor						fatty acid alpha-oxidation|nervous system development	peroxisomal matrix	electron carrier activity|L-ascorbic acid binding|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|phytanoyl-CoA dioxygenase activity|protein binding				0		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	GTTAACCAGATGTGACATGTAT	0.322													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14471520	14471520	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14471520delA	uc001imv.2	-						FRMD4A_uc001imw.1_Intron			Q9P2Q2	FRM4A_HUMAN	Homo sapiens mRNA for KIAA1294 protein, partial cds.							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						CTTTGCCTTCACCACGGATGT	0.453													4	2	---	---	---	---	
SPAG6	9576	broad.mit.edu	37	10	22679776	22679776	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22679776delA	uc001iri.2	+						SPAG6_uc001irj.2_Intron|SPAG6_uc010qct.1_Intron|SPAG6_uc009xkh.2_Intron	NM_012443	NP_036575	O75602	SPAG6_HUMAN	sperm associated antigen 6 isoform 1						cell projection organization|spermatid development	axoneme|cilium|cytoplasm|flagellum|microtubule	binding			breast(1)	1						TAACCAAATTAAAAAGCAAAG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29274560	29274561	+	IGR	DEL	AG	-	-	rs3069175		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29274560_29274561delAG								BAMBI (302692 upstream) : LYZL1 (303429 downstream)																							GCAGGAAAACAGGGGTCAGATG	0.500													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29282867	29282867	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29282867delA								BAMBI (310999 upstream) : LYZL1 (295123 downstream)																							ctctgtatagaaaaaaaaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31477382	31477382	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31477382delG								ZNF438 (156516 upstream) : LOC220930 (128076 downstream)																							TTGCTATTGTGGGAAAACAGA	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	35115406	35115407	+	IGR	DEL	AC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35115406_35115407delAC								PARD3 (11483 upstream) : CUL2 (183401 downstream)																							ctcaaaaaCAacacacacacac	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46095812	46095813	+	IGR	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46095812_46095813insT								MARCH8 (5458 upstream) : ANUBL1 (15227 downstream)																							tccttacagtcttttttttcct	0.000													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47096410	47096411	+	Intron	INS	-	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47096410_47096411insG	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						GTAGTGTGGCTGGAttggcctg	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54096820	54096820	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54096820delC								DKK1 (19404 upstream) : MBL2 (428321 downstream)																							GTGGTCTACTCCATCTCACTA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	57471058	57471059	+	IGR	INS	-	A	A	rs149256630	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57471058_57471059insA								PCDH15 (83356 upstream) : ZWINT (646140 downstream)																							CTTTCAGTTAGAAAAAAAACCC	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	64782965	64782965	+	IGR	DEL	A	-	-	rs74456024		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64782965delA								EGR2 (204038 upstream) : NRBF2 (110042 downstream)																							aatgagagagaaaaaaaaaga	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	67444816	67444816	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67444816delT								ANXA2P3 (858182 upstream) : CTNNA3 (234909 downstream)																							ACATCAGGCATTTTTTTCCTT	0.398													4	2	---	---	---	---	
TTC18	118491	broad.mit.edu	37	10	75067060	75067060	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75067060delA	uc009xrc.2	-						TTC18_uc001jty.2_Intron|TTC18_uc009xrd.1_Intron	NM_145170	NP_660153	Q5T0N1	TTC18_HUMAN	tetratricopeptide repeat domain 18								binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)					actgaagaacaaaaaaaaata	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	76526667	76526667	+	IGR	DEL	A	-	-	rs5786152		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76526667delA								ADK (57608 upstream) : MYST4 (59712 downstream)																							GGGAACACCCACACCAGGGAA	0.488													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80300087	80300087	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80300087delC	uc010qlp.1	+											SubName: Full=cDNA FLJ57363;																		ACACAAAGAACCCCAGAAAAA	0.343													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	84096754	84096754	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84096754delT	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		AGGGTTTTTCTTTTTTTTTCT	0.338													4	2	---	---	---	---	
FAM190B	54462	broad.mit.edu	37	10	86098048	86098048	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86098048delA	uc001kdh.1	+						FAM190B_uc001kdg.1_Intron|FAM190B_uc010qmd.1_Intron	NM_018999	NP_061872	Q9H7U1	F190B_HUMAN	granule cell antiserum positive 14											ovary(3)|skin(1)	4						agaaaaacttaaaaaaaaaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	86423703	86423703	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86423703delT								FAM190B (145427 upstream) : GRID1 (935609 downstream)																							CTTGGGAGTCTTTTTTTCCTG	0.428													4	2	---	---	---	---	
LIPA	3988	broad.mit.edu	37	10	90984237	90984238	+	Intron	DEL	TG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90984237_90984238delTG	uc001kga.3	-						LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron|LIPA_uc010qnf.1_Intron|LIPA_uc009xtq.2_Intron|LIPA_uc009xtr.1_5'Flank	NM_000235	NP_000226	P38571	LICH_HUMAN	lipase A precursor						lipid catabolic process	lysosome	lipase activity|sterol esterase activity				0		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		GGATTTCATATGTGTGTGTGTG	0.287													4	2	---	---	---	---	
CRTAC1	55118	broad.mit.edu	37	10	99693173	99693173	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99693173delC	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)		TTCTTGACTTCCCTCAGTTGG	0.488													4	2	---	---	---	---	
COL17A1	1308	broad.mit.edu	37	10	105839148	105839149	+	Intron	DEL	TG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105839148_105839149delTG	uc001kxr.2	-						COL17A1_uc010qqv.1_Intron|COL17A1_uc009xxp.1_Intron	NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen						cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		tgtgcatgtatgtgtgtgtgtg	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	108309963	108309963	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108309963delA								None (None upstream) : SORCS1 (23459 downstream)																							CAGCCACAAGAAAAAAAAAGA	0.512													4	2	---	---	---	---	
ATRNL1	26033	broad.mit.edu	37	10	117591279	117591280	+	Intron	INS	-	C	C	rs138558681		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117591279_117591280insC	uc001lcg.2	+						ATRNL1_uc010qsm.1_Intron|ATRNL1_uc010qsn.1_Intron	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor							integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		gtcaagtgagtttttttttttc	0.054													6	4	---	---	---	---	
ATRNL1	26033	broad.mit.edu	37	10	117591283	117591284	+	Intron	INS	-	TTG	TTG	rs144672238		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117591283_117591284insTTG	uc001lcg.2	+						ATRNL1_uc010qsm.1_Intron|ATRNL1_uc010qsn.1_Intron	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor							integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		agtgagtttttttttttcaagt	0.064													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	118342225	118342225	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118342225delA								PNLIP (14859 upstream) : PNLIPRP1 (8265 downstream)																							CATTGGGGTTAAAATGATATT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	119565340	119565340	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119565340delT								EMX2 (256284 upstream) : RAB11FIP2 (199089 downstream)																							GAGCATGGAATTTTTGGTATC	0.353													4	2	---	---	---	---	
CHST15	51363	broad.mit.edu	37	10	125846196	125846196	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125846196delT	uc001lhm.2	-						CHST15_uc001lhn.2_Intron|CHST15_uc010que.1_Intron|CHST15_uc001lho.2_Intron	NM_015892	NP_056976	Q7LFX5	CHSTF_HUMAN	B cell RAG associated protein						hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity			ovary(1)	1						ctcctcctcctcctcctctat	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125984148	125984149	+	IGR	DEL	CA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125984148_125984149delCA								CHST15 (130942 upstream) : OAT (101723 downstream)																							TCTGTGCATGCACACACACACA	0.579													11	5	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127582669	127582670	+	Intron	DEL	AT	-	-	rs141033053		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127582669_127582670delAT	uc001ljg.1	-						FANK1_uc010quk.1_5'Flank|FANK1_uc001ljh.3_5'Flank|FANK1_uc009yan.2_5'Flank	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				ACTTAAAAAAATATATATAGAA	0.297													4	2	---	---	---	---	
DOCK1	1793	broad.mit.edu	37	10	128775915	128775916	+	Intron	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128775915_128775916insT	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		ACAAGTCCTGCTCTTGGAACTG	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	129338032	129338032	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129338032delA								DOCK1 (87251 upstream) : NPS (9581 downstream)																							GAGTATCATTAAAAAAAAAAG	0.279													2	4	---	---	---	---	
KNDC1	85442	broad.mit.edu	37	10	134992084	134992084	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134992084delC	uc001llz.1	+						KNDC1_uc001lma.1_Intron	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		GGGTTCCGGTCCCCCCTCTGC	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	514295	514295	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:514295delT								RNH1 (7022 upstream) : HRAS (17948 downstream)																							cccccagccAttttttttttg	0.000													3	3	---	---	---	---	
BRSK2	9024	broad.mit.edu	37	11	1465901	1465901	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1465901delC	uc001lti.2	+						BRSK2_uc009ycv.1_Intron|BRSK2_uc001lth.1_Intron|BRSK2_uc001ltj.2_Intron|BRSK2_uc001ltk.2_Intron|BRSK2_uc001ltl.2_Intron|BRSK2_uc001ltm.2_Intron|BRSK2_uc001ltn.2_Intron|BRSK2_uc010qwx.1_Intron	NM_003957	NP_003948	Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2						establishment of cell polarity|neuron differentiation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		tccctccgctccccaggcccc	0.353													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	5975058	5975058	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5975058delT								OR56A3 (5536 upstream) : OR56A5 (13727 downstream)																							CTATACTACCTTTATATCAAG	0.254													4	2	---	---	---	---	
SYT9	143425	broad.mit.edu	37	11	7325399	7325400	+	Intron	DEL	TT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7325399_7325400delTT	uc001mfe.2	+						SYT9_uc001mfd.2_Intron|SYT9_uc009yfi.2_Intron	NM_175733	NP_783860	Q86SS6	SYT9_HUMAN	synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		ttgtaggtggttttaagaatga	0.050													4	2	---	---	---	---	
ST5	6764	broad.mit.edu	37	11	8733601	8733602	+	Intron	DEL	AG	-	-	rs71978018		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8733601_8733602delAG	uc001mgt.2	-						ST5_uc009yfr.2_Intron|ST5_uc001mgu.2_Intron|ST5_uc001mgv.2_Intron|ST5_uc010rbq.1_Intron|ST5_uc010rbp.1_Intron|ST5_uc009yfs.2_5'Flank	NM_213618	NP_998783	P78524	ST5_HUMAN	suppression of tumorigenicity 5 isoform 1						positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		aggcaatggcagagagagaggg	0.020													4	2	---	---	---	---	
ZNF143	7702	broad.mit.edu	37	11	9544709	9544709	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9544709delT	uc001mhr.2	+						ZNF143_uc009yfu.2_Intron|ZNF143_uc010rby.1_Intron	NM_003442	NP_003433	P52747	ZN143_HUMAN	zinc finger protein 143						regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|zinc ion binding				0				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		agaatattgattttttttttc	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	22070823	22070823	+	IGR	DEL	G	-	-	rs7939685	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22070823delG								NELL1 (473596 upstream) : ANO5 (143899 downstream)																							TTTTGTTtttgtttgtttgtt	0.303													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	26869813	26869813	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26869813delT								SLC5A12 (124839 upstream) : FIBIN (145815 downstream)																							ggccatttgatttttctgtgc	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	31127952	31127952	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31127952delA	uc009yjk.1	-						uc009yjl.1_Intron|DCDC1_uc001msu.1_Intron					RecName: Full=Doublecortin domain-containing protein 5;																		TTTCTCCTTTAAAAAGGGACA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	39984746	39984746	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39984746delT								None (None upstream) : LRRC4C (151007 downstream)																							GCCACGTTGATTTTTTTTTCT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56241756	56241756	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56241756delA								OR5M3 (3783 upstream) : OR5M8 (16155 downstream)																							ACATTCCCACAAAAAAAATGT	0.333													4	2	---	---	---	---	
PATL1	219988	broad.mit.edu	37	11	59436377	59436378	+	5'UTR	INS	-	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59436377_59436378insG	uc001noe.3	-	1					PATL1_uc009yms.1_5'UTR	NM_152716	NP_689929	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog						cytoplasmic mRNA processing body assembly|deadenylation-dependent decapping of nuclear-transcribed mRNA	cytoplasmic mRNA processing body	protein binding|RNA binding			ovary(1)	1						ATTCTTGgggaggggggcaggg	0.401													4	2	---	---	---	---	
C11orf95	65998	broad.mit.edu	37	11	63535170	63535170	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63535170delA	uc010rmv.1	-						C11orf95_uc001nxr.2_5'Flank|C11orf95_uc001nxs.2_5'Flank	NM_001144936	NP_001138408	C9JLR9	CK095_HUMAN	hypothetical protein LOC65998							intracellular	zinc ion binding				0						GGCCTGGAGGAAACCCTCAAG	0.582													4	2	---	---	---	---	
MACROD1	28992	broad.mit.edu	37	11	63839896	63839896	+	Intron	DEL	A	-	-	rs34047031		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63839896delA	uc001nyh.2	-							NM_014067	NP_054786	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1												0						CGGCTCatttaaaaaaaaaaa	0.284													4	2	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70849707	70849707	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70849707delA	uc001oqc.2	-							NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			tactaaaaagaaaaaaaaatc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	73492707	73492707	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73492707delT								RAB6A (20506 upstream) : MRPL48 (6210 downstream)																							GCCTCCCTACTTTTTTTTTTC	0.398													4	3	---	---	---	---	
GAB2	9846	broad.mit.edu	37	11	77994931	77994931	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77994931delT	uc001ozh.2	-						GAB2_uc001ozg.2_Intron	NM_080491	NP_536739	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2 isoform a						osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity			ovary(5)|lung(1)	6	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			tctgagattcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	82007659	82007660	+	Intron	INS	-	T	T	rs138009929	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82007659_82007660insT	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																		ttctctttatattttgtgcatc	0.000													4	3	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	84348888	84348888	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84348888delA	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				AGTAAGAGGTAAAATCTGATT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91518404	91518404	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91518404delT								MIR1261 (916034 upstream) : FAT3 (566858 downstream)																							GACATAGAGATTTTTTTTTCT	0.358													4	2	---	---	---	---	
MAML2	84441	broad.mit.edu	37	11	95980376	95980376	+	Intron	DEL	A	-	-	rs75115900		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95980376delA	uc001pfw.1	-							NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				CAGACCATGCAAAAAAAAAAT	0.378			T	MECT1|CRTC3	salivary gland mucoepidermoid								4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99300663	99300664	+	Intron	INS	-	A	A	rs149359602	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99300663_99300664insA	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	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)		cagaccatggtaaaaaaaaaag	0.000													4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99802162	99802163	+	Intron	INS	-	T	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99802162_99802163insT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	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)		AATAACCTTGGTTTTTTTTACT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	101471522	101471522	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101471522delT								TRPC6 (16863 upstream) : ANGPTL5 (289884 downstream)																							AACCAAAATATTTAGGTGTTG	0.303													4	2	---	---	---	---	
PPP2R1B	5519	broad.mit.edu	37	11	111633278	111633278	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111633278delT	uc001plx.1	-						PPP2R1B_uc001plw.1_Intron|PPP2R1B_uc010rwi.1_Intron|PPP2R1B_uc010rwj.1_Intron|PPP2R1B_uc010rwk.1_Intron|PPP2R1B_uc010rwl.1_Intron	NM_002716	NP_002707	P30154	2AAB_HUMAN	beta isoform of regulatory subunit A, protein								protein binding				0		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		CCAGCAGttcttttttttttt	0.249													3	3	---	---	---	---	
PTS	5805	broad.mit.edu	37	11	112101759	112101759	+	Intron	DEL	A	-	-	rs2904867	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112101759delA	uc001pnj.3	+						PTS_uc009yyo.2_Intron	NM_000317	NP_000308	Q03393	PTPS_HUMAN	6-pyruvoyltetrahydropterin synthase						cellular amino acid metabolic process|central nervous system development|tetrahydrobiopterin biosynthetic process	mitochondrion	6-pyruvoyltetrahydropterin synthase activity|metal ion binding				0		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)		ttttttttttaaataGGCACA	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114703466	114703466	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114703466delA								FAM55B (125814 upstream) : CADM1 (336487 downstream)																							GGAGAAGGAGAAAAAAAAATA	0.428													4	2	---	---	---	---	
GRIK4	2900	broad.mit.edu	37	11	120619863	120619863	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120619863delT	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)	CCTATAGTACTTTTTTTTTGC	0.498													3	3	---	---	---	---	
GRIK4	2900	broad.mit.edu	37	11	120783121	120783122	+	Intron	INS	-	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120783121_120783122insG	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)	GGAATCTTTCAGGGAAAAGAGC	0.327													4	2	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126573492	126573492	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126573492delA	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		gctgtaatccaaatgctgggc	0.159													4	2	---	---	---	---	
FLI1	2313	broad.mit.edu	37	11	128664361	128664362	+	Intron	DEL	GA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128664361_128664362delGA	uc010sbu.1	+						FLI1_uc010sbt.1_Intron|FLI1_uc010sbv.1_Intron|FLI1_uc009zci.2_Intron	NM_002017	NP_002008	Q01543	FLI1_HUMAN	Friend leukemia virus integration 1						hemostasis|organ morphogenesis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2266)	bone(2210)|soft_tissue(48)|autonomic_ganglia(4)|central_nervous_system(4)|lung(3)|ovary(2)|pancreas(2)	2273	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		CATCTATCTGGAGAGAGAGAGA	0.396			T	EWSR1	Ewing sarcoma								4	2	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131316929	131316930	+	Intron	INS	-	AAT	AAT	rs138419791	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131316929_131316930insAAT	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						CCAAAGCTGGAAATTATTTTTG	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134620986	134620986	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134620986delA								B3GAT1 (339174 upstream) : None (None downstream)																							ATAGGAGCCTAAATCCCAAGT	0.458													4	2	---	---	---	---	
WNK1	65125	broad.mit.edu	37	12	996697	996697	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:996697delT	uc001qio.3	+						WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TTGATACTAATTTTTTTTTTA	0.318													3	3	---	---	---	---	
CACNA2D4	93589	broad.mit.edu	37	12	2025609	2025609	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2025609delT	uc001qjp.2	-						CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GAGACAGGGCTGGGAGTCATT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	2147244	2147244	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2147244delC								DCP1B (33567 upstream) : CACNA1C (15172 downstream)																							CCCAAAAGCACCCAGACAAAA	0.438													4	2	---	---	---	---	
NRIP2	83714	broad.mit.edu	37	12	2940767	2940767	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2940767delA	uc001qlc.2	-						NRIP2_uc010sed.1_Intron	NM_031474	NP_113662	Q9BQI9	NRIP2_HUMAN	nuclear receptor interacting protein 2						proteolysis|transcription, DNA-dependent	cytoplasm|nucleus	aspartic-type endopeptidase activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			aaaaccaaacaaaaaaaaCTC	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	5057845	5057845	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5057845delG								KCNA1 (30425 upstream) : KCNA5 (95240 downstream)																							TTGGCGACAAGGGGGCTATAT	0.398													4	2	---	---	---	---	
ETV6	2120	broad.mit.edu	37	12	11818922	11818922	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11818922delT	uc001qzz.2	+							NM_001987	NP_001978	P41212	ETV6_HUMAN	ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				CTGATCATCCTTTTTTTTGAT	0.468			T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								4	2	---	---	---	---	
KIAA0528	9847	broad.mit.edu	37	12	22650621	22650621	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22650621delG	uc001rfq.2	-						KIAA0528_uc010sir.1_Intron|KIAA0528_uc010sis.1_Intron|KIAA0528_uc010sit.1_Intron|KIAA0528_uc010siu.1_Intron|KIAA0528_uc001rfr.2_Intron|KIAA0528_uc009ziy.1_Intron	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847								protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						CAAACTGGGTGGGGATCAGTA	0.368													4	2	---	---	---	---	
SOX5	6660	broad.mit.edu	37	12	24628535	24628535	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24628535delC	uc001rfx.2	-						SOX5_uc001rfy.2_Intron	NM_152989	NP_694534	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform b						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						ACAATGAGTACCCAGCAAGAG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38478810	38478811	+	IGR	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38478810_38478811insA								None (None upstream) : ALG10B (231746 downstream)																							TCCTCCGTCTGAAAAAAAAAGA	0.515													4	2	---	---	---	---	
DIP2B	57609	broad.mit.edu	37	12	51057899	51057899	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51057899delA	uc001rwv.2	+						DIP2B_uc001rwu.2_Intron|DIP2B_uc009zls.1_Intron	NM_173602	NP_775873	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6						CTTCTTTGGGAGGCACTCAAT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55983622	55983623	+	IGR	INS	-	A	A	rs112752869		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55983622_55983623insA								OR6C4 (37684 upstream) : OR10P1 (47053 downstream)																							aaagaacacagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
TMEM5	10329	broad.mit.edu	37	12	64195604	64195604	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64195604delA	uc001srq.1	+						TMEM5_uc001srr.1_Intron|TMEM5_uc001srs.1_Intron	NM_014254	NP_055069	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5							integral to plasma membrane					0		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		accctgcctcaaaaaaaaaac	0.139													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	76359028	76359028	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76359028delA								KRR1 (453610 upstream) : PHLDA1 (60200 downstream)																							TGATTTGAAGAAAAAAAAAGA	0.368													2	4	---	---	---	---	
ZDHHC17	23390	broad.mit.edu	37	12	77247216	77247216	+	3'UTR	DEL	T	-	-	rs10714920		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77247216delT	uc001syk.1	+	17						NM_015336	NP_056151	Q8IUH5	ZDH17_HUMAN	huntingtin interacting protein 14						lipoprotein transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|protein binding|protein-cysteine S-palmitoleyltransferase activity|signal transducer activity|zinc ion binding				0						TTCCTTGGAGTTTTTTTTCAT	0.299													3	3	---	---	---	---	
TMTC2	160335	broad.mit.edu	37	12	83489010	83489010	+	Intron	DEL	T	-	-	rs80203455		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83489010delT	uc001szt.2	+						TMTC2_uc010suk.1_Intron	NM_152588	NP_689801	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat							endoplasmic reticulum|integral to membrane	binding			ovary(2)	2						tttttttttgttttttttttt	0.010													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	88041943	88041943	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88041943delG								MGAT4C (809262 upstream) : C12orf50 (331873 downstream)																							tgggaagaatggcaTATACAT	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97624724	97624724	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97624724delA								NEDD1 (277263 upstream) : RMST (234075 downstream)																							aggcctggagaaaaaaaaata	0.109													4	2	---	---	---	---	
C12orf75	387882	broad.mit.edu	37	12	105722573	105722573	+	5'Flank	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105722573delA	uc001tlh.3	+						C12orf75_uc001tli.3_5'Flank	NM_001145199	NP_001138671	Q8TAD7	OCC1_HUMAN	hypothetical protein LOC387882												0						tgtgtttaacaggagaatgca	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	110072013	110072015	+	IGR	DEL	ACC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110072013_110072015delACC								MVK (36943 upstream) : C12orf34 (80175 downstream)																							catccccataaccaccaccacca	0.143													4	2	---	---	---	---	
PPP1CC	5501	broad.mit.edu	37	12	111179001	111179001	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111179001delT	uc001tru.2	-							NM_002710	NP_002701	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma						cell division|glycogen metabolic process|mitotic prometaphase|triglyceride catabolic process	cleavage furrow|condensed chromosome kinetochore|cytosol|midbody|MLL5-L complex|nuclear speck|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|protein binding|protein kinase binding|protein serine/threonine phosphatase activity			lung(2)|central_nervous_system(1)	3						TTTTTTGTTGTTTTTTTTTTA	0.308													4	2	---	---	---	---	
CUX2	23316	broad.mit.edu	37	12	111475587	111475588	+	Intron	DEL	TT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111475587_111475588delTT	uc001tsa.1	+							NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6						AACTTTCTACTTTTTTTTTTTA	0.401													4	3	---	---	---	---	
TMEM116	89894	broad.mit.edu	37	12	112380768	112380768	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112380768delT	uc001ttc.1	-						TMEM116_uc001ttd.1_Intron|TMEM116_uc001tte.1_Intron|TMEM116_uc001ttf.1_Intron|TMEM116_uc001ttg.1_Intron|TMEM116_uc001tth.1_Intron|TMEM116_uc001tti.1_Intron	NM_138341	NP_612350	Q8NCL8	TM116_HUMAN	transmembrane protein 116							integral to membrane				ovary(1)	1						TTTTACACACttttttttttt	0.189													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114624373	114624373	+	IGR	DEL	A	-	-	rs146319536		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114624373delA								RBM19 (220197 upstream) : TBX5 (167363 downstream)																							ATTTCCAGGCAAAAAAAAAAA	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115779157	115779158	+	IGR	INS	-	T	T	rs72086853		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115779157_115779158insT								TBX3 (657188 upstream) : MED13L (617225 downstream)																							TTGCTATTTTCTTTTTTttttt	0.203													4	2	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119447691	119447691	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119447691delC	uc001txa.1	+							NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						TTCAGATGTTCCCCCTTCGAC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	125354124	125354125	+	IGR	DEL	AA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125354124_125354125delAA								SCARB1 (5605 upstream) : UBC (42069 downstream)																							Gagggaaaggaaaaagaggaag	0.257													4	2	---	---	---	---	
FBRSL1	57666	broad.mit.edu	37	12	133104201	133104201	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133104201delC	uc001ukf.2	+							NM_001142641	NP_001136113	Q9HCM7	FBSL_HUMAN	fibrosin-like 1											central_nervous_system(2)	2						ttgagggctgcggggctgcgg	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27375943	27375943	+	IGR	DEL	A	-	-	rs75120926		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27375943delA								GPR12 (41021 upstream) : USP12 (266495 downstream)																							GTTTGACATCAGGGGTCTCAG	0.488													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	40204257	40204258	+	IGR	DEL	TG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40204257_40204258delTG								LHFP (26901 upstream) : COG6 (25506 downstream)																							gtggtgtgtatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	40683169	40683169	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40683169delT								COG6 (317367 upstream) : LOC646982 (238104 downstream)																							AATCCCTTGCTTTTTagaggc	0.269													4	2	---	---	---	---	
ENOX1	55068	broad.mit.edu	37	13	43967723	43967726	+	Intron	DEL	TGGA	-	-	rs35153723		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43967723_43967726delTGGA	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron	NM_001127615	NP_001121087	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		gacaggtgggtggatggatggatg	0.127													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	45681235	45681235	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45681235delT								KIAA1704 (73493 upstream) : GTF2F2 (13396 downstream)																							AAAATGAGAAtttttttttga	0.035													3	3	---	---	---	---	
LCP1	3936	broad.mit.edu	37	13	46730961	46730961	+	Intron	DEL	T	-	-	rs67497284		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46730961delT	uc001vaz.3	-						LCP1_uc001vba.3_Intron	NM_002298	NP_002289	P13796	PLSL_HUMAN	L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)		ttttcttttcttttttttttt	0.159			T	BCL6	NHL 								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	53442437	53442437	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53442437delA								PCDH8 (19663 upstream) : OLFM4 (160535 downstream)																							TGTGGTATTTAAAAAGATCTG	0.323													4	2	---	---	---	---	
PRR20A	122183	broad.mit.edu	37	13	57722080	57722082	+	Intron	DEL	CTC	-	-	rs140840239		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57722080_57722082delCTC	uc010the.1	+							NM_198441	NP_940843	P86480	PR20D_HUMAN	proline rich 20												0						ACGCCTGCCACTCCTCTCTTTTT	0.512													4	2	---	---	---	---	
TDRD3	81550	broad.mit.edu	37	13	61055922	61055922	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61055922delT	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		tgccttgtagtttttgcttag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	76793856	76793857	+	IGR	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76793856_76793857insA								LMO7 (359852 upstream) : KCTD12 (660447 downstream)																							TTTTTGAAAGGAAAAAAAAATG	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	81684449	81684451	+	IGR	DEL	GTG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81684449_81684451delGTG								SPRY2 (769363 upstream) : None (None downstream)																							TTGGAAATCTGTGGTGGTGATAT	0.330													4	2	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94659867	94659867	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94659867delT	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				TTTGTCGTCCTTTTCCCCCTT	0.373													4	2	---	---	---	---	
CLYBL	171425	broad.mit.edu	37	13	100305926	100305926	+	Intron	DEL	T	-	-	rs73564226	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100305926delT	uc001vok.2	+						CLYBL_uc010tix.1_Intron|CLYBL_uc010tiy.1_Intron	NM_206808	NP_996531	Q8N0X4	CLYBL_HUMAN	citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					tagctttttctttttttttcA	0.323													5	3	---	---	---	---	
NALCN	259232	broad.mit.edu	37	13	101818757	101818757	+	Intron	DEL	T	-	-	rs75307676		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101818757delT	uc001vox.1	-						NALCN_uc001voy.2_Intron	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					tgccaaactgttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105056816	105056817	+	IGR	INS	-	CAAA	CAAA	rs142390330	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105056816_105056817insCAAA								None (None upstream) : None (None downstream)																							CCGAACCTTTGCAAACACTGTG	0.252													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106590694	106590694	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106590694delT								DAOA (447312 upstream) : EFNB2 (551404 downstream)																							TCTGCTTCCATTTTTTTTTAT	0.378													9	4	---	---	---	---	
EFNB2	1948	broad.mit.edu	37	13	107171776	107171777	+	Intron	INS	-	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107171776_107171777insG	uc001vqi.2	-							NM_004093	NP_004084	P52799	EFNB2_HUMAN	ephrin B2 precursor						cell differentiation|cell-cell signaling|interspecies interaction between organisms|nervous system development	integral to plasma membrane	ephrin receptor binding			ovary(1)	1	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					AATAAATGTGTGGGGGGGGAGG	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19413163	19413163	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19413163delG								OR11H12 (34591 upstream) : POTEG (140202 downstream)																							GGACTGCTGAGTTGGCATGGC	0.493													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20376811	20376812	+	IGR	INS	-	CT	CT			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20376811_20376812insCT								OR4K2 (31440 upstream) : OR4K5 (11954 downstream)																							AACCTCTTTTCCTCTCTCTCAC	0.485													4	2	---	---	---	---	
RBM23	55147	broad.mit.edu	37	14	23373732	23373732	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23373732delT	uc001whg.2	-						RBM23_uc001whh.2_Intron|RBM23_uc001whi.2_Intron|RBM23_uc010tne.1_Intron|RBM23_uc001whj.2_Intron|RBM23_uc001whk.1_Intron	NM_001077351	NP_001070819	Q86U06	RBM23_HUMAN	RNA binding motif protein 23 isoform 1						mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)		AAAGGTGGACTTTTTTTTTTT	0.104													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	29781361	29781361	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29781361delA								C14orf23 (517362 upstream) : PRKD1 (264328 downstream)																							TGGCATCCCCAAAATAACAAA	0.433													4	2	---	---	---	---	
PRKD1	5587	broad.mit.edu	37	14	30142573	30142573	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30142573delC	uc001wqh.2	-							NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1						cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		GAATGCGTCACCGTCTTTCAC	0.363													4	2	---	---	---	---	
NPAS3	64067	broad.mit.edu	37	14	33607715	33607715	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33607715delG	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		AATTAAGGATGGAAAAAAAGT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	36560465	36560465	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36560465delT								BRMS1L (219297 upstream) : MBIP (207299 downstream)																							gtggcttccattttagacatc	0.065													4	2	---	---	---	---	
TTLL5	23093	broad.mit.edu	37	14	76237822	76237822	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76237822delT	uc001xrx.2	+						TTLL5_uc010ask.1_Intron|TTLL5_uc001xrz.2_Intron|TTLL5_uc001xry.1_Intron	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)		TCTATTCTTCTTTTTTTCCCT	0.189													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	92678470	92678471	+	IGR	INS	-	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92678470_92678471insG								CPSF2 (47927 upstream) : SLC24A4 (110454 downstream)																							AGGCCTCCGGTGGGGGGCTACA	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	92735757	92735760	+	IGR	DEL	TTTT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92735757_92735760delTTTT								CPSF2 (105214 upstream) : SLC24A4 (53165 downstream)																							ctccagcttcttttaagatttttt	0.108													2	4	---	---	---	---	
SLC24A4	123041	broad.mit.edu	37	14	92864234	92864235	+	Intron	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92864234_92864235insA	uc001yak.2	+						SLC24A4_uc001yai.2_Intron|SLC24A4_uc010twm.1_Intron|SLC24A4_uc001yaj.2_Intron	NM_153646	NP_705932	Q8NFF2	NCKX4_HUMAN	solute carrier family 24 member 4 isoform 1							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			breast(2)|ovary(1)	3		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		TATTTAGCATTCATAGAATAAG	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	94260952	94260953	+	IGR	INS	-	C	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94260952_94260953insC								PRIMA1 (6186 upstream) : C14orf86 (110123 downstream)																							ttgaagtgtttcccccaaaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97523967	97523968	+	IGR	INS	-	A	A	rs147056985	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97523967_97523968insA								VRK1 (176017 upstream) : C14orf64 (867979 downstream)																							TACACTCATGGAAAAAAAAATC	0.391													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97756587	97756587	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97756587delC								VRK1 (408637 upstream) : C14orf64 (635360 downstream)																							gagtccctgtcctagcttcct	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98702594	98702594	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98702594delA								C14orf64 (258133 upstream) : C14orf177 (475356 downstream)																							CAGCTACGTGAAAGGGCTGAG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101461091	101461091	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101461091delA								SNORD114-31 (1446 upstream) : MIR379 (27312 downstream)																							ATTCACGGATAATGAATTAAT	0.274													4	2	---	---	---	---	
RCOR1	23186	broad.mit.edu	37	14	103187889	103187889	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103187889delA	uc001ymb.2	+							NM_015156	NP_055971	Q9UKL0	RCOR1_HUMAN	REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1						ccctgactttaaaaaaaaaaa	0.164													5	3	---	---	---	---	
KIAA0284	283638	broad.mit.edu	37	14	105356241	105356245	+	Intron	DEL	AAATG	-	-	rs61996002	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105356241_105356245delAAATG	uc010axb.2	+						INF2_uc010tyi.1_Intron|KIAA0284_uc001ypr.2_Intron|KIAA0284_uc001yps.2_Intron|KIAA0284_uc001ypt.2_Intron	NM_001112726	NP_001106197	Q9Y4F5	K0284_HUMAN	hypothetical protein LOC283638 isoform 1							cytoplasm|microtubule				breast(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000472)|OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0149)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.178)		atggatggacaaatggatggatgga	0.210													6	3	---	---	---	---	
KIAA0284	283638	broad.mit.edu	37	14	105356248	105356254	+	Intron	DEL	TGGATGG	-	-	rs79560126	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105356248_105356254delTGGATGG	uc010axb.2	+						INF2_uc010tyi.1_Intron|KIAA0284_uc001ypr.2_Intron|KIAA0284_uc001yps.2_Intron|KIAA0284_uc001ypt.2_Intron	NM_001112726	NP_001106197	Q9Y4F5	K0284_HUMAN	hypothetical protein LOC283638 isoform 1							cytoplasm|microtubule				breast(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000472)|OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0149)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.178)		gacaaatggatggatggatggatggat	0.193													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20107786	20107787	+	IGR	INS	-	AA	AA			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20107786_20107787insAA								None (None upstream) : GOLGA6L6 (629307 downstream)																							gaaatgaaatgatgaaatgatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20858819	20858819	+	IGR	DEL	T	-	-	rs113324872		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20858819delT								GOLGA8C (77793 upstream) : BCL8 (11237 downstream)																							tttgatggcatttttttttac	0.000													3	4	---	---	---	---	
LOC646214	646214	broad.mit.edu	37	15	21941542	21941545	+	5'Flank	DEL	ACTT	-	-	rs138766428		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21941542_21941545delACTT	uc010tzj.1	-							NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						GGGCAATCTGACTTACACCTTAAT	0.446													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26382908	26382908	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26382908delA								ATP10A (272591 upstream) : GABRB3 (405787 downstream)																							AATAAAAACCATAAAAAGGCT	0.418													4	2	---	---	---	---	
HERC2	8924	broad.mit.edu	37	15	28369563	28369563	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28369563delA	uc001zbj.2	-							NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GTTTGACTGTAAAAAAAATTA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	32295828	32295828	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32295828delA								OTUD7A (132836 upstream) : CHRNA7 (26898 downstream)																							AAATCCAAGGAAAAAAGTTAA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	36720337	36720337	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36720337delC								ATPBD4 (881933 upstream) : C15orf41 (151475 downstream)																							TACTGAATAGCCCCCTTCTGG	0.303													4	2	---	---	---	---	
CASC5	57082	broad.mit.edu	37	15	40929363	40929363	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40929363delT	uc010bbs.1	+						CASC5_uc010bbt.1_Intron	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		tctctttttcttttttctttc	0.030													4	3	---	---	---	---	
UBR1	197131	broad.mit.edu	37	15	43390737	43390737	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43390737delA	uc001zqq.2	-						UBR1_uc010udk.1_Intron	NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		ACTGATTTATAAAAGTATCTA	0.239													4	2	---	---	---	---	
WDR76	79968	broad.mit.edu	37	15	44143777	44143777	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44143777delT	uc001zti.1	+							NM_024908	NP_079184	Q9H967	WDR76_HUMAN	WD repeat domain 76												0		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)		GTTAAATTTCTTTTTTTTTTC	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	51482617	51482617	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51482617delT								TNFAIP8L3 (85144 upstream) : CYP19A1 (17638 downstream)																							CATTGTTTTCTTTTTTTGCAC	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	60586303	60586303	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60586303delA								FOXB1 (257895 upstream) : ANXA2 (53048 downstream)																							TGGATGAAACAAAAAGGGGAA	0.318													4	2	---	---	---	---	
GLCE	26035	broad.mit.edu	37	15	69494606	69494606	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69494606delA	uc002ary.1	+							NM_015554	NP_056369	O94923	GLCE_HUMAN	D-glucuronyl C5-epimerase						heparan sulfate proteoglycan biosynthetic process|heparin biosynthetic process	Golgi membrane|integral to membrane	UDP-glucuronate 5'-epimerase activity			ovary(2)	2						TTACCCAATTAAAAAAAAAAA	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	73208960	73208961	+	IGR	INS	-	C	C	rs150097629	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73208960_73208961insC								ADPGK (132293 upstream) : NEO1 (135914 downstream)																							TATCATATTCAAATTCAGTTTA	0.322													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	73324679	73324679	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73324679delC								ADPGK (248012 upstream) : NEO1 (20196 downstream)																							ACCCAACACTCCGAGATAATG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	74052575	74052575	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74052575delT								C15orf59 (8759 upstream) : TBC1D21 (113393 downstream)																							CTCCATGCCCTTGACATCCAG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	74462916	74462916	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74462916delT								ISLR2 (33775 upstream) : ISLR (3171 downstream)																							CATCAGGATCTTTTTTTTTGC	0.413													4	2	---	---	---	---	
C15orf27	123591	broad.mit.edu	37	15	76393399	76393399	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76393399delA	uc002bbq.2	+						C15orf27_uc010bkp.2_Intron	NM_152335	NP_689548	Q2M3C6	CO027_HUMAN	hypothetical protein LOC123591							integral to membrane					0						TTGAGCTTTTAATGGTGGTCT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78248342	78248342	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78248342delG								LOC645752 (29154 upstream) : LOC91450 (37234 downstream)																							aggaatagcaggagggggatt	0.000													4	2	---	---	---	---	
KIAA1199	57214	broad.mit.edu	37	15	81189647	81189647	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81189647delT	uc002bfw.1	+						KIAA1199_uc010unn.1_Intron	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						CAACACAATCTTTTTGGCTGC	0.383													4	2	---	---	---	---	
MESDC1	59274	broad.mit.edu	37	15	81296130	81296130	+	3'UTR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81296130delT	uc002bfz.2	+	1						NM_022566	NP_072088	Q9H1K6	MESD1_HUMAN	mesoderm development candidate 1												0						TTTGTATGTCTTTTTTTTTTT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	82134058	82134058	+	IGR	DEL	A	-	-	rs80042069		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82134058delA								TMC3 (467640 upstream) : MEX3B (200070 downstream)																							CTTGAGGCAGAAAAAAAAAAA	0.373													3	4	---	---	---	---	
AP3B2	8120	broad.mit.edu	37	15	83360356	83360356	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83360356delA	uc010uoh.1	-						AP3B2_uc010uoi.1_Intron|AP3B2_uc010uoj.1_Intron|AP3B2_uc010uok.1_Intron	NM_004644	NP_004635	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)			TTTCTTCtttaaaaaaaaaaa	0.303													4	2	---	---	---	---	
ACAN	176	broad.mit.edu	37	15	89409240	89409240	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89409240delA	uc010upo.1	+						ACAN_uc010upp.1_Intron|ACAN_uc002bna.2_Intron|uc002bnb.1_5'Flank	NM_013227	NP_037359	E7EX88	E7EX88_HUMAN	aggrecan isoform 2 precursor						cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CAGGGCCGTGAAAAAAAAAAT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94677799	94677799	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94677799delT								None (None upstream) : MCTP2 (97002 downstream)																							CTCGTAGCCCTTTAATAGAAG	0.418													4	2	---	---	---	---	
SPATA8	145946	broad.mit.edu	37	15	97325800	97325800	+	5'Flank	DEL	C	-	-	rs67145880		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97325800delC	uc002bue.2	+						uc002bub.2_5'Flank|uc002buc.1_5'Flank|uc010uro.1_5'Flank|uc010urp.1_5'Flank	NM_173499	NP_775770	Q6RVD6	SPAT8_HUMAN	spermatogenesis associated 8											ovary(1)|skin(1)	2	Melanoma(26;0.0142)|Lung NSC(78;0.041)|all_lung(78;0.0468)		OV - Ovarian serous cystadenocarcinoma(32;0.0718)			ACCCAGCCAACCCTGACTGGT	0.562													4	3	---	---	---	---	
LRRC28	123355	broad.mit.edu	37	15	99878082	99878084	+	Intron	DEL	GAT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99878082_99878084delGAT	uc002bva.1	+						LRRC28_uc010urs.1_Intron|LRRC28_uc002bvb.1_Intron|LRRC28_uc010urt.1_Intron|LRRC28_uc002bvc.1_Intron|LRRC28_uc010uru.1_Intron|LRRC28_uc002bvd.1_Intron	NM_144598	NP_653199	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28												0	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			CAAGCAAGAGgatgatgatgatg	0.414													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	1340114	1340114	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1340114delA								TPSD1 (31620 upstream) : UBE2I (19066 downstream)																							GACAGAGATGAAGGAGACAGC	0.662													4	2	---	---	---	---	
ZNF75A	7627	broad.mit.edu	37	16	3358947	3358947	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3358947delT	uc002cut.3	+						ZNF75A_uc002cuv.3_Intron	NM_153028	NP_694573	Q96N20	ZN75A_HUMAN	zinc finger protein 75a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1						CATTGTTTGGTTTTTTTTTTA	0.408													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6605037	6605037	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6605037delG	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		atgagaagctggggagaggcc	0.104													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6955929	6955929	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6955929delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		ATTGACTTCCTTCTGCCCTTG	0.517													4	2	---	---	---	---	
MKL2	57496	broad.mit.edu	37	16	14279923	14279923	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14279923delA	uc010uza.1	+						MKL2_uc002dcg.2_Intron|MKL2_uc002dch.2_5'Flank	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein						cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5						AATTTTCCTTAAAAAAAATCA	0.398													4	2	---	---	---	---	
BFAR	51283	broad.mit.edu	37	16	14744025	14744025	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14744025delA	uc002dco.2	+						BFAR_uc002dcm.2_3'UTR|BFAR_uc002dcn.2_3'UTR|BFAR_uc002dcp.2_Intron|BFAR_uc010uzh.1_Intron	NM_016561	NP_057645	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator						anti-apoptosis|apoptosis	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	structural molecule activity|zinc ion binding			ovary(1)|skin(1)	2						ctaaaaatacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	23394540	23394540	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23394540delT								SCNN1B (1921 upstream) : COG7 (5276 downstream)																							ttcttttttctttttttttga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	25213802	25213803	+	IGR	DEL	CA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25213802_25213803delCA								LCMT1 (24251 upstream) : AQP8 (14482 downstream)																							CACACACGTGCACACACACACA	0.351													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	25598471	25598471	+	IGR	DEL	A	-	-	rs11356345		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25598471delA								ZKSCAN2 (329616 upstream) : HS3ST4 (104876 downstream)																							TGAGTGGCAGATGTCTGTTTT	0.433													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32544622	32544622	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32544622delT								HERC2P4 (380748 upstream) : TP53TG3B (140219 downstream)																							aaaagaaaggtttagctctag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34926473	34926473	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34926473delC								LOC146481 (211506 upstream) : None (None downstream)																							cattagacttcccagggttgg	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	47955707	47955707	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47955707delT								PHKB (220274 upstream) : ABCC12 (161177 downstream)																							GTCAGCTCACTAGATGGAAGC	0.234													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	53084808	53084808	+	IGR	DEL	T	-	-	rs71727356		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53084808delT								TOX3 (503094 upstream) : CHD9 (4137 downstream)																							CCTCACCCTCttttttttttg	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55041272	55041272	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55041272delT								IRX5 (72879 upstream) : IRX6 (317199 downstream)																							CGTGACTTTATTTTTTTTTTT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	61577803	61577804	+	IGR	INS	-	CTA	CTA	rs139743022	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61577803_61577804insCTA								None (None upstream) : CDH8 (109431 downstream)																							gatgttagctgctactactact	0.025													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	65771179	65771179	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65771179delC								LOC283867 (160976 upstream) : CDH5 (629346 downstream)																							ATTGCCAACTCCAGGCCAATC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	65797704	65797704	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65797704delA								LOC283867 (187501 upstream) : CDH5 (602821 downstream)																							CAGTATCTTCAAAGGGTATCA	0.473													4	2	---	---	---	---	
HYDIN	54768	broad.mit.edu	37	16	71226168	71226168	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71226168delT	uc002ezr.2	-						HYDIN_uc002ezv.2_Intron|HYDIN_uc010vmc.1_Intron|HYDIN_uc010vmd.1_Intron|HYDIN_uc002ezw.3_Intron	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)				ctgcccctccttcgttaatgt	0.070													4	2	---	---	---	---	
ADAMTS18	170692	broad.mit.edu	37	16	77457799	77457800	+	Intron	DEL	AG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77457799_77457800delAG	uc002ffc.3	-						ADAMTS18_uc002ffe.1_Intron|ADAMTS18_uc010vni.1_Intron	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						TAGCTGGTAAAGAGAGAGAGAG	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	80490935	80490935	+	IGR	DEL	A	-	-	rs113028442		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80490935delA								MAF (856313 upstream) : DYNLRB2 (83919 downstream)																							AATAAGAACTAAAAAAAAAAA	0.209													2	4	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	82933641	82933642	+	Intron	DEL	CT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82933641_82933642delCT	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		atcttgattgctctctctctct	0.129													4	2	---	---	---	---	
NLRP1	22861	broad.mit.edu	37	17	5452089	5452089	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5452089delC	uc002gci.2	-						NLRP1_uc002gcg.1_Intron|NLRP1_uc002gck.2_Intron|NLRP1_uc002gcj.2_Intron|NLRP1_uc002gcl.2_Intron|NLRP1_uc002gch.3_Intron|NLRP1_uc010clh.2_Intron	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1						defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding			lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	9		Colorectal(1115;3.48e-05)				cagcagtagtccctgctgacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5920898	5920898	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5920898delA								NLRP1 (433066 upstream) : WSCD1 (51539 downstream)																							GGAAGGCAGGATCTTTCCTCT	0.507													4	2	---	---	---	---	
CLEC10A	10462	broad.mit.edu	37	17	6980639	6980639	+	Intron	DEL	A	-	-	rs68032848		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6980639delA	uc002gek.2	-						CLEC10A_uc002gej.2_Intron|CLEC10A_uc002gel.2_Intron|CLEC10A_uc010clv.1_Intron	NM_182906	NP_878910	Q8IUN9	CLC10_HUMAN	C-type lectin, superfamily member 14 isoform 1						endocytosis|innate immune response	integral to membrane|plasma membrane	sugar binding				0						cagtgcccccatcaccattcc	0.015													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	7937785	7937785	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7937785delT								GUCY2D (14127 upstream) : ALOX15B (4573 downstream)																							GCGATGGTTCTTTTTTTTTTT	0.234													4	3	---	---	---	---	
PIK3R5	23533	broad.mit.edu	37	17	8786196	8786200	+	Intron	DEL	TTTCT	-	-	rs148961517		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8786196_8786200delTTTCT	uc002glt.2	-						PIK3R5_uc010vuz.1_Intron|PIK3R5_uc002glu.3_Intron	NM_014308	NP_055123	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5						platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						gctgccctaatttctcttctggacc	0.000													5	4	---	---	---	---	
STX8	9482	broad.mit.edu	37	17	9387702	9387702	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9387702delA	uc002glx.2	-							NM_004853	NP_004844	Q9UNK0	STX8_HUMAN	syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1						ACCTAAGCTCAAAAAAAAAAA	0.294													4	3	---	---	---	---	
GAS7	8522	broad.mit.edu	37	17	9823286	9823287	+	Intron	INS	-	TG	TG	rs144704447		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9823286_9823287insTG	uc002gmg.1	-						GAS7_uc010vvc.1_Intron|GAS7_uc002gmh.1_Intron|GAS7_uc010vvd.1_Intron|GAS7_uc002gmi.2_Intron|GAS7_uc002gmj.1_Intron|GAS7_uc010coh.1_Intron	NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2						GGTTCTCATTTtgtgtgtgtgt	0.421			T	MLL	AML*								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	10162586	10162586	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10162586delA								GAS7 (60718 upstream) : MYH13 (41597 downstream)																							CTAAAAAAACAAAAAAAACAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13570893	13570893	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13570893delC								HS3ST3A1 (65649 upstream) : CDRT15P (356922 downstream)																							aaatcagagacccccccagcg	0.000													4	2	---	---	---	---	
CCDC144A	9720	broad.mit.edu	37	17	16665299	16665299	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16665299delA	uc002gqk.1	+						CCDC144A_uc002gql.1_Intron|LOC162632_uc010cpj.1_Intron	NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A												0						TAGGGAAAGTAAAAAAAAAAT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	18315107	18315108	+	RNA	INS	-	CT	CT	rs148626885	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18315107_18315108insCT	uc002gtt.1	+	1		c.635_636insCT								Homo sapiens cDNA FLJ35934 fis, clone TESTI2011315.																		gccctcttctcctcactgtctt	0.134													4	5	---	---	---	---	
ALDH3A1	218	broad.mit.edu	37	17	19643966	19643966	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19643966delT	uc010cqu.2	-						ALDH3A1_uc010vzd.1_Intron|ALDH3A1_uc002gwj.2_Intron|ALDH3A1_uc010cqv.2_Intron|ALDH3A1_uc002gwk.2_Intron|ALDH3A1_uc002gwl.1_Intron	NM_001135168	NP_001128640	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3A1						cellular aldehyde metabolic process	cytosol|endoplasmic reticulum	alcohol dehydrogenase (NADP+) activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(1)|pancreas(1)	2	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)	NADH(DB00157)	gtgcattatcttttttttttc	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21508509	21508509	+	IGR	DEL	A	-	-	rs113427058		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21508509delA								C17orf51 (30778 upstream) : FAM27L (316861 downstream)																							aaattcatagaaaaaaaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	22258033	22258033	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22258033delT								FLJ36000 (344963 upstream) : None (None downstream)																							tgaaacactcttttagtagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25274969	25274974	+	IGR	DEL	ATTTGG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25274969_25274974delATTTGG								None (None upstream) : WSB1 (346132 downstream)																							tggaaatcttatttgggttatgttct	0.073													4	2	---	---	---	---	
ADAP2	55803	broad.mit.edu	37	17	29258667	29258669	+	Intron	DEL	CCA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29258667_29258669delCCA	uc002hfx.2	+						ADAP2_uc010csk.2_Intron|ADAP2_uc002hfy.2_Intron|ADAP2_uc010csl.2_Intron	NM_018404	NP_060874	Q9NPF8	ADAP2_HUMAN	centaurin-alpha 2 protein						heart development|regulation of ARF GTPase activity	mitochondrial envelope|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding, bridging|zinc ion binding	p.?(1)		ovary(1)	1						agggagacccccatctctacaaa	0.044													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	32486045	32486045	+	5'Flank	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32486045delT	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)	TCTGTTGTCCTTTTTTTTTTT	0.294													3	3	---	---	---	---	
SLFN14	342618	broad.mit.edu	37	17	33879682	33879683	+	Intron	INS	-	AT	AT	rs147667480	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33879682_33879683insAT	uc010ctu.1	-							NM_001129820	NP_001123292	P0C7P3	SLN14_HUMAN	schlafen family member 14								ATP binding			central_nervous_system(1)	1						tatatatacacatatatataca	0.134													4	2	---	---	---	---	
AATF	26574	broad.mit.edu	37	17	35391334	35391334	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35391334delA	uc002hni.2	+						AATF_uc002hnj.2_Intron	NM_012138	NP_036270	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|negative regulation of superoxide anion generation|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to DNA damage stimulus	centrosome|focal adhesion|nucleolus	leucine zipper domain binding|sequence-specific DNA binding transcription factor activity				0		Breast(25;0.00607)				TTATAAGGAGAAAGGGCTATC	0.308													4	2	---	---	---	---	
CISD3	284106	broad.mit.edu	37	17	36889192	36889193	+	Intron	DEL	AC	-	-	rs67033100		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36889192_36889193delAC	uc010wds.1	+							NM_001136498	NP_001129970	P0C7P0	CISD3_HUMAN	CDGSH iron sulfur domain 3 precursor							mitochondrion	2 iron, 2 sulfur cluster binding|metal ion binding				0						AGACTCAGAGacacacacacac	0.347													4	2	---	---	---	---	
SP2	6668	broad.mit.edu	37	17	45999891	45999892	+	Intron	DEL	TT	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45999891_45999892delTT	uc002imk.2	+						SP2_uc002iml.2_Intron	NM_003110	NP_003101	Q02086	SP2_HUMAN	Sp2 transcription factor						immune response|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|histone deacetylase binding|zinc ion binding				0						GACCAGAAACtttttttttttt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	46597351	46597351	+	IGR	DEL	A	-	-	rs77829919		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46597351delA								SKAP1 (89757 upstream) : HOXB1 (9456 downstream)																							TCTCCCTAGGAGGGGGGTCCT	0.358													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	49423803	49423803	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49423803delT								UTP18 (48513 upstream) : CA10 (283872 downstream)																							TTTTGTGTTCTTTTGTGGATC	0.259													4	2	---	---	---	---	
CA10	56934	broad.mit.edu	37	17	50007339	50007339	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50007339delT	uc002itw.3	-						CA10_uc002itv.3_Intron|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			CACTTACAGCTTTTTGATGAG	0.348													4	2	---	---	---	---	
TUBD1	51174	broad.mit.edu	37	17	57966088	57966089	+	Intron	INS	-	T	T	rs11462592		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57966088_57966089insT	uc002ixw.1	-						TUBD1_uc010ddf.1_Intron|TUBD1_uc010ddg.1_Intron|TUBD1_uc010ddh.1_Intron|TUBD1_uc010wok.1_Intron|TUBD1_uc002ixx.1_Intron|TUBD1_uc010wol.1_Intron|TUBD1_uc010ddi.1_Intron	NM_016261	NP_057345	Q9UJT1	TBD_HUMAN	delta-tubulin						cell differentiation|microtubule-based movement|multicellular organismal development|protein polymerization|spermatogenesis	centriole|microtubule|nucleus	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)			tgttttttgtcttttttttttc	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	60493862	60493862	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60493862delT								EFCAB3 (25 upstream) : METTL2A (7374 downstream)																							TTCCTAAATCttttttttttt	0.154													4	2	---	---	---	---	
MARCH10	162333	broad.mit.edu	37	17	60795200	60795200	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60795200delC	uc010ddr.2	-						MARCH10_uc002jag.3_Intron|MARCH10_uc010dds.2_Intron|MARCH10_uc002jah.2_Intron|uc002jaj.1_Intron|uc002jak.2_Intron	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190								ligase activity|zinc ion binding				0						accatctcttcccacccagat	0.184													4	2	---	---	---	---	
AXIN2	8313	broad.mit.edu	37	17	63590223	63590223	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63590223delT	uc010den.1	-							NM_004655	NP_004646	Q9Y2T1	AXIN2_HUMAN	axin 2						cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2						ACCACAACTCTTTTTTTTTTT	0.418									Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				3	3	---	---	---	---	
PITPNC1	26207	broad.mit.edu	37	17	65627963	65627963	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65627963delT	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549	Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			TGGGAAGAGATTTTTTTTTTT	0.403													6	3	---	---	---	---	
GPS1	2873	broad.mit.edu	37	17	80012101	80012102	+	Intron	DEL	TG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80012101_80012102delTG	uc002kdl.1	+						RFNG_uc002kdj.2_5'Flank|GPS1_uc002kdk.1_Intron|GPS1_uc010dij.1_Intron|GPS1_uc002kdm.1_Intron|GPS1_uc002kdn.1_Intron|GPS1_uc002kdo.1_Intron|GPS1_uc010wvh.1_Intron	NM_004127	NP_004118	Q13098	CSN1_HUMAN	G protein pathway suppressor 1 isoform 2						cell cycle|cullin deneddylation|inactivation of MAPK activity|JNK cascade	cytoplasm|signalosome	GTPase inhibitor activity|protein binding			central_nervous_system(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)			GTGTGGCTTCTGTGTGTGTGCA	0.624													4	2	---	---	---	---	
POTEC	388468	broad.mit.edu	37	18	14537537	14537537	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14537537delA	uc010dln.2	-						POTEC_uc010xaj.1_Intron	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2											skin(3)	3						GGAAAAATTGAAAAAAAAAAG	0.284													8	4	---	---	---	---	
LOC644669	644669	broad.mit.edu	37	18	15326233	15326233	+	5'Flank	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15326233delA	uc002ktd.1	-							NR_027417				Homo sapiens cDNA FLJ40312 fis, clone TESTI2029880.												0						gattcagttcaacttgggctt	0.080													4	2	---	---	---	---	
CDH2	1000	broad.mit.edu	37	18	25747303	25747303	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25747303delT	uc002kwg.2	-							NM_001792	NP_001783	P19022	CADH2_HUMAN	cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4						ATTTAGTGGCTTGACACCATA	0.358													4	2	---	---	---	---	
SLC14A2	8170	broad.mit.edu	37	18	43064695	43064696	+	Intron	DEL	TC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43064695_43064696delTC	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron|uc002lbc.1_Intron|uc002lbd.1_Intron	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4						TAACTCACTGTCTCTCTCTCTC	0.431													5	3	---	---	---	---	
PSTPIP2	9050	broad.mit.edu	37	18	43566574	43566574	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43566574delC	uc002lbp.3	-						PSTPIP2_uc002lbq.3_Intron	NM_024430	NP_077748	Q9H939	PPIP2_HUMAN	proline-serine-threonine phosphatase interacting							membrane				ovary(1)	1						TAGGGCCTTGCCCCTTTCCAT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	44992903	44992903	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44992903delC	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																		TGCCTTCTTTCCTGACCATGG	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68607176	68607176	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68607176delG								SOCS6 (609742 upstream) : None (None downstream)																							TCCTCTCTGTGGAGTATCAGT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	74022593	74022594	+	IGR	DEL	AC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74022593_74022594delAC								C18orf62 (883004 upstream) : ZNF516 (49025 downstream)																							GATACACTGTACACACACACGT	0.505													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75669395	75669397	+	IGR	DEL	CAA	-	-	rs150771226		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75669395_75669397delCAA								GALR1 (687301 upstream) : None (None downstream)																							actatcaccccaacaactccaac	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76498852	76498852	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76498852delC								None (None upstream) : SALL3 (241423 downstream)																							tctcacatagcccacacacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	3131445	3131446	+	IGR	DEL	AC	-	-	rs66993077		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3131445_3131446delAC								GNA11 (9993 upstream) : GNA15 (4745 downstream)																							aaaaaaaaaaacaaaaaaaaaa	0.347													4	2	---	---	---	---	
LRG1	116844	broad.mit.edu	37	19	4540284	4540285	+	5'Flank	INS	-	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4540284_4540285insG	uc002mau.2	-						PLIN5_uc002mat.1_5'Flank	NM_052972	NP_443204	P02750	A2GL_HUMAN	leucine-rich alpha-2-glycoprotein 1 precursor							extracellular region|membrane				ovary(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCTGATTTTTGGGGGGCATCC	0.475													4	2	---	---	---	---	
TMEM146	257062	broad.mit.edu	37	19	5753884	5753884	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5753884delA	uc002mda.2	+						TMEM146_uc010duj.1_Intron	NM_152784	NP_689997	Q86XM0	TM146_HUMAN	transmembrane protein 146 precursor							integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3						accctgtctcaaaaaaaaaag	0.209													4	2	---	---	---	---	
TNFSF9	8744	broad.mit.edu	37	19	6530396	6530397	+	5'Flank	DEL	AG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6530396_6530397delAG	uc002mfh.2	+							NM_003811	NP_003802	P41273	TNFL9_HUMAN	tumor necrosis factor (ligand) superfamily,						apoptosis|cell proliferation|cell-cell signaling|immune response|signal transduction	extracellular space|integral to membrane	cytokine activity|tumor necrosis factor receptor binding			central_nervous_system(1)	1						agtcagaggcagagagagagaa	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	8773556	8773557	+	IGR	DEL	TG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8773556_8773557delTG								ADAMTS10 (97968 upstream) : ACTL9 (34194 downstream)																							tgtgtgtgcatgtgtgtgtgtg	0.287													4	2	---	---	---	---	
ICAM3	3385	broad.mit.edu	37	19	10446140	10446141	+	Intron	DEL	AC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10446140_10446141delAC	uc002mob.2	-						RAVER1_uc002moa.2_5'Flank|ICAM3_uc010dxd.1_Intron|ICAM3_uc010xlf.1_3'UTR	NM_002162	NP_002153	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3 precursor						cell-cell adhesion|regulation of immune response	integral to plasma membrane	integrin binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			TCTTCACAGGACACACACACAG	0.614													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	11192318	11192318	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11192318delT								SMARCA4 (19359 upstream) : LDLR (7739 downstream)																							CAGAACATTCTTTTTTTTTTC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13292877	13292877	+	IGR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13292877delG								IER2 (27161 upstream) : CACNA1A (24379 downstream)																							ATCTGTGTGTGGGGGGGTGTT	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31553016	31553016	+	IGR	DEL	A	-	-	rs71335104		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31553016delA								ZNF536 (504051 upstream) : DKFZp566F0947 (87767 downstream)																							acacacacacaaaaaaaaAAA	0.214													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	35950327	35950327	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35950327delT								FFAR2 (7660 upstream) : KRTDAP (27903 downstream)																							TTTGCCCCACTTTTTTTTTTC	0.453													4	2	---	---	---	---	
ZNF568	374900	broad.mit.edu	37	19	37425207	37425207	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37425207delT	uc002ofc.2	+						ZNF568_uc010efg.2_Intron|ZNF568_uc010xtn.1_Intron|ZNF568_uc002ofd.2_Intron|ZNF568_uc010efe.2_Intron|ZNF568_uc010eff.1_Intron	NM_198539	NP_940941	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ttctagtatcttttttttttt	0.000													2	4	---	---	---	---	
ZNF585A	199704	broad.mit.edu	37	19	37645152	37645152	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37645152delA	uc002ofo.1	-						ZNF585A_uc002ofm.1_Intron|ZNF585A_uc002ofn.1_Intron	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)			acagatgtggaaaaAGTAAGG	0.199													4	2	---	---	---	---	
BCKDHA	593	broad.mit.edu	37	19	41920223	41920223	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41920223delG	uc002oqq.2	+						CYP2F1_uc010xvw.1_Intron|BCKDHA_uc002oqm.3_Intron|BCKDHA_uc002oqp.1_Intron|BCKDHA_uc002oqr.2_Intron|BCKDHA_uc010xvz.1_Intron	NM_000709	NP_000700	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha						branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|alpha-ketoacid dehydrogenase activity|carboxy-lyase activity|metal ion binding|protein binding				0						GGACTCTGGAGGGGGCAGTCT	0.443													4	2	---	---	---	---	
DMRTC2	63946	broad.mit.edu	37	19	42352414	42352414	+	Intron	DEL	A	-	-	rs79959130		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42352414delA	uc002ors.2	+						DMRTC2_uc002orr.1_Intron|DMRTC2_uc010xwe.1_Intron	NM_001040283	NP_001035373	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2						cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0						actccatctcaaaaaaaaaaa	0.244													3	3	---	---	---	---	
KCNN4	3783	broad.mit.edu	37	19	44288148	44288149	+	5'Flank	DEL	TC	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44288148_44288149delTC	uc002oxl.2	-						KCNN4_uc010eja.1_5'Flank	NM_002250	NP_002241	O15554	KCNN4_HUMAN	intermediate conductance calcium-activated						defense response	voltage-gated potassium channel complex	calcium-activated potassium channel activity|calmodulin binding			ovary(2)	2		Prostate(69;0.0352)			Clotrimazole(DB00257)|Halothane(DB01159)|Quinine(DB00468)	tcctcttgggtctctctctctc	0.139													4	2	---	---	---	---	
DKFZp434J0226	93429	broad.mit.edu	37	19	46715889	46715891	+	Intron	DEL	CCA	-	-	rs34244695		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46715889_46715891delCCA	uc010xxw.1	+							NR_027003				Homo sapiens mRNA; cDNA DKFZp434J0226 (from clone DKFZp434J0226).												0						TGGAATTTCTCCACCACCAGAAC	0.394													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	48274929	48274929	+	IGR	DEL	A	-	-	rs151315925		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48274929delA								GLTSCR2 (788 upstream) : SEPW1 (6913 downstream)																							actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	52062228	52062228	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52062228delA								SIGLEC6 (27164 upstream) : ZNF175 (12303 downstream)																							ACCAGGAATGAAAAAGTCTGG	0.338													4	2	---	---	---	---	
ZNF805	390980	broad.mit.edu	37	19	57773719	57773720	+	3'UTR	DEL	AA	-	-	rs72332740		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57773719_57773720delAA	uc010ygt.1	+	4					ZNF805_uc010ygu.1_3'UTR	NM_001023563	NP_001018857	Q5CZA5	ZN805_HUMAN	zinc finger protein 805 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TGTAACCAAGAAAAAAAAAAAA	0.327													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	58413072	58413073	+	IGR	INS	-	A	A	rs59723971		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58413072_58413073insA								ZNF814 (12630 upstream) : ZNF417 (4070 downstream)																							tggcacagatgcagaggacaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	5272768	5272768	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5272768delT								CDS2 (100781 upstream) : PROKR2 (9919 downstream)																							ACATGCTCCATTTTTTTTTTT	0.353													4	2	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9381869	9381870	+	Intron	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9381869_9381870insA	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron|PLCB4_uc002wnh.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						GCcatccacttaaaaaaaattt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16947406	16947406	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16947406delT								OTOR (214598 upstream) : PCSK2 (259346 downstream)																							TCTTGCCACAttttttttcat	0.264													4	2	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17272320	17272320	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17272320delT	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)	GTATAGAAGGTTTTTATTTta	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22263730	22263731	+	5'Flank	INS	-	A	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22263730_22263731insA	uc002wsk.1	-											Homo sapiens mRNA; cDNA DKFZp781N2119 (from clone DKFZp781N2119).																		aactccttttcaaaaaaatttt	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	24053655	24053655	+	IGR	DEL	A	-	-	rs1626172	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24053655delA								GGTLC1 (84239 upstream) : TMEM90B (396180 downstream)																							TTGCCACCATAAAAAAAAATC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26252112	26252113	+	IGR	INS	-	T	T	rs36126165		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26252112_26252113insT								MIR663 (63198 upstream) : None (None downstream)																							acttcctctgggaatcatgaat	0.000													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29628987	29628988	+	Intron	INS	-	C	C	rs138771657		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29628987_29628988insC	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						tctctctctcttttttaacagc	0.119													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29636482	29636482	+	Intron	DEL	T	-	-	rs62891160		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29636482delT	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						CTTTGCAATATATTTTCCTCC	0.114													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	38046117	38046117	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38046117delA								LOC339568 (192726 upstream) : None (None downstream)																							CTGATGTGTGAGCCGTCTTTG	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	39297796	39297797	+	IGR	INS	-	A	A	rs143445558	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39297796_39297797insA								None (None upstream) : MAFB (16722 downstream)																							gcgacctgcatagtcacacagg	0.188													4	2	---	---	---	---	
CSE1L	1434	broad.mit.edu	37	20	47674727	47674727	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47674727delT	uc002xty.2	+						CSE1L_uc010zyg.1_Intron|CSE1L_uc010ghx.2_5'Flank	NM_001316	NP_001307	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like protein						apoptosis|cell proliferation|intracellular protein transport	cytoplasm|nucleus	importin-alpha export receptor activity			large_intestine(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			GTCCTTCAGCTTTTTTTTCTA	0.333													4	2	---	---	---	---	
B4GALT5	9334	broad.mit.edu	37	20	48266358	48266358	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48266358delA	uc002xuu.3	-							NM_004776	NP_004767	O43286	B4GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	galactosyltransferase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)			CAAGTAATAGAAAATGTGCCT	0.368													4	2	---	---	---	---	
ZNF831	128611	broad.mit.edu	37	20	57783650	57783651	+	Intron	DEL	TG	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57783650_57783651delTG	uc002yan.2	+							NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831							intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)					TGCACAGAATTGTGTGTGTGTG	0.535													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10754260	10754261	+	IGR	DEL	TC	-	-	rs112973473		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10754260_10754261delTC								None (None upstream) : TPTE (152482 downstream)																							ctgtgaaacttctgtgtgatgc	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11052980	11052984	+	Intron	DEL	TAATC	-	-	rs148507295		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11052980_11052984delTAATC	uc002yit.1	-							NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AATAAATCATTAATCTAACAATGGA	0.229													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	24638544	24638545	+	IGR	INS	-	ACAC	ACAC	rs142970893	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24638544_24638545insACAC								None (None upstream) : None (None downstream)																							ACCTCATTTATacacacacaca	0.129													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	38670155	38670156	+	IGR	INS	-	G	G	rs138552748	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38670155_38670156insG								DSCR3 (30322 upstream) : DYRK1A (69703 downstream)																							actgaatgcctgggaccaagtg	0.163													4	2	---	---	---	---	
DYRK1A	1859	broad.mit.edu	37	21	38763436	38763436	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38763436delG	uc002ywi.2	+						DYRK1A_uc002ywg.1_Intron|DYRK1A_uc010gno.1_Intron|DYRK1A_uc002ywh.1_Intron	NM_101395	NP_567824	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation						nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4						ctagtgccctggttctttgga	0.015													4	2	---	---	---	---	
BACE2	25825	broad.mit.edu	37	21	42572130	42572130	+	Intron	DEL	A	-	-	rs112085931		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42572130delA	uc002yyw.2	+						BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron	NM_012105	NP_036237	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2 isoform A						membrane protein ectodomain proteolysis|negative regulation of amyloid precursor protein biosynthetic process|peptide hormone processing	cell surface|endoplasmic reticulum|endosome|Golgi apparatus|integral to membrane	aspartic-type endopeptidase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				aaaaaaaaACAAAAAAAAAAC	0.199													4	2	---	---	---	---	
SLC37A1	54020	broad.mit.edu	37	21	43962247	43962247	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43962247delT	uc002zbi.2	+						SLC37A1_uc002zbj.2_Intron	NM_018964	NP_061837	P57057	GLPT_HUMAN	solute carrier family 37 member 1						carbohydrate transport|transmembrane transport	integral to membrane					0						TCTGGCTGGGTTTTTTTTCCT	0.378													4	2	---	---	---	---	
PDE9A	5152	broad.mit.edu	37	21	44138682	44138682	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44138682delT	uc002zbm.2	+						PDE9A_uc002zbn.2_Intron|PDE9A_uc002zbo.2_Intron|PDE9A_uc002zbp.2_Intron|PDE9A_uc002zbq.2_Intron|PDE9A_uc002zbs.2_Intron|PDE9A_uc002zbr.2_Intron|PDE9A_uc002zbt.2_Intron|PDE9A_uc002zbu.2_Intron|PDE9A_uc002zbv.2_Intron|PDE9A_uc002zbw.2_Intron|PDE9A_uc002zbx.2_Intron|PDE9A_uc002zby.2_Intron|PDE9A_uc002zbz.2_Intron|PDE9A_uc002zca.2_Intron|PDE9A_uc002zcb.2_Intron|PDE9A_uc002zcc.2_Intron|PDE9A_uc002zcd.2_Intron|PDE9A_uc002zce.2_Intron|PDE9A_uc002zcf.2_Intron|PDE9A_uc002zcg.2_Intron	NM_002606	NP_002597	O76083	PDE9A_HUMAN	phosphodiesterase 9A isoform a						platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2						atccatgaagtttttttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16156727	16156728	+	Intron	INS	-	G	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16156727_16156728insG	uc002zkr.3	-						uc002zks.3_Intron					Homo sapiens cDNA FLJ12852 fis, clone NT2RP2003445.																		GAAACAGGGTTGGGGTGACCGA	0.683													3	4	---	---	---	---	
MICAL3	57553	broad.mit.edu	37	22	18432933	18432933	+	Intron	DEL	T	-	-	rs68119234		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18432933delT	uc002zng.3	-						MICAL3_uc002znh.2_Intron|MICAL3_uc002znl.1_Intron|MICAL3_uc010grf.2_Intron|MICAL3_uc011agm.1_Intron	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		CAGCTGTCTAttttttttttt	0.229													4	2	---	---	---	---	
CLTCL1	8218	broad.mit.edu	37	22	19258329	19258329	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19258329delA	uc002zpb.2	-						CLTCL1_uc011agv.1_Intron|CLTCL1_uc011agw.1_Intron	NM_007098	NP_009029	P53675	CLH2_HUMAN	clathrin, heavy polypeptide-like 1 isoform 1						anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)					AGAAAGATATAAAAAAAAAAT	0.224			T	?	ALCL								4	2	---	---	---	---	
SLC2A11	66035	broad.mit.edu	37	22	24223698	24223698	+	Intron	DEL	A	-	-	rs35177865		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24223698delA	uc002zyn.3	+						SLC2A11_uc002zyl.1_Intron|SLC2A11_uc002zym.3_Intron|SLC2A11_uc002zyo.3_Intron|SLC2A11_uc011ajc.1_Intron|SLC2A11_uc002zyp.3_Intron	NM_001024938	NP_001020109	Q9BYW1	GTR11_HUMAN	glucose transporter protein 10 isoform c							integral to membrane|plasma membrane	sugar transmembrane transporter activity			ovary(1)	1						gaggaactgcaaaatcacaca	0.114													3	5	---	---	---	---	
SEZ6L	23544	broad.mit.edu	37	22	26638505	26638505	+	Intron	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26638505delC	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6						GGTTTAAGAACCACGACTATT	0.189													4	2	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	33872710	33872711	+	Intron	INS	-	G	G	rs149874072	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33872710_33872711insG	uc003and.3	-						LARGE_uc011amd.1_Intron|LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|LARGE_uc010gwq.1_Intron	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				AAAGAATACTAGGTATTAACTA	0.416													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35162928	35162941	+	IGR	DEL	TGTGTATGTGTGTG	-	-	rs66886119	by1000genomes	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35162928_35162941delTGTGTATGTGTGTG								LARGE (844344 upstream) : ISX (299188 downstream)																							tctgtgtgtatgtgtatgtgtgtgtgtgtgtgtg	0.304													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	37146540	37146540	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37146540delA								CACNG2 (47637 upstream) : IFT27 (7715 downstream)																							aaatgctattaaaagcttttt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48014632	48014632	+	IGR	DEL	C	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48014632delC								TBC1D22A (444910 upstream) : FAM19A5 (870656 downstream)																							ACCATTCTGTCCCACACACAA	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49483018	49483019	+	IGR	DEL	CA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49483018_49483019delCA								FAM19A5 (335276 upstream) : C22orf34 (325157 downstream)																							ACcacacaggcacacacacaca	0.238													4	3	---	---	---	---	
C22orf34	348645	broad.mit.edu	37	22	50022841	50022841	+	Intron	DEL	G	-	-	rs66525271		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50022841delG	uc003bit.3	-						C22orf34_uc003biq.2_Intron					RecName: Full=Uncharacterized protein C22orf34;												0						GCTGCTGTGTGGGTCCCTGTT	0.567													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	10399407	10399407	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10399407delT								CLCN4 (193710 upstream) : MID1 (14190 downstream)																							TTGTTTTCTCTTGATGTCAGT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	22801393	22801394	+	IGR	INS	-	A	A	rs75750656		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22801393_22801394insA								ZNF645 (508819 upstream) : DDX53 (216693 downstream)																							tggttatggctaaaaaaaaggg	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	30798191	30798191	+	IGR	DEL	A	-	-	rs34505146		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30798191delA								GK (49467 upstream) : TAB3 (47369 downstream)																							acacgaggtgaaaaaaaaggt	0.000													4	2	---	---	---	---	
USP9X	8239	broad.mit.edu	37	X	41078697	41078697	+	Intron	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41078697delT	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						TGTGTTTTGATTTTTTTTTTT	0.234													5	3	---	---	---	---	
GPR173	54328	broad.mit.edu	37	X	53085072	53085075	+	Intron	DEL	GTGT	-	-	rs112784276		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53085072_53085075delGTGT	uc004dru.2	+							NM_018969	NP_061842	Q9NS66	GP173_HUMAN	G protein-coupled receptor 173							integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1						TGTATTTGGAgtgtgtgtgtgtgt	0.328													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	89806147	89806147	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89806147delT								TGIF2LX (628267 upstream) : PABPC5 (883450 downstream)																							gaatcctccctcaatcattct	0.000													4	2	---	---	---	---	
APLN	8862	broad.mit.edu	37	X	128781212	128781212	+	3'UTR	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128781212delG	uc004eus.2	-	3						NM_017413	NP_059109	Q9ULZ1	APEL_HUMAN	apelin preproprotein						immune response|lactation|signal transduction		hormone activity				0						GATGGGGTGTGGGGGCAGGAA	0.577													4	2	---	---	---	---	
BCORL1	63035	broad.mit.edu	37	X	129171119	129171119	+	Intron	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129171119delA	uc004evb.1	+						BCORL1_uc004evc.1_Intron	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7						agactgtctcaaaaaaaaaaG	0.229													4	2	---	---	---	---	
ZNF75D	7626	broad.mit.edu	37	X	134383351	134383352	+	Intron	DEL	CA	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134383351_134383352delCA	uc004eym.2	-									P51815	ZN75D_HUMAN	Homo sapiens mRNA; cDNA DKFZp451F083 (from clone DKFZp451F083); complete cds.						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						CGTGCATGTGCACACACACACA	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	139551653	139551653	+	IGR	DEL	A	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139551653delA								CXorf66 (503976 upstream) : SOX3 (33499 downstream)																							CACCCGGCTCAAAAAAAAAAG	0.284													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	151064898	151064898	+	IGR	DEL	T	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151064898delT								CNGA2 (150862 upstream) : MAGEA4 (16098 downstream)																							tcctcatcgctttttcctttt	0.000													4	2	---	---	---	---	
HCFC1	3054	broad.mit.edu	37	X	153228022	153228022	+	Intron	DEL	G	-	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153228022delG	uc004fjp.2	-							NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1						cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ACTCTGTGCTGGGGGAGGAGT	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59014683	59014684	+	IGR	DEL	AT	-	-	rs10534960		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59014683_59014684delAT								None (None upstream) : None (None downstream)																							acaaaacagaatgagagttccc	0.035													6	3	---	---	---	---	
