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
FAM41C	284593	broad.mit.edu	37	1	809846	809846	+	RNA	SNP	A	G	G	rs117421153	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:809846A>G	uc001abt.3	-	2		c.747T>C				NR_027055				Homo sapiens family with sequence similarity 41, member C, mRNA (cDNA clone IMAGE:5201580), partial cds.												0						GCTGCATTTTAAAGCACTTTT	0.453													3	28	---	---	---	---	PASS
RERE	473	broad.mit.edu	37	1	8419828	8419828	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8419828G>A	uc001ape.2	-	20	4424	c.3614C>T	c.(3613-3615)GCG>GTG	p.A1205V	RERE_uc001apf.2_Missense_Mutation_p.A1205V|RERE_uc001apd.2_Missense_Mutation_p.A651V	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	1205	Potential.				multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		ACTCACAGCCGCCCGCTCTGC	0.542													10	11	---	---	---	---	PASS
PPIE	10450	broad.mit.edu	37	1	40229518	40229518	+	3'UTR	SNP	C	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40229518C>T	uc001cdw.2	+	11					BMP8B_uc001cdz.1_Intron|BMP8B_uc001cea.1_Intron|PPIE_uc001cdv.2_3'UTR	NM_006112	NP_006103	Q9UNP9	PPIE_HUMAN	peptidylprolyl isomerase E isoform 1						protein folding|regulation of transcription, DNA-dependent	catalytic step 2 spliceosome	cyclosporin A binding|nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|protein binding|RNA binding				0	all_cancers(7;1.63e-13)|all_lung(5;2.27e-16)|all_epithelial(6;1.35e-15)|Lung NSC(20;1.49e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;2.7e-17)|all cancers(16;5.5e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TGTGCAGCTACTATGGGGTAC	0.552													19	72	---	---	---	---	PASS
BTF3L4	91408	broad.mit.edu	37	1	52525496	52525496	+	Intron	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52525496T>C	uc001ctk.2	+						BTF3L4_uc001ctl.2_Intron|BTF3L4_uc010onh.1_Intron|BTF3L4_uc001ctm.2_5'UTR	NM_152265	NP_689478	Q96K17	BT3L4_HUMAN	basic transcription factor 3-like 4 isoform 1											large_intestine(1)	1						AATCTATTTTTCCCCCCCTAG	0.408													35	64	---	---	---	---	PASS
WLS	79971	broad.mit.edu	37	1	68611602	68611602	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68611602T>C	uc001def.1	-	9	1499	c.1228A>G	c.(1228-1230)AAG>GAG	p.K410E	uc001deb.1_Intron|uc001dec.1_Intron|WLS_uc001dee.2_Missense_Mutation_p.K408E|WLS_uc001deg.1_Missense_Mutation_p.K319E|WLS_uc009wbf.1_Missense_Mutation_p.K365E	NM_024911	NP_079187	Q5T9L3	WLS_HUMAN	G protein-coupled receptor 177 isoform 1	410	Cytoplasmic (Potential).				multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Wnt receptor signaling pathway	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	signal transducer activity				0						CTGGACTGCTTCCCACTGATG	0.517													49	73	---	---	---	---	PASS
CDC14A	8556	broad.mit.edu	37	1	100964760	100964760	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100964760G>A	uc001dtg.3	+	15	2185	c.1697G>A	c.(1696-1698)CGA>CAA	p.R566Q	CDC14A_uc010oui.1_Missense_Mutation_p.R508Q|CDC14A_uc001dtf.2_Missense_Mutation_p.R566Q|CDC14A_uc009wed.1_Missense_Mutation_p.R273Q|CDC14A_uc009wee.2_Missense_Mutation_p.R566Q	NM_003672	NP_003663	Q9UNH5	CC14A_HUMAN	CDC14 homolog A isoform 1	566					cell cycle|cell division|cell proliferation	centrosome|nucleus|spindle	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			large_intestine(1)	1		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		ACCATCCTCCGACCCTCCTAC	0.572													49	67	---	---	---	---	PASS
SCARNA2	677766	broad.mit.edu	37	1	109642843	109642843	+	RNA	SNP	C	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109642843C>A	uc001dwo.1	+	1		c.29C>A				NR_003023				Homo sapiens cDNA clone IMAGE:6602628, partial cds.												0						GGCCTGGGTCCTGGGTGTTGT	0.647													12	19	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142803398	142803398	+	Intron	SNP	C	A	A	rs1920859	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142803398C>A	uc001eiw.1	+						uc001ejb.2_RNA|uc001ejc.2_5'Flank					Homo sapiens PNAS-130 mRNA, complete cds.																		cttctgagctcctcaagtgat	0.100													3	13	---	---	---	---	PASS
ANKRD34A	284615	broad.mit.edu	37	1	145474166	145474166	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145474166C>G	uc001enq.1	+	4	2131	c.838C>G	c.(838-840)CTG>GTG	p.L280V	NBPF10_uc001emp.3_Intron|LIX1L_uc001enr.2_5'Flank	NM_001039888	NP_001034977	Q69YU3	AN34A_HUMAN	ankyrin repeat domain 34	280	Pro-rich.										0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TGGCCTGACCCTGACCGGTCG	0.662													35	52	---	---	---	---	PASS
SETDB1	9869	broad.mit.edu	37	1	150923430	150923430	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150923430T>C	uc001evu.2	+	13	2267	c.2077T>C	c.(2077-2079)TGT>CGT	p.C693R	SETDB1_uc009wmf.2_Missense_Mutation_p.C694R|SETDB1_uc001evv.2_Missense_Mutation_p.C693R|SETDB1_uc009wmg.1_Missense_Mutation_p.C693R	NM_001145415	NP_001138887	Q15047	SETB1_HUMAN	SET domain, bifurcated 1 isoform 1	693					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|Golgi apparatus|nucleus|plasma membrane	DNA binding|histone-lysine N-methyltransferase activity|protein binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCCCCTATCCTGTGTCAATGA	0.458													46	98	---	---	---	---	PASS
IGSF9	57549	broad.mit.edu	37	1	159897631	159897631	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159897631G>A	uc001fur.2	-	20	3475	c.3277C>T	c.(3277-3279)CCT>TCT	p.P1093S	IGSF9_uc001fuq.2_Missense_Mutation_p.P1077S|CCDC19_uc001ful.2_5'Flank|TAGLN2_uc001fun.1_5'Flank|TAGLN2_uc001fuo.1_5'Flank|TAGLN2_uc010piy.1_5'Flank|IGSF9_uc001fup.2_Missense_Mutation_p.P239S	NM_001135050	NP_001128522	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9 isoform a	1093	Cytoplasmic (Potential).					cell junction|integral to membrane|synapse				ovary(2)|central_nervous_system(2)|large_intestine(1)	5	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			ATGTCCCCAGGGAATTCTGAG	0.517													33	72	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228400286	228400286	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228400286G>A	uc009xez.1	+	2	846	c.802G>A	c.(802-804)GAG>AAG	p.E268K	OBSCN_uc001hsn.2_Missense_Mutation_p.E268K|uc001hsm.1_RNA	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	268	Ig-like 3.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				GCCCAAGCCCGAGACGGTGTG	0.687													16	55	---	---	---	---	PASS
RHOB	388	broad.mit.edu	37	2	20647327	20647327	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20647327A>G	uc002rdv.2	+	1	493	c.101A>G	c.(100-102)TAC>TGC	p.Y34C		NM_004040	NP_004031	P62745	RHOB_HUMAN	ras homolog gene family, member B precursor	34	Effector region (Potential).				angiogenesis|axon guidance|cell adhesion|endosome to lysosome transport|negative regulation of cell cycle|platelet activation|positive regulation of angiogenesis|protein transport|regulation of small GTPase mediated signal transduction|Rho protein signal transduction|transformed cell apoptosis	cytosol|late endosome membrane|nucleus|plasma membrane	GTP binding|GTPase activity|protein binding			ovary(1)|lung(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)	all_epithelial(98;4.19e-09)|Lung NSC(108;0.00452)|Ovarian(717;0.0164)		OV - Ovarian serous cystadenocarcinoma(76;1.14e-22)|Epithelial(75;7.84e-19)		CCCGAGGTGTACGTGCCCACC	0.637													26	44	---	---	---	---	PASS
TP53I3	9540	broad.mit.edu	37	2	24307066	24307066	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24307066A>G	uc002rey.1	-	2	191	c.131T>C	c.(130-132)TTA>TCA	p.L44S	LOC375190_uc002rew.2_Intron|TP53I3_uc002rex.1_Missense_Mutation_p.L44S|TP53I3_uc002rez.1_Missense_Mutation_p.L44S|TP53I3_uc010ykk.1_5'UTR	NM_147184	NP_671713	Q53FA7	QORX_HUMAN	tumor protein p53 inducible protein 3	44					induction of apoptosis by oxidative stress|NADP metabolic process		NADPH binding|NADPH:quinone reductase activity|protein homodimerization activity|quinone binding|zinc ion binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TACCTGCATTAAGTCCGCCCG	0.667											OREG0014492	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	22	23	---	---	---	---	PASS
TMEM214	54867	broad.mit.edu	37	2	27258869	27258869	+	Silent	SNP	C	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27258869C>T	uc002ria.3	+	5	779	c.669C>T	c.(667-669)ATC>ATT	p.I223I	TMEM214_uc010yle.1_RNA|TMEM214_uc002rib.3_Silent_p.I178I	NM_017727	NP_060197	Q6NUQ4	TM214_HUMAN	transmembrane protein 214 isoform 1	223						integral to membrane	protein binding				0						GCATCTGTATCCAGGCCATCC	0.512													22	29	---	---	---	---	PASS
FLJ40330	645784	broad.mit.edu	37	2	89104958	89104958	+	Intron	SNP	A	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89104958A>G	uc010fhg.2	+						FLJ40330_uc010fhh.2_Intron|FLJ40330_uc010fhi.1_RNA	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						AATTCAAATCATTGATTTCTG	0.289													3	6	---	---	---	---	PASS
GPR155	151556	broad.mit.edu	37	2	175301104	175301104	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175301104C>A	uc002uit.2	-	17	2744	c.2353G>T	c.(2353-2355)GAC>TAC	p.D785Y	GPR155_uc002uiu.2_Missense_Mutation_p.D785Y|GPR155_uc002uiv.2_Missense_Mutation_p.D785Y|GPR155_uc010fqs.2_Missense_Mutation_p.D757Y	NM_001033045	NP_001028217	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155 isoform 9	785	DEP.				intracellular signal transduction|transmembrane transport	integral to membrane				ovary(1)	1						CTCACCAGGTCACAGCCACAG	0.488													33	76	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196729403	196729403	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196729403T>C	uc002utj.3	-	41	7077	c.6976A>G	c.(6976-6978)ATT>GTT	p.I2326V		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2326	AAA 4 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						ATCCTGGAAATTCTGCTGATG	0.463													75	102	---	---	---	---	PASS
STRADB	55437	broad.mit.edu	37	2	202344965	202344965	+	3'UTR	SNP	T	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202344965T>G	uc002uyd.3	+	12						NM_018571	NP_061041	Q9C0K7	STRAB_HUMAN	STE20-related kinase adaptor beta						activation of protein kinase activity|cell cycle arrest|insulin receptor signaling pathway|protein export from nucleus|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|protein binding|protein kinase activity			skin(2)|stomach(1)|lung(1)	4						CTTCTGTATTTCTAGGTACAA	0.368													5	157	---	---	---	---	PASS
DNAH1	25981	broad.mit.edu	37	3	52387249	52387249	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52387249T>C	uc011bef.1	+	19	3419	c.3158T>C	c.(3157-3159)CTG>CCG	p.L1053P	DNAH1_uc003ddt.1_Missense_Mutation_p.L1053P	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1053	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GCTGAGCAGCTGGAGAAGAAC	0.577													14	36	---	---	---	---	PASS
CACNA1D	776	broad.mit.edu	37	3	53845394	53845394	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53845394G>C	uc003dgv.3	+	48	6610	c.6447G>C	c.(6445-6447)GAG>GAC	p.E2149D	CACNA1D_uc003dgu.3_Missense_Mutation_p.E2169D|CACNA1D_uc003dgy.3_Missense_Mutation_p.E2125D|CACNA1D_uc003dgw.3_Missense_Mutation_p.E1816D|CACNA1D_uc011bes.1_RNA	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	2149	Cytoplasmic (Potential).				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)	GGGATGAGGAGGACCTGGCGG	0.622													24	37	---	---	---	---	PASS
CCDC14	64770	broad.mit.edu	37	3	123634543	123634543	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123634543T>C	uc011bjx.1	-	13	2036	c.1945A>G	c.(1945-1947)AAG>GAG	p.K649E	CCDC14_uc003egv.3_Missense_Mutation_p.K290E|CCDC14_uc003egx.3_Missense_Mutation_p.K449E|CCDC14_uc010hrt.2_Missense_Mutation_p.K608E|CCDC14_uc003egy.3_Missense_Mutation_p.K449E|CCDC14_uc003egz.2_Intron	NM_022757	NP_073594	Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	649						centrosome					0		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		GAGAGAAGCTTTGCCATGCTA	0.363													12	179	---	---	---	---	PASS
ZNF732	654254	broad.mit.edu	37	4	265156	265156	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:265156G>C	uc011buu.1	-	3	1501	c.1487C>G	c.(1486-1488)ACT>AGT	p.T496S	ZNF732_uc010ibb.1_Intron	NM_001137608	NP_001131080	B4DXR9	ZN732_HUMAN	zinc finger protein 732	497					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTTCTCTCCAGTATGAATTGT	0.378													10	14	---	---	---	---	PASS
PIGG	54872	broad.mit.edu	37	4	493095	493095	+	5'UTR	SNP	C	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:493095C>T	uc003gak.3	+	1					PIGG_uc003gaj.3_5'UTR|PIGG_uc011bux.1_RNA|PIGG_uc010ibf.2_5'UTR|PIGG_uc003gal.3_Intron|ZNF721_uc003gag.2_5'UTR|ZNF721_uc010ibe.2_5'UTR|ZNF721_uc003gah.1_RNA|PIGG_uc003gai.2_RNA|PIGG_uc011buw.1_5'UTR|PIGG_uc003gam.2_5'UTR|PIGG_uc003gan.2_5'UTR	NM_001127178	NP_001120650	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	CP2 mannose-ethanolamine phosphotransferase activity			central_nervous_system(2)|ovary(1)|skin(1)	4						CAGGTGGGGTCGGTTCCGCAT	0.652													6	9	---	---	---	---	PASS
ADAMTS12	81792	broad.mit.edu	37	5	33576716	33576716	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33576716G>A	uc003jia.1	-	19	3578	c.3415C>T	c.(3415-3417)CCT>TCT	p.P1139S	ADAMTS12_uc010iuq.1_Missense_Mutation_p.P1054S	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1139	Spacer 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						GGAGTCACAGGCCAAGTGATA	0.483										HNSCC(64;0.19)			61	82	---	---	---	---	PASS
PCDHA6	56142	broad.mit.edu	37	5	140209828	140209828	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140209828T>C	uc003lho.2	+	1	2179	c.2152T>C	c.(2152-2154)TAC>CAC	p.Y718H	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc011dab.1_Missense_Mutation_p.Y718H	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	718	Helical; (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTACTGCTGTACACAGCGCT	0.692													31	56	---	---	---	---	PASS
HK3	3101	broad.mit.edu	37	5	176317826	176317826	+	Silent	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176317826G>A	uc003mfa.2	-	5	623	c.531C>T	c.(529-531)GAC>GAT	p.D177D	HK3_uc003mez.2_5'Flank	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3	177	Glucose-binding (Potential).|Regulatory.				glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	7	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACCTCACCCTGTCCAAGCCCG	0.597													5	94	---	---	---	---	PASS
HIST1H4E	8367	broad.mit.edu	37	6	26205069	26205069	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26205069T>C	uc003ngy.2	+	1	197	c.197T>C	c.(196-198)GTG>GCG	p.V66A		NM_003545	NP_003536	P62805	H4_HUMAN	histone cluster 1, H4e	66					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding	p.V66V(1)		ovary(1)	1		all_hematologic(11;0.196)				CTGGAAAACGTGATTCGTGAT	0.567													50	67	---	---	---	---	PASS
UNC5CL	222643	broad.mit.edu	37	6	41002736	41002736	+	Silent	SNP	A	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41002736A>G	uc003opi.2	-	2	167	c.78T>C	c.(76-78)CTT>CTC	p.L26L	UNC5CL_uc010jxe.1_Silent_p.L26L	NM_173561	NP_775832	Q8IV45	UN5CL_HUMAN	unc-5 homolog C-like	26	Helical; Signal-anchor for type III membrane protein; (Potential).				signal transduction	cytoplasm|integral to membrane				ovary(2)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)					ATTGGGCCAGAAGGAGGACAC	0.602													50	63	---	---	---	---	PASS
PEX6	5190	broad.mit.edu	37	6	42931981	42931981	+	3'UTR	SNP	C	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42931981C>G	uc003otf.2	-	17					uc003ote.1_5'Flank|PEX6_uc010jya.2_RNA	NM_000287	NP_000278	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6						protein import into peroxisome matrix, translocation|protein stabilization	cytosol|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)	1			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			TTGGCAGCAGCCTGAGGAGGA	0.612													19	19	---	---	---	---	PASS
GPR110	266977	broad.mit.edu	37	6	46977033	46977033	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46977033A>T	uc003oyt.2	-	11	2337	c.2138T>A	c.(2137-2139)ATA>AAA	p.I713K	GPR110_uc011dwl.1_Missense_Mutation_p.I401K	NM_153840	NP_722582	Q5T601	GP110_HUMAN	G-protein coupled receptor 110 isoform 1	713	Helical; Name=4; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|pancreas(1)	3						AATGACAGATATAATGAGAGG	0.478													25	43	---	---	---	---	PASS
PEX3	8504	broad.mit.edu	37	6	143811741	143811741	+	3'UTR	SNP	T	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143811741T>A	uc003qjl.2	+	12						NM_003630	NP_003621	P56589	PEX3_HUMAN	peroxisomal biogenesis factor 3						protein import into peroxisome membrane|transmembrane transport	integral to peroxisomal membrane	protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(155;5.73e-06)|GBM - Glioblastoma multiforme(68;0.0117)		TAAAACCTGATTTGAAAACAA	0.433													4	11	---	---	---	---	PASS
RBM16	22828	broad.mit.edu	37	6	155123148	155123148	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155123148C>A	uc003qqa.2	+	8	882	c.650C>A	c.(649-651)CCC>CAC	p.P217H	RBM16_uc011efj.1_Missense_Mutation_p.P283H|RBM16_uc011efk.1_Missense_Mutation_p.P262H|RBM16_uc003qpz.2_Missense_Mutation_p.P217H|RBM16_uc010kji.2_Missense_Mutation_p.P238H	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16	217	Gln-rich.				mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)		CAACAGAAGCCCCAGCCTTCC	0.428													77	82	---	---	---	---	PASS
ARID1B	57492	broad.mit.edu	37	6	157511244	157511244	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157511244G>A	uc003qqn.2	+	15	3860	c.3708G>A	c.(3706-3708)ATG>ATA	p.M1236I	ARID1B_uc003qqo.2_Missense_Mutation_p.M1196I|ARID1B_uc003qqp.2_Missense_Mutation_p.M1183I	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1241					chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GGAACTCCATGACTCCAAACG	0.517													65	148	---	---	---	---	PASS
SNX13	23161	broad.mit.edu	37	7	17833769	17833769	+	3'UTR	SNP	A	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17833769A>G	uc003stw.1	-	25					SNX13_uc003stv.2_Missense_Mutation_p.F925S|SNX13_uc010kuc.2_Missense_Mutation_p.F722S|SNX13_uc010kub.2_Missense_Mutation_p.F331S			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;						cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)					AAGTTCACGGAATTTATACTG	0.358													35	6	---	---	---	---	PASS
FKBP9L	360132	broad.mit.edu	37	7	55755682	55755682	+	Intron	SNP	G	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55755682G>C	uc010kzl.2	-						FKBP9L_uc010kzk.2_5'UTR|FKBP9L_uc003tqt.2_Intron|FKBP9L_uc011kcs.1_Intron	NR_003949				SubName: Full=cDNA, FLJ79189, highly similar to FK506-binding protein 9 (EC 5.2.1.8);												0						GTGTTCCTAtgagaagaacac	0.214													42	68	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94055151	94055151	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94055151T>A	uc003ung.1	+	44	3396	c.2925T>A	c.(2923-2925)CAT>CAA	p.H975Q	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	975					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CTGGCAAACATGGAAACCGTG	0.567										HNSCC(75;0.22)			10	30	---	---	---	---	PASS
SLC26A3	1811	broad.mit.edu	37	7	107418619	107418619	+	Splice_Site	SNP	C	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107418619C>A	uc003ver.2	-	13	1725	c.1514_splice	c.e13+1	p.F505_splice	SLC26A3_uc003ves.2_Splice_Site_p.F470_splice	NM_000111	NP_000102	P40879	S26A3_HUMAN	solute carrier family 26, member 3						excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)|skin(1)	4						TGAGCACTCACAATTGGGTCC	0.483													3	39	---	---	---	---	PASS
RBM28	55131	broad.mit.edu	37	7	127965927	127965927	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127965927A>C	uc003vmp.2	-	11	1262	c.1147T>G	c.(1147-1149)TTC>GTC	p.F383V	RBM28_uc003vmo.2_5'UTR|RBM28_uc011koj.1_Missense_Mutation_p.F242V|RBM28_uc011kok.1_Missense_Mutation_p.F330V	NM_018077	NP_060547	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	383	RRM 3.				mRNA processing|RNA splicing	Golgi apparatus|nucleolus|spliceosomal complex	nucleotide binding|RNA binding			ovary(2)	2						TGAGTCATGAACTGGGCAAAT	0.443													25	87	---	---	---	---	PASS
ARHGEF5	7984	broad.mit.edu	37	7	144060770	144060770	+	Silent	SNP	T	C	C	rs141931104	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144060770T>C	uc003wel.2	+	2	1126	c.1008T>C	c.(1006-1008)AAT>AAC	p.N336N	ARHGEF5_uc003wek.2_Silent_p.N336N	NM_005435	NP_005426	Q12774	ARHG5_HUMAN	rho guanine nucleotide exchange factor 5	336					intracellular signal transduction|regulation of Rho protein signal transduction	intracellular	GTP binding|protein binding|Rho guanyl-nucleotide exchange factor activity			skin(2)	2	Melanoma(164;0.14)					CAGAAGAGAATAGGGCGGACT	0.512													6	452	---	---	---	---	PASS
ATG9B	285973	broad.mit.edu	37	7	150715068	150715068	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150715068G>A	uc011kvc.1	-	8	2018	c.1942C>T	c.(1942-1944)CGT>TGT	p.R648C	ATG9B_uc003wig.3_RNA	NM_173681	NP_775952	Q674R7	ATG9B_HUMAN	ATG9 autophagy related 9 homolog B	648	Cytoplasmic (By similarity).				autophagic vacuole assembly	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane				ovary(1)	1	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCCAGGGCACGAGGGCGGAAC	0.592											OREG0018444	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	69	---	---	---	---	PASS
LRRCC1	85444	broad.mit.edu	37	8	86019572	86019572	+	Silent	SNP	G	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86019572G>T	uc003ycw.2	+	1	196	c.42G>T	c.(40-42)GTG>GTT	p.V14V	LRRCC1_uc010lzz.1_RNA|LRRCC1_uc010maa.1_5'UTR|LRRCC1_uc003ycx.2_5'UTR|LRRCC1_uc003ycy.2_5'Flank	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	14					cell division|mitosis	centriole|nucleus					0						aggcggAAGTGGAAAACGAAG	0.527													4	8	---	---	---	---	PASS
FREM1	158326	broad.mit.edu	37	9	14846003	14846003	+	Silent	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14846003G>A	uc003zlm.2	-	8	1938	c.1348C>T	c.(1348-1350)CTA>TTA	p.L450L	FREM1_uc010mic.2_RNA	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	450	CSPG 2.				cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)		ACGGTGACTAGCCGGACAGCA	0.473													14	21	---	---	---	---	PASS
MLLT3	4300	broad.mit.edu	37	9	20346391	20346391	+	3'UTR	SNP	A	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20346391A>C	uc003zoe.2	-	11					MLLT3_uc011lne.1_3'UTR|MLLT3_uc011lnf.1_3'UTR	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)		aaaaaaaaaaaccaaaaaaaa	0.303			T	MLL	ALL								5	23	---	---	---	---	PASS
CREB3	10488	broad.mit.edu	37	9	35736669	35736669	+	Silent	SNP	A	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35736669A>G	uc003zxv.2	+	9	1515	c.1062A>G	c.(1060-1062)GGA>GGG	p.G354G	CREB3_uc010mla.2_Silent_p.G273G	NM_006368	NP_006359	O43889	CREB3_HUMAN	cAMP responsive element binding protein 3	378	Lumenal (Potential).|Pro-rich.				chemotaxis|induction of positive chemotaxis|interspecies interaction between organisms|negative regulation of cell cycle|positive regulation of calcium ion transport|positive regulation of cell migration|positive regulation of transcription, DNA-dependent|reactivation of latent virus|regulation of cell proliferation	cytosol|endoplasmic reticulum|endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|integral to membrane|nucleus|nucleus	cAMP response element binding protein binding|CCR1 chemokine receptor binding|DNA binding|protein dimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity				0	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)	GBM - Glioblastoma multiforme(74;0.0285)		GGAAGGGAGGATGGCTTCCTA	0.592											OREG0019176	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	80	144	---	---	---	---	PASS
PALM2-AKAP2	445815	broad.mit.edu	37	9	112898812	112898812	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112898812C>A	uc004bei.2	+	9	1876	c.1684C>A	c.(1684-1686)CAG>AAG	p.Q562K	PALM2-AKAP2_uc004bek.3_Missense_Mutation_p.Q330K|PALM2-AKAP2_uc004bej.3_Missense_Mutation_p.Q330K|PALM2-AKAP2_uc004bel.1_Missense_Mutation_p.Q140K|AKAP2_uc011lwi.1_Missense_Mutation_p.Q188K|AKAP2_uc004bem.2_Missense_Mutation_p.Q188K|PALM2-AKAP2_uc010mtw.1_Missense_Mutation_p.Q148K|AKAP2_uc011lwj.1_Missense_Mutation_p.Q99K|PALM2-AKAP2_uc004ben.2_Missense_Mutation_p.Q99K	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2	99							enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6						CGAGGCGACCCAGCCAGAACC	0.582													4	91	---	---	---	---	PASS
VAV2	7410	broad.mit.edu	37	9	136649535	136649535	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136649535T>C	uc004ces.2	-	18	1584	c.1538A>G	c.(1537-1539)AAC>AGC	p.N513S	VAV2_uc004cer.2_Missense_Mutation_p.N503S|VAV2_uc004cet.1_Missense_Mutation_p.N52S	NM_001134398	NP_001127870	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor isoform	513					angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		TGGCTTGATGTTTGACCTGGC	0.552													66	85	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	17110165	17110165	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17110165A>G	uc001ioo.2	-	21	2958	c.2906T>C	c.(2905-2907)CTG>CCG	p.L969P		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	969	CUB 5.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TAAATGAATCAGGTGATTAGG	0.413													74	99	---	---	---	---	PASS
PLCE1	51196	broad.mit.edu	37	10	96043555	96043555	+	Silent	SNP	C	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96043555C>T	uc001kjk.2	+	21	5438	c.4804C>T	c.(4804-4806)CTG>TTG	p.L1602L	PLCE1_uc010qnx.1_Silent_p.L1586L|PLCE1_uc001kjm.2_Silent_p.L1294L|PLCE1_uc001kjp.2_5'Flank|uc001kjo.1_Intron	NM_016341	NP_057425	Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1 isoform 1	1602					activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)				AGACAACATTCTGGAAGACAG	0.373													40	62	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093448	1093448	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093448C>A	uc001lsx.1	+	31	12380	c.12353C>A	c.(12352-12354)ACC>AAC	p.T4118N		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4118						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gtgaccccaaccccgacaccc	0.000													4	32	---	---	---	---	PASS
SCUBE2	57758	broad.mit.edu	37	11	9043470	9043470	+	Silent	SNP	G	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9043470G>T	uc001mhh.1	-	21	2880	c.2800C>A	c.(2800-2802)CGA>AGA	p.R934R	SCUBE2_uc001mhi.1_Silent_p.R906R|SCUBE2_uc001mhj.1_Silent_p.R742R	NM_020974	NP_066025	Q9NQ36	SCUB2_HUMAN	CEGP1 protein precursor	934						extracellular region	calcium ion binding			ovary(1)|skin(1)	2				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		CTGCCATCTCGAACTATGTCT	0.433													6	129	---	---	---	---	PASS
NUCB2	4925	broad.mit.edu	37	11	17351711	17351711	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17351711T>C	uc001mmw.2	+	12	1285	c.1040T>C	c.(1039-1041)CTA>CCA	p.L347P	NUCB2_uc009ygz.2_Missense_Mutation_p.L317P|NUCB2_uc009yha.2_RNA|NUCB2_uc001mmx.3_RNA|uc001mmy.1_5'Flank	NM_005013	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2 precursor	347	Binds to necdin (By similarity).					cytosol|ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|plasma membrane	calcium ion binding|DNA binding				0						GAGGAAGAACTAAAAGAATAT	0.308													8	11	---	---	---	---	PASS
SYT12	91683	broad.mit.edu	37	11	66816272	66816272	+	3'UTR	SNP	G	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66816272G>T	uc009yrl.2	+	8					SYT12_uc001oju.2_3'UTR	NM_177963	NP_808878	Q8IV01	SYT12_HUMAN	synaptotagmin XII							cell junction|integral to membrane|synaptic vesicle membrane				ovary(1)	1						CTGGAGCCCGGTACCCACTCA	0.637													3	13	---	---	---	---	PASS
ANGPTL5	253935	broad.mit.edu	37	11	101771272	101771272	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101771272C>A	uc001pgl.2	-	7	1146	c.550G>T	c.(550-552)GAC>TAC	p.D184Y		NM_178127	NP_835228	Q86XS5	ANGL5_HUMAN	angiopoietin-like 5 precursor	184	Fibrinogen C-terminal.				signal transduction	extracellular space	receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.043)		BRCA - Breast invasive adenocarcinoma(274;0.0328)		TAATCCATGTCACACATTACC	0.353													4	116	---	---	---	---	PASS
DYRK4	8798	broad.mit.edu	37	12	4702286	4702286	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4702286A>T	uc001qmx.2	+	4	397	c.237A>T	c.(235-237)AAA>AAT	p.K79N	DYRK4_uc009zeh.1_Missense_Mutation_p.K194N|DYRK4_uc001qmy.1_Missense_Mutation_p.K79N	NM_003845	NP_003836	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	79						Golgi apparatus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|skin(1)	3			Colorectal(7;0.103)			CTCCTGAGAAATTTAGCAAGA	0.537													28	63	---	---	---	---	PASS
LOH12CR1	118426	broad.mit.edu	37	12	12618552	12618552	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12618552C>T	uc001ral.2	+	4	799	c.433C>T	c.(433-435)CAG>TAG	p.Q145*	LOH12CR1_uc009zhu.2_Nonsense_Mutation_p.Q97*	NM_058169	NP_477517	Q969J3	L12R1_HUMAN	LOH1CR12	145										ovary(1)	1		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.0205)		GTATGCCGAGCAGATCCAGAA	0.527													38	49	---	---	---	---	PASS
PLEKHA9	51054	broad.mit.edu	37	12	45568052	45568052	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45568052T>C	uc001rom.1	-	3	634	c.97A>G	c.(97-99)ATT>GTT	p.I33V	PLEKHA9_uc009zke.2_Missense_Mutation_p.I33V	NM_015899	NP_056983			pleckstrin homology domain containing, family A												0	Lung SC(27;0.192)|Renal(347;0.236)			GBM - Glioblastoma multiforme(48;0.173)		CCCACATCAATTCCCTCCTCA	0.428													159	248	---	---	---	---	PASS
GOLGA3	2802	broad.mit.edu	37	12	133384990	133384990	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133384990T>G	uc001ukz.1	-	5	1224	c.665A>C	c.(664-666)AAG>ACG	p.K222T	GOLGA3_uc001ula.1_Missense_Mutation_p.K222T|GOLGA3_uc001ulb.2_Missense_Mutation_p.K222T	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	222	Golgi-targeting domain.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		GCTGCCCACCTTAGGCCCCCG	0.502													170	255	---	---	---	---	PASS
FNDC3A	22862	broad.mit.edu	37	13	49772609	49772609	+	Silent	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49772609T>C	uc001vcm.2	+	23	3191	c.2886T>C	c.(2884-2886)TTT>TTC	p.F962F	FNDC3A_uc001vcn.2_Silent_p.F962F|FNDC3A_uc001vco.2_RNA|FNDC3A_uc001vcq.2_Silent_p.F906F	NM_001079673	NP_001073141	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	962	Fibronectin type-III 8.					Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		GTGTTGCCTTTAGCCACCAGA	0.448													10	172	---	---	---	---	PASS
LMO7	4008	broad.mit.edu	37	13	76335071	76335071	+	Translation_Start_Site	SNP	A	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76335071A>G	uc001vjv.2	+	1	275	c.-485A>G	c.(-487--483)ATAAT>ATGAT		LMO7_uc010thv.1_Missense_Mutation_p.N124D|LMO7_uc001vjt.1_Missense_Mutation_p.N72D|LMO7_uc010thw.1_Missense_Mutation_p.N33D|LMO7_uc001vju.1_RNA	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		TTCACAGGATAATATAAACGT	0.368													24	38	---	---	---	---	PASS
OR4K17	390436	broad.mit.edu	37	14	20585888	20585888	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20585888C>T	uc001vwo.1	+	1	323	c.323C>T	c.(322-324)GCC>GTC	p.A108V		NM_001004715	NP_001004715	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K,	80	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)	3	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		GCTTCTTTTGCCACCCCTAAG	0.398													7	500	---	---	---	---	PASS
CHD8	57680	broad.mit.edu	37	14	21873953	21873953	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21873953A>G	uc001was.1	-	15	2235	c.2141T>C	c.(2140-2142)TTC>TCC	p.F714S	CHD8_uc001war.1_Missense_Mutation_p.F610S|CHD8_uc001wav.1_Missense_Mutation_p.F156S	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	993	Helicase ATP-binding.				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)		CGGTTCCAAGAAATGAAGCAA	0.398													227	52	---	---	---	---	PASS
KIAA0247	9766	broad.mit.edu	37	14	70170292	70170292	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70170292G>A	uc001xlk.2	+	3	618	c.302G>A	c.(301-303)AGC>AAC	p.S101N	KIAA0247_uc010aqz.2_Missense_Mutation_p.S76N	NM_014734	NP_055549	Q92537	K0247_HUMAN	hypothetical protein LOC9766 precursor	101	Sushi.|Extracellular (Potential).					integral to membrane				ovary(3)	3				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)		ATGGAGATTAGCTGCCGTCTC	0.493													51	7	---	---	---	---	PASS
TPM1	7168	broad.mit.edu	37	15	63354948	63354948	+	Intron	SNP	C	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63354948C>T	uc002alg.2	+						TPM1_uc002alh.2_Intron|TPM1_uc010bgn.2_Intron|TPM1_uc002ali.2_Intron|TPM1_uc002alj.2_Intron|TPM1_uc002alk.2_Intron|TPM1_uc002all.2_Intron|TPM1_uc002alm.2_Intron|TPM1_uc010uie.1_Intron|TPM1_uc002alp.2_Intron|TPM1_uc010uif.1_Silent_p.C256C|TPM1_uc002alr.2_Intron|TPM1_uc002als.2_Intron|TPM1_uc010uig.1_Intron|TPM1_uc002alt.2_Intron|TPM1_uc010bgp.2_Intron	NM_001018005	NP_001018005	P09493	TPM1_HUMAN	tropomyosin 1 alpha chain isoform 1						cardiac muscle contraction|cellular component movement|cellular response to reactive oxygen species|muscle filament sliding|negative regulation of cell migration|positive regulation of ATPase activity|positive regulation of cell adhesion|positive regulation of heart rate by epinephrine|positive regulation of stress fiber assembly|regulation of muscle contraction|ruffle organization|sarcomere organization|ventricular cardiac muscle tissue morphogenesis|wound healing	bleb|cytosol|muscle thin filament tropomyosin|ruffle membrane|stress fiber	actin binding|structural constituent of cytoskeleton|structural constituent of muscle				0						CGCTCCTTTGCACTTGCACAT	0.423													10	13	---	---	---	---	PASS
ODF3L1	161753	broad.mit.edu	37	15	76019874	76019874	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76019874G>A	uc002bax.1	+	4	1040	c.818G>A	c.(817-819)CGT>CAT	p.R273H		NM_175881	NP_787077	Q8IXM7	OD3L1_HUMAN	outer dense fiber of sperm tails 3-like 1	273											0						ATCGACATTCGTGACTGAGGC	0.527													4	107	---	---	---	---	PASS
ANPEP	290	broad.mit.edu	37	15	90349564	90349564	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90349564G>T	uc002bop.3	-	2	543	c.251C>A	c.(250-252)TCC>TAC	p.S84Y		NM_001150	NP_001141	P15144	AMPN_HUMAN	membrane alanine aminopeptidase precursor	84	Extracellular.|Metalloprotease.				angiogenesis|cell differentiation|interspecies interaction between organisms	cytosol|ER-Golgi intermediate compartment|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|receptor activity|zinc ion binding			ovary(3)|skin(1)	4	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)	CACCCGGTAGGAATCGGGTTT	0.612													55	63	---	---	---	---	PASS
MPG	4350	broad.mit.edu	37	16	133207	133207	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:133207G>A	uc002cfn.2	+	4	790	c.472G>A	c.(472-474)GTG>ATG	p.V158M	MPG_uc002cfm.2_Missense_Mutation_p.V141M|MPG_uc010bqp.2_Missense_Mutation_p.V141M|MPG_uc002cfo.2_Missense_Mutation_p.V153M	NM_002434	NP_002425	P29372	3MG_HUMAN	N-methylpurine-DNA glycosylase isoform a	158					depurination|DNA dealkylation involved in DNA repair	nucleoplasm	alkylbase DNA N-glycosylase activity|damaged DNA binding|identical protein binding			ovary(1)|skin(1)	2		all_cancers(16;9.01e-08)|all_epithelial(16;7.64e-07)|Hepatocellular(780;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)				GACCCTGTACGTGTACATCAT	0.642								BER_DNA_glycosylases					100	169	---	---	---	---	PASS
KIAA0430	9665	broad.mit.edu	37	16	15729509	15729509	+	Intron	SNP	G	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15729509G>T	uc002ddr.2	-						KIAA0430_uc002ddq.2_Intron|KIAA0430_uc010uzv.1_Intron|KIAA0430_uc010uzw.1_Intron|KIAA0430_uc010uzx.1_Missense_Mutation_p.R278S	NM_014647	NP_055462	Q9Y4F3	LKAP_HUMAN	limkain b1							peroxisome	nucleotide binding|RNA binding				0						AAAAAGATACGAACCTTGTTT	0.403													3	64	---	---	---	---	PASS
CNOT1	23019	broad.mit.edu	37	16	58589212	58589212	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58589212G>C	uc002env.2	-	21	3127	c.2834C>G	c.(2833-2835)CCT>CGT	p.P945R	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Missense_Mutation_p.P940R|CNOT1_uc002enx.2_Missense_Mutation_p.P945R|CNOT1_uc002enz.1_Missense_Mutation_p.P374R	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	945					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GGATCCAAAAGGCTTGCGTAA	0.428													86	139	---	---	---	---	PASS
PFAS	5198	broad.mit.edu	37	17	8168629	8168629	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8168629G>C	uc002gkr.2	+	19	2445	c.2304G>C	c.(2302-2304)TGG>TGC	p.W768C	PFAS_uc010vuv.1_Missense_Mutation_p.W344C|PFAS_uc002gks.2_5'Flank	NM_012393	NP_036525	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	768					'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process	cytosol	ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	GCGGGAACTGGATGTGGGCAG	0.627													37	119	---	---	---	---	PASS
ZNF823	55552	broad.mit.edu	37	19	11833020	11833020	+	Silent	SNP	G	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11833020G>T	uc002msm.2	-	4	1455	c.1329C>A	c.(1327-1329)CCC>CCA	p.P443P	ZNF823_uc010xmd.1_Silent_p.P261P|ZNF823_uc010dyi.1_Silent_p.P399P	NM_001080493	NP_001073962	P16415	ZN823_HUMAN	ZFP-36 for a zinc finger protein	443					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						GACATTTATAGGGTTTCACTC	0.433										HNSCC(68;0.2)			4	101	---	---	---	---	PASS
NACC1	112939	broad.mit.edu	37	19	13249317	13249317	+	3'UTR	SNP	C	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13249317C>G	uc002mwm.2	+	6						NM_052876	NP_443108	Q96RE7	NACC1_HUMAN	transcriptional repressor NAC1						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization|transcription, DNA-dependent	cytoplasm|nuclear body					0						CTCCCCAGGACCCGCGGTGGG	0.682													5	4	---	---	---	---	PASS
AKAP8L	26993	broad.mit.edu	37	19	15491165	15491165	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15491165C>T	uc002naw.1	-	14	1808	c.1709G>A	c.(1708-1710)GGG>GAG	p.G570E	AKAP8_uc002nav.2_5'Flank|AKAP8_uc010xog.1_5'Flank|AKAP8L_uc002nax.1_RNA|AKAP8L_uc010xoh.1_Missense_Mutation_p.G509E	NM_014371	NP_055186	Q9ULX6	AKP8L_HUMAN	A kinase (PRKA) anchor protein 8-like	570				EEEKEQEEAEGGALDEGAQGEAAGISEGAEGVPAQPPVPPE PA -> RRRRSRRRLRAVPWTRGRRAKRQGFRRAQRACRRS LPCPQSQP (in Ref. 3; AAF86048).		cytoplasm|nuclear matrix	DEAD/H-box RNA helicase binding|DNA binding|zinc ion binding			ovary(1)	1						GCCCTGCGCCCCCTCGTCCAG	0.751													5	3	---	---	---	---	PASS
PRODH2	58510	broad.mit.edu	37	19	36303703	36303703	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36303703A>G	uc002obx.1	-	2	251	c.233T>C	c.(232-234)CTC>CCC	p.L78P		NM_021232	NP_067055	Q9UF12	PROD2_HUMAN	kidney and liver proline oxidase 1	78					glutamate biosynthetic process|proline catabolic process		proline dehydrogenase activity			ovary(2)	2	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ACAGGTCCGGAGCATCCTGGG	0.622													12	31	---	---	---	---	PASS
SRC	6714	broad.mit.edu	37	20	36024642	36024642	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36024642G>A	uc002xgx.2	+	8	1080	c.631G>A	c.(631-633)GAC>AAC	p.D211N	SRC_uc002xgy.2_Missense_Mutation_p.D211N	NM_005417	NP_005408	P12931	SRC_HUMAN	proto-oncogene tyrosine-protein kinase SRC	211	SH2.				axon guidance|bone resorption|cell junction assembly|cellular membrane organization|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular protein kinase cascade|leukocyte migration|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of integrin activation|Ras protein signal transduction|regulation of bone resorption|regulation of vascular permeability|response to interleukin-1|signal complex assembly|T cell costimulation	caveola|cytosol|mitochondrial inner membrane	ATP binding|heme binding|integrin binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|SH3/SH2 adaptor activity			large_intestine(10)|lung(1)|central_nervous_system(1)|endometrium(1)	13		Myeloproliferative disorder(115;0.00878)			Dasatinib(DB01254)	CCGCAAGCTGGACAGCGGCGG	0.642													42	9	---	---	---	---	PASS
TP53RK	112858	broad.mit.edu	37	20	45315610	45315610	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45315610T>C	uc002xsk.2	-	2	767	c.544A>G	c.(544-546)ATA>GTA	p.I182V	SLC13A3_uc002xsg.1_5'Flank|SLC13A3_uc010gho.1_5'Flank|TP53RK_uc002xsj.2_3'UTR	NM_033550	NP_291028	Q96S44	PRPK_HUMAN	p53-related protein kinase	182	Protein kinase.				lipopolysaccharide biosynthetic process	membrane|nucleus	ATP binding|p53 binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0		Myeloproliferative disorder(115;0.0122)				CCAAAGTCTATGAGCACAATG	0.502													9	171	---	---	---	---	PASS
ARFGAP1	55738	broad.mit.edu	37	20	61907896	61907896	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61907896G>T	uc002yem.2	+	4	347	c.235G>T	c.(235-237)GGG>TGG	p.G79W	ARFGAP1_uc011aas.1_Missense_Mutation_p.G26W|ARFGAP1_uc011aat.1_5'UTR|ARFGAP1_uc002yel.2_Missense_Mutation_p.G79W|ARFGAP1_uc002yen.2_Missense_Mutation_p.G79W	NM_018209	NP_060679	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating	79	Arf-GAP.				COPI coating of Golgi vesicle|protein transport|regulation of ARF GTPase activity|retrograde vesicle-mediated transport, Golgi to ER	cytosol|Golgi-associated vesicle membrane	ARF GTPase activator activity|zinc ion binding			pancreas(1)	1	all_cancers(38;1.59e-09)					GAAAGCTGGTGGGAATGCTAA	0.517													4	90	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	11014987	11014987	+	RNA	SNP	A	G	G			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11014987A>G	uc002yis.1	-	7		c.1459T>C						P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CTATAGTTTCAATAGCAGACT	0.388													5	38	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11098920	11098920	+	5'UTR	SNP	A	G	G	rs78230864		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11098920A>G	uc002yit.1	-	1					BAGE_uc002yix.2_RNA	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)		gggagataccagagaccctaa	0.000													3	7	---	---	---	---	PASS
MSL3	10943	broad.mit.edu	37	X	11786748	11786748	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11786748G>T	uc004cuw.2	+	10	1333	c.1228G>T	c.(1228-1230)GGG>TGG	p.G410W	MSL3_uc004cux.2_Missense_Mutation_p.G351W|MSL3_uc011mig.1_Missense_Mutation_p.G261W|MSL3_uc011mih.1_Missense_Mutation_p.G398W|MSL3_uc004cuy.2_Missense_Mutation_p.G244W	NM_078629	NP_523353	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3-like 1 isoform a	410					histone H4-K16 acetylation|multicellular organismal development|transcription from RNA polymerase II promoter	MSL complex	DNA binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						TAGCAAGGAAGGGAGTGCTGT	0.388													4	74	---	---	---	---	PASS
UTS2	10911	broad.mit.edu	37	1	7960477	7960480	+	Intron	DEL	GAAG	-	-	rs112148287		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7960477_7960480delGAAG	uc001aoq.2	-							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)		aagaaggaaagaaggaaggaagga	0.098													4	2	---	---	---	---	
SPEN	23013	broad.mit.edu	37	1	16265061	16265063	+	Intron	DEL	TTT	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16265061_16265063delTTT	uc001axk.1	+						SPEN_uc010obp.1_Intron	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator						interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GAAAAAAAGCTTTTTTTTTTTTT	0.365													5	3	---	---	---	---	
SPATA21	374955	broad.mit.edu	37	1	16729987	16729987	+	Intron	DEL	C	-	-	rs57948110		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16729987delC	uc001ayn.2	-						SPATA21_uc001ayl.1_Intron|SPATA21_uc010occ.1_Intron	NM_198546	NP_940948	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21								calcium ion binding			ovary(2)|breast(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		tcttttttttctttttttttt	0.010													5	3	---	---	---	---	
TMEM39B	55116	broad.mit.edu	37	1	32542594	32542594	+	Intron	DEL	T	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32542594delT	uc010ogv.1	+						TMEM39B_uc010ogt.1_Intron|TMEM39B_uc010ogu.1_Intron|TMEM39B_uc001bue.3_Intron|TMEM39B_uc001buf.3_Intron|TMEM39B_uc010ogw.1_Intron	NM_018056	NP_060526	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B							integral to membrane					0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TTACATCCCATCTTGGAGTTT	0.537													18	11	---	---	---	---	
CCDC18	343099	broad.mit.edu	37	1	93721741	93721766	+	Intron	DEL	ATACTCATTGTATGTTAAATTTTAAC	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93721741_93721766delATACTCATTGTATGTTAAATTTTAAC	uc001dpq.2	+						CCDC18_uc001dpr.1_Intron	NM_206886	NP_996769	Q5T9S5	CCD18_HUMAN	sarcoma antigen NY-SAR-41											ovary(2)|breast(2)|pancreas(1)	5		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		ACAGTGGGTGATACTCATTGTATGTTAAATTTTAACATACTCATTG	0.265													4	2	---	---	---	---	
ATP5F1	515	broad.mit.edu	37	1	111992603	111992603	+	Intron	DEL	T	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111992603delT	uc001ebc.2	+						WDR77_uc001ebb.2_5'Flank|WDR77_uc010owd.1_5'Flank|WDR77_uc010owe.1_5'Flank|ATP5F1_uc009wgf.1_Intron|ATP5F1_uc001ebd.3_Intron	NM_001688	NP_001679	P24539	AT5F1_HUMAN	ATP synthase, H+ transporting, mitochondrial F0						ATP catabolic process|respiratory electron transport chain	mitochondrial matrix|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)	hydrogen ion transporting ATP synthase activity, rotational mechanism|protein binding				0		all_cancers(81;8.16e-06)|all_epithelial(167;5.63e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		TTTCCGATAATTTTGGGACAC	0.428													22	12	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154728394	154728396	+	Intron	DEL	AGA	-	-	rs149878824	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154728394_154728396delAGA	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			gaagaagaagagaagaagaagag	0.000													5	3	---	---	---	---	
FER1L5	90342	broad.mit.edu	37	2	97362036	97362036	+	Intron	DEL	T	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97362036delT	uc010fia.2	+						FER1L5_uc002sws.3_Intron|FER1L5_uc010fib.1_Intron|FER1L5_uc002swt.3_Intron|FER1L5_uc010yus.1_Intron	NM_001113382	NP_001106853	A0AVI2	FR1L5_HUMAN	fer-1-like 5 isoform 2							integral to membrane				ovary(1)	1						cttttcaatcttttttttttt	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106219011	106219018	+	Intron	DEL	GAAGGAAG	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106219011_106219018delGAAGGAAG	uc002tdf.2	-											Homo sapiens hypothetical protein LOC285000, mRNA (cDNA clone IMAGE:3925223), partial cds.																		gagagagagagaaggaaggaaggaagga	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129098917	129098919	+	IGR	DEL	GTG	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129098917_129098919delGTG								HS6ST1 (22746 upstream) : None (None downstream)																							ggtattggtagtggtggtgatgg	0.103													4	3	---	---	---	---	
SLC4A10	57282	broad.mit.edu	37	2	162729068	162729068	+	Intron	DEL	A	-	-	rs5835886		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162729068delA	uc002ubx.3	+						SLC4A10_uc010fpa.1_Intron|SLC4A10_uc010zcr.1_Intron|SLC4A10_uc002uby.3_Intron|SLC4A10_uc010zcs.1_Intron	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate						bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5						TTGCCTATTCAAAAAAAAAAA	0.303													5	3	---	---	---	---	
CNTN6	27255	broad.mit.edu	37	3	1424468	1424468	+	Intron	DEL	T	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1424468delT	uc003boz.2	+						CNTN6_uc011asj.1_Intron|CNTN6_uc003bpa.2_Intron	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6 precursor						axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		ATTTTTCTAATTGGCATTCCA	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	5281022	5281023	+	IGR	INS	-	AC	AC	rs111598174		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5281022_5281023insAC								EDEM1 (19373 upstream) : None (None downstream)																							acacacaccatacacacacacc	0.000													6	5	---	---	---	---	
GALNTL2	117248	broad.mit.edu	37	3	15957585	15957586	+	Intron	DEL	GT	-	-	rs57111858		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15957585_15957586delGT	uc003caq.3	+							NM_054110	NP_473451	Q8N3T1	GLTL2_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1						AAGAAAgtgcgtgtgtgtgtgt	0.109													5	3	---	---	---	---	
GAP43	2596	broad.mit.edu	37	3	115401993	115401996	+	Intron	DEL	CGCA	-	-	rs139086285	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115401993_115401996delCGCA	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		cgcgcgcgcgcgcacacacacaca	0.206													2	4	---	---	---	---	
LSAMP	4045	broad.mit.edu	37	3	116163562	116163563	+	Intron	DEL	AC	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116163562_116163563delAC	uc003ebt.2	-						LSAMP_uc011bis.1_Intron|LSAMP_uc010hqq.1_RNA	NM_002338	NP_002329	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		TAAAACAGGGacacacacacac	0.317													3	4	---	---	---	---	
DIRC2	84925	broad.mit.edu	37	3	122564455	122564456	+	Intron	DEL	TT	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122564455_122564456delTT	uc003efw.3	+						DIRC2_uc010hrl.2_Intron|DIRC2_uc010hrm.2_Intron	NM_032839	NP_116228	Q96SL1	DIRC2_HUMAN	disrupted in renal carcinoma 2						transport	integral to membrane					0				GBM - Glioblastoma multiforme(114;0.0614)		ttccagcacgtttttttttttt	0.099													4	2	---	---	---	---	
SLC12A8	84561	broad.mit.edu	37	3	124935692	124935695	+	Intron	DEL	ACAC	-	-	rs67876548		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124935692_124935695delACAC	uc003ehw.3	-							NM_024628	NP_078904	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8						potassium ion transport	integral to membrane	symporter activity				0						aaagcagtgtacacacacacacac	0.000													4	2	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131256125	131256127	+	Intron	DEL	CTG	-	-	rs74985864		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131256125_131256127delCTG	uc003eok.2	-						CPNE4_uc011blq.1_Intron|CPNE4_uc003eol.2_Intron|CPNE4_uc003eom.2_Intron|CPNE4_uc003eoj.2_Intron	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						Tttttcttttctgtttttttttt	0.167													4	2	---	---	---	---	
NPHP3	27031	broad.mit.edu	37	3	132402202	132402202	+	Intron	DEL	A	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132402202delA	uc003epe.1	-						NPHP3_uc003eoz.1_Intron|NPHP3_uc003epd.1_Intron	NM_153240	NP_694972	Q7Z494	NPHP3_HUMAN	nephrocystin 3						maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1						TTTATACCATAAAATCATTCA	0.328													28	17	---	---	---	---	
GABRG1	2565	broad.mit.edu	37	4	46050388	46050391	+	Intron	DEL	GAAG	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46050388_46050391delGAAG	uc003gxb.2	-							NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)		ATGGAATAGAgaaggaaggaagga	0.225													4	3	---	---	---	---	
HMGCS1	3157	broad.mit.edu	37	5	43297941	43297941	+	Intron	DEL	A	-	-	rs75413713		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43297941delA	uc003jnr.3	-						HMGCS1_uc003jnp.3_5'Flank|HMGCS1_uc003jnq.3_Intron	NM_001098272	NP_001091742	Q01581	HMCS1_HUMAN	hydroxymethylglutaryl-CoA synthase 1						cholesterol biosynthetic process|isoprenoid biosynthetic process	cytosol|soluble fraction	hydroxymethylglutaryl-CoA synthase activity				0						actcggtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	77965309	77965312	+	IGR	DEL	GAGA	-	-	rs57667593		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77965309_77965312delGAGA								LHFPL2 (20661 upstream) : ARSB (107727 downstream)																							ggaagggggggagagagagagaga	0.010													4	2	---	---	---	---	
HSD17B4	3295	broad.mit.edu	37	5	118867262	118867265	+	Intron	DEL	GGGT	-	-	rs59962115		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118867262_118867265delGGGT	uc003ksj.2	+						HSD17B4_uc011cwg.1_Intron|HSD17B4_uc011cwh.1_Intron|HSD17B4_uc011cwi.1_Intron|HSD17B4_uc003ksk.3_Intron|HSD17B4_uc011cwj.1_Intron|HSD17B4_uc010jcn.1_Intron|HSD17B4_uc010jco.1_Intron	NM_000414	NP_000405	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity			ovary(1)|pancreas(1)	2		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)	NADH(DB00157)	GTCCAAAGGGGGgtgtgtgtgtgt	0.265													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	143161545	143161546	+	IGR	DEL	GT	-	-	rs111278908		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143161545_143161546delGT								NR3C1 (346468 upstream) : HMHB1 (30180 downstream)																							tgtgtttaaggtgtgtgtgtgt	0.124													4	2	---	---	---	---	
CANX	821	broad.mit.edu	37	5	179153578	179153578	+	Intron	DEL	A	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179153578delA	uc003mkk.2	+						CANX_uc011dgp.1_Intron|CANX_uc003mkl.2_Intron|CANX_uc011dgq.1_Intron	NM_001746	NP_001737	P27824	CALX_HUMAN	calnexin precursor						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein secretion	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane|melanosome	calcium ion binding|sugar binding|unfolded protein binding				0	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)	ctctgtctccaaaaaaaaaaa	0.119													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	42467818	42467818	+	IGR	DEL	A	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42467818delA								TRERF1 (47953 upstream) : UBR2 (64240 downstream)																							AGTTTATGTTAAAAAAAAAAA	0.343													5	4	---	---	---	---	
KIAA0240	23506	broad.mit.edu	37	6	42789978	42789978	+	Intron	DEL	T	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42789978delT	uc003osn.1	+						KIAA0240_uc003osm.1_Intron|KIAA0240_uc011duw.1_Intron|KIAA0240_uc003oso.1_Intron|KIAA0240_uc003osp.1_Intron	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506											ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)			TCAGTAAttcttttttttttt	0.124													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	88994155	88994156	+	IGR	DEL	TG	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88994155_88994156delTG								CNR1 (118388 upstream) : RNGTT (325833 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
MAN1A1	4121	broad.mit.edu	37	6	119515172	119515172	+	Intron	DEL	A	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119515172delA	uc003pym.1	-							NM_005907	NP_005898	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		TCACTGTTACATTTAAATTCC	0.313													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134013763	134013764	+	Intron	INS	-	AC	AC	rs144873970	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134013763_134013764insAC	uc003qeg.1	-											Homo sapiens cDNA FLJ36194 fis, clone TESTI2027615.																		taaaaaaGCAAacacacacaca	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	157691443	157691445	+	IGR	DEL	CCT	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157691443_157691445delCCT								ARID1B (161042 upstream) : C6orf35 (18610 downstream)																							caccaccatccctaccaccacca	0.005													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	2515855	2515855	+	IGR	DEL	G	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2515855delG								CHST12 (41641 upstream) : LFNG (43624 downstream)																							GGCCAGCTCTGGGGGGACCTT	0.617													4	2	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23827361	23827362	+	Intron	DEL	AC	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23827361_23827362delAC	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_Intron|STK31_uc003swv.1_5'Flank	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						gtATGATTGTacacacacacac	0.094													3	3	---	---	---	---	
AGFG2	3268	broad.mit.edu	37	7	100146360	100146360	+	Intron	DEL	T	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100146360delT	uc003uvf.2	+						AGFG2_uc003uvg.1_Intron|AGFG2_uc010lgy.2_5'Flank	NM_006076	NP_006067	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			central_nervous_system(1)	1						TCTTTCACCCTTTCTCCCTCC	0.453													26	24	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114529061	114529062	+	IGR	INS	-	T	T			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114529061_114529062insT								FOXP2 (197969 upstream) : MDFIC (33147 downstream)																							tccttccttccttccttccttc	0.000													6	3	---	---	---	---	
TSGA14	95681	broad.mit.edu	37	7	130039660	130039661	+	Intron	INS	-	A	A	rs55710117		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130039660_130039661insA	uc003vpz.2	-						TSGA14_uc003vpy.2_Intron|TSGA14_uc010lmf.2_Intron|TSGA14_uc003vqa.2_Intron|TSGA14_uc011kpg.1_Intron	NM_018718	NP_061188	Q9BYV8	CEP41_HUMAN	testis specific, 14						G2/M transition of mitotic cell cycle	centrosome|cytosol					0	Melanoma(18;0.0435)					gactctgtctcaaaaaaaaaaa	0.223													3	3	---	---	---	---	
PODXL	5420	broad.mit.edu	37	7	131241030	131241035	+	In_Frame_Del	DEL	GGCGAC	-	-	rs11277659		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131241030_131241035delGGCGAC	uc003vqw.3	-	1	342_347	c.84_89delGTCGCC	c.(82-90)CCGTCGCCC>CCC	p.28_30PSP>P	PODXL_uc003vqx.3_In_Frame_Del_p.28_30PSP>P	NM_001018111	NP_001018121	O00592	PODXL_HUMAN	podocalyxin-like isoform 1 precursor	28_30	Extracellular (Potential).				cell adhesion|epithelial tube formation|negative regulation of cell-cell adhesion|positive regulation of cell migration|positive regulation of cell-cell adhesion mediated by integrin|regulation of microvillus assembly	actin cytoskeleton|apical plasma membrane|centrosome|filopodium|integral to plasma membrane|lamellipodium|membrane raft|microvillus membrane|nucleolus|ruffle				breast(2)|pancreas(1)	3	Melanoma(18;0.162)					ATTCTGGGAGggcgacggcgacggcg	0.573													5	4	---	---	---	---	
FGL1	2267	broad.mit.edu	37	8	17726303	17726303	+	Intron	DEL	A	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17726303delA	uc003wxx.2	-						FGL1_uc003wxy.2_Intron|FGL1_uc003wxz.2_Intron|FGL1_uc003wya.2_Intron|FGL1_uc003wyb.2_Intron|FGL1_uc003wyc.2_Intron|FGL1_uc003wyd.2_Intron|FGL1_uc003wye.2_Intron|FGL1_uc003wyf.2_Intron	NM_201553	NP_963847	Q08830	FGL1_HUMAN	fibrinogen-like 1 precursor						signal transduction	fibrinogen complex	receptor binding				0				Colorectal(111;0.0573)|COAD - Colon adenocarcinoma(73;0.215)		TTTTAAAATTAAGTTTATTTC	0.318													10	14	---	---	---	---	
PTK2B	2185	broad.mit.edu	37	8	27183744	27183745	+	Intron	DEL	TG	-	-	rs113539724		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27183744_27183745delTG	uc003xfn.1	+						PTK2B_uc003xfo.1_Intron|PTK2B_uc003xfp.1_Intron|PTK2B_uc003xfq.1_Intron	NM_173174	NP_775266	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a						apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			lung(3)|ovary(1)|skin(1)	5		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)		CTCgtgtgtatgtgtgtgtgtg	0.436													3	3	---	---	---	---	
EPHX2	2053	broad.mit.edu	37	8	27382625	27382626	+	Intron	DEL	GC	-	-	rs3076741		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27382625_27382626delGC	uc003xfu.2	+						EPHX2_uc010lut.1_Intron|EPHX2_uc010luu.2_Intron|EPHX2_uc010luv.2_Intron|EPHX2_uc003xfv.2_Intron|EPHX2_uc010luw.2_Intron	NM_001979	NP_001970	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic						aromatic compound catabolic process|cellular calcium ion homeostasis|drug metabolic process|inflammatory response|positive regulation of vasodilation|reactive oxygen species metabolic process|regulation of blood pressure|response to toxin|xenobiotic metabolic process	cytosol|focal adhesion|Golgi apparatus|nucleolus|peroxisome|soluble fraction	epoxide hydrolase activity|metal ion binding|protein homodimerization activity			ovary(1)	1		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)	Tamoxifen(DB00675)	gtgtgtgtgtgCGCGCGCGCGC	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	4781394	4781395	+	IGR	INS	-	T	T	rs55660551		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4781394_4781395insT								AK3 (39351 upstream) : RCL1 (11439 downstream)																							tcatcttcctcttttttttttt	0.238													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68398095	68398095	+	IGR	DEL	C	-	-	rs74487823		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68398095delC								FAM27B (603906 upstream) : MIR1299 (604144 downstream)																							CCATGCTTAGCTTGGGTTTCT	0.353													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68482651	68482652	+	IGR	DEL	AA	-	-	rs112257348		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68482651_68482652delAA								FAM27B (688462 upstream) : MIR1299 (519587 downstream)																							tttcaaaaataaaaaaaaaaga	0.000													5	4	---	---	---	---	
C9orf102	375748	broad.mit.edu	37	9	98678837	98678838	+	Intron	INS	-	A	A	rs144815828	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98678837_98678838insA	uc004avt.3	+						C9orf102_uc010mrx.1_Intron|C9orf102_uc011lum.1_Intron|C9orf102_uc010mry.1_Intron|C9orf102_uc010mrz.2_Intron	NM_001010895	NP_001010895	Q5T890	RAD26_HUMAN	RAD26L hypothetical protein						DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding				0		Acute lymphoblastic leukemia(62;0.0559)				ATTCTGTATGGAAAAAATTGTT	0.297													3	8	---	---	---	---	
PALM2-AKAP2	445815	broad.mit.edu	37	9	112894313	112894314	+	Intron	DEL	GT	-	-	rs112145897		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112894313_112894314delGT	uc004bei.2	+						PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron|AKAP2_uc011lwi.1_Intron|AKAP2_uc004bem.2_Intron|PALM2-AKAP2_uc010mtw.1_Intron|AKAP2_uc011lwj.1_Intron	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6						AGTAACTAGCgtgtgtgtgtgt	0.193													5	3	---	---	---	---	
C5	727	broad.mit.edu	37	9	123722359	123722360	+	Intron	INS	-	A	A	rs140399863	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123722359_123722360insA	uc004bkv.2	-							NM_001735	NP_001726	P01031	CO5_HUMAN	complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)	TGCTGAGGAATAAAAACTTTGC	0.322													5	3	---	---	---	---	
SARDH	1757	broad.mit.edu	37	9	136550476	136550477	+	Intron	INS	-	G	G	rs9409845	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136550476_136550477insG	uc004cep.3	-						SARDH_uc004ceo.2_Intron|SARDH_uc011mdn.1_Intron|SARDH_uc011mdo.1_Intron|SARDH_uc004cen.2_Intron	NM_001134707	NP_001128179	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase precursor						glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|sarcosine dehydrogenase activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		GGAAAGGCCCCGGGGACCTGCC	0.525													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29346514	29346523	+	IGR	DEL	ACACACACAT	-	-	rs74261619	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29346514_29346523delACACACACAT								BAMBI (374646 upstream) : LYZL1 (231467 downstream)																							acacacacacacacacacaTATATATATAT	0.324													2	4	---	---	---	---	
SLC25A16	8034	broad.mit.edu	37	10	70266207	70266207	+	Intron	DEL	A	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70266207delA	uc001joi.2	-						SLC25A16_uc010qix.1_Intron|SLC25A16_uc010qiy.1_Intron|SLC25A16_uc001joj.2_Intron	NM_152707	NP_689920	P16260	GDC_HUMAN	solute carrier family 25, member 16						coenzyme biosynthetic process|pantothenate metabolic process	integral to membrane|mitochondrial inner membrane	binding|solute:solute antiporter activity				0						ctcaaaaattaaaaaaaaaaa	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	70968942	70968943	+	IGR	INS	-	TTTT	TTTT	rs147863098	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70968942_70968943insTTTT								SUPV3L1 (93 upstream) : HKDC1 (11116 downstream)																							ttgtgtgtgtgtttgtttgtTT	0.267													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81788176	81788176	+	IGR	DEL	A	-	-	rs35380147		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81788176delA								MBL1P (77393 upstream) : LOC219347 (17815 downstream)																							AGCTGTGCATATCTGGACTCC	0.443													3	3	---	---	---	---	
TCF7L2	6934	broad.mit.edu	37	10	114710870	114710870	+	Intron	DEL	C	-	-	rs72101402		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114710870delC	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_5'Flank|TCF7L2_uc010qrs.1_5'Flank|TCF7L2_uc010qrt.1_5'Flank	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		TTTTTTTCTACCCCCCCCTCG	0.502													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134206019	134206020	+	IGR	INS	-	G	G	rs142843997		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134206019_134206020insG								LRRC27 (11009 upstream) : PWWP2B (4682 downstream)																							atgatggtgatgtgataatggt	0.000													8	7	---	---	---	---	
SAA3P	6290	broad.mit.edu	37	11	18136968	18136969	+	Intron	DEL	TA	-	-	rs111233296		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18136968_18136969delTA	uc001mnt.2	-							NR_026576				Homo sapiens truncated serum amyloid A3 precursor (SAA3) mRNA, complete cds.												0						gtgtgtgtgttagtgtgtgtgt	0.000											OREG0020820	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	20681856	20681859	+	IGR	DEL	TGTG	-	-	rs113800770		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20681856_20681859delTGTG								SLC6A5 (5248 upstream) : NELL1 (9258 downstream)																							CTTTGATCATtgtgtgtgtgtgtg	0.230													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42010455	42010462	+	IGR	DEL	AAAAGAAA	-	-	rs72331687		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42010455_42010462delAAAAGAAA								LRRC4C (529132 upstream) : None (None downstream)																							agaaagaaagaaaagaaagaaagaaaga	0.130													4	2	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	5693297	5693298	+	Intron	INS	-	C	C	rs148573998	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5693297_5693298insC	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						TTTAATGAACACCCCCCCCCCG	0.460													4	2	---	---	---	---	
BAZ2A	11176	broad.mit.edu	37	12	56999208	56999208	+	Intron	DEL	T	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56999208delT	uc001slq.1	-						BAZ2A_uc001slp.1_Intron|BAZ2A_uc009zov.1_5'Flank|BAZ2A_uc009zow.1_Intron	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A						chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0						TTTTATGTAAttttttttttt	0.174													3	3	---	---	---	---	
NAP1L1	4673	broad.mit.edu	37	12	76462515	76462516	+	Intron	INS	-	ACAC	ACAC	rs35120003		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76462515_76462516insACAC	uc001sxw.2	-						NAP1L1_uc001sxv.2_Intron|NAP1L1_uc001sxz.2_Intron|NAP1L1_uc001sxx.2_Intron|NAP1L1_uc001sxy.2_Intron|NAP1L1_uc010sty.1_Intron|NAP1L1_uc010stz.1_Intron|NAP1L1_uc010sua.1_Intron|NAP1L1_uc001syb.2_Intron|NAP1L1_uc001sya.2_Intron|NAP1L1_uc001syc.2_Intron	NM_139207	NP_631946	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1						DNA replication|nucleosome assembly|positive regulation of cell proliferation	chromatin assembly complex|melanosome	protein binding			ovary(1)|skin(1)	2		Colorectal(145;0.09)				ACCCGCCCCTTacacacacaca	0.342													7	4	---	---	---	---	
C12orf29	91298	broad.mit.edu	37	12	88441882	88441883	+	Intron	INS	-	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88441882_88441883insA	uc001tao.2	+						C12orf29_uc001tap.2_Intron|C12orf29_uc009zsk.2_Intron	NM_001009894	NP_001009894	Q8N999	CL029_HUMAN	hypothetical protein LOC91298												0						agaccagctataaaaaaaaaaa	0.040													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97465866	97465869	+	IGR	DEL	CACA	-	-	rs57987918		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97465866_97465869delCACA								NEDD1 (118405 upstream) : RMST (392930 downstream)																							AGCATGTGTGcacacacacacaca	0.225													4	2	---	---	---	---	
GCN1L1	10985	broad.mit.edu	37	12	120588740	120588741	+	Intron	INS	-	A	A			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120588740_120588741insA	uc001txo.2	-							NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis						regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					gactccgtctcaaaaaaaaaaa	0.208													4	2	---	---	---	---	
POLE	5426	broad.mit.edu	37	12	133240810	133240810	+	Intron	DEL	C	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133240810delC	uc001uks.1	-						POLE_uc010tbq.1_Intron|POLE_uc009zyu.1_Intron	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon						base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)		AGccttccctccttccttcct	0.274								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					32	25	---	---	---	---	
C13orf28	122258	broad.mit.edu	37	13	113053532	113053540	+	Intron	DEL	TGGGAGAGG	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113053532_113053540delTGGGAGAGG	uc001vsd.1	+							NM_145248	NP_660291	Q96KW9	SPAC7_HUMAN	hypothetical protein LOC122258 precursor							extracellular region					0	all_lung(23;0.000633)|Lung NSC(43;0.0161)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0997)|Medulloblastoma(90;0.163)					CCAGCTGTAATGGGAGAGGTAGGAGGCAG	0.469													20	12	---	---	---	---	
ACOT2	10965	broad.mit.edu	37	14	74036674	74036675	+	Intron	INS	-	C	C	rs139052625	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74036674_74036675insC	uc001xon.3	+						ACOT1_uc010tuc.1_Intron|ACOT2_uc001xom.2_Intron	NM_006821	NP_006812	P49753	ACOT2_HUMAN	acyl-CoA thioesterase 2						acyl-CoA metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process	mitochondrion	carboxylesterase activity|palmitoyl-CoA hydrolase activity|protein binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0033)|OV - Ovarian serous cystadenocarcinoma(108;0.0639)		TTATGTGTATgcccccccgccg	0.272													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	75771990	75771990	+	IGR	DEL	A	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75771990delA								FOS (23055 upstream) : JDP2 (122519 downstream)																							tattttttttagagagtcttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20148686	20148725	+	IGR	DEL	ATTTTGTCCGCCGCCGCCGCGGCTTTCTACCCGCCGCGGC	-	-	rs71114078		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20148686_20148725delATTTTGTCCGCCGCCGCCGCGGCTTTCTACCCGCCGCGGC								None (None upstream) : GOLGA6L6 (588369 downstream)																							CATCTCCACTATTTTGTCCGCCGCCGCCGCGGCTTTCTACCCGCCGCGGCATTTTGCCCC	0.592													8	4	---	---	---	---	
ARHGAP11A	9824	broad.mit.edu	37	15	32928531	32928531	+	Frame_Shift_Del	DEL	G	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32928531delG	uc001zgy.1	+	12	2279	c.1557delG	c.(1555-1557)ATGfs	p.M519fs	ARHGAP11A_uc010ubw.1_Frame_Shift_Del_p.M330fs|ARHGAP11A_uc010ubx.1_Frame_Shift_Del_p.M330fs	NM_014783	NP_055598	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A isoform 1	519					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			skin(3)|breast(2)|urinary_tract(1)	6		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		ATTACCGGATGTCTTGGACAG	0.383													72	58	---	---	---	---	
UBR1	197131	broad.mit.edu	37	15	43237806	43237806	+	Intron	DEL	T	-	-	rs11352938		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43237806delT	uc001zqq.2	-							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)		AAAAGGGATATTTTCCCTTCA	0.393													5	3	---	---	---	---	
AP4E1	23431	broad.mit.edu	37	15	51257153	51257154	+	Intron	DEL	CA	-	-	rs55825810		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51257153_51257154delCA	uc001zyx.1	+							NM_007347	NP_031373	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1						intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		ctccccctaccacacacacaca	0.000													6	3	---	---	---	---	
TRIP4	9325	broad.mit.edu	37	15	64737449	64737449	+	Intron	DEL	T	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64737449delT	uc002anm.2	+							NM_016213	NP_057297	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ligand-dependent nuclear receptor binding|transcription coactivator activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3						agccTGTAAGTCATAATCTTT	0.104													11	8	---	---	---	---	
TEKT5	146279	broad.mit.edu	37	16	10746623	10746630	+	Intron	DEL	ACACACAC	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10746623_10746630delACACACAC	uc002czz.1	-							NM_144674	NP_653275	Q96M29	TEKT5_HUMAN	tektin 5						microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2						acacaggcaaacacacacacacacacac	0.163													4	2	---	---	---	---	
IL21R	50615	broad.mit.edu	37	16	27460779	27460780	+	3'UTR	INS	-	TG	TG	rs147165457	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27460779_27460780insTG	uc002doq.1	+	9					IL21R_uc002dor.1_3'UTR|IL21R_uc002dos.1_3'UTR|uc002dot.2_RNA	NM_181078	NP_851564	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor precursor						natural killer cell activation	integral to membrane	interleukin-21 receptor activity			ovary(2)|lung(1)|breast(1)	4						gtgcatatgcatgtgtgtgtgt	0.381			T	BCL6	NHL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29249936	29249937	+	Intron	INS	-	CA	CA			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29249936_29249937insCA	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		catagtaaatgcacacacacac	0.035													4	2	---	---	---	---	
STX1B	112755	broad.mit.edu	37	16	31004014	31004015	+	3'UTR	INS	-	GGGGTGGAGGA	GGGGTGGAGGA	rs143292802	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31004014_31004015insGGGGTGGAGGA	uc010cad.2	-	10						NM_052874	NP_443106	P61266	STX1B_HUMAN	syntaxin 1B						intracellular protein transport|neurotransmitter transport|synaptic transmission	integral to plasma membrane	extracellular-glutamate-gated ion channel activity|SNAP receptor activity				0						GGTCTGCCGTGGGGGTGGGGCT	0.653													4	4	---	---	---	---	
AKAP10	11216	broad.mit.edu	37	17	19871514	19871515	+	Intron	INS	-	A	A	rs34802640		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19871514_19871515insA	uc002gwo.2	-						AKAP10_uc002gwp.1_Intron|AKAP10_uc010cqw.1_Intron|AKAP10_uc010vze.1_Intron	NM_007202	NP_009133	O43572	AKA10_HUMAN	A-kinase anchor protein 10 precursor						blood coagulation|protein localization	cytosol|mitochondrion|plasma membrane	signal transducer activity			skin(1)	1	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					actccgtctccaaaaaaaaaaa	0.099													5	3	---	---	---	---	
ITGA3	3675	broad.mit.edu	37	17	48157869	48157870	+	Intron	INS	-	GA	GA	rs2018134	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48157869_48157870insGA	uc010dbl.2	+						ITGA3_uc010dbm.2_Intron	NM_002204	NP_002195	P26006	ITA3_HUMAN	integrin alpha 3 isoform a precursor						blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|leukocyte migration	cell surface|integrin complex	protein binding|receptor activity			ovary(2)|pancreas(1)	3						tgtgtgtgtgtgatttgcgtgt	0.282													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	56419372	56419375	+	Intron	DEL	AAGG	-	-	rs112446080		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56419372_56419375delAAGG	uc010dct.1	+						uc010dcu.1_Intron|uc002ivz.2_Intron|uc010dcv.1_Intron|uc002iwa.2_Intron|uc002iwb.2_Intron|uc002iwc.2_Intron					Homo sapiens cDNA FLJ20264 fis, clone COLF7912.																		aagaaagaaaaaggaaggaaggaa	0.005													4	3	---	---	---	---	
SLC39A11	201266	broad.mit.edu	37	17	70769817	70769818	+	Intron	DEL	CC	-	-	rs58841287		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70769817_70769818delCC	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron	NM_001159770	NP_001153242	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1						cacacacacacCCAGTATATAA	0.228													3	3	---	---	---	---	
C17orf56	146705	broad.mit.edu	37	17	79204128	79204134	+	Intron	DEL	TGAGTGC	-	-	rs150422103		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79204128_79204134delTGAGTGC	uc002jzu.1	-						C17orf56_uc002jzr.1_Intron|C17orf56_uc002jzs.1_Intron|C17orf56_uc002jzt.1_Intron|C17orf56_uc002jzv.1_Intron|uc002jzw.1_RNA	NM_144679	NP_653280	Q96N21	CQ056_HUMAN	hypothetical protein LOC146705							integral to membrane					0	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			cagtgtaCTGTGAGTGCTGCAGAGTTT	0.338											OREG0024811	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
EFNA2	1943	broad.mit.edu	37	19	1298419	1298420	+	Intron	DEL	TA	-	-	rs34685801		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1298419_1298420delTA	uc002lry.1	+							NM_001405	NP_001396	O43921	EFNA2_HUMAN	ephrin-A2 precursor						cell-cell signaling	anchored to membrane|plasma membrane	ephrin receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GATGTACGATTAGGAGTTTTAA	0.569													6	6	---	---	---	---	
SH2D3A	10045	broad.mit.edu	37	19	6760567	6760567	+	Intron	DEL	A	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6760567delA	uc002mft.2	-						SH2D3A_uc010xjg.1_Intron	NM_005490	NP_005481	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A						JNK cascade|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			breast(2)	2						agactcagtcaaaaaaaaaaa	0.234													8	4	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7153471	7153481	+	Intron	DEL	CACACACCACA	-	-	rs72347224		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7153471_7153481delCACACACCACA	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	acacccacgccacacaccacacacacaccac	0.171													4	2	---	---	---	---	
CLEC17A	388512	broad.mit.edu	37	19	14702710	14702711	+	Intron	INS	-	TGTG	TGTG			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14702710_14702711insTGTG	uc010dzn.1	+						CLEC17A_uc002mzh.1_Intron|CLEC17A_uc010xnt.1_Intron|CLEC17A_uc010xnu.1_Intron|CLEC17A_uc010dzo.1_Intron			Q6ZS10	CL17A_HUMAN	SubName: Full=CLEC17A protein;							cell surface|integral to membrane	fucose binding|mannose binding|metal ion binding|receptor activity				0						CCGGAGAAAAAtgtgtgtgtgt	0.228													5	3	---	---	---	---	
EMR2	30817	broad.mit.edu	37	19	14866107	14866108	+	Intron	DEL	AT	-	-	rs141637468	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14866107_14866108delAT	uc002mzp.1	-						EMR2_uc010dzs.1_Intron|EMR2_uc010xnw.1_Intron|EMR2_uc002mzo.1_Intron|EMR2_uc002mzq.1_Intron|EMR2_uc002mzr.1_Intron|EMR2_uc002mzs.1_Intron|EMR2_uc002mzt.1_Intron|EMR2_uc002mzu.1_Intron|EMR2_uc010xnx.1_Intron|EMR2_uc010xny.1_Intron	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone						cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			lung(2)|ovary(1)|skin(1)	4						aaaaaaaaaaatacaaaaatta	0.000													4	2	---	---	---	---	
FOSB	2354	broad.mit.edu	37	19	45976377	45976385	+	3'UTR	DEL	TGGCCTCCC	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45976377_45976385delTGGCCTCCC	uc002pbx.3	+	4					ERCC1_uc002pbu.1_Intron|FOSB_uc010eke.2_3'UTR|FOSB_uc002pby.3_3'UTR|FOSB_uc010eka.1_3'UTR|FOSB_uc010ekb.1_3'UTR|FOSB_uc010ekc.1_3'UTR|FOSB_uc010ekf.2_3'UTR|FOSB_uc010ekd.1_3'UTR|FOSB_uc010ekg.2_3'UTR|FOSB_uc002pca.3_3'UTR	NM_006732	NP_006723	P53539	FOSB_HUMAN	FBJ murine osteosarcoma viral oncogene homolog B						behavior|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(2)|lung(1)	3		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00814)|Epithelial(262;0.18)|GBM - Glioblastoma multiforme(486;0.242)		AGTGGGTGTGTGGCCTCCCTGGCTCCTCC	0.450													7	5	---	---	---	---	
FLT3LG	2323	broad.mit.edu	37	19	49982452	49982452	+	Intron	DEL	T	-	-	rs33951493		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49982452delT	uc010yau.1	+						FLT3LG_uc002pnv.2_Intron|FLT3LG_uc002pnw.2_Intron|FLT3LG_uc002pnu.2_Intron|FLT3LG_uc002pnx.2_Intron|FLT3LG_uc010yav.1_Intron	NM_001459	NP_001450	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand precursor						positive regulation of cell proliferation|signal transduction	extracellular space|integral to membrane|plasma membrane|soluble fraction	cytokine activity				0		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		AGTTTACCAAttttttttttt	0.249													4	3	---	---	---	---	
NLRP2	55655	broad.mit.edu	37	19	55511961	55511961	+	Intron	DEL	A	-	-	rs34129339		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55511961delA	uc002qij.2	+						NLRP2_uc010yfp.1_Intron|NLRP2_uc010esn.2_Intron|NLRP2_uc010eso.2_Intron|NLRP2_uc010esp.2_Intron	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2						apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		actgtcttttaaaaaaaaaaa	0.194													7	5	---	---	---	---	
TNNT1	7138	broad.mit.edu	37	19	55648876	55648877	+	Intron	INS	-	C	C			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55648876_55648877insC	uc002qjb.3	-						TNNT1_uc002qiz.3_Intron|TNNT1_uc002qja.3_Intron|TNNT1_uc002qjc.3_Intron|TNNT1_uc002qje.3_Intron|TNNT1_uc002qjd.3_Intron	NM_003283	NP_003274	P13805	TNNT1_HUMAN	troponin T1, skeletal, slow isoform a						muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		aggagtccagaccccagcccct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	7750863	7750864	+	IGR	DEL	CA	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7750863_7750864delCA								BMP2 (989953 upstream) : HAO1 (112767 downstream)																							TGCAGGATCGcacacacacaca	0.233													4	2	---	---	---	---	
TPX2	22974	broad.mit.edu	37	20	30348186	30348186	+	Intron	DEL	T	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30348186delT	uc002wwp.1	+						TPX2_uc010gdv.1_Intron	NM_012112	NP_036244	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated protein homolog						activation of protein kinase activity|apoptosis|cell division|cell proliferation|mitosis|regulation of mitotic spindle organization	cytoplasm|microtubule|nucleus|spindle pole	ATP binding|GTP binding|protein kinase binding			large_intestine(1)|ovary(1)	2			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			TAACATAGAAttttttttttt	0.139													4	3	---	---	---	---	
WISP2	8839	broad.mit.edu	37	20	43343904	43343905	+	Intron	DEL	GC	-	-	rs1980802	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43343904_43343905delGC	uc002xmn.2	+						uc002xml.1_Intron|uc002xmm.1_Intron|WISP2_uc002xmo.1_5'UTR|WISP2_uc002xmp.2_5'UTR|WISP2_uc002xmq.2_5'UTR	NM_003881	NP_003872	O76076	WISP2_HUMAN	WNT1 inducible signaling pathway protein 2						cell adhesion|cell-cell signaling|signal transduction	extracellular region|soluble fraction	insulin-like growth factor binding			skin(1)	1		Myeloproliferative disorder(115;0.0122)				gtgtgtgtgagcgcgcgcgcgc	0.297													5	3	---	---	---	---	
SLC13A3	64849	broad.mit.edu	37	20	45228901	45228901	+	Intron	DEL	A	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45228901delA	uc002xsf.1	-						SLC13A3_uc010ghn.1_Intron|SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron	NM_022829	NP_073740	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	ggaaggaaggaaaggaaagga	0.020													1	6	---	---	---	---	
PRPF6	24148	broad.mit.edu	37	20	62626969	62626969	+	Intron	DEL	T	-	-	rs113295997		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62626969delT	uc002yho.2	+						PRPF6_uc002yhp.2_Intron	NM_012469	NP_036601	O94906	PRP6_HUMAN	PRP6 pre-mRNA processing factor 6 homolog						assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)					ctccttctccttttttttttt	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	21646916	21646917	+	IGR	INS	-	AGGAAGGT	AGGAAGGT	rs142229684	by1000genomes	TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21646916_21646917insAGGAAGGT								None (None upstream) : C21orf131 (467997 downstream)																							ggaaggaaggaaggaaggaagg	0.005													4	2	---	---	---	---	
PCNT	5116	broad.mit.edu	37	21	47768704	47768704	+	Intron	DEL	T	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47768704delT	uc002zji.3	+						PCNT_uc002zjj.2_Intron|PCNT_uc010gqk.1_Intron	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					aatttttgtattttttttttt	0.000													4	2	---	---	---	---	
FAAH2	158584	broad.mit.edu	37	X	57458220	57458220	+	Intron	DEL	G	-	-	rs6521622		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57458220delG	uc004dvc.2	+							NM_174912	NP_777572	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2							integral to membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|hydrolase activity			ovary(3)	3						ttgtttttttgttttttttgg	0.060										HNSCC(52;0.14)			4	3	---	---	---	---	
MCF2	4168	broad.mit.edu	37	X	138687316	138687316	+	Intron	DEL	T	-	-	rs35352084		TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138687316delT	uc004fau.2	-						MCF2_uc004fav.2_Intron|MCF2_uc011mwl.1_Intron|MCF2_uc010nsh.1_Intron|MCF2_uc011mwm.1_Intron|MCF2_uc011mwn.1_Intron|MCF2_uc004faw.2_Intron|MCF2_uc011mwo.1_Intron	NM_005369	NP_005360	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|membrane|membrane fraction	protein binding|Rho guanyl-nucleotide exchange factor activity			lung(1)|pleura(1)	2	Acute lymphoblastic leukemia(192;0.000127)					TATCCATGACTTTTTTTTTTT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58978027	58978027	+	IGR	DEL	T	-	-			TCGA-A3-3363-01A-01D-0966-08	TCGA-A3-3363-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58978027delT								None (None upstream) : None (None downstream)																							ttccattgcattccattccat	0.020													20	12	---	---	---	---	
