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
NBPF1	55672	broad.mit.edu	37	1	16918727	16918727	+	5'UTR	SNP	G	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918727G>C	uc009vos.1	-	6					NBPF1_uc010oce.1_5'UTR	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CGAGGTGCCTGAACTCAGAGC	0.463													3	15	---	---	---	---	PASS
SLC30A2	7780	broad.mit.edu	37	1	26370857	26370857	+	Intron	SNP	C	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26370857C>G	uc001blh.1	-						SLC30A2_uc001blg.1_Missense_Mutation_p.S117T	NM_032513	NP_115902	Q9BRI3	ZNT2_HUMAN	solute carrier family 30, member 2 isoform 2						positive regulation of sequestering of zinc ion|zinc ion transport	integral to membrane|late endosome|lysosomal membrane	cation transmembrane transporter activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.09e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00614)|READ - Rectum adenocarcinoma(331;0.0649)		GGAGAAGAGGCTGATGAGCAT	0.587													9	20	---	---	---	---	PASS
DENND2D	79961	broad.mit.edu	37	1	111731357	111731357	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111731357C>G	uc001eak.1	-	10	1266	c.1066G>C	c.(1066-1068)GAC>CAC	p.D356H	DENND2D_uc001eal.1_Missense_Mutation_p.D353H	NM_024901	NP_079177	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	356										ovary(1)	1		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		CCAAGAGAGTCTAAGATGTCA	0.478													12	365	---	---	---	---	PASS
CACNA1S	779	broad.mit.edu	37	1	201030579	201030579	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201030579A>T	uc001gvv.2	-	25	3298	c.3071T>A	c.(3070-3072)ATA>AAA	p.I1024K		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	1024	III.|Extracellular (Potential).|Dihydropyridine binding (By similarity).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	ATTGGAGTCTATGGCCTTGTA	0.542													20	47	---	---	---	---	PASS
NAV1	89796	broad.mit.edu	37	1	201687817	201687817	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201687817C>A	uc001gwu.2	+	3	1507	c.1160C>A	c.(1159-1161)TCC>TAC	p.S387Y		NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1	387					cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4						GACCTCAAGTCCGGCTACATG	0.607													45	138	---	---	---	---	PASS
LAMB3	3914	broad.mit.edu	37	1	209799337	209799337	+	Silent	SNP	C	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209799337C>T	uc001hhg.2	-	13	2022	c.1632G>A	c.(1630-1632)CCG>CCA	p.P544P	LAMB3_uc009xco.2_Silent_p.P544P|LAMB3_uc001hhh.2_Silent_p.P544P|LAMB3_uc010psl.1_Intron|hsa-mir-4260|MI0015859_5'Flank	NM_001017402	NP_001017402	Q13751	LAMB3_HUMAN	laminin, beta 3 precursor	544	Laminin EGF-like 6.				cell adhesion|epidermis development|hemidesmosome assembly		structural molecule activity			central_nervous_system(2)|skin(2)|large_intestine(1)|ovary(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		TGTCGCAGCCCGGGCCCTCTG	0.627													13	31	---	---	---	---	PASS
GPATCH2	55105	broad.mit.edu	37	1	217604349	217604349	+	3'UTR	SNP	A	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217604349A>G	uc001hlf.1	-	10						NM_018040	NP_060510	Q9NW75	GPTC2_HUMAN	G patch domain containing 2							intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		CTATGGCAGGACTGTATGCAG	0.353													5	2	---	---	---	---	PASS
CDC42BPA	8476	broad.mit.edu	37	1	227216801	227216801	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227216801A>G	uc001hqr.2	-	29	4827	c.3884T>C	c.(3883-3885)CTG>CCG	p.L1295P	CDC42BPA_uc001hqq.2_Missense_Mutation_p.L594P|CDC42BPA_uc001hqs.2_Missense_Mutation_p.L1214P|CDC42BPA_uc009xes.2_Missense_Mutation_p.L1267P|CDC42BPA_uc010pvs.1_Missense_Mutation_p.L1275P|CDC42BPA_uc001hqp.2_Missense_Mutation_p.L451P|CDC42BPA_uc001hqt.2_Missense_Mutation_p.L173P|CDC42BPA_uc001hqu.1_Missense_Mutation_p.L502P	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	1308	CNH.				actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				AGTTTCTGACAGCTTGTAAAA	0.468													18	51	---	---	---	---	PASS
AKT3	10000	broad.mit.edu	37	1	243859016	243859016	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243859016C>T	uc001iab.1	-	2	130	c.49G>A	c.(49-51)GAA>AAA	p.E17K	AKT3_uc001hzz.1_Missense_Mutation_p.E17K	NM_005465	NP_005456	Q9Y243	AKT3_HUMAN	AKT3 kinase isoform 1	17	PH.				signal transduction	Golgi apparatus|nucleus|plasma membrane	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|lung(1)|breast(1)|central_nervous_system(1)	4	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			TTTATATATTCTCCTACATGA	0.348													11	47	---	---	---	---	PASS
TPO	7173	broad.mit.edu	37	2	1499872	1499872	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1499872G>A	uc002qww.2	+	12	2209	c.2118G>A	c.(2116-2118)ATG>ATA	p.M706I	TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Missense_Mutation_p.M649I|TPO_uc002qwr.2_Missense_Mutation_p.M706I|TPO_uc002qwx.2_Missense_Mutation_p.M649I|TPO_uc010yio.1_Missense_Mutation_p.M533I|TPO_uc010yip.1_Missense_Mutation_p.M706I|TPO_uc002qwy.1_Missense_Mutation_p.M46I|TPO_uc002qwz.2_Intron	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a	706	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GGGTGCCCATGGATGCCTTCC	0.562													14	28	---	---	---	---	PASS
SDC1	6382	broad.mit.edu	37	2	20403634	20403634	+	Silent	SNP	C	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20403634C>T	uc002rdo.1	-	3	866	c.567G>A	c.(565-567)GAG>GAA	p.E189E	SDC1_uc002rdp.1_Silent_p.E189E|SDC1_uc010exv.2_Intron	NM_002997	NP_002988	P18827	SDC1_HUMAN	syndecan 1 precursor	189	Extracellular (Potential).				lipid metabolic process|lipoprotein metabolic process|myoblast development|striated muscle cell development	cytoplasm|extracellular region|focal adhesion|integral to plasma membrane	cytoskeletal protein binding|protein C-terminus binding			ovary(4)|skin(1)	5	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			OV - Ovarian serous cystadenocarcinoma(76;0.221)		CAGCAGCCCTCTCGGTGGCAG	0.612													11	69	---	---	---	---	PASS
COL3A1	1281	broad.mit.edu	37	2	189871705	189871705	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189871705C>T	uc002uqj.1	+	44	3361	c.3244C>T	c.(3244-3246)CGA>TGA	p.R1082*		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	1082	Triple-helical region.				axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)	TGCTGGTTCCCGAGGTGCTCC	0.363													4	70	---	---	---	---	PASS
FN1	2335	broad.mit.edu	37	2	216245654	216245654	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216245654C>G	uc002vfa.2	-	33	5580	c.5314G>C	c.(5314-5316)GAT>CAT	p.D1772H	FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Missense_Mutation_p.D1772H|FN1_uc002vfe.2_Missense_Mutation_p.D1681H|FN1_uc002vff.2_Missense_Mutation_p.D1681H|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Missense_Mutation_p.D1772H|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_5'UTR|FN1_uc010zjp.1_Intron|FN1_uc002vfk.1_5'Flank|FN1_uc010fva.1_5'Flank|FN1_uc010fvb.1_5'Flank|FN1_uc010fvc.1_Missense_Mutation_p.D134H|FN1_uc010fvd.1_Intron	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	1773	Heparin-binding 2.|Fibronectin type-III 13.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TCTTCACCATCAGGTGCAGGG	0.542													17	110	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10183763	10183763	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183763A>T	uc003bvc.2	+	1	445	c.232A>T	c.(232-234)AAT>TAT	p.N78Y	VHL_uc003bvd.2_Missense_Mutation_p.N78Y	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	78			N -> H (in VHLD; type I).|N -> T (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.N78K(6)|p.N78I(3)|p.F76fs*80(2)|p.F76fs*81(2)|p.N78H(2)|p.N78S(2)|p.N78T(1)|p.S72_V87>L(1)|p.C77_N78>Y(1)|p.R60fs*35(1)|p.V74fs*51(1)|p.N78_R79insN(1)|p.C77fs*53(1)|p.N78Y(1)|p.N78fs*81(1)|p.V74fs*77(1)|p.N78D(1)|p.N78fs*54(1)|p.C77_R79del(1)|p.N78fs*80(1)|p.C77*(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CATCTTCTGCAATCGCAGTCC	0.721		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				4	4	---	---	---	---	PASS
CELSR3	1951	broad.mit.edu	37	3	48682540	48682540	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48682540G>A	uc003cul.2	-	25	8181	c.7900C>T	c.(7900-7902)CCA>TCA	p.P2634S	CELSR3_uc003cuf.1_Missense_Mutation_p.P2731S|CELSR3_uc010hkf.2_5'Flank|CELSR3_uc010hkg.2_Missense_Mutation_p.P617S	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	2634	Cytoplasmic (Potential).				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		ACGTTGCGTGGCTCAACCTGC	0.652													3	26	---	---	---	---	PASS
PROS1	5627	broad.mit.edu	37	3	93643109	93643109	+	Splice_Site	SNP	C	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93643109C>A	uc003drb.3	-	3	576	c.235_splice	c.e3-1	p.D79_splice	PROS1_uc010hoo.2_Splice_Site|PROS1_uc003dqz.3_Splice_Site	NM_000313	NP_000304	P07225	PROS_HUMAN	protein S, alpha preproprotein						leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|post-translational protein modification|proteolysis	endoplasmic reticulum membrane|extracellular region|Golgi lumen|Golgi membrane|platelet alpha granule lumen	calcium ion binding|endopeptidase inhibitor activity			large_intestine(1)	1					Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)	AAAAATAATCCTAGAAAGAAG	0.154													5	44	---	---	---	---	PASS
AHSG	197	broad.mit.edu	37	3	186335181	186335181	+	Intron	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186335181G>A	uc003fqk.3	+						AHSG_uc003fqj.2_Nonsense_Mutation_p.W205*|AHSG_uc003fql.3_Intron|AHSG_uc003fqm.3_Intron|AHSG_uc010hyp.2_Intron	NM_001622	NP_001613	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein						acute-phase response|negative regulation of bone mineralization|negative regulation of insulin receptor signaling pathway|pinocytosis|positive regulation of phagocytosis|regulation of inflammatory response|skeletal system development	extracellular space	cysteine-type endopeptidase inhibitor activity|protein binding				0	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		CAGTTCGGTGGCACTTCGGGA	0.537											OREG0015968	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	37	---	---	---	---	PASS
ADD1	118	broad.mit.edu	37	4	2906737	2906737	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2906737A>G	uc003gfr.2	+	10	1596	c.1408A>G	c.(1408-1410)ACT>GCT	p.T470A	ADD1_uc003gfn.2_Intron|ADD1_uc003gfo.2_Missense_Mutation_p.T470A|ADD1_uc003gfp.2_Missense_Mutation_p.T470A|ADD1_uc003gfq.2_Missense_Mutation_p.T470A|ADD1_uc003gfs.2_Missense_Mutation_p.T470A|ADD1_uc003gft.3_Missense_Mutation_p.T470A	NM_001119	NP_001110	P35611	ADDA_HUMAN	adducin 1 (alpha) isoform a	470					actin filament bundle assembly|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|positive regulation of protein binding	cytosol|F-actin capping protein complex|nucleus|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding|transcription factor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CAAGTCGAAGACTAAGGTGTG	0.542													18	48	---	---	---	---	PASS
SLIT2	9353	broad.mit.edu	37	4	20550708	20550708	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20550708A>C	uc003gpr.1	+	24	2650	c.2446A>C	c.(2446-2448)ATT>CTT	p.I816L	SLIT2_uc003gps.1_Missense_Mutation_p.I808L	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	816	LRR 19.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						TCTGAGATGTATTCCTCCTCG	0.353													27	96	---	---	---	---	PASS
PTPN13	5783	broad.mit.edu	37	4	87692395	87692395	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87692395G>C	uc003hpz.2	+	31	5355	c.4875G>C	c.(4873-4875)GAG>GAC	p.E1625D	PTPN13_uc003hpy.2_Missense_Mutation_p.E1630D|PTPN13_uc003hqa.2_Missense_Mutation_p.E1606D|PTPN13_uc003hqb.2_Missense_Mutation_p.E1434D|PTPN13_uc003hqc.1_5'UTR	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	1625						cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CATGTGTGGAGCAAAGCACCA	0.443													10	16	---	---	---	---	PASS
AGA	175	broad.mit.edu	37	4	178352921	178352921	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178352921A>T	uc003iuu.1	-	9	1044	c.982T>A	c.(982-984)TTC>ATC	p.F328I	AGA_uc010irt.1_RNA	NM_000027	NP_000018	P20933	ASPG_HUMAN	aspartylglucosaminidase precursor	328					asparagine catabolic process via L-aspartate|protein deglycosylation|protein maturation	endoplasmic reticulum|intermediate filament cytoskeleton|lysosome|microtubule cytoskeleton	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)		TAAACCATGAAACTAAACTGA	0.343													16	73	---	---	---	---	PASS
TERT	7015	broad.mit.edu	37	5	1294723	1294723	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1294723G>A	uc003jcb.1	-	2	336	c.278C>T	c.(277-279)GCG>GTG	p.A93V	TERT_uc003jca.1_Missense_Mutation_p.A93V|TERT_uc003jcc.1_Missense_Mutation_p.A93V|TERT_uc003jcd.1_RNA|TERT_uc003jce.1_RNA	NM_198253	NP_937983	O14746	TERT_HUMAN	telomerase reverse transcriptase isoform 1	93	RNA-interacting domain 1.|GQ motif.				anti-apoptosis|DNA strand elongation|replicative senescence|telomere formation via telomerase|telomere maintenance via telomerase	cytoplasm|nucleolus|PML body|telomerase holoenzyme complex	protein homodimerization activity|telomeric DNA binding|telomeric RNA binding|telomeric template RNA reverse transcriptase activity			lung(7)|ovary(2)|central_nervous_system(2)|skin(1)	12	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CACGTTCTTCGCGCCGCGCTC	0.612									TERT_Mutation-Associated_Haematological_Disorders|Congenital_Dyskeratosis|Pulmonary_Fibrosis_Idiopathic				5	16	---	---	---	---	PASS
PKD2L2	27039	broad.mit.edu	37	5	137230170	137230170	+	Silent	SNP	T	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137230170T>G	uc003lby.2	+	4	452	c.396T>G	c.(394-396)CGT>CGG	p.R132R	PKD2L2_uc010jep.1_Silent_p.R72R|PKD2L2_uc003lbw.1_Silent_p.R132R|PKD2L2_uc003lbx.2_Silent_p.R132R	NM_014386	NP_055201	Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	132	Polycystin motif.|Extracellular (Potential).					integral to membrane	calcium ion binding|ion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CCAGAGTTCGTCAACTAAAAG	0.373													33	178	---	---	---	---	PASS
TUBB	203068	broad.mit.edu	37	6	30692126	30692126	+	Silent	SNP	C	A	A	rs146810731		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30692126C>A	uc003nrl.2	+	4	1414	c.1287C>A	c.(1285-1287)ACC>ACA	p.T429T	TUBB_uc003nrk.1_Intron|TUBB_uc011dmq.1_Silent_p.T357T	NM_178014	NP_821133	P07437	TBB5_HUMAN	tubulin, beta	429					cellular component movement|G2/M transition of mitotic cell cycle|microtubule-based movement|natural killer cell mediated cytotoxicity|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|MHC class I protein binding			ovary(1)	1					Colchicine(DB01394)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)	AGGATGCCACCGCAGAAGAGG	0.572													20	54	---	---	---	---	PASS
HIVEP2	3097	broad.mit.edu	37	6	143094139	143094139	+	Silent	SNP	T	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143094139T>A	uc003qjd.2	-	5	2480	c.1737A>T	c.(1735-1737)CCA>CCT	p.P579P		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	579					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		CCACGGTCCCTGGATAGAATA	0.507													31	109	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21657267	21657267	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21657267G>A	uc003svc.2	+	23	4172	c.4141G>A	c.(4141-4143)GTC>ATC	p.V1381I		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1381	Stem (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						GGAAGTCCGCGTCTGGGATGC	0.483									Kartagener_syndrome				24	37	---	---	---	---	PASS
IFRD1	3475	broad.mit.edu	37	7	112097100	112097100	+	Intron	SNP	C	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112097100C>T	uc003vgh.2	+						IFRD1_uc011kmn.1_Intron|IFRD1_uc003vgi.2_Missense_Mutation_p.A139V|IFRD1_uc003vgj.2_Intron|IFRD1_uc011kmo.1_Intron|IFRD1_uc011kmp.1_Intron	NM_001007245	NP_001007246	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1						multicellular organismal development|myoblast cell fate determination		binding			kidney(1)|central_nervous_system(1)	2						AAAGGTAATGCCCTTATTTTT	0.353													19	110	---	---	---	---	PASS
NCAPG2	54892	broad.mit.edu	37	7	158472689	158472689	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158472689A>C	uc003wnv.1	-	11	1254	c.1109T>G	c.(1108-1110)ATG>AGG	p.M370R	NCAPG2_uc010lqu.1_Missense_Mutation_p.M162R|NCAPG2_uc003wnw.1_RNA|NCAPG2_uc003wnx.1_Missense_Mutation_p.M370R|NCAPG2_uc011kwe.1_Missense_Mutation_p.M370R	NM_017760	NP_060230	Q86XI2	CNDG2_HUMAN	leucine zipper protein 5	370					cell division|chromosome condensation|mitosis	nucleus	methylated histone residue binding			ovary(1)|breast(1)|kidney(1)	3	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		TTCACTATCCATTTCAATAGC	0.393													88	140	---	---	---	---	PASS
DHTKD1	55526	broad.mit.edu	37	10	12111000	12111000	+	5'UTR	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12111000G>A	uc001ild.3	+	1						NM_018706	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain						glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			TCGGGCTCCCGCCTTAGCATG	0.706													6	20	---	---	---	---	PASS
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	Missense_Mutation	SNP	A	G	G	rs2257765		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38654432A>G	uc010qex.1	+	5	599	c.524A>G	c.(523-525)AAT>AGT	p.N175S	HSD17B7P2_uc001izq.2_RNA|HSD17B7P2_uc001izo.1_RNA|HSD17B7P2_uc001izp.1_Missense_Mutation_p.N173S					SubName: Full=cDNA FLJ60462, highly similar to 3-keto-steroid reductase (EC 1.1.1.270);												0						TCATCTCGCAATGCAAGGAAA	0.453													6	106	---	---	---	---	PASS
OR52B4	143496	broad.mit.edu	37	11	4388624	4388624	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4388624A>G	uc010qye.1	-	1	902	c.902T>C	c.(901-903)ATC>ACC	p.I301T		NM_001005161	NP_001005161	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B,	301	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTGTTCCTGGATTTGCTTGGT	0.403													13	81	---	---	---	---	PASS
SLC17A6	57084	broad.mit.edu	37	11	22397548	22397548	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22397548C>G	uc001mqk.2	+	10	1608	c.1195C>G	c.(1195-1197)CTG>GTG	p.L399V		NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent	399	Helical; (Potential).				sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity	p.L399M(1)		ovary(3)|breast(1)	4						GGAAGCCACACTGCTCCTGGT	0.388													29	122	---	---	---	---	PASS
OR5M8	219484	broad.mit.edu	37	11	56258042	56258042	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56258042G>A	uc001nix.1	-	1	805	c.805C>T	c.(805-807)CAG>TAG	p.Q269*		NM_001005282	NP_001005282	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M,	269	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	Esophageal squamous(21;0.00352)					ATTTTACCCTGTTCAACAGAT	0.368													21	131	---	---	---	---	PASS
OR5M8	219484	broad.mit.edu	37	11	56258050	56258050	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56258050G>C	uc001nix.1	-	1	797	c.797C>G	c.(796-798)TCT>TGT	p.S266C		NM_001005282	NP_001005282	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M,	266	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	Esophageal squamous(21;0.00352)					CTGTTCAACAGATTCCTTTGA	0.378													21	121	---	---	---	---	PASS
C11orf24	53838	broad.mit.edu	37	11	68029933	68029933	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68029933G>A	uc001onr.3	-	4	972	c.530C>T	c.(529-531)ACC>ATC	p.T177I	C11orf24_uc001ons.2_Missense_Mutation_p.T177I	NM_022338	NP_071733	Q96F05	CK024_HUMAN	hypothetical protein LOC53838 precursor	177	Extracellular (Potential).					integral to membrane					0						AGTGGACGGGGTCCGCCCTGT	0.627													8	41	---	---	---	---	PASS
RPS3	6188	broad.mit.edu	37	11	75113456	75113456	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75113456C>T	uc001owh.2	+	4	346	c.316C>T	c.(316-318)CGT>TGT	p.R106C	RPS3_uc001owg.2_Missense_Mutation_p.R106C|RPS3_uc001owi.2_Missense_Mutation_p.R106C|RPS3_uc001owk.1_Intron|SNORD15B_uc001owl.1_5'Flank	NM_001005	NP_000996	P23396	RS3_HUMAN	ribosomal protein S3	106					activation of caspase activity|endocrine pancreas development|induction of apoptosis|negative regulation of DNA repair|negative regulation of NF-kappaB transcription factor activity|response to DNA damage stimulus|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleus|ruffle membrane	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|endonuclease activity|iron-sulfur cluster binding|mRNA binding|NF-kappaB binding|protein kinase binding|structural constituent of ribosome				0						AGAGTCTCTGCGTTACAAACT	0.473													42	153	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92533045	92533045	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92533045A>G	uc001pdj.3	+	9	6883	c.6866A>G	c.(6865-6867)CAG>CGG	p.Q2289R		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2289	Cadherin 21.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ATTTTCGATCAGCCTACATAC	0.413										TCGA Ovarian(4;0.039)			11	33	---	---	---	---	PASS
PIWIL4	143689	broad.mit.edu	37	11	94308185	94308185	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94308185G>C	uc001pfa.2	+	3	398	c.187G>C	c.(187-189)GGT>CGT	p.G63R	PIWIL4_uc010rue.1_RNA|PIWIL4_uc009ywk.1_RNA	NM_152431	NP_689644	Q7Z3Z4	PIWL4_HUMAN	piwi-like 4	63					cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|meiosis|multicellular organismal development|piRNA metabolic process|regulation of translation|spermatogenesis	nucleus|piP-body	piRNA binding			skin(1)	1		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GATATCTTCTGGTGATGCTGG	0.348													23	53	---	---	---	---	PASS
MMP20	9313	broad.mit.edu	37	11	102482517	102482517	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102482517T>G	uc001phc.2	-	3	505	c.492A>C	c.(490-492)GAA>GAC	p.E164D		NM_004771	NP_004762	O60882	MMP20_HUMAN	matrix metalloproteinase 20 preproprotein	164					proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)		TAATATCCGCTTCTCCTGAGT	0.453													22	68	---	---	---	---	PASS
A2M	2	broad.mit.edu	37	12	9248234	9248234	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9248234G>C	uc001qvk.1	-	16	2027	c.1914C>G	c.(1912-1914)GAC>GAG	p.D638E	A2M_uc009zgk.1_Missense_Mutation_p.D488E	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	638					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	AGTCTTCATTGTCCTGGTCAT	0.393													11	200	---	---	---	---	PASS
KCNJ8	3764	broad.mit.edu	37	12	21918783	21918783	+	Silent	SNP	G	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21918783G>T	uc001rff.2	-	3	1487	c.1149C>A	c.(1147-1149)CGC>CGA	p.R383R		NM_004982	NP_004973	Q15842	IRK8_HUMAN	potassium inwardly-rectifying channel J8	383	Cytoplasmic (By similarity).					voltage-gated potassium channel complex					0					Levosimendan(DB00922)	TCATGGAGTTGCGCTTCCTCA	0.458													54	277	---	---	---	---	PASS
DDX11	1663	broad.mit.edu	37	12	31242307	31242307	+	Intron	SNP	T	C	C	rs4031315		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31242307T>C	uc001rjt.1	+						DDX11_uc010sjw.1_3'UTR|DDX11_uc010sjx.1_Intron|DDX11_uc001rjr.1_Intron|DDX11_uc001rjs.1_Intron|DDX11_uc001rju.1_Intron|DDX11_uc001rjv.1_Intron|DDX11_uc001rjw.1_Intron|DDX11_uc001rjx.1_5'UTR|DDX11_uc009zjn.1_Intron	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GGCACCATCTTTTTGCCTCTT	0.537										Multiple Myeloma(12;0.14)			3	34	---	---	---	---	PASS
RAN	5901	broad.mit.edu	37	12	131357432	131357432	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131357432C>T	uc001uir.2	+	3	153	c.88C>T	c.(88-90)CAT>TAT	p.H30Y	RAN_uc010tbk.1_5'UTR|RAN_uc010tbl.1_5'UTR|RAN_uc001uis.2_Missense_Mutation_p.H50Y	NM_006325	NP_006316	P62826	RAN_HUMAN	ras-related nuclear protein	30					androgen receptor signaling pathway|cell division|DNA metabolic process|mitosis|mitotic spindle organization|positive regulation of transcription, DNA-dependent|protein export from nucleus|RNA export from nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|melanosome|nuclear pore|nucleoplasm	androgen receptor binding|chromatin binding|GTP binding|GTPase activity|transcription coactivator activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		CGTGAAACGTCATTTGACTGG	0.403													17	195	---	---	---	---	PASS
THSD1	55901	broad.mit.edu	37	13	52952408	52952408	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52952408G>A	uc001vgo.2	-	5	2242	c.1697C>T	c.(1696-1698)GCG>GTG	p.A566V	THSD1_uc001vgp.2_Missense_Mutation_p.A513V|THSD1_uc010tgz.1_Missense_Mutation_p.A187V|THSD1_uc010aea.2_Missense_Mutation_p.A27V	NM_018676	NP_061146	Q9NS62	THSD1_HUMAN	thrombospondin type I domain-containing 1	566	Cytoplasmic (Potential).					extracellular region|integral to membrane|intracellular membrane-bounded organelle				ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		GCTGGGGGCCGCATCAATGGC	0.542													59	152	---	---	---	---	PASS
LOC646214	646214	broad.mit.edu	37	15	21936872	21936872	+	RNA	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21936872G>A	uc010tzj.1	-	1		c.3868C>T				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						TGACTTTAGGGCCATAAGCCT	0.512													20	173	---	---	---	---	PASS
CSK	1445	broad.mit.edu	37	15	75092775	75092775	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75092775G>A	uc010bkb.1	+	7	668	c.485G>A	c.(484-486)GGA>GAA	p.G162E	CSK_uc002ays.2_Missense_Mutation_p.G162E|CSK_uc010bkc.1_5'UTR	NM_001127190	NP_001120662	P41240	CSK_HUMAN	c-src tyrosine kinase	162	SH2.				blood coagulation|epidermal growth factor receptor signaling pathway|T cell costimulation|T cell receptor signaling pathway	centrosome|cytosol|Golgi apparatus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein C-terminus binding			lung(2)|central_nervous_system(1)	3						GACGCAGATGGACTCTGTACG	0.617											OREG0023291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	41	---	---	---	---	PASS
CHRNB4	1143	broad.mit.edu	37	15	78917389	78917389	+	3'UTR	SNP	G	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78917389G>T	uc002bed.1	-	6					CHRNB4_uc002bee.1_Missense_Mutation_p.L202I|uc002bef.1_5'Flank	NM_000750	NP_000741	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4						regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0						TATTTACTTAGGGCCTCATCA	0.592													6	19	---	---	---	---	PASS
CHRNB4	1143	broad.mit.edu	37	15	78917390	78917390	+	3'UTR	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78917390G>A	uc002bed.1	-	6					CHRNB4_uc002bee.1_Silent_p.A201A|uc002bef.1_5'Flank	NM_000750	NP_000741	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4						regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0						ATTTACTTAGGGCCTCATCAG	0.587													6	19	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	90835636	90835636	+	5'Flank	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90835636G>A	uc010uqe.1	-											DQ594729																		TGTCCAGAACGAGAACAAGAG	0.582													23	72	---	---	---	---	PASS
PRSS36	146547	broad.mit.edu	37	16	31160816	31160816	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31160816A>G	uc002ebd.2	-	3	136	c.77T>C	c.(76-78)CTC>CCC	p.L26P	PRSS36_uc010vff.1_5'UTR|PRSS36_uc010vfg.1_Missense_Mutation_p.L26P|PRSS36_uc010vfh.1_Missense_Mutation_p.L26P	NM_173502	NP_775773	Q5K4E3	POLS2_HUMAN	protease, serine, 36 precursor	26					proteolysis	cytoplasm|proteinaceous extracellular matrix	serine-type endopeptidase activity			ovary(1)	1						GGTAGGACTGAGAGCTGGGAG	0.592													10	107	---	---	---	---	PASS
WDR81	124997	broad.mit.edu	37	17	1633775	1633775	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1633775T>C	uc002fti.2	+	2	349	c.88T>C	c.(88-90)TAT>CAT	p.Y30H	WDR81_uc002fth.2_Missense_Mutation_p.Y206H|WDR81_uc010vqp.1_Missense_Mutation_p.Y54H|WDR81_uc002ftj.2_Missense_Mutation_p.Y1257H|WDR81_uc010vqq.1_5'UTR	NM_001163811	NP_001157283	Q562E7	WDR81_HUMAN	WD repeat domain 81 isoform 4	30										skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GACGTCTTGTTATGTTGGTAA	0.642													6	20	---	---	---	---	PASS
DNAH2	146754	broad.mit.edu	37	17	7680805	7680805	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7680805C>A	uc002giu.1	+	32	5114	c.5100C>A	c.(5098-5100)AAC>AAA	p.N1700K		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	1700	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TCAGGGGGAACTTGACCAAGA	0.493													145	435	---	---	---	---	PASS
MED9	55090	broad.mit.edu	37	17	17380342	17380342	+	5'UTR	SNP	C	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17380342C>T	uc002grh.1	+	1						NM_018019	NP_060489	Q9NWA0	MED9_HUMAN	mediator complex subunit 9						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		protein binding				0						TCTGGCTAACCTACCCCCGGA	0.617													15	68	---	---	---	---	PASS
JUP	3728	broad.mit.edu	37	17	39927930	39927930	+	Silent	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39927930G>A	uc002hxq.2	-	2	454	c.177C>T	c.(175-177)ACC>ACT	p.T59T	JUP_uc010wfs.1_Silent_p.T59T|JUP_uc002hxr.2_Silent_p.T59T|JUP_uc002hxs.2_Silent_p.T59T	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin	59					adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		GGGTGTAAGTGGTGGTTTTCT	0.632													10	78	---	---	---	---	PASS
SLC4A1	6521	broad.mit.edu	37	17	42338113	42338113	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42338113C>T	uc002igf.3	-	5	388	c.239G>A	c.(238-240)CGC>CAC	p.R80H	SLC4A1_uc002igg.3_Missense_Mutation_p.R80H	NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member	80	Cytoplasmic.				bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		TTGCACCCAGCGCGCCGCCTC	0.617													13	57	---	---	---	---	PASS
FOSB	2354	broad.mit.edu	37	19	45974303	45974303	+	Intron	SNP	T	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45974303T>G	uc002pbx.3	+						ERCC1_uc002pbu.1_Intron|FOSB_uc002pbw.2_3'UTR|FOSB_uc010eke.2_Intron|FOSB_uc002pby.3_Intron|FOSB_uc010eka.1_Intron|FOSB_uc010ekb.1_Intron|FOSB_uc010ekc.1_Intron|FOSB_uc010ekf.2_Intron|FOSB_uc010ekd.1_Intron|FOSB_uc010ekg.2_Intron|FOSB_uc002pca.3_Intron	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)		AAGGCCTCAGTGTTACAGAAA	0.537													2	3	---	---	---	---	PASS
EML2	24139	broad.mit.edu	37	19	46136177	46136177	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46136177T>C	uc002pcn.2	-	6	487	c.452A>G	c.(451-453)CAC>CGC	p.H151R	EML2_uc002pco.2_RNA|EML2_uc002pcp.2_Missense_Mutation_p.H35R|EML2_uc010xxl.1_Missense_Mutation_p.H298R|EML2_uc010xxm.1_Missense_Mutation_p.H352R|EML2_uc010xxn.1_RNA|EML2_uc010xxo.1_Missense_Mutation_p.H151R|EML2_uc010ekj.2_Missense_Mutation_p.H151R|EML2_uc010ekk.1_5'Flank	NM_012155	NP_036287	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like	151	WD 1.				sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		GCCCAGCACGTGTAAGGTGGA	0.622													13	36	---	---	---	---	PASS
FUT1	2523	broad.mit.edu	37	19	49253332	49253332	+	3'UTR	SNP	C	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49253332C>T	uc002pkk.2	-	4						NM_000148	NP_000139	P19526	FUT1_HUMAN	fucosyltransferase 1						L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to plasma membrane|membrane fraction	galactoside 2-alpha-L-fucosyltransferase activity			ovary(1)	1		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		ATACGGGCACCCATTTGCTTC	0.478													3	5	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57327329	57327329	+	Silent	SNP	T	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57327329T>C	uc002qnu.2	-	7	2832	c.2481A>G	c.(2479-2481)GGA>GGG	p.G827G	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Silent_p.G798G|PEG3_uc002qnv.2_Silent_p.G827G|PEG3_uc002qnw.2_Silent_p.G703G|PEG3_uc002qnx.2_Silent_p.G701G|PEG3_uc010etr.2_Silent_p.G827G	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	827					apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TGTATTCCCTTCCTTCAGAGG	0.453													13	134	---	---	---	---	PASS
MATN4	8785	broad.mit.edu	37	20	43922450	43922450	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43922450G>A	uc002xnn.2	-	10	1890	c.1703C>T	c.(1702-1704)GCG>GTG	p.A568V	MATN4_uc002xno.2_Missense_Mutation_p.A527V|MATN4_uc002xnp.2_Missense_Mutation_p.A486V	NM_003833	NP_003824	O95460	MATN4_HUMAN	matrilin 4 isoform 1 precursor	609	Potential.					extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)				CTCCAGGCGCGCCGTCAGCTG	0.687													3	37	---	---	---	---	PASS
CHM	1121	broad.mit.edu	37	X	85213896	85213896	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85213896A>C	uc004eet.2	-	6	819	c.789T>G	c.(787-789)ATT>ATG	p.I263M	CHM_uc011mqz.1_Missense_Mutation_p.I115M	NM_000390	NP_000381	P24386	RAE1_HUMAN	choroideremia isoform a	263					intracellular protein transport|protein geranylgeranylation|response to stimulus|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(1)	1		all_lung(315;5.41e-06)				GAAATGCAAGAATCCTGGTAA	0.353													42	51	---	---	---	---	PASS
UTY	7404	broad.mit.edu	37	Y	15361721	15361721	+	3'UTR	SNP	A	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:15361721A>G	uc004fsx.1	-	28					UTY_uc004fsw.1_Intron|UTY_uc010nwx.1_3'UTR	NM_007125	NP_009056	O14607	UTY_HUMAN	tetratricopeptide repeat protein isoform 3						chromatin modification	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						CTCATTTAATATTCATGGAAC	0.308													8	11	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14272	14272	+	RNA	SNP	C	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14272C>T	uc004cox.3	+	1		c.1936C>T			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		TCCTCCCGAATCAACCCTGAC	0.423													6	8	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	12293343	12293351	+	Intron	DEL	TTCCTTCCC	-	-	rs112549370		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12293343_12293351delTTCCTTCCC	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		cttcattcctttccttcccttccttccct	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92195738	92195739	+	IGR	INS	-	AGGA	AGGA			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92195738_92195739insAGGA								FKSG73 (65244 upstream) : None (None downstream)																							gggagggaaagaggaaggaagg	0.045													7	4	---	---	---	---	
MARCH7	64844	broad.mit.edu	37	2	160616015	160616015	+	Intron	DEL	T	-	-	rs34264670		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160616015delT	uc002uax.2	+						MARCH7_uc010foq.2_Intron|MARCH7_uc010zcn.1_Intron|MARCH7_uc010for.2_Intron|MARCH7_uc002uay.2_Intron	NM_022826	NP_073737	Q9H992	MARH7_HUMAN	axotrophin								ligase activity|zinc ion binding				0						AATTTCataattttttttttt	0.279													5	3	---	---	---	---	
MYO3B	140469	broad.mit.edu	37	2	171258312	171258313	+	Intron	INS	-	TTTTT	TTTTT	rs78393302		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171258312_171258313insTTTTT	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						ctttctttttcttttttttttt	0.233													4	4	---	---	---	---	
ACAD11	84129	broad.mit.edu	37	3	132360471	132360473	+	Intron	DEL	GAG	-	-	rs71974303		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132360471_132360473delGAG	uc003eov.3	-						ACAD11_uc003eoy.2_Intron	NM_032169	NP_115545	Q709F0	ACD11_HUMAN	putative acyl-CoA dehydrogenase							peroxisome	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|transferase activity, transferring phosphorus-containing groups			ovary(1)	1						ggaggaagaagaggaggaagaag	0.020													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197866710	197866712	+	IGR	DEL	GAG	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197866710_197866712delGAG								LOC348840 (59168 upstream) : FAM157A (12525 downstream)																							gacaatggatgaggaggagggag	0.025													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	76010090	76010091	+	IGR	INS	-	GAAG	GAAG	rs34335133		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76010090_76010091insGAAG								PARM1 (34767 upstream) : RCHY1 (394264 downstream)																							AAGACGAAGAAgaaggaaggaa	0.208													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	79569453	79569454	+	Intron	INS	-	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79569453_79569454insT	uc003hlf.2	+						uc003hlg.2_Intron|uc003hlh.2_Intron|uc003hli.2_Intron					Homo sapiens cDNA FLJ32651 fis, clone SYNOV2001581.																		ttccttccttcctccctccctc	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	88802901	88802902	+	IGR	INS	-	GGGA	GGGA	rs140375271	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88802901_88802902insGGGA								MEPE (34959 upstream) : SPP1 (93900 downstream)																							aagagagagggggaaggaagga	0.054													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	105918246	105918247	+	IGR	INS	-	T	T	rs145057012		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105918246_105918247insT								CXXC4 (502188 upstream) : TET2 (149696 downstream)																							tttttttttccttttttttttt	0.183													4	2	---	---	---	---	
C5orf33	133686	broad.mit.edu	37	5	36207548	36207549	+	Intron	INS	-	A	A	rs34974252		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36207548_36207549insA	uc003jkf.3	-						C5orf33_uc003jke.3_Intron|C5orf33_uc010iux.2_Intron|C5orf33_uc003jkg.3_Intron|C5orf33_uc011cov.1_Intron	NM_001085411	NP_001078880	Q4G0N4	NAKD1_HUMAN	hypothetical protein LOC133686 isoform 1								NAD+ kinase activity				0	all_lung(31;5.63e-05)		Epithelial(62;0.0254)|all cancers(62;0.0805)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TAGAAGAAATTAAAAAAAAAAA	0.302													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	61129109	61129110	+	IGR	INS	-	GAAG	GAAG	rs7707571	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61129109_61129110insGAAG								FLJ37543 (126747 upstream) : KIF2A (472879 downstream)																							aatgaatgaatgaaggaaggaa	0.149													4	4	---	---	---	---	
CANX	821	broad.mit.edu	37	5	179153577	179153578	+	Intron	INS	-	A	A			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179153577_179153578insA	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)	actctgtctccaaaaaaaaaaa	0.119													3	3	---	---	---	---	
XPO5	57510	broad.mit.edu	37	6	43521248	43521249	+	Intron	DEL	AC	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43521248_43521249delAC	uc003ovp.2	-							NM_020750	NP_065801	Q9HAV4	XPO5_HUMAN	exportin 5						gene silencing by RNA	cytosol|nucleoplasm	protein binding|tRNA binding			skin(2)|breast(1)|kidney(1)	4	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			AAGCTTTAAAacacacacacac	0.356													3	3	---	---	---	---	
TPD52L1	7164	broad.mit.edu	37	6	125493246	125493249	+	Intron	DEL	CTTT	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125493246_125493249delCTTT	uc003pzu.1	+						TPD52L1_uc003pzv.1_Intron|TPD52L1_uc003pzw.1_Intron|TPD52L1_uc003pzx.1_Intron|TPD52L1_uc003pzy.1_Intron	NM_003287	NP_003278	Q16890	TPD53_HUMAN	tumor protein D52-like 1 isoform 1						DNA fragmentation involved in apoptotic nuclear change|G2/M transition of mitotic cell cycle|induction of apoptosis|positive regulation of JNK cascade|positive regulation of MAP kinase activity	perinuclear region of cytoplasm	caspase activator activity|protein heterodimerization activity|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)		ctttctttccctttctttctttct	0.069													4	3	---	---	---	---	
ARID1B	57492	broad.mit.edu	37	6	157360839	157360839	+	Intron	DEL	C	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157360839delC	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron|ARID1B_uc003qqq.1_Intron	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		ttctttctttcctttctttcc	0.020													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	3337336	3337338	+	IGR	DEL	GAG	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3337336_3337338delGAG								CARD11 (253757 upstream) : SDK1 (3742 downstream)																							agtggaagaagaggaggaggagg	0.094													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	16772067	16772070	+	IGR	DEL	TTCC	-	-	rs6953755	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16772067_16772070delTTCC								BZW2 (25919 upstream) : TSPAN13 (21281 downstream)																							ctttctttctttccttccttcctt	0.010													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	55659699	55659699	+	IGR	DEL	C	-	-	rs140374894		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55659699delC								VOPP1 (19499 upstream) : LOC442308 (53613 downstream)																							CTCAGCTGCACCCCCCCTCTT	0.587													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	96377119	96377130	+	IGR	DEL	CTTCCTTCCTTT	-	-	rs71956221		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96377119_96377130delCTTCCTTCCTTT								SHFM1 (37916 upstream) : DLX6AS (220698 downstream)																							tccttccttccttccttcctttcttccttcct	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	73068487	73068488	+	IGR	INS	-	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73068487_73068488insT								TRPA1 (80668 upstream) : KCNB2 (381138 downstream)																							tccttccttccttccttccttc	0.059													4	2	---	---	---	---	
ANKRD46	157567	broad.mit.edu	37	8	101535131	101535136	+	Intron	DEL	ACATAT	-	-	rs147227610	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101535131_101535136delACATAT	uc003yjm.2	-						ANKRD46_uc003yjn.1_Intron|ANKRD46_uc003yjo.1_Intron|ANKRD46_uc003yjp.1_Intron	NM_198401	NP_940683	Q86W74	ANR46_HUMAN	ankyrin repeat domain 46							integral to membrane					0	all_cancers(14;5.07e-05)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000353)|all_lung(17;0.000998)		Epithelial(11;2.61e-11)|all cancers(13;5.03e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.49e-06)|STAD - Stomach adenocarcinoma(118;0.0957)			acacacacacacatatatatatatac	0.209													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138676648	138676649	+	IGR	INS	-	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138676648_138676649insT								None (None upstream) : FAM135B (465619 downstream)																							tctttccttccttTTTTTTTTT	0.213													10	5	---	---	---	---	
ANKRD20A4	728747	broad.mit.edu	37	9	69391298	69391299	+	Intron	INS	-	TA	TA			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69391298_69391299insTA	uc004afn.2	+						ANKRD20A4_uc010mnw.1_Intron	NM_001098805	NP_001092275	Q4UJ75	A20A4_HUMAN	ankyrin repeat domain 20 family, member A4												0						CTACTCCATCTTATACATTAGG	0.317													5	3	---	---	---	---	
KIAA1529	57653	broad.mit.edu	37	9	100133212	100133213	+	Intron	INS	-	GGC	GGC	rs142691576	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100133212_100133213insGGC	uc011lut.1	+						KIAA1529_uc004axe.1_Intron|KIAA1529_uc004axg.1_Intron|KIAA1529_uc004axh.1_Intron|KIAA1529_uc011luw.1_Intron	NM_020893	NP_065944			hypothetical protein LOC57653											ovary(4)|large_intestine(2)|skin(1)	7		Acute lymphoblastic leukemia(62;0.154)				TGGCCATTATTGGCTGTTTTAA	0.277													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	116500495	116500496	+	IGR	INS	-	C	C			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116500495_116500496insC								RGS3 (140478 upstream) : ZNF618 (138066 downstream)																							cttccttccttcctttcttccc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	133834137	133834139	+	IGR	DEL	CCG	-	-	rs145336475	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133834137_133834139delCCG								FIBCD1 (19682 upstream) : LAMC3 (50365 downstream)																							accaccaccaccgccatcaccat	0.000													4	2	---	---	---	---	
ANKRD26	22852	broad.mit.edu	37	10	27301763	27301763	+	Intron	DEL	T	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27301763delT	uc001ith.2	-						ANKRD26_uc001itg.2_Intron|ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4						aaaaaaagaaTTACATGAGAA	0.184													58	27	---	---	---	---	
C10orf71	118461	broad.mit.edu	37	10	50534969	50534970	+	In_Frame_Ins	INS	-	ACACACACACAC	ACACACACACAC	rs66701434		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50534969_50534970insACACACACACAC	uc010qgp.1	+	4	2407_2408	c.2068_2069insACACACACACAC	c.(2068-2070)AAC>AACACACACACACAC	p.702_703insTHTH		NM_199459	NP_955629	Q711Q0	CJ071_HUMAN	hypothetical protein LOC118461 isoform 2	Error:Variant_position_missing_in_Q711Q0_after_alignment											0						CAAAACAAGCAacacacacaca	0.406													6	3	---	---	---	---	
CHKA	1119	broad.mit.edu	37	11	67831875	67831875	+	Intron	DEL	A	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67831875delA	uc001onj.2	-						CHKA_uc001onk.2_Intron	NM_001277	NP_001268	P35790	CHKA_HUMAN	choline kinase alpha isoform a						lipid transport|phosphatidylethanolamine biosynthetic process	cytoplasm	ATP binding|choline kinase activity|drug binding|ethanolamine kinase activity|signal transducer activity			ovary(1)|central_nervous_system(1)	2					Choline(DB00122)	actctgtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	75170074	75170081	+	IGR	DEL	AAGGAAGA	-	-	rs117628501	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75170074_75170081delAAGGAAGA								ATXN7L3B (234851 upstream) : KCNC2 (263816 downstream)																							ggaaggaaggaaggaagaaaggaagaaa	0.038													6	10	---	---	---	---	
TRPV4	59341	broad.mit.edu	37	12	110230071	110230071	+	Intron	DEL	G	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110230071delG	uc001tpj.1	-						TRPV4_uc001tpg.1_Intron|TRPV4_uc001tph.1_Intron|TRPV4_uc001tpi.1_Intron|TRPV4_uc001tpk.1_Intron|TRPV4_uc001tpl.1_Intron	NM_021625	NP_067638	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel,						actin cytoskeleton reorganization|actin filament organization|calcium ion import|cell death|cell volume homeostasis|cell-cell junction assembly|cellular hypotonic response|cortical microtubule organization|elevation of cytosolic calcium ion concentration|microtubule polymerization|negative regulation of neuron projection development|osmosensory signaling pathway|positive regulation of microtubule depolymerization|response to mechanical stimulus	cortical actin cytoskeleton|filopodium|focal adhesion|growth cone|integral to membrane|lamellipodium|ruffle membrane	actin filament binding|alpha-tubulin binding|beta-tubulin binding|calcium channel activity|calmodulin binding|microtubule binding|protein binding|protein kinase C binding|SH2 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						aaaaaaaaaagaaCTCAGCAA	0.284													9	4	---	---	---	---	
MED13L	23389	broad.mit.edu	37	12	116469529	116469530	+	Intron	INS	-	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116469529_116469530insG	uc001tvw.2	-							NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		agaaaagaaaagaaaagaaaag	0.005													3	3	---	---	---	---	
KNTC1	9735	broad.mit.edu	37	12	123107166	123107166	+	Intron	DEL	A	-	-	rs75934693		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123107166delA	uc001ucv.2	+						KNTC1_uc010taf.1_Intron|GPR81_uc001ucw.1_Intron	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		TAAGTTAATTAAAAAAAAAAA	0.209													4	2	---	---	---	---	
CDX2	1045	broad.mit.edu	37	13	28538846	28538858	+	Intron	DEL	AAAAAAAAAAAAA	-	-	rs66744020		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28538846_28538858delAAAAAAAAAAAAA	uc001urv.2	-							NM_001265	NP_001256	Q99626	CDX2_HUMAN	caudal type homeobox 2						organ morphogenesis|transcription from RNA polymerase II promoter		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)	1	all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155)	Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199)		atctctgtttaaaaaaaaaaaaaaaaaaaaaaa	0.211			T	ETV6	AML								6	9	---	---	---	---	
PDS5B	23047	broad.mit.edu	37	13	33315050	33315050	+	Intron	DEL	T	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33315050delT	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		CCTTTCAACCTTTTTTTTTTT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	54394435	54394437	+	IGR	DEL	CAC	-	-	rs139166998		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54394435_54394437delCAC								OLFM4 (768249 upstream) : MIR1297 (491670 downstream)																							TGAAAaccatcaccaccaccacc	0.246													3	3	---	---	---	---	
KLHL1	57626	broad.mit.edu	37	13	70293328	70293345	+	Intron	DEL	GTGTGTGTGTGTGTGAGA	-	-	rs71966264		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70293328_70293345delGTGTGTGTGTGTGTGAGA	uc001vip.2	-						KLHL1_uc010thm.1_Intron	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		gtgtgtgtgtgtgtgtgtgtgtgtgagagagagagaga	0.220													2	4	---	---	---	---	
C14orf21	161424	broad.mit.edu	37	14	24772593	24772593	+	Intron	DEL	T	-	-	rs112529240		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24772593delT	uc001wol.1	+						C14orf21_uc001wom.1_Intron	NM_174913	NP_777573	Q86U38	CN021_HUMAN	hypothetical protein LOC161424								RNA binding			breast(2)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(265;0.0185)		ACCCAGCTAAttttttttttt	0.313													4	2	---	---	---	---	
C14orf179	112752	broad.mit.edu	37	14	76527155	76527156	+	Intron	INS	-	CCTCCCTC	CCTCCCTC	rs142190540	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76527155_76527156insCCTCCCTC	uc010asm.1	+						C14orf179_uc001xsf.2_Intron|C14orf179_uc010asl.1_Intron|C14orf179_uc001xsg.2_Intron|C14orf179_uc010tve.1_Intron	NM_001102564	NP_001096034	Q96FT9	IFT43_HUMAN	hypothetical protein LOC112752 isoform 2						cilium morphogenesis|intraflagellar retrograde transport						0				BRCA - Breast invasive adenocarcinoma(234;0.0199)		ttccctcccttcctccctccct	0.000													5	3	---	---	---	---	
TRIP11	9321	broad.mit.edu	37	14	92439370	92439370	+	Intron	DEL	T	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92439370delT	uc001xzy.2	-						TRIP11_uc010auf.1_Intron	NM_004239	NP_004230	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)		ATACTGGCACttttttttttt	0.119			T	PDGFRB	AML								4	3	---	---	---	---	
CAPN3	825	broad.mit.edu	37	15	42677730	42677731	+	Intron	DEL	AG	-	-	rs79988905	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42677730_42677731delAG	uc001zpn.1	+						CAPN3_uc001zpk.1_Intron|CAPN3_uc001zpl.1_Intron|CAPN3_uc010udf.1_Intron|CAPN3_uc010udg.1_Intron|CAPN3_uc001zpo.1_Intron|CAPN3_uc001zpp.1_Intron	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a						muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		ATACACACACagagagagagag	0.347											OREG0023085	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SOLH	6650	broad.mit.edu	37	16	601069	601070	+	Intron	INS	-	G	G			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:601069_601070insG	uc002chi.2	+						SOLH_uc002chj.2_5'Flank	NM_005632	NP_005623	O75808	CAN15_HUMAN	small optic lobes						proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)	2		Hepatocellular(780;0.00335)				CCGGTCGGTGAGGTCCCCGGTC	0.762													4	2	---	---	---	---	
SCNN1B	6338	broad.mit.edu	37	16	23354829	23354830	+	Intron	DEL	AA	-	-	rs10655638		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23354829_23354830delAA	uc002dln.2	+							NM_000336	NP_000327	P51168	SCNNB_HUMAN	sodium channel, nonvoltage-gated 1, beta						excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	ggaaggaaggaaaaggaaggaa	0.010													4	3	---	---	---	---	
PRKCB	5579	broad.mit.edu	37	16	24032529	24032556	+	Intron	DEL	TTCTTTCTTTCTTTCTTTCTTTCTTTCC	-	-	rs147959262	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24032529_24032556delTTCTTTCTTTCTTTCTTTCTTTCTTTCC	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	ctttctttctttctttctttctttctttctttctttccttccttcctt	0.000													4	2	---	---	---	---	
ZC3H18	124245	broad.mit.edu	37	16	88690882	88690883	+	Intron	INS	-	AGC	AGC	rs143096278	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88690882_88690883insAGC	uc002fky.2	+						ZC3H18_uc010voz.1_Intron|ZC3H18_uc010chw.2_Intron|ZC3H18_uc002fkz.2_5'Flank	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18							nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		GTCCAGGCACGAGCGTGCTCAC	0.653													3	3	---	---	---	---	
RHOT1	55288	broad.mit.edu	37	17	30477376	30477376	+	Intron	DEL	T	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30477376delT	uc002hgz.2	+						RHOT1_uc002hgw.2_Intron|RHOT1_uc002hgy.2_Intron|RHOT1_uc002hha.2_Intron|RHOT1_uc010csv.2_Intron|RHOT1_uc002hgx.2_Intron|RHOT1_uc010wby.1_Intron|RHOT1_uc002hhb.2_Intron|RHOT1_uc002hgv.2_Intron	NM_018307	NP_060777	Q8IXI2	MIRO1_HUMAN	ras homolog gene family, member T1 isoform 3						apoptosis|cellular homeostasis|mitochondrion transport along microtubule|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to mitochondrial outer membrane|plasma membrane	calcium ion binding|GTP binding|GTPase activity|protein binding			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)				GCTAATGAACTTTTTTTTTTT	0.313													4	3	---	---	---	---	
NPEPPS	9520	broad.mit.edu	37	17	45646982	45646982	+	Intron	DEL	T	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45646982delT	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010dba.1_Intron	NM_006310	NP_006301	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0						TATTAAGAGCttttttttttt	0.169													4	2	---	---	---	---	
CALCOCO2	10241	broad.mit.edu	37	17	46928942	46928944	+	In_Frame_Del	DEL	GAT	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46928942_46928944delGAT	uc002iof.2	+	7	733_735	c.654_656delGAT	c.(652-657)AAGATG>AAG	p.M219del	CALCOCO2_uc010wlp.1_In_Frame_Del_p.M240del|CALCOCO2_uc010wlq.1_In_Frame_Del_p.M147del|CALCOCO2_uc010wlr.1_In_Frame_Del_p.M243del|CALCOCO2_uc010wls.1_In_Frame_Del_p.M177del	NM_005831	NP_005822	Q13137	CACO2_HUMAN	calcium binding and coiled-coil domain 2	219	Potential.				response to interferon-gamma|viral reproduction	cytoskeleton|Golgi apparatus|nucleus|perinuclear region of cytoplasm|soluble fraction	protein homodimerization activity			ovary(1)	1						AAAACCAGAAGATGTCCTCAGAA	0.419													55	24	---	---	---	---	
MRC2	9902	broad.mit.edu	37	17	60738939	60738942	+	Intron	DEL	TTCC	-	-	rs66648705	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60738939_60738942delTTCC	uc002jad.2	+						MRC2_uc002jac.2_Intron	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2						endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|skin(1)	3						ccttccttcattccttccttcctt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	78950793	78950793	+	IGR	DEL	A	-	-	rs112496455		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78950793delA								RPTOR (10620 upstream) : CHMP6 (14848 downstream)																							tttgacaattaaaaaaaaaaa	0.129													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35660163	35660170	+	IGR	DEL	CTTCCTTC	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35660163_35660170delCTTCCTTC								CELF4 (514163 upstream) : None (None downstream)																							ttcttcttttcttccttccttccttcct	0.260													6	4	---	---	---	---	
ONECUT3	390874	broad.mit.edu	37	19	1768998	1768999	+	Intron	INS	-	GGA	GGA	rs138220122	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1768998_1768999insGGA	uc010xgr.1	+							NM_001080488	NP_001073957	O60422	ONEC3_HUMAN	one cut homeobox 3						endocrine pancreas development		sequence-specific DNA binding				0		Acute lymphoblastic leukemia(61;4.66e-11)|all_hematologic(61;4.59e-07)		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)		gtggaggtgatggtggaggtgg	0.000											OREG0025124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7174851	7174852	+	Intron	DEL	TG	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7174851_7174852delTG	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)	GGTATTTCTTtgtgtgtgtgtg	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	10055883	10055895	+	IGR	DEL	GGGAGGGAGGGAG	-	-	rs111802762		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10055883_10055895delGGGAGGGAGGGAG								OLFM2 (8813 upstream) : COL5A3 (14342 downstream)																							aaggaaggaagggagggagggagggaaggaagg	0.146													4	2	---	---	---	---	
SFRS16	11129	broad.mit.edu	37	19	45571210	45571211	+	Intron	DEL	GT	-	-			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45571210_45571211delGT	uc002pak.2	+						SFRS16_uc002pal.2_Intron|SFRS16_uc010xxh.1_Intron|SFRS16_uc002pam.2_Intron	NM_007056	NP_008987	Q8N2M8	CLASR_HUMAN	splicing factor, arginine/serine-rich 16						mRNA processing|RNA splicing	nucleus					0		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		TGAGGCTGGGGTCAGAGGTGGC	0.634													21	10	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	52086153	52086154	+	Intron	INS	-	AAAG	AAAG	rs116779353	by1000genomes	TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52086153_52086154insAAAG	uc002xwo.2	+						uc002xwp.1_Intron	NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			gaaagatagatagagagggagg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10547386	10547387	+	Intron	INS	-	AC	AC			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10547386_10547387insAC	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		acagaataggtacacacacaca	0.000													6	3	---	---	---	---	
SON	6651	broad.mit.edu	37	21	34929319	34929320	+	Intron	INS	-	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34929319_34929320insT	uc002yse.1	+						SON_uc002ysb.1_Intron|SON_uc002ysc.2_Intron|SON_uc002ysd.2_Intron|SON_uc002ysf.1_Intron|SON_uc002ysg.2_Intron	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F						anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6						TAGTTTTTTCCTTTTTTTTTTT	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	28006886	28006887	+	IGR	INS	-	T	T			TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28006886_28006887insT								MIAT (891937 upstream) : MN1 (137379 downstream)																							ggagggaggaagggagggaggg	0.109													4	2	---	---	---	---	
OSBP2	23762	broad.mit.edu	37	22	31298126	31298127	+	Intron	DEL	CC	-	-	rs56186828		TCGA-BP-5009-01A-01D-1462-08	TCGA-BP-5009-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31298126_31298127delCC	uc003aiy.1	+						OSBP2_uc011ala.1_Intron|OSBP2_uc010gwc.1_Intron|OSBP2_uc011alb.1_Intron|OSBP2_uc003aiz.1_Intron|OSBP2_uc003aja.1_Intron|OSBP2_uc011alc.1_Intron|OSBP2_uc003ajb.2_Intron|OSBP2_uc011ald.1_Intron|OSBP2_uc010gwd.1_Intron	NM_030758	NP_110385	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2 isoform a						lipid transport	membrane	lipid binding			breast(1)|skin(1)	2						AAAAAAAAAACCAAAAAAAAAA	0.282													10	5	---	---	---	---	
