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
FBXO42	54455	broad.mit.edu	37	1	16578281	16578281	+	Intron	SNP	C	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16578281C>A	uc001ayg.2	-						FBXO42_uc001aye.3_Intron|FBXO42_uc001ayf.2_Intron	NM_018994	NP_061867	Q6P3S6	FBX42_HUMAN	F-box protein 42											upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		ACTGTCCCACCTGGAAGACAA	0.398													3	28	---	---	---	---	PASS
MAP3K6	9064	broad.mit.edu	37	1	27684232	27684232	+	Missense_Mutation	SNP	C	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27684232C>G	uc001bny.1	-	22	3300	c.3051G>C	c.(3049-3051)GAG>GAC	p.E1017D	MAP3K6_uc009vsw.1_Missense_Mutation_p.E1009D	NM_004672	NP_004663	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase	1017	Potential.				activation of JUN kinase activity		ATP binding|magnesium ion binding|MAP kinase kinase kinase activity			breast(4)|lung(3)|ovary(1)|central_nervous_system(1)	9		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GGTGCAGATTCTCCGCCAGCG	0.667											OREG0013282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	15	---	---	---	---	PASS
CGN	57530	broad.mit.edu	37	1	151508792	151508792	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151508792C>T	uc009wmw.2	+	19	3421	c.3277C>T	c.(3277-3279)CGG>TGG	p.R1093W	CGN_uc010pde.1_Missense_Mutation_p.R87W	NM_020770	NP_065821	Q9P2M7	CING_HUMAN	cingulin	1087	Potential.					myosin complex|tight junction	actin binding|motor activity			ovary(2)|pancreas(1)	3	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			TGAAGACGAGCGGCAGCATGT	0.473													29	35	---	---	---	---	PASS
SNTG2	54221	broad.mit.edu	37	2	1271203	1271203	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1271203G>A	uc002qwq.2	+	14	1272	c.1144G>A	c.(1144-1146)GAG>AAG	p.E382K	SNTG2_uc010ewi.2_Missense_Mutation_p.E255K	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	382	PH.				central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		TTTTGACTTTGAGGACCAGAG	0.522													5	16	---	---	---	---	PASS
HPCAL1	3241	broad.mit.edu	37	2	10566867	10566867	+	Missense_Mutation	SNP	G	C	C			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10566867G>C	uc002raj.2	+	5	876	c.502G>C	c.(502-504)GAA>CAA	p.E168Q	HPCAL1_uc002rak.2_Missense_Mutation_p.E168Q|HPCAL1_uc002ral.2_Missense_Mutation_p.E168Q|HPCAL1_uc010exe.2_RNA|HPCAL1_uc010exf.2_Missense_Mutation_p.E168Q	NM_002149	NP_002140	P37235	HPCL1_HUMAN	hippocalcin-like 1	168	EF-hand 4.|3 (Potential).						calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)		GTCCTTGGAAGAATTCATCAG	0.582													77	111	---	---	---	---	PASS
AFF3	3899	broad.mit.edu	37	2	100623202	100623202	+	Silent	SNP	C	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100623202C>A	uc002tag.2	-	6	1001	c.765G>T	c.(763-765)TCG>TCT	p.S255S	AFF3_uc002taf.2_Silent_p.S280S|AFF3_uc010fiq.1_Silent_p.S255S|AFF3_uc010yvr.1_Silent_p.S409S|AFF3_uc002tah.1_Silent_p.S280S|AFF3_uc010fir.1_Silent_p.S332S|AFF3_uc002tai.2_Silent_p.S177S	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1	255					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						CGCTGGTTTCCGAAGACGACT	0.592													3	46	---	---	---	---	PASS
GLI2	2736	broad.mit.edu	37	2	121744182	121744182	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121744182C>T	uc010flp.2	+	12	2315	c.2285C>T	c.(2284-2286)CCG>CTG	p.P762L	GLI2_uc002tmq.1_Missense_Mutation_p.P434L|GLI2_uc002tmr.1_Missense_Mutation_p.P417L|GLI2_uc002tmt.3_Missense_Mutation_p.P434L|GLI2_uc002tmu.3_Missense_Mutation_p.P417L|GLI2_uc002tmw.1_Missense_Mutation_p.P745L	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	762					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				CCTCCCCTCCCGGGAAGTGGT	0.597													32	33	---	---	---	---	PASS
ROBO1	6091	broad.mit.edu	37	3	78987932	78987932	+	Missense_Mutation	SNP	C	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78987932C>G	uc003dqe.2	-	4	526	c.318G>C	c.(316-318)GAG>GAC	p.E106D	ROBO1_uc003dqb.2_Missense_Mutation_p.E67D|ROBO1_uc003dqc.2_Missense_Mutation_p.E67D|ROBO1_uc003dqd.2_Missense_Mutation_p.E67D	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	106	Extracellular (Potential).|Ig-like C2-type 1.				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TCTCCACTCTCTCTCCCCCTT	0.478													36	2	---	---	---	---	PASS
MRPL3	11222	broad.mit.edu	37	3	131220486	131220486	+	Missense_Mutation	SNP	C	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131220486C>G	uc003eoh.2	-	2	330	c.166G>C	c.(166-168)GAA>CAA	p.E56Q	MRPL3_uc011blo.1_5'UTR|MRPL3_uc011blp.1_Missense_Mutation_p.E83Q	NM_007208	NP_009139	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	56					translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0						GGGACATTTTCTTCAGAAAGA	0.378													110	135	---	---	---	---	PASS
WDR49	151790	broad.mit.edu	37	3	167196719	167196719	+	Missense_Mutation	SNP	C	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167196719C>A	uc003fev.1	-	15	2347	c.2041G>T	c.(2041-2043)GCC>TCC	p.A681S	WDR49_uc003feu.1_Missense_Mutation_p.A506S|WDR49_uc011bpd.1_Missense_Mutation_p.A646S|WDR49_uc003few.1_3'UTR	NM_178824	NP_849146	Q8IV35	WDR49_HUMAN	WD repeat domain 49	681										large_intestine(1)|ovary(1)|skin(1)	3						AATTGCTTGGCTTTTCGTTCA	0.313													15	12	---	---	---	---	PASS
ATP13A5	344905	broad.mit.edu	37	3	193049049	193049049	+	Missense_Mutation	SNP	C	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193049049C>A	uc011bsq.1	-	12	1324	c.1324G>T	c.(1324-1326)GTC>TTC	p.V442F		NM_198505	NP_940907	Q4VNC0	AT135_HUMAN	ATPase type 13A5	442	Helical; (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|skin(4)|large_intestine(2)	11	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		ACTGGAGGGACAGTCACGGTG	0.502													3	51	---	---	---	---	PASS
WDR17	116966	broad.mit.edu	37	4	177046324	177046324	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177046324C>T	uc003iuj.2	+	6	836	c.680C>T	c.(679-681)ACG>ATG	p.T227M	WDR17_uc003iuk.2_Missense_Mutation_p.T203M|WDR17_uc003ium.3_Missense_Mutation_p.T203M|WDR17_uc003iul.1_Intron	NM_170710	NP_733828	Q8IZU2	WDR17_HUMAN	WD repeat domain 17 isoform 1	227	WD 4.									ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		GATCCAGTTACGGCCTTGGAA	0.363													41	2	---	---	---	---	PASS
HSD17B4	3295	broad.mit.edu	37	5	118814681	118814681	+	Missense_Mutation	SNP	C	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118814681C>G	uc003ksj.2	+	8	710	c.587C>G	c.(586-588)GCG>GGG	p.A196G	HSD17B4_uc011cwg.1_Missense_Mutation_p.A172G|HSD17B4_uc011cwh.1_Missense_Mutation_p.A178G|HSD17B4_uc011cwi.1_Missense_Mutation_p.A221G|HSD17B4_uc003ksk.3_Missense_Mutation_p.A49G|HSD17B4_uc011cwj.1_Missense_Mutation_p.A49G|HSD17B4_uc010jcn.1_5'UTR	NM_000414	NP_000405	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	196	NAD.|(3R)-hydroxyacyl-CoA dehydrogenase.				bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity			ovary(1)|pancreas(1)	2		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)	NADH(DB00157)	GCTCCTAATGCGGGATCACGG	0.408													5	76	---	---	---	---	PASS
TRA2A	29896	broad.mit.edu	37	7	23552514	23552514	+	Missense_Mutation	SNP	T	C	C			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23552514T>C	uc003swi.2	-	4	738	c.524A>G	c.(523-525)GAG>GGG	p.E175G	TRA2A_uc011jzb.1_RNA|TRA2A_uc011jzc.1_Missense_Mutation_p.E74G|TRA2A_uc011jzd.1_Missense_Mutation_p.E74G|TRA2A_uc010kuo.1_RNA	NM_013293	NP_037425	Q13595	TRA2A_HUMAN	transformer-2 alpha	175	RRM.				nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|RNA binding			ovary(1)	1						CAAATTTACCTCCTTTGAGTC	0.333													42	21	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48336912	48336912	+	Intron	SNP	A	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48336912A>G	uc003toq.2	+						ABCA13_uc010kys.1_Intron	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						ACTGAGGGTAAGTATGTGGTT	0.318													3	11	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77766275	77766275	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77766275C>T	uc003yav.2	+	10	7370	c.6983C>T	c.(6982-6984)GCT>GTT	p.A2328V	ZFHX4_uc003yau.1_Missense_Mutation_p.A2373V|ZFHX4_uc003yaw.1_Missense_Mutation_p.A2328V	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2328						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ACGGATGCAGCTAAAAACGCT	0.512										HNSCC(33;0.089)			49	56	---	---	---	---	PASS
DNTT	1791	broad.mit.edu	37	10	98064245	98064245	+	5'UTR	SNP	G	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98064245G>A	uc001kmf.2	+	1					DNTT_uc001kmg.2_5'UTR	NM_004088	NP_004079	P04053	TDT_HUMAN	terminal deoxynucleotidyltransferase isoform 1						DNA modification	nucleus	DNA binding|DNA nucleotidylexotransferase activity|DNA-directed DNA polymerase activity|metal ion binding			ovary(1)	1		Colorectal(252;0.0815)|all_hematologic(284;0.224)		Epithelial(162;7.97e-08)|all cancers(201;1.89e-06)		GGCAGCAGCAGCCTCTTCCCA	0.602													4	22	---	---	---	---	PASS
MTA2	9219	broad.mit.edu	37	11	62361993	62361993	+	Nonsense_Mutation	SNP	C	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62361993C>A	uc001ntq.1	-	16	2068	c.1687G>T	c.(1687-1689)GAG>TAG	p.E563*	TUT1_uc001nto.2_5'Flank|MTA2_uc010rlx.1_Nonsense_Mutation_p.E390*	NM_004739	NP_004730	O94776	MTA2_HUMAN	metastasis-associated protein 2	563					chromatin assembly or disassembly	NuRD complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2						CTCACAGTCTCATAGGCCCGT	0.542													4	105	---	---	---	---	PASS
PDZRN4	29951	broad.mit.edu	37	12	41582515	41582515	+	5'Flank	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41582515C>T	uc010skn.1	+							NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				ACCGCGCCCGCGGCTGCGGCC	0.741													5	4	---	---	---	---	PASS
UNG	7374	broad.mit.edu	37	12	109537062	109537062	+	Silent	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109537062C>T	uc001tnz.1	+	3	478	c.408C>T	c.(406-408)ACC>ACT	p.T136T	UNG_uc001toa.1_Silent_p.T127T	NM_080911	NP_550433	P13051	UNG_HUMAN	uracil-DNA glycosylase isoform UNG2	136					base-excision repair|interspecies interaction between organisms	mitochondrion|nucleus	protein binding|uracil DNA N-glycosylase activity			lung(1)|central_nervous_system(1)	2						AAGTCTTCACCTGGACCCAGA	0.358								BER_DNA_glycosylases	Immune_Deficiency_with_Hyper-IgM				33	42	---	---	---	---	PASS
CDK5RAP3	80279	broad.mit.edu	37	17	46054123	46054123	+	Missense_Mutation	SNP	G	A	A	rs34460325		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46054123G>A	uc002imr.2	+	9	928	c.844G>A	c.(844-846)GAC>AAC	p.D282N	CDK5RAP3_uc010wlc.1_Missense_Mutation_p.D302N|CDK5RAP3_uc002imq.1_Missense_Mutation_p.D57N|CDK5RAP3_uc002imu.2_Missense_Mutation_p.D126N|CDK5RAP3_uc002ims.2_Missense_Mutation_p.D195N|CDK5RAP3_uc002imv.2_Missense_Mutation_p.D126N|CDK5RAP3_uc002imw.2_Missense_Mutation_p.D126N|CDK5RAP3_uc002imx.2_Missense_Mutation_p.D57N	NM_176096	NP_788276	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	282					brain development|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation		neuronal Cdc2-like kinase binding				0						TGAGGGGACTGACTCTGGCAT	0.502													24	44	---	---	---	---	PASS
LIMD2	80774	broad.mit.edu	37	17	61776286	61776286	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61776286G>A	uc002jbj.3	-	4	275	c.97C>T	c.(97-99)CGG>TGG	p.R33W	LIMD2_uc002jbk.3_Missense_Mutation_p.A34V|LIMD2_uc002jbl.3_Missense_Mutation_p.R33W	NM_030576	NP_085053	Q9BT23	LIMD2_HUMAN	LIM domain containing 2	33							zinc ion binding				0						ACCTGGGCCCGCAGGCTGAAG	0.662													4	99	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	19	19478779	19478779	+	IGR	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19478779C>T								KIAA0892 (9217 upstream) : GATAD2A (17863 downstream)																							GGCCACCCCTCAGGGGACACT	0.617													6	6	---	---	---	---	PASS
LRFN1	57622	broad.mit.edu	37	19	39805231	39805231	+	Missense_Mutation	SNP	A	C	C			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39805231A>C	uc002okw.2	-	1	746	c.746T>G	c.(745-747)TTC>TGC	p.F249C		NM_020862	NP_065913	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III	249	Extracellular (Potential).					cell junction|integral to membrane|postsynaptic density|postsynaptic membrane				ovary(2)	2	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GTTGCCGCCGAAGCTGACGGT	0.692													10	22	---	---	---	---	PASS
ZNF404	342908	broad.mit.edu	37	19	44378036	44378036	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44378036C>T	uc002oxs.3	-	2	330	c.321G>A	c.(319-321)ATG>ATA	p.M107I		NM_001033719	NP_001028891	Q494X3	ZN404_HUMAN	zinc finger protein 404	110					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)				TTTTGAATATCATTTGACTAA	0.328													23	186	---	---	---	---	PASS
CEP250	11190	broad.mit.edu	37	20	34054842	34054842	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34054842C>T	uc002xcm.2	+	9	1215	c.544C>T	c.(544-546)CGG>TGG	p.R182W	CEP250_uc010zve.1_5'UTR|CEP250_uc010gfe.1_RNA|CEP250_uc010zvd.1_RNA|CEP250_uc002xco.2_5'UTR	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2	182					centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			CAGTCTATGGCGGGAGGTTGT	0.532													30	46	---	---	---	---	PASS
ZNF334	55713	broad.mit.edu	37	20	45130587	45130587	+	Missense_Mutation	SNP	T	C	C			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45130587T>C	uc002xsc.2	-	5	1575	c.1391A>G	c.(1390-1392)AAT>AGT	p.N464S	ZNF334_uc002xsa.2_Missense_Mutation_p.N487S|ZNF334_uc002xsb.2_Missense_Mutation_p.N426S|ZNF334_uc002xsd.2_Missense_Mutation_p.N426S|ZNF334_uc010ghl.2_Missense_Mutation_p.N463S	NM_018102	NP_060572	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334 isoform a	464	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)				CCCACATTCATTACATTCATA	0.363													66	68	---	---	---	---	PASS
COL18A1	80781	broad.mit.edu	37	21	46888159	46888159	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46888159G>A	uc011afs.1	+	2	1376	c.1355G>A	c.(1354-1356)CGC>CAC	p.R452H	COL18A1_uc002zhg.2_Missense_Mutation_p.R37H|COL18A1_uc002zhi.2_Missense_Mutation_p.R217H	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	452					cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		TTTGCAGAGCGCATCAGCGAG	0.667													3	37	---	---	---	---	PASS
SGSM1	129049	broad.mit.edu	37	22	25320198	25320198	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25320198G>A	uc003abg.2	+	26	3561	c.3404G>A	c.(3403-3405)CGG>CAG	p.R1135Q	SGSM1_uc003abh.2_Missense_Mutation_p.R1074Q|SGSM1_uc010guu.1_Missense_Mutation_p.R1080Q|SGSM1_uc003abj.2_Missense_Mutation_p.R1019Q|SGSM1_uc003abi.1_Missense_Mutation_p.R1055Q	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1	1135						Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5						AAGCTGGCGCGGGACCTCGTG	0.562													10	24	---	---	---	---	PASS
ATRX	546	broad.mit.edu	37	X	76814318	76814318	+	Splice_Site	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76814318C>T	uc004ecp.3	-	29	6559	c.6327_splice	c.e29-1	p.R2109_splice	ATRX_uc004ecq.3_Splice_Site_p.R2071_splice|ATRX_uc004eco.3_Splice_Site_p.R1894_splice	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1						DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	TAATCGTCCTCTGAAAATGAA	0.274			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						22	11	---	---	---	---	PASS
TAF7L	54457	broad.mit.edu	37	X	100538563	100538563	+	Missense_Mutation	SNP	G	A	A	rs145455495		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100538563G>A	uc004ehb.2	-	4	424	c.412C>T	c.(412-414)CGC>TGC	p.R138C	TAF7L_uc004eha.2_Missense_Mutation_p.R52C|TAF7L_uc004ehc.1_Missense_Mutation_p.R52C	NM_024885	NP_079161	Q5H9L4	TAF7L_HUMAN	TATA box binding protein-associated factor, RNA	138					cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription initiation from RNA polymerase II promoter	cytoplasm|transcription factor TFIID complex	binding			breast(1)	1						ACTGCATGGCGCCCATCAGCT	0.398													115	128	---	---	---	---	PASS
AGRN	375790	broad.mit.edu	37	1	970550	970552	+	Intron	DEL	GGG	-	-	rs80124228		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:970550_970552delGGG	uc001ack.1	+							NM_198576	NP_940978	O00468	AGRIN_HUMAN	agrin precursor						axon guidance|clustering of voltage-gated sodium channels|muscarinic acetylcholine receptor signaling pathway|receptor clustering	basal lamina	laminin binding|structural constituent of cytoskeleton			central_nervous_system(2)|breast(1)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		GGCTAGCGGTGGGGGGGGGGGGG	0.650													12	6	---	---	---	---	
SLC35A3	23443	broad.mit.edu	37	1	100480733	100480734	+	Intron	DEL	AG	-	-	rs140167739	by1000genomes	TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100480733_100480734delAG	uc001dsp.1	+						SLC35A3_uc001dsq.1_Intron|SLC35A3_uc009wdy.1_Intron|SLC35A3_uc001dsr.1_Intron|SLC35A3_uc001dss.1_Intron	NM_012243	NP_036375	Q9Y2D2	S35A3_HUMAN	solute carrier family 35 member 3A						UDP-N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	sugar:hydrogen symporter activity|UDP-N-acetylglucosamine transmembrane transporter activity				0		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.124)|all cancers(265;0.198)|Lung(183;0.199)		aaaaaaaaaaagaaaGTAATCT	0.114													4	2	---	---	---	---	
IGFN1	91156	broad.mit.edu	37	1	201195812	201195812	+	Intron	DEL	A	-	-	rs34207437		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201195812delA	uc001gwc.2	+						IGFN1_uc001gwb.2_Intron	NM_178275	NP_840059			RecName: Full=Immunoglobulin-like and fibronectin type III domain-containing protein 1; AltName: Full=EEF1A2-binding protein 1; AltName: Full=KY-interacting protein 1;											ovary(2)|pancreas(1)	3						TATTAGCTACAAAAAAAAATC	0.363													3	3	---	---	---	---	
WDR35	57539	broad.mit.edu	37	2	20141610	20141611	+	Intron	INS	-	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20141610_20141611insA	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron|WDR35_uc002rdk.3_Intron	NM_001006657	NP_001006658	Q9P2L0	WDR35_HUMAN	WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTTTAAAGACAAAAAAAAAGT	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64602903	64602905	+	IGR	DEL	CAC	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64602903_64602905delCAC								PELI1 (231298 upstream) : HSPC159 (78422 downstream)																							ccaccaccatcaccaccatcacc	0.000													6	4	---	---	---	---	
C2orf27A	29798	broad.mit.edu	37	2	132491392	132491392	+	Intron	DEL	T	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132491392delT	uc002ttf.1	+							NM_013310	NP_037442	Q580R0	CB027_HUMAN	hypothetical protein LOC29798												0						atatatttaatttttttattt	0.274													9	5	---	---	---	---	
ROBO1	6091	broad.mit.edu	37	3	78663959	78663959	+	Intron	DEL	A	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78663959delA	uc003dqe.2	-						ROBO1_uc003dqb.2_Intron|ROBO1_uc003dqc.2_Intron|ROBO1_uc003dqd.2_Intron|ROBO1_uc010hoh.2_Intron|ROBO1_uc011bgl.1_Intron	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GCCTAAGGAGAAAAAAAAAAA	0.403													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	29769921	29769922	+	IGR	INS	-	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29769921_29769922insG								HCG4 (9071 upstream) : HLA-G (24834 downstream)																							TAGGATCTCATGCCCTGCCTCC	0.510													4	6	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32552253	32552254	+	Intron	INS	-	G	G	rs149553038	by1000genomes	TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32552253_32552254insG	uc003obk.3	-						HLA-DRB1_uc011dqa.1_5'Flank|HLA-DRB6_uc003obo.1_5'Flank|HLA-DRB1_uc003obp.3_Intron|HLA-DRB1_uc011dqb.1_5'Flank|HLA-DRB1_uc011dqc.1_5'Flank	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						GTGCGGGCGCTGGAACCTTAAC	0.698													3	4	---	---	---	---	
SGK1	6446	broad.mit.edu	37	6	134492496	134492497	+	Intron	INS	-	TG	TG	rs141268381	by1000genomes	TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134492496_134492497insTG	uc003qen.3	-						SGK1_uc003qeo.3_Intron|SGK1_uc011ect.1_Intron|SGK1_uc011ecu.1_Intron|SGK1_uc011ecv.1_Intron|SGK1_uc011ecw.1_Intron	NM_005627	NP_005618	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1 isoform						apoptosis|response to stress|sodium ion transport	endoplasmic reticulum|nucleus|plasma membrane	ATP binding|protein binding|protein serine/threonine kinase activity			skin(3)|stomach(1)|lung(1)|central_nervous_system(1)	6	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		gtgtgtgtgtttgtgtgtgtgt	0.356													6	5	---	---	---	---	
MTMR9	66036	broad.mit.edu	37	8	11157337	11157337	+	Intron	DEL	T	-	-	rs3840697		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11157337delT	uc003wtm.2	+						MTMR9_uc010lrx.2_Intron|MTMR9_uc011kxa.1_Intron	NM_015458	NP_056273	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9							cytoplasm	phosphatase activity|protein binding				0			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		GGCAGATGCCTTTGTTAGATA	0.343													2	6	---	---	---	---	
NR4A3	8013	broad.mit.edu	37	9	102589219	102589220	+	Intron	INS	-	T	T	rs142732047	by1000genomes	TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102589219_102589220insT	uc004baf.1	+						NR4A3_uc004bae.2_Intron|NR4A3_uc004bag.1_Intron|NR4A3_uc004bai.2_Intron	NM_006981	NP_008912	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|thyroid hormone receptor activity|zinc ion binding		EWSR1/NR4A3(140)|TAF15/NR4A3(33)	bone(173)	173		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				AAAAACCGCCGTTTTTTACCAT	0.386			T	EWSR1	extraskeletal myxoid chondrosarcoma								9	7	---	---	---	---	
RALGPS1	9649	broad.mit.edu	37	9	129739855	129739856	+	Intron	INS	-	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129739855_129739856insT	uc004bqo.1	+						RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron	NM_014636	NP_055451	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1						ATTTGGTCTTGTTTTTTATCTC	0.337													10	6	---	---	---	---	
INSC	387755	broad.mit.edu	37	11	15134193	15134194	+	Intron	INS	-	G	G	rs148001480	by1000genomes	TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15134193_15134194insG	uc001mly.2	+						INSC_uc001mlz.2_5'Flank	NM_001031853	NP_001027024	Q1MX18	INSC_HUMAN	inscuteable isoform a						cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5						tATTGGGAAGTGGGGGGGGGGC	0.401													9	4	---	---	---	---	
DYNC1H1	1778	broad.mit.edu	37	14	102450009	102450010	+	Intron	INS	-	T	T	rs77079653		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102450009_102450010insT	uc001yks.2	+							NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1						cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						tttgtttggtgttttttttttg	0.134													6	3	---	---	---	---	
RTF1	23168	broad.mit.edu	37	15	41771141	41771142	+	Intron	INS	-	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41771141_41771142insT	uc001zny.2	+							NM_015138	NP_055953	Q92541	RTF1_HUMAN	Paf1/RNA polymerase II complex component						histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		TTGTAATTGCCTTTTTTTTTTT	0.470													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	56038833	56038833	+	IGR	DEL	G	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56038833delG								PRTG (3656 upstream) : NEDD4 (80298 downstream)																							aaaaaaaaaagaaGCTCCTGG	0.279													5	3	---	---	---	---	
LCMT1	51451	broad.mit.edu	37	16	25123136	25123137	+	5'UTR	DEL	GT	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25123136_25123137delGT	uc002dnx.1	+	1					LCMT1_uc002dny.1_5'UTR|LCMT1_uc002dnz.1_5'UTR|LCMT1_uc002doa.1_5'UTR|LCMT1_uc002dnw.1_RNA	NM_016309	NP_057393	Q9UIC8	LCMT1_HUMAN	leucine carboxyl methyltransferase 1 isoform a								protein binding|protein C-terminal carboxyl O-methyltransferase activity|S-adenosylmethionine-dependent methyltransferase activity				0				GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)	GGCTCGCGCCGTCCCCCGCCGC	0.683													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32176904	32176904	+	IGR	DEL	G	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32176904delG								HERC2P4 (13030 upstream) : TP53TG3B (507937 downstream)																							AAAAAAAAAAGAAATCAAAGC	0.284													4	2	---	---	---	---	
TRPV1	7442	broad.mit.edu	37	17	3494199	3494200	+	Intron	INS	-	C	C	rs140971657	by1000genomes	TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3494199_3494200insC	uc010vrr.1	-						TRPV1_uc010vro.1_Intron|TRPV1_uc010vrp.1_Intron|TRPV1_uc010vrq.1_Intron|TRPV1_uc010vrs.1_Intron|TRPV1_uc010vrt.1_Intron|TRPV1_uc010vru.1_Intron	NM_080706	NP_542437	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel,						cell surface receptor linked signaling pathway|chemosensory behavior|thermoception	cell junction|dendritic spine membrane|integral to plasma membrane|postsynaptic membrane	ATP binding|calcium channel activity|calmodulin binding			ovary(1)	1				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	GGACAACCATGCCCCCCTGCTT	0.649													2	6	---	---	---	---	
FXR2	9513	broad.mit.edu	37	17	7495379	7495380	+	Intron	DEL	TC	-	-	rs138014385		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7495379_7495380delTC	uc002gia.1	-						MPDU1_uc010vuc.1_Intron|SOX15_uc002ghy.1_5'Flank|SOX15_uc002ghz.1_5'Flank	NM_004860	NP_004851	P51116	FXR2_HUMAN	fragile X mental retardation syndrome related							cytosolic large ribosomal subunit	protein binding|RNA binding				0				READ - Rectum adenocarcinoma(115;0.17)		CATGATCCAGTCTCTCTTACTT	0.470													3	3	---	---	---	---	
RPL26	6154	broad.mit.edu	37	17	8285267	8285268	+	Intron	DEL	AG	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8285267_8285268delAG	uc002glh.1	-							NM_000987	NP_000978	P61254	RL26_HUMAN	ribosomal protein L26						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0						aaaaaaaaaaaGATTTTCACCA	0.193													4	2	---	---	---	---	
ITGB3	3690	broad.mit.edu	37	17	45377704	45377705	+	Intron	INS	-	GT	GT	rs145406552		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45377704_45377705insGT	uc002ilj.2	+						ITGB3_uc010wkr.1_Intron	NM_000212	NP_000203	P05106	ITB3_HUMAN	integrin beta chain, beta 3 precursor						activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)	CTTACAGGCGCGCGCGCGCgtg	0.520													4	2	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	58888881	58888882	+	Intron	INS	-	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58888881_58888882insA	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			AGTTCAGAGGTAAaaaaaaaaa	0.252													4	2	---	---	---	---	
LOC651250	651250	broad.mit.edu	37	17	66122028	66122029	+	RNA	DEL	AA	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66122028_66122029delAA	uc002jgq.2	+	6		c.1151_1152delAA			LOC651250_uc002kit.2_RNA|LOC651250_uc002jgo.1_Intron	NR_027418				Homo sapiens cDNA FLJ33831 fis, clone CTONG2003937.												0						TTCGTGAGCTaaaaaaaaaaaa	0.267													4	2	---	---	---	---	
SRP68	6730	broad.mit.edu	37	17	74036119	74036126	+	Intron	DEL	TCACTCAA	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74036119_74036126delTCACTCAA	uc002jqk.1	-						SRP68_uc010wsu.1_Intron|SRP68_uc002jql.1_Intron|SRP68_uc002jqj.1_Intron	NM_014230	NP_055045	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa						response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding			ovary(1)	1						aggggccatctcactcaatcactcaatc	0.082													4	2	---	---	---	---	
ZNF562	54811	broad.mit.edu	37	19	9764668	9764669	+	Intron	INS	-	T	T	rs145922849		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9764668_9764669insT	uc010xks.1	-						ZNF562_uc002mly.2_Intron|ZNF562_uc002mlx.2_Intron|ZNF562_uc010xkt.1_Intron|ZNF562_uc010xku.1_Intron|ZNF562_uc010xkv.1_Intron|ZNF562_uc010xkw.1_Intron	NM_001130032	NP_001123504	Q6V9R5	ZN562_HUMAN	zinc finger protein 562 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTAATGTTTAAttttttttttt	0.119													3	3	---	---	---	---	
PRKCG	5582	broad.mit.edu	37	19	54396035	54396036	+	Intron	DEL	CG	-	-	rs41275812	by1000genomes	TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54396035_54396036delCG	uc002qcq.1	+						PRKCG_uc010eqz.1_Intron|PRKCG_uc010yef.1_Intron|PRKCG_uc010yeg.1_Intron|PRKCG_uc010yeh.1_Intron	NM_002739	NP_002730	P05129	KPCG_HUMAN	protein kinase C, gamma						activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|synaptic transmission	cytosol	ATP binding|protein kinase C activity|zinc ion binding			lung(4)|ovary(2)|pancreas(2)|large_intestine(1)	9	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)		cacacacacacgcacacacacg	0.213													5	3	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62074205	62074207	+	Intron	DEL	CAC	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62074205_62074207delCAC	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	ccatcaccatcaccaccaccatc	0.000													4	2	---	---	---	---	
SLC2A11	66035	broad.mit.edu	37	22	24199261	24199261	+	Intron	DEL	G	-	-	rs71184919		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24199261delG	uc002zyn.3	+						SLC2A11_uc002zyl.1_Intron|SLC2A11_uc002zym.3_Intron|SLC2A11_uc002zyo.3_Intron|SLC2A11_uc011ajc.1_5'UTR|SLC2A11_uc011ajd.1_5'Flank|SLC2A11_uc002zyp.3_5'Flank	NM_001024938	NP_001020109	Q9BYW1	GTR11_HUMAN	glucose transporter protein 10 isoform c							integral to membrane|plasma membrane	sugar transmembrane transporter activity			ovary(1)	1						GTGTGTGTGTGGGGGGGGGGG	0.612													2	7	---	---	---	---	
CACNA1I	8911	broad.mit.edu	37	22	39994293	39994294	+	Intron	INS	-	GCCCT	GCCCT	rs148307297	by1000genomes	TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39994293_39994294insGCCCT	uc003ayc.2	+						CACNA1I_uc003ayd.2_Intron|CACNA1I_uc003aye.2_Intron|CACNA1I_uc003ayf.2_Intron	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,						axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)	cgccccgccccgccctgcccTC	0.327													3	4	---	---	---	---	
FAM19A5	25817	broad.mit.edu	37	22	49103825	49103837	+	Intron	DEL	TCCTGACCATCTG	-	-	rs141710021		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49103825_49103837delTCCTGACCATCTG	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436	Q7Z5A7	F19A5_HUMAN	family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)		GGTGCTAAATTCCTGACCATCTGTCCTGGGGCA	0.620													5	8	---	---	---	---	
