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
CPSF3L	54973	broad.mit.edu	37	1	1249171	1249171	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1249171A>C	uc001aee.1	-	9	956	c.898T>G	c.(898-900)TTT>GTT	p.F300V	CPSF3L_uc009vjy.1_RNA|CPSF3L_uc001aef.1_Missense_Mutation_p.F306V|CPSF3L_uc009vjz.1_Missense_Mutation_p.F278V|CPSF3L_uc010nyj.1_Missense_Mutation_p.F271V|CPSF3L_uc001aeg.1_Missense_Mutation_p.F176V|CPSF3L_uc001aeh.1_Missense_Mutation_p.F199V|CPSF3L_uc001aei.1_Missense_Mutation_p.F202V|CPSF3L_uc001aej.1_Missense_Mutation_p.F127V|CPSF3L_uc001aek.1_Missense_Mutation_p.F42V	NM_017871	NP_060341	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor	300						Golgi apparatus|nucleus	hydrolase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;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)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		TTGAACTCAAACATGTTCCTC	0.587													30	85	---	---	---	---	PASS
MIIP	60672	broad.mit.edu	37	1	12081816	12081816	+	Silent	SNP	G	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12081816G>T	uc001ato.1	+	2	213	c.33G>T	c.(31-33)CGG>CGT	p.R11R		NM_021933	NP_068752	Q5JXC2	MIIP_HUMAN	invasion inhibitory protein 45	11										ovary(1)	1						CACAGCTGCGGCTGCTCAATC	0.677													8	25	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16918717	16918717	+	5'UTR	SNP	C	T	T	rs3872321	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918717C>T	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)		AAACAAGGTTCGAGGTGCCTG	0.478													5	23	---	---	---	---	PASS
UBXN10	127733	broad.mit.edu	37	1	20517187	20517187	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20517187C>T	uc001bdb.2	+	2	217	c.133C>T	c.(133-135)CGG>TGG	p.R45W		NM_152376	NP_689589	Q96LJ8	UBX10_HUMAN	UBX domain protein 10	45										ovary(1)	1						CGCCAAGGGACGGACAAGACC	0.537													45	108	---	---	---	---	PASS
ATP1B1	481	broad.mit.edu	37	1	169100955	169100955	+	RNA	SNP	A	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169100955A>T	uc001gfs.1	+	6		c.1199A>T						P05026	AT1B1_HUMAN	Synthetic construct DNA, clone: pF1KB8186, Homo sapiens ATP1B1 gene for ATPase, Na+/K+ transporting, beta 1 polypeptide, without stop codon, in Flexi system.						ATP biosynthetic process|blood coagulation|leukocyte migration	sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	all_hematologic(923;0.208)					AATGTAAATTAAAGTGTAGCA	0.313													6	8	---	---	---	---	PASS
ZBTB37	84614	broad.mit.edu	37	1	173834625	173834625	+	5'Flank	SNP	A	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173834625A>G	uc009wwp.1	+						GAS5_uc001gji.2_RNA|GAS5_uc001gjj.2_RNA|GAS5_uc001gjk.2_RNA|SNORD81_uc009wwi.1_5'Flank|SNORD47_uc001gjl.2_5'Flank|SNORD80_uc009wwj.1_5'Flank|SNORD79_uc009wwk.1_5'Flank|ZBTB37_uc001gjp.1_5'Flank|ZBTB37_uc001gjq.3_5'Flank|ZBTB37_uc001gjr.2_5'Flank	NM_001122770	NP_001116242	Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AAGGTATGACAGGAACTGTCT	0.348													16	36	---	---	---	---	PASS
GAS5	60674	broad.mit.edu	37	1	173835706	173835706	+	Splice_Site	SNP	C	A	A	rs112023202		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173835706C>A	uc001gji.2	-	3		c.157_splice	c.e3-1		GAS5_uc001gjj.2_Splice_Site|GAS5_uc001gjk.2_RNA|SNORD81_uc009wwi.1_5'Flank|SNORD47_uc001gjl.2_5'Flank|SNORD80_uc009wwj.1_5'Flank|SNORD79_uc009wwk.1_5'Flank|SNORD78_uc009wwl.2_5'Flank|SNORD44_uc001gjn.1_5'Flank|SNORD77_uc009wwm.1_5'Flank|ZBTB37_uc001gjp.1_5'Flank|ZBTB37_uc001gjq.3_5'Flank|ZBTB37_uc009wwp.1_5'Flank|ZBTB37_uc001gjr.2_5'Flank					Homo sapiens mRNA; cDNA DKFZp564D0164 (from clone DKFZp564D0164).												0						TCTTTAGGACCTGGGAAGAAA	0.418													11	26	---	---	---	---	PASS
CFH	3075	broad.mit.edu	37	1	196642242	196642242	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196642242G>A	uc001gtj.3	+	2	433	c.193G>A	c.(193-195)GTA>ATA	p.V65I	CFH_uc001gti.3_Missense_Mutation_p.V65I|CFH_uc009wyw.2_Missense_Mutation_p.V65I|CFH_uc009wyx.2_Missense_Mutation_p.V65I	NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	65	Sushi 1.				complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6						TGTAATAATGGTATGCAGGAA	0.378													51	116	---	---	---	---	PASS
SDCCAG8	10806	broad.mit.edu	37	1	243581274	243581274	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243581274T>A	uc001hzw.2	+	15	1905	c.1749T>A	c.(1747-1749)AAT>AAA	p.N583K	SDCCAG8_uc010pyk.1_Missense_Mutation_p.N438K|SDCCAG8_uc010pyl.1_Missense_Mutation_p.N395K|SDCCAG8_uc001hzx.2_Intron	NM_006642	NP_006633	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	583	Mediates interaction with OFD1.|Gln-rich.|Potential.|Sufficient for homodimerization (By similarity).				establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		TTCTAGAAAATGAACAGTATT	0.373													44	127	---	---	---	---	PASS
PXDN	7837	broad.mit.edu	37	2	1653137	1653137	+	Silent	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1653137C>T	uc002qxa.2	-	17	2479	c.2415G>A	c.(2413-2415)ACG>ACA	p.T805T		NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	805					extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TGACGGTCTCCGTCCCGATCA	0.652													24	38	---	---	---	---	PASS
UGP2	7360	broad.mit.edu	37	2	64069233	64069233	+	5'UTR	SNP	A	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64069233A>C	uc002scm.2	+	1					UGP2_uc002scl.2_Intron|UGP2_uc010ypx.1_5'Flank	NM_006759	NP_006750	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2 isoform a						glycogen biosynthetic process|phosphorylation|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	metal ion binding|protein binding|UTP:glucose-1-phosphate uridylyltransferase activity				0						CGGTTGTTAAAGCAGGAGAGG	0.363													14	37	---	---	---	---	PASS
NCRNA00164	554226	broad.mit.edu	37	2	132905792	132905792	+	RNA	SNP	G	C	C	rs143919579	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132905792G>C	uc002tti.3	-	7		c.1099C>G			NCRNA00164_uc002ttj.3_RNA	NR_027019				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						TGTTCCTTCAGATGTTCCTTC	0.443													4	18	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152397301	152397301	+	Silent	SNP	T	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152397301T>C	uc010fnx.2	-	109	15785	c.15594A>G	c.(15592-15594)GAA>GAG	p.E5198E	NEB_uc002txr.2_Silent_p.E1621E	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	5198	Nebulin 141.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGGTGGCAAGTTCAACATACA	0.418													23	68	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170011038	170011038	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170011038T>G	uc002ues.2	-	66	12440	c.12227A>C	c.(12226-12228)GAG>GCG	p.E4076A		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	4076	Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	TTGAAGATACTCTGAGAACCT	0.393													55	117	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179479674	179479674	+	Silent	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179479674C>T	uc010zfg.1	-	209	41180	c.40956G>A	c.(40954-40956)GAG>GAA	p.E13652E	uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.E7347E|TTN_uc010zfi.1_Silent_p.E7280E|TTN_uc010zfj.1_Silent_p.E7155E	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	14579							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTTGccttcctcaagacctg	0.303													3	22	---	---	---	---	PASS
SSFA2	6744	broad.mit.edu	37	2	182757372	182757372	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182757372G>A	uc002uoi.2	+	2	564	c.242G>A	c.(241-243)TGG>TAG	p.W81*	SSFA2_uc010zfn.1_Nonsense_Mutation_p.W81*|SSFA2_uc002uoh.2_Nonsense_Mutation_p.W81*|SSFA2_uc002uoj.2_Nonsense_Mutation_p.W81*|SSFA2_uc002uok.2_RNA|SSFA2_uc010zfo.1_5'UTR	NM_001130445	NP_001123917	P28290	SSFA2_HUMAN	sperm specific antigen 2 isoform 1	81						cytoplasm|plasma membrane	actin binding			breast(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			ATCGCGATATGGCTCAAGGAC	0.682													19	55	---	---	---	---	PASS
CDCP1	64866	broad.mit.edu	37	3	45134910	45134910	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45134910C>G	uc003com.2	-	6	1621	c.1486G>C	c.(1486-1488)GGC>CGC	p.G496R		NM_022842	NP_073753	Q9H5V8	CDCP1_HUMAN	CUB domain-containing protein 1 isoform 1	496	CUB.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		CAGAAGGAGCCGAAGTACAGG	0.597													24	47	---	---	---	---	PASS
BOC	91653	broad.mit.edu	37	3	112969403	112969403	+	Silent	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112969403C>T	uc003dzx.2	+	4	720	c.99C>T	c.(97-99)AAC>AAT	p.N33N	BOC_uc010hqi.2_Silent_p.N33N|BOC_uc003dzy.2_Silent_p.N33N|BOC_uc003dzz.2_Silent_p.N33N|BOC_uc003dzw.1_Silent_p.N33N|BOC_uc003eaa.1_Silent_p.N33N	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	33	Extracellular (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)			TTCCTCCAGACGAGGTCCCTC	0.552													27	88	---	---	---	---	PASS
FAM162A	26355	broad.mit.edu	37	3	122123119	122123119	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122123119G>A	uc003eez.2	+	3	262	c.172G>A	c.(172-174)GTG>ATG	p.V58M	FAM162A_uc011bjq.1_Missense_Mutation_p.V58M	NM_014367	NP_055182	Q96A26	F162A_HUMAN	growth and transformation-dependent protein	58						integral to membrane				ovary(1)	1						TTACAACAGAGTGCCTTTACA	0.373													22	30	---	---	---	---	PASS
SLC41A3	54946	broad.mit.edu	37	3	125725761	125725761	+	Intron	SNP	T	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125725761T>G	uc003eij.2	-						SLC41A3_uc003eii.2_3'UTR|SLC41A3_uc003eil.2_3'UTR|SLC41A3_uc003eik.2_Intron|SLC41A3_uc011bkh.1_3'UTR	NM_001008485	NP_001008485	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3 isoform 1							integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(114;0.167)		GAGGCAGGGGTCAACCATCCC	0.522													5	43	---	---	---	---	PASS
SAMD7	344658	broad.mit.edu	37	3	169646258	169646258	+	Silent	SNP	G	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169646258G>T	uc003fgd.2	+	7	1200	c.933G>T	c.(931-933)CTG>CTT	p.L311L	SAMD7_uc003fge.2_Silent_p.L311L|SAMD7_uc011bpo.1_Silent_p.L212L	NM_182610	NP_872416	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	311										skin(1)	1	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)			CACATGCACTGGTTACAATTG	0.388													7	256	---	---	---	---	PASS
TP63	8626	broad.mit.edu	37	3	189590896	189590896	+	Intron	SNP	T	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189590896T>C	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron|TP63_uc003fsa.2_3'UTR|TP63_uc003fsb.2_Intron|TP63_uc003fsc.2_Intron|TP63_uc003fsd.2_Intron|TP63_uc010hzd.1_Intron	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		TAGCAGATTGTCATAGATTCA	0.403									Hay-Wells_syndrome	HNSCC(45;0.13)			14	43	---	---	---	---	PASS
ZNF595	152687	broad.mit.edu	37	4	53233	53233	+	5'UTR	SNP	C	A	A	rs7658521		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53233C>A	uc003fzv.1	+	1					ZNF595_uc003fzu.1_RNA|ZNF718_uc003fzt.3_5'Flank|ZNF595_uc010iay.1_RNA|ZNF595_uc011bus.1_5'UTR|ZNF595_uc011but.1_5'UTR	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		CTGGCTCCTGCGAGGGCTTGG	0.627													6	39	---	---	---	---	PASS
YTHDC1	91746	broad.mit.edu	37	4	69188621	69188621	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69188621C>A	uc003hdx.2	-	11	1800	c.1447G>T	c.(1447-1449)GAA>TAA	p.E483*	YTHDC1_uc003hdy.2_Nonsense_Mutation_p.E465*	NM_001031732	NP_001026902	Q96MU7	YTDC1_HUMAN	splicing factor YT521-B isoform 1	483	YTH.									upper_aerodigestive_tract(1)|ovary(1)	2						GTTCCACATTCAAGTTCAATT	0.373													46	123	---	---	---	---	PASS
ABCE1	6059	broad.mit.edu	37	4	146041212	146041212	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146041212C>A	uc003ijx.2	+	11	1491	c.1051C>A	c.(1051-1053)CCA>ACA	p.P351T	ABCE1_uc003ijy.2_Missense_Mutation_p.P351T|ABCE1_uc010iot.2_RNA	NM_001040876	NP_001035809	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E, member 1	351	ABC transporter 2.				interspecies interaction between organisms|response to virus|RNA catabolic process	mitochondrion	ATP binding|ATPase activity|electron carrier activity|iron-sulfur cluster binding|ribonuclease inhibitor activity			skin(1)	1	all_hematologic(180;0.151)					GTATAAATATCCAGGAATGAA	0.353													29	73	---	---	---	---	PASS
CCDC110	256309	broad.mit.edu	37	4	186382284	186382284	+	Silent	SNP	G	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186382284G>A	uc003ixu.3	-	5	343	c.267C>T	c.(265-267)AAC>AAT	p.N89N	CCDC110_uc003ixv.3_Intron|CCDC110_uc011ckt.1_Silent_p.N89N	NM_152775	NP_689988	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110 isoform a	89						nucleus				central_nervous_system(1)	1		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		TAATACTTTTGTTCAATATTT	0.299													8	233	---	---	---	---	PASS
POLR3G	10622	broad.mit.edu	37	5	89781415	89781415	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89781415G>A	uc003kjq.2	+	2	231	c.31G>A	c.(31-33)GCT>ACT	p.A11T	POLR3G_uc011cuc.1_Missense_Mutation_p.A11T	NM_006467	NP_006458	O15318	RPC7_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	11					innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|regulation of transcription from RNA polymerase III promoter|response to virus	DNA-directed RNA polymerase III complex	DNA-directed RNA polymerase activity				0		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;2.74e-31)|Epithelial(54;8.2e-26)|all cancers(79;3.86e-22)		AGGACGTGCTGCTTATACCTT	0.398													54	157	---	---	---	---	PASS
SLC36A1	206358	broad.mit.edu	37	5	150853235	150853235	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150853235G>C	uc003luc.2	+	8	942	c.725G>C	c.(724-726)AGG>ACG	p.R242T	GM2A_uc011dcs.1_Intron|SLC36A1_uc003lub.1_Missense_Mutation_p.R242T|SLC36A1_uc010jhw.1_Missense_Mutation_p.R242T	NM_078483	NP_510968	Q7Z2H8	S36A1_HUMAN	solute carrier family 36 member 1	242	Extracellular (Potential).				cellular nitrogen compound metabolic process|ion transport	endoplasmic reticulum|integral to membrane|lysosomal membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			skin(1)	1		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)|all_neural(839;0.138)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glycine(DB00145)|L-Alanine(DB00160)	GTCTTTCAGAGGATCCCAGAC	0.398													123	296	---	---	---	---	PASS
ODZ2	57451	broad.mit.edu	37	5	167673803	167673803	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167673803T>A	uc010jjd.2	+	27	5832	c.5832T>A	c.(5830-5832)TTT>TTA	p.F1944L	ODZ2_uc003lzr.3_Missense_Mutation_p.F1714L|ODZ2_uc003lzt.3_Missense_Mutation_p.F1317L|ODZ2_uc010jje.2_Missense_Mutation_p.F1208L	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		AGTATATATTTGAGTATGACT	0.512													7	488	---	---	---	---	PASS
DTNBP1	84062	broad.mit.edu	37	6	15615585	15615585	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15615585T>G	uc003nbm.2	-	6	572	c.401A>C	c.(400-402)CAT>CCT	p.H134P	DTNBP1_uc003nbl.2_Missense_Mutation_p.H53P|DTNBP1_uc003nbn.2_RNA|DTNBP1_uc003nbo.2_RNA|DTNBP1_uc003nbp.2_Missense_Mutation_p.H134P|DTNBP1_uc010jph.2_Missense_Mutation_p.H121P	NM_032122	NP_115498	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1 isoform a	134	Potential.				actin cytoskeleton reorganization|cellular membrane organization|neuron projection morphogenesis|post-Golgi vesicle-mediated transport|regulation of dopamine receptor signaling pathway	axon part|BLOC-1 complex|cell junction|dendritic spine|endoplasmic reticulum membrane|endosome membrane|growth cone|melanosome membrane|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|synaptic vesicle membrane|synaptosome	identical protein binding				0	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			GTCTTCCAGATGCAGCAGGTT	0.383									Hermansky-Pudlak_syndrome				53	146	---	---	---	---	PASS
TULP1	7287	broad.mit.edu	37	6	35479476	35479476	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35479476G>T	uc003okv.3	-	4	310	c.298C>A	c.(298-300)CGC>AGC	p.R100S	TULP1_uc003okw.3_Intron	NM_003322	NP_003313	O00294	TULP1_HUMAN	tubby like protein 1	100					dendrite development|eye photoreceptor cell development|phagocytosis|photoreceptor cell maintenance|positive regulation of phagocytosis	cell junction|cytoplasm|extracellular region|photoreceptor inner segment|photoreceptor outer segment|synapse	actin filament binding|phosphatidylinositol-4,5-bisphosphate binding			ovary(2)|central_nervous_system(1)	3						CGGGGGTCGCGCTTCTTGGCC	0.726													6	11	---	---	---	---	PASS
PHIP	55023	broad.mit.edu	37	6	79650693	79650693	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79650693T>G	uc003pir.2	-	40	5409	c.5183A>C	c.(5182-5184)GAT>GCT	p.D1728A	PHIP_uc003piq.2_Missense_Mutation_p.D752A|PHIP_uc011dyp.1_Missense_Mutation_p.D1727A|IRAK1BP1_uc010kbg.1_Intron|PHIP_uc003pio.3_Missense_Mutation_p.D614A	NM_017934	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1728					insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		GACTAGGAGATCTGCATCTAA	0.373													141	382	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152529239	152529239	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152529239C>G	uc010kiw.2	-	125	23294	c.22692G>C	c.(22690-22692)CAG>CAC	p.Q7564H	SYNE1_uc010kiv.2_Missense_Mutation_p.Q2088H|SYNE1_uc003qos.3_Missense_Mutation_p.Q2088H|SYNE1_uc003qot.3_Missense_Mutation_p.Q7493H|SYNE1_uc003qou.3_Missense_Mutation_p.Q7564H|SYNE1_uc003qor.3_Missense_Mutation_p.Q464H	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7564	HAT 11.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGCGCTGCCACTGGCGAATCT	0.517										HNSCC(10;0.0054)			3	117	---	---	---	---	PASS
MICALL2	79778	broad.mit.edu	37	7	1489860	1489860	+	Intron	SNP	G	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1489860G>A	uc003skj.3	-						MICALL2_uc003skl.1_RNA	NM_182924	NP_891554	Q8IY33	MILK2_HUMAN	MICAL-like 2 isoform 1							cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		GTGAGGCCGGGGCGGGGGCCA	0.567													43	112	---	---	---	---	PASS
MACC1	346389	broad.mit.edu	37	7	20180451	20180451	+	3'UTR	SNP	C	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20180451C>G	uc003sus.3	-	7					MACC1_uc010kug.2_3'UTR	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3						cacacacagacacacacacac	0.159													3	49	---	---	---	---	PASS
SPAM1	6677	broad.mit.edu	37	7	123595133	123595133	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123595133G>A	uc003vld.2	+	5	1439	c.1037G>A	c.(1036-1038)CGA>CAA	p.R346Q	SPAM1_uc003vle.2_Missense_Mutation_p.R346Q|SPAM1_uc011koa.1_Missense_Mutation_p.R2Q|SPAM1_uc003vlf.3_Missense_Mutation_p.R346Q|SPAM1_uc010lku.2_Missense_Mutation_p.R346Q	NM_153189	NP_694859	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 2	346					binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)	AGTATAATGCGAAGTATGGTA	0.294													68	279	---	---	---	---	PASS
SLC7A13	157724	broad.mit.edu	37	8	87229763	87229763	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87229763A>G	uc003ydq.1	-	3	1213	c.1115T>C	c.(1114-1116)ATA>ACA	p.I372T	SLC7A13_uc003ydr.1_Missense_Mutation_p.I363T	NM_138817	NP_620172	Q8TCU3	S7A13_HUMAN	solute carrier family 7, (cationic amino acid	372	Helical; Name=10; (Potential).					integral to membrane	amino acid transmembrane transporter activity			central_nervous_system(1)	1						CATTAATAATATAGACCATAA	0.323													43	76	---	---	---	---	PASS
RANBP6	26953	broad.mit.edu	37	9	6014375	6014375	+	Silent	SNP	G	A	A	rs146563217		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6014375G>A	uc003zjr.2	-	1	1244	c.1233C>T	c.(1231-1233)TCC>TCT	p.S411S	RANBP6_uc011lmf.1_Intron|RANBP6_uc003zjs.2_Intron	NM_012416	NP_036548	O60518	RNBP6_HUMAN	RAN binding protein 6	411	HEAT 3.				protein transport	cytoplasm|nucleus	binding			ovary(3)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		AAAGCAAAACGGAGTTAACTG	0.433													29	82	---	---	---	---	PASS
WNK2	65268	broad.mit.edu	37	9	95997219	95997219	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95997219C>T	uc004ati.1	+	4	1205	c.1205C>T	c.(1204-1206)GCG>GTG	p.A402V	WNK2_uc011lud.1_Missense_Mutation_p.A402V|WNK2_uc004atj.2_Missense_Mutation_p.A402V|WNK2_uc004atk.2_Missense_Mutation_p.A39V|WNK2_uc010mrc.1_Missense_Mutation_p.A402V|WNK2_uc010mrd.1_Missense_Mutation_p.A39V	NM_006648	NP_006639	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	402	Protein kinase.				intracellular protein kinase cascade		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1)	12						TGCCAGAATGCGGCCCAGATC	0.587													3	48	---	---	---	---	PASS
C10orf18	54906	broad.mit.edu	37	10	5790452	5790452	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5790452A>C	uc001iij.2	+	15	5693	c.5068A>C	c.(5068-5070)ATG>CTG	p.M1690L	C10orf18_uc001iik.2_Missense_Mutation_p.M534L	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	1690										ovary(1)|central_nervous_system(1)	2						AGCAGGCAGAATGGCCAGTTT	0.463													17	58	---	---	---	---	PASS
ABLIM1	3983	broad.mit.edu	37	10	116307474	116307474	+	Silent	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116307474C>T	uc010qsg.1	-	5	834	c.735G>A	c.(733-735)CAG>CAA	p.Q245Q	ABLIM1_uc010qsh.1_Silent_p.Q185Q|ABLIM1_uc010qsi.1_Silent_p.Q185Q|ABLIM1_uc010qsk.1_Silent_p.Q169Q|ABLIM1_uc009xyp.2_Silent_p.Q179Q|ABLIM1_uc009xyo.2_Silent_p.Q93Q	NM_002313	NP_002304	O14639	ABLM1_HUMAN	actin-binding LIM protein 1 isoform a	245	LIM zinc-binding 3.				axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		CCAAGTGCCACTGCTTATCCA	0.567													9	64	---	---	---	---	PASS
OR4C15	81309	broad.mit.edu	37	11	55321820	55321820	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55321820C>A	uc010rig.1	+	1	38	c.38C>A	c.(37-39)GCA>GAA	p.A13E		NM_001001920	NP_001001920	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C,	Error:Variant_position_missing_in_Q8NGM1_after_alignment					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						AATAATTTTGCACTTGGATGT	0.318										HNSCC(20;0.049)			64	175	---	---	---	---	PASS
PITPNM1	9600	broad.mit.edu	37	11	67266179	67266179	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67266179A>G	uc001olx.2	-	9	1561	c.1372T>C	c.(1372-1374)TCC>CCC	p.S458P	PITPNM1_uc001olw.2_5'Flank|PITPNM1_uc001oly.2_Missense_Mutation_p.S458P|PITPNM1_uc001olz.2_Missense_Mutation_p.S458P	NM_004910	NP_004901	O00562	PITM1_HUMAN	phosphatidylinositol transfer protein,	458					brain development|lipid metabolic process|phototransduction|protein transport	cleavage furrow|endoplasmic reticulum membrane|Golgi cisterna membrane|lipid particle|membrane fraction|midbody	metal ion binding|phosphatidylinositol transporter activity			lung(2)|central_nervous_system(1)	3						TCGAAGGCGGAGCTCAGCGTC	0.667													21	56	---	---	---	---	PASS
NARS2	79731	broad.mit.edu	37	11	78154737	78154737	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78154737C>A	uc001ozi.2	-	12	1608	c.1232G>T	c.(1231-1233)CGA>CTA	p.R411L	NARS2_uc010rsq.1_Missense_Mutation_p.R184L	NM_024678	NP_078954	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial	411					asparaginyl-tRNA aminoacylation	mitochondrial matrix	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding			ovary(2)	2	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	GAAATGGTATCGTTCTTCTCT	0.408													17	70	---	---	---	---	PASS
EXPH5	23086	broad.mit.edu	37	11	108389044	108389044	+	Silent	SNP	G	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108389044G>T	uc001pkk.2	-	5	660	c.549C>A	c.(547-549)GTC>GTA	p.V183V	EXPH5_uc010rvy.1_5'UTR|EXPH5_uc010rvz.1_Silent_p.V27V|EXPH5_uc010rwa.1_Silent_p.V107V	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	183					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTGGCTTTGGGACAAATGTAC	0.418													35	87	---	---	---	---	PASS
APOA5	116519	broad.mit.edu	37	11	116661335	116661335	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116661335G>A	uc001ppr.2	-	3	618	c.610C>T	c.(610-612)CGC>TGC	p.R204C	ZNF259_uc001ppp.2_5'Flank|ZNF259_uc009yzd.2_5'Flank|ZNF259_uc001ppq.2_5'Flank|APOA5_uc009yze.2_Missense_Mutation_p.R204C|APOA5_uc009yzf.2_Missense_Mutation_p.R204C|APOA5_uc009yzg.2_Missense_Mutation_p.R230C	NM_052968	NP_443200	Q6Q788	APOA5_HUMAN	apolipoprotein AV precursor	204					acylglycerol homeostasis|cholesterol homeostasis|lipid transport|lipoprotein metabolic process|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of receptor-mediated endocytosis|positive regulation of triglyceride catabolic process|positive regulation of very-low-density lipoprotein particle remodeling|tissue regeneration|triglyceride catabolic process|triglyceride homeostasis	chylomicron|high-density lipoprotein particle|very-low-density lipoprotein particle	enzyme binding|heparin binding|lipoprotein lipase activator activity|low-density lipoprotein particle receptor binding|phosphatidylcholine binding				0	all_hematologic(175;0.0487)	all_cancers(61;3.31e-09)|all_epithelial(67;8.03e-06)|Breast(348;0.0126)|Melanoma(852;0.0153)|Acute lymphoblastic leukemia(157;0.0257)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0433)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;4.93e-06)|all cancers(92;0.000123)|OV - Ovarian serous cystadenocarcinoma(223;0.149)		TGCACGTGGCGCCCGATGCCG	0.701													8	21	---	---	---	---	PASS
GPR84	53831	broad.mit.edu	37	12	54757575	54757575	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54757575A>G	uc001sfu.2	-	2	151	c.61T>C	c.(61-63)TAT>CAT	p.Y21H		NM_020370	NP_065103	Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	21	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			breast(2)	2						ACTGCAACATAACGATAGCCC	0.582													14	17	---	---	---	---	PASS
FAM19A2	338811	broad.mit.edu	37	12	62147529	62147529	+	Splice_Site	SNP	T	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62147529T>A	uc001sqw.2	-	4	1773	c.260_splice	c.e4-1	p.A87_splice	FAM19A2_uc001sqv.2_Splice_Site|FAM19A2_uc001sqx.2_Splice_Site_p.A87_splice|FAM19A2_uc001sqy.2_Splice_Site	NM_178539	NP_848634	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)		CTATTGAAGCTATAAGAGAGA	0.388													43	154	---	---	---	---	PASS
C12orf51	283450	broad.mit.edu	37	12	112688106	112688106	+	Silent	SNP	G	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112688106G>C	uc009zwc.2	-	18	2544	c.2526C>G	c.(2524-2526)ACC>ACG	p.T842T	C12orf51_uc010syk.1_Silent_p.T664T|C12orf51_uc001tts.2_Silent_p.T655T|C12orf51_uc001ttt.3_Silent_p.T653T	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						CTTCCTCTATGGTCAGAGGCA	0.557													47	126	---	---	---	---	PASS
FLT3	2322	broad.mit.edu	37	13	28597599	28597599	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28597599T>C	uc001urw.2	-	19	2388	c.2306A>G	c.(2305-2307)GAA>GGA	p.E769G	FLT3_uc010aao.2_RNA|FLT3_uc010tdn.1_Missense_Mutation_p.E769G	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3 precursor	769	Protein kinase.|Cytoplasmic (Potential).				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)	TTTTTGGTTTTCATATTCAAT	0.363			Mis|O		AML|ALL								15	165	---	---	---	---	PASS
PCDH20	64881	broad.mit.edu	37	13	61987113	61987113	+	Silent	SNP	C	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61987113C>A	uc001vid.3	-	2	1483	c.1119G>T	c.(1117-1119)CTG>CTT	p.L373L	PCDH20_uc010thj.1_Silent_p.L373L	NM_022843	NP_073754	Q8N6Y1	PCD20_HUMAN	protocadherin 20	346	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|breast(1)|central_nervous_system(1)	6		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		TGTTTTCATCCAGGTGAAATA	0.438													52	245	---	---	---	---	PASS
KIAA0317	9870	broad.mit.edu	37	14	75136411	75136411	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75136411T>G	uc001xqb.2	-	15	2360	c.1855A>C	c.(1855-1857)AGT>CGT	p.S619R	KIAA0317_uc010tut.1_Missense_Mutation_p.S458R	NM_001039479	NP_001034568	O15033	K0317_HUMAN	hypothetical protein LOC9870	619	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|intracellular	ubiquitin-protein ligase activity			ovary(2)|kidney(1)|central_nervous_system(1)|pancreas(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00404)		TCCATCTCACTCATGTCATTG	0.398													60	158	---	---	---	---	PASS
WHAMML1	339005	broad.mit.edu	37	15	23205108	23205108	+	RNA	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23205108C>T	uc001yvg.2	-	2		c.687G>A			WHAMML1_uc010ayc.2_RNA|WHAMML1_uc010ayd.2_RNA|WHAMML1_uc010aye.1_RNA	NR_003521				Homo sapiens mRNA; cDNA DKFZp313L2232 (from clone DKFZp313L2232).												0						GTGGTTGCCACGGTAACTAAT	0.393													3	37	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34115263	34115263	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34115263C>T	uc001zhi.2	+	81	11132	c.11062C>T	c.(11062-11064)CAG>TAG	p.Q3688*	RYR3_uc010bar.2_Nonsense_Mutation_p.Q3683*	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3688					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGGTCTTATGCAGTCTTGCAG	0.438													4	105	---	---	---	---	PASS
TP53BP1	7158	broad.mit.edu	37	15	43748602	43748602	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43748602T>G	uc001zrs.2	-	12	2337	c.2189A>C	c.(2188-2190)AAG>ACG	p.K730T	TP53BP1_uc010udp.1_Missense_Mutation_p.K730T|TP53BP1_uc001zrq.3_Missense_Mutation_p.K735T|TP53BP1_uc001zrr.3_Missense_Mutation_p.K735T|TP53BP1_uc010udq.1_Missense_Mutation_p.K735T	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3	730					double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		TATTGCCAACTTTTGAGGGGA	0.413								Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					5	279	---	---	---	---	PASS
CORO1A	11151	broad.mit.edu	37	16	30199863	30199863	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30199863G>C	uc002dww.2	+	10	1369	c.1247G>C	c.(1246-1248)AGG>ACG	p.R416T	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|CORO1A_uc010bzq.2_Missense_Mutation_p.R416T|CORO1A_uc010bzr.2_Intron|CORO1A_uc002dwx.2_Missense_Mutation_p.R310T|CORO1A_uc002dwy.1_3'UTR|LOC606724_uc002dwz.1_5'Flank	NM_007074	NP_009005	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	416					cell-substrate adhesion|innate immune response|leukocyte chemotaxis|negative regulation of actin nucleation|phagolysosome assembly|positive chemotaxis|regulation of cell shape|uropod organization	actin filament|cortical actin cytoskeleton|lamellipodium|phagocytic cup|phagocytic vesicle membrane	actin filament binding|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein homodimerization activity				0						GGGCGCAGGAGGGCAGCACCA	0.672													8	23	---	---	---	---	PASS
SRCAP	10847	broad.mit.edu	37	16	30740445	30740445	+	Silent	SNP	T	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30740445T>C	uc002dze.1	+	26	6202	c.5817T>C	c.(5815-5817)CGT>CGC	p.R1939R	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Silent_p.R1734R	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	1939					interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			TCGGCCCTCGTTCTCCTGGCC	0.592													31	84	---	---	---	---	PASS
CES4	51716	broad.mit.edu	37	16	55794605	55794605	+	5'UTR	SNP	G	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55794605G>C	uc002eik.2	+	1					CES4_uc010cce.2_5'UTR	NR_003276				RecName: Full=Inactive carboxylesterase 4; AltName: Full=Placental carboxylesterase 3;          Short=PCE-3; Flags: Precursor;												0						CGCGGCTTGGGGTGAGTCCTT	0.582													4	27	---	---	---	---	PASS
GAST	2520	broad.mit.edu	37	17	39872101	39872101	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39872101C>A	uc002hxl.2	+	3	315	c.283C>A	c.(283-285)CGC>AGC	p.R95S	JUP_uc010wfs.1_Intron	NM_000805	NP_000796	P01350	GAST_HUMAN	gastrin preproprotein	95		Cleavage.				extracellular region	hormone activity				0		Breast(137;0.000307)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			CTTCGGCCGCCGCAGTGCTGA	0.557													3	55	---	---	---	---	PASS
CNP	1267	broad.mit.edu	37	17	40120540	40120540	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40120540C>T	uc002hyl.1	+	2	602	c.458C>T	c.(457-459)GCG>GTG	p.A153V	CNP_uc002hyk.1_Missense_Mutation_p.A153V|CNP_uc010wfz.1_Intron|CNP_uc002hym.1_Missense_Mutation_p.A133V|CNP_uc010wga.1_Intron	NM_033133	NP_149124	P09543	CN37_HUMAN	2',3'-cyclic nucleotide 3' phosphodiesterase	153					cell killing|cyclic nucleotide catabolic process|RNA metabolic process|synaptic transmission	extracellular space|melanosome	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity|ATP binding|protein binding				0		all_cancers(22;2.38e-06)|all_epithelial(22;6.79e-05)|Breast(137;0.000143)		UCEC - Uterine corpus endometrioid carcinoma (308;0.171)		CCCAAGACGGCGTGGCGGCTG	0.597													5	48	---	---	---	---	PASS
HSD17B1	3292	broad.mit.edu	37	17	40706578	40706578	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40706578A>G	uc002hzw.2	+	5	1663	c.695A>G	c.(694-696)CAG>CGG	p.Q232R	HSD17B1_uc002hzx.2_Missense_Mutation_p.Q233R|HSD17B1_uc010wgm.1_RNA|uc002hzy.2_5'UTR|HSD17B1_uc010cyi.2_Missense_Mutation_p.Q263R	NM_000413	NP_000404	P14061	DHB1_HUMAN	hydroxysteroid (17-beta) dehydrogenase 1	232					estrogen biosynthetic process	cytosol	binding|estradiol 17-beta-dehydrogenase activity				0		all_cancers(22;5.59e-08)|all_epithelial(22;7e-07)|Ovarian(249;0.0261)		BRCA - Breast invasive adenocarcinoma(366;0.129)	NADH(DB00157)	GAGGCGGCGCAGAACCCTGAG	0.692													12	21	---	---	---	---	PASS
ITGA2B	3674	broad.mit.edu	37	17	42457990	42457990	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42457990C>T	uc002igt.1	-	14	1449	c.1417G>A	c.(1417-1419)GCC>ACC	p.A473T	ITGA2B_uc002igu.1_5'UTR	NM_000419	NP_000410	P08514	ITA2B_HUMAN	integrin alpha 2b preproprotein	473	Extracellular (Potential).|FG-GAP 7.				axon guidance|integrin-mediated signaling pathway|platelet activation|platelet degranulation	integrin complex|platelet alpha granule membrane	identical protein binding|receptor activity			ovary(2)|lung(1)	3		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Tirofiban(DB00775)	ACCTGGTTGGCCCCGTAAGCT	0.592													4	87	---	---	---	---	PASS
COL1A1	1277	broad.mit.edu	37	17	48267076	48267076	+	Silent	SNP	A	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48267076A>T	uc002iqm.2	-	38	2757	c.2631T>A	c.(2629-2631)CCT>CCA	p.P877P		NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein	877	Triple-helical region.				axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1)	382					Collagenase(DB00048)|Palifermin(DB00039)	CAGCAGCACCAGGGAAACCAG	0.622			T	PDGFB|USP6	dermatofibrosarcoma protuberans|aneurysmal bone cyst 		Osteogenesis imperfecta						13	36	---	---	---	---	PASS
DSG1	1828	broad.mit.edu	37	18	28911765	28911765	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28911765C>T	uc002kwp.2	+	6	831	c.619C>T	c.(619-621)CCA>TCA	p.P207S		NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	207	Extracellular (Potential).|Cadherin 2.				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			TTCAGATTCACCAATGTTTAT	0.343													5	246	---	---	---	---	PASS
ZNF396	252884	broad.mit.edu	37	18	32948335	32948335	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32948335A>C	uc010xcf.1	-	5	1114	c.982T>G	c.(982-984)TCA>GCA	p.S328A		NM_145756	NP_665699	Q96N95	ZN396_HUMAN	zinc finger protein 396	Error:Variant_position_missing_in_Q96N95_after_alignment					viral reproduction	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						CCTGAAAGTGACCTGGGGCAC	0.373													36	186	---	---	---	---	PASS
SIRT6	51548	broad.mit.edu	37	19	4180866	4180866	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4180866T>A	uc002lzo.2	-	2	167	c.107A>T	c.(106-108)GAA>GTA	p.E36V	ANKRD24_uc010dtt.1_5'Flank|SIRT6_uc002lzn.2_5'UTR|SIRT6_uc002lzp.2_Missense_Mutation_p.E36V|SIRT6_uc010xid.1_Intron|SIRT6_uc002lzq.2_Missense_Mutation_p.E36V|SIRT6_uc002lzr.2_Intron	NM_016539	NP_057623	Q8N6T7	SIRT6_HUMAN	sirtuin 6	36	Deacetylase sirtuin-type.				chromatin silencing|protein ADP-ribosylation	nuclear telomeric heterochromatin|nucleoplasm	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|protein binding|zinc ion binding			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.023)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTCGCCAGTTCCCACACCTT	0.627													16	42	---	---	---	---	PASS
ZNF358	140467	broad.mit.edu	37	19	7584511	7584511	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7584511C>T	uc002mgn.2	+	2	553	c.383C>T	c.(382-384)ACT>ATT	p.T128I		NM_018083	NP_060553	Q9NW07	ZN358_HUMAN	zinc finger protein 358	128					embryonic forelimb morphogenesis|neural tube development|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1						TCTGGCCTCACTGCCACCCCC	0.557													35	66	---	---	---	---	PASS
ZNF627	199692	broad.mit.edu	37	19	11725352	11725352	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11725352C>T	uc002msk.2	+	2	222	c.14C>T	c.(13-15)GCC>GTC	p.A5V	ZNF627_uc010dyf.2_5'UTR	NM_145295	NP_660338	Q7L945	ZN627_HUMAN	zinc finger protein 627	5	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						GATTCAGTGGCCTTTGAGGAT	0.423													48	106	---	---	---	---	PASS
PRDX2	7001	broad.mit.edu	37	19	12907780	12907780	+	3'UTR	SNP	G	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12907780G>C	uc002mvd.2	-	6						NM_005809	NP_005800	P32119	PRDX2_HUMAN	peroxiredoxin 2 isoform a						anti-apoptosis|cell redox homeostasis|hydrogen peroxide catabolic process|removal of superoxide radicals		thioredoxin peroxidase activity				0						TGTGGAGTTTGGAGGGGCAGG	0.637											OREG0025274	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	5	---	---	---	---	PASS
ZNF527	84503	broad.mit.edu	37	19	37879644	37879644	+	Silent	SNP	G	A	A	rs73930983		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37879644G>A	uc010efk.1	+	5	804	c.693G>A	c.(691-693)ACG>ACA	p.T231T	ZNF527_uc002ogf.3_Silent_p.T199T|ZNF527_uc010xtq.1_RNA	NM_032453	NP_115829	Q8NB42	ZN527_HUMAN	zinc finger protein 527	231					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACCAGAGTACGTACCTTAGTA	0.348													51	162	---	---	---	---	PASS
CYTH2	9266	broad.mit.edu	37	19	48975743	48975743	+	Intron	SNP	C	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48975743C>A	uc002pjj.3	+						uc002pjg.2_5'Flank|CYTH2_uc010xzr.1_Silent_p.T132T|CYTH2_uc002pji.2_Intron	NM_017457	NP_059431	Q99418	CYH2_HUMAN	cytohesin 2 isoform 1						actin cytoskeleton organization|endocytosis|regulation of ARF protein signal transduction|regulation of cell adhesion	cytoplasm|membrane fraction|plasma membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1						TCCCTCCCACCCCCCAGACCC	0.662													16	6	---	---	---	---	PASS
POLD1	5424	broad.mit.edu	37	19	50905132	50905132	+	Silent	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50905132C>T	uc002psb.3	+	4	470	c.414C>T	c.(412-414)TGC>TGT	p.C138C	POLD1_uc002psc.3_Silent_p.C138C|POLD1_uc010enx.2_RNA|POLD1_uc010eny.2_Silent_p.C138C	NM_002691	NP_002682	P28340	DPOD1_HUMAN	DNA-directed DNA polymerase delta 1	138					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|DNA synthesis involved in DNA repair|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|response to UV|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	delta DNA polymerase complex|nucleoplasm|nucleotide-excision repair complex	3'-5'-exodeoxyribonuclease activity|chromatin binding|DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding|protein binding			upper_aerodigestive_tract(1)|central_nervous_system(1)	2		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		TCTCTGTCTGCTGCCACATCC	0.711								DNA_polymerases_(catalytic_subunits)					31	60	---	---	---	---	PASS
EPB41L1	2036	broad.mit.edu	37	20	34778270	34778270	+	Silent	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34778270C>T	uc002xfb.2	+	10	1269	c.1098C>T	c.(1096-1098)GTC>GTT	p.V366V	EPB41L1_uc002xeu.2_Silent_p.V304V|EPB41L1_uc010zvo.1_Silent_p.V366V|EPB41L1_uc002xev.2_Silent_p.V366V|EPB41L1_uc002xew.2_Silent_p.V269V|EPB41L1_uc002xex.2_Silent_p.V335V|EPB41L1_uc002xey.2_Silent_p.V293V|EPB41L1_uc002xez.2_Silent_p.V304V	NM_012156	NP_036288	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	366	FERM.				cortical actin cytoskeleton organization|synaptic transmission	cytoskeleton|cytosol|extrinsic to membrane|plasma membrane	actin binding|structural molecule activity			ovary(2)|pancreas(1)	3	Breast(12;0.0239)					TGTGGAAGGTCTGCATCGAGC	0.537													9	28	---	---	---	---	PASS
RBPJL	11317	broad.mit.edu	37	20	43938268	43938268	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43938268T>C	uc002xns.2	+	3	265	c.193T>C	c.(193-195)TGT>CGT	p.C65R	MATN4_uc002xnn.2_5'Flank|MATN4_uc002xno.2_5'Flank|MATN4_uc002xnp.2_5'Flank|MATN4_uc002xnr.1_5'Flank|RBPJL_uc002xnt.2_Missense_Mutation_p.C65R	NM_014276	NP_055091	Q9UBG7	RBPJL_HUMAN	recombining binding protein L	65					signal transduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				GCAGCAACAGTGTGAACAGAC	0.617													22	46	---	---	---	---	PASS
PIGT	51604	broad.mit.edu	37	20	44049024	44049024	+	Silent	SNP	G	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44049024G>C	uc002xoh.1	+	7	895	c.822G>C	c.(820-822)CTG>CTC	p.L274L	PIGT_uc010ghb.1_Silent_p.L264L|PIGT_uc010zwt.1_RNA|PIGT_uc010ghd.1_Silent_p.L181L|PIGT_uc010ghc.1_RNA|PIGT_uc010ghe.1_Silent_p.L237L|PIGT_uc010ghf.1_Silent_p.L227L|PIGT_uc002xoj.1_Silent_p.L274L|PIGT_uc002xok.1_Silent_p.L239L|PIGT_uc010zwu.1_Silent_p.L12L|PIGT_uc002xoi.1_RNA|PIGT_uc010zwv.1_Silent_p.L12L|PIGT_uc010zww.1_Silent_p.L218L|PIGT_uc010zwx.1_Silent_p.L109L|PIGT_uc010zwy.1_Silent_p.L172L|PIGT_uc010zwz.1_Silent_p.L12L|PIGT_uc010zxa.1_Silent_p.L112L|PIGT_uc002xol.1_Silent_p.L130L|PIGT_uc010zxb.1_5'UTR	NM_015937	NP_057021	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	274	Lumenal (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			pancreas(1)	1		Myeloproliferative disorder(115;0.0122)				CCTGCCCCCTGGCTTCAGAGA	0.612													4	26	---	---	---	---	PASS
BPIL2	254240	broad.mit.edu	37	22	32853321	32853321	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32853321A>T	uc003amn.2	-	1	53	c.53T>A	c.(52-54)CTC>CAC	p.L18H	BPIL2_uc010gwo.2_5'UTR|BPIL2_uc011amb.1_5'UTR|BPIL2_uc003amo.3_Missense_Mutation_p.L18H	NM_174932	NP_777592	Q8NFQ6	BPIL2_HUMAN	bactericidal/permeability-increasing	18						extracellular region	lipopolysaccharide binding|phospholipid binding			ovary(1)|skin(1)	2						TGAGACATAGAGATTCCACAG	0.433											OREG0003513	type=REGULATORY REGION|Gene=BPIL2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	43	110	---	---	---	---	PASS
UPK3A	7380	broad.mit.edu	37	22	45683306	45683306	+	Silent	SNP	A	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45683306A>C	uc003bfy.2	+	3	468	c.462A>C	c.(460-462)GCA>GCC	p.A154A	UPK3A_uc010gzy.2_Intron	NM_006953	NP_008884	O75631	UPK3A_HUMAN	uroplakin 3A precursor	154	Lumenal (Potential).				epithelial cell differentiation	endoplasmic reticulum membrane|integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TCTGTAACGCACCCCTGTCGG	0.602													4	6	---	---	---	---	PASS
MTMR8	55613	broad.mit.edu	37	X	63568632	63568632	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:63568632T>A	uc004dvs.2	-	6	708	c.640A>T	c.(640-642)ACT>TCT	p.T214S	MTMR8_uc011mou.1_Missense_Mutation_p.T214S|MTMR8_uc004dvt.1_Missense_Mutation_p.T214S	NM_017677	NP_060147	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	214	Myotubularin phosphatase.					nuclear envelope	protein tyrosine phosphatase activity			ovary(2)|breast(2)	4						ACACAGCGAGTGTAAAATCCA	0.433													27	66	---	---	---	---	PASS
RGAG4	340526	broad.mit.edu	37	X	71351148	71351148	+	Silent	SNP	C	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71351148C>A	uc010nlh.1	-	1	604	c.243G>T	c.(241-243)GGG>GGT	p.G81G	NHSL2_uc011mqa.1_Intron|RGAG4_uc004eaj.1_RNA|NHSL2_uc004eak.1_5'Flank|NHSL2_uc010nli.2_5'Flank	NM_001024455	NP_001019626	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	81										ovary(2)|skin(1)	3	Renal(35;0.156)					GCAGTTCTCCCCCGGGAATGA	0.597													30	61	---	---	---	---	PASS
GUCY2F	2986	broad.mit.edu	37	X	108691325	108691325	+	Silent	SNP	C	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108691325C>T	uc004eod.3	-	6	1818	c.1542G>A	c.(1540-1542)ACG>ACA	p.T514T	GUCY2F_uc011msq.1_RNA	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	514	Cytoplasmic (Potential).				intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8						GATTGATAAACGTTACATCCT	0.289													54	116	---	---	---	---	PASS
RAB33A	9363	broad.mit.edu	37	X	129306270	129306270	+	Silent	SNP	G	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129306270G>T	uc004evl.2	+	1	498	c.234G>T	c.(232-234)GTG>GTT	p.V78V	RAB33A_uc010nre.2_RNA	NM_004794	NP_004785	Q14088	RB33A_HUMAN	Ras-related protein Rab-33A	78					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding				0						AGAAGACCGTGGAAATCGAGG	0.622													26	101	---	---	---	---	PASS
SLITRK4	139065	broad.mit.edu	37	X	142717613	142717613	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142717613C>A	uc004fbx.2	-	2	1688	c.1312G>T	c.(1312-1314)GAG>TAG	p.E438*	SLITRK4_uc004fby.2_Nonsense_Mutation_p.E438*	NM_173078	NP_775101	Q8IW52	SLIK4_HUMAN	slit and trk like 4 protein precursor	438	Extracellular (Potential).|LRR 9.					integral to membrane				upper_aerodigestive_tract(1)|large_intestine(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)					TAGAGTCTCTCAATTTGATTG	0.363													6	227	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	153627003	153627003	+	5'UTR	SNP	C	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153627003C>A	uc010nuv.1	-	1					RPL10_uc004fkm.2_Intron|RPL10_uc004fko.2_Intron|RPL10_uc004fkn.1_Intron|RPL10_uc004fkp.1_Intron|RPL10_uc004fkq.1_5'Flank|RPL10_uc004fkr.1_5'Flank|SNORA70_uc010nux.1_5'Flank					Homo sapiens cDNA, FLJ97181.																		GTCTTGGGAACTGACCCTATG	0.547													10	73	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	4274160	4274163	+	IGR	DEL	CTTT	-	-	rs11801817		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4274160_4274163delCTTT								LOC100133612 (440283 upstream) : LOC284661 (197948 downstream)																							tccttccttcctttcttccttcct	0.078													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	29691887	29691888	+	IGR	INS	-	TTTCTTTCTCTTCTTTCTTTC	TTTCTTTCTCTTCTTTCTTTC	rs139763080	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29691887_29691888insTTTCTTTCTCTTCTTTCTTTC								PTPRU (38572 upstream) : None (None downstream)																							ttctttttctttttctttctct	0.035													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	72969498	72969499	+	IGR	INS	-	CTCC	CTCC	rs146980338	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72969498_72969499insCTCC								NEGR1 (221093 upstream) : None (None downstream)																							tctctctccctctctctttctt	0.030													5	3	---	---	---	---	
ST7L	54879	broad.mit.edu	37	1	113126863	113126864	+	Intron	INS	-	A	A	rs76579294		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113126863_113126864insA	uc001ecd.2	-						ST7L_uc009wgh.2_Intron|ST7L_uc001ecc.2_Intron|ST7L_uc010owg.1_Intron|ST7L_uc010owh.1_Intron|ST7L_uc001ece.2_Intron|ST7L_uc001ecf.2_Intron|ST7L_uc001ecg.2_Intron|ST7L_uc010owi.1_Intron|ST7L_uc001ech.2_Intron|ST7L_uc001eci.2_Intron|ST7L_uc009wgi.1_Intron|ST7L_uc010owj.1_Intron	NM_017744	NP_060214	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7-like isoform 1						negative regulation of cell growth	integral to membrane	binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCCATCTTTAGAAAAAAAAAAA	0.317													4	3	---	---	---	---	
C1orf125	126859	broad.mit.edu	37	1	179335499	179335500	+	Intron	INS	-	T	T	rs35129223		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179335499_179335500insT	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmn.1_Intron|C1orf125_uc010pnl.1_Intron|C1orf125_uc001gmp.2_Intron	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1												0						TAGTTGTCATCTTTTTTTTTTT	0.431													4	4	---	---	---	---	
ELF3	1999	broad.mit.edu	37	1	201980096	201980096	+	5'UTR	DEL	T	-	-	rs60246030		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201980096delT	uc001gxg.3	+	1					ELF3_uc001gxi.3_Intron|ELF3_uc001gxh.3_Intron	NM_004433	NP_004424	P78545	ELF3_HUMAN	E74-like factor 3 (ets domain transcription						epidermis development|epithelial cell differentiation|inflammatory response|mammary gland involution|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0						TGGTCTGAGATCTTGGAGCCC	0.622													4	2	---	---	---	---	
HHIPL2	79802	broad.mit.edu	37	1	222711950	222711950	+	Intron	DEL	A	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222711950delA	uc001hnh.1	-							NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2 precursor						carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)		taaaaaTATTAAAATAAAAAG	0.214													47	26	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	223352884	223352885	+	IGR	INS	-	CTTT	CTTT	rs61837572	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223352884_223352885insCTTT								TLR5 (36260 upstream) : SUSD4 (41278 downstream)																							ttccttccttcctttctttctt	0.045													4	2	---	---	---	---	
ATAD2B	54454	broad.mit.edu	37	2	24103433	24103433	+	Intron	DEL	A	-	-	rs75314008		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24103433delA	uc002rek.3	-						ATAD2B_uc010yki.1_Intron|ATAD2B_uc010exx.1_Intron	NM_017552	NP_060022	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B								ATP binding|nucleoside-triphosphatase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					actctgtctcaaaaaaaaaaa	0.179													5	3	---	---	---	---	
SOS1	6654	broad.mit.edu	37	2	39224748	39224749	+	Intron	DEL	TT	-	-	rs149992654		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39224748_39224749delTT	uc002rrk.3	-						SOS1_uc002rrj.3_Intron	NM_005633	NP_005624	Q07889	SOS1_HUMAN	son of sevenless homolog 1						apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)				AAGACTTAAATTTTTTTTTTTT	0.198									Noonan_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	44293377	44293377	+	IGR	DEL	G	-	-	rs61062797		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44293377delG								LRPPRC (70233 upstream) : PPM1B (102623 downstream)																							TTTTTGTTTTGTTTTTTTTTT	0.313													4	5	---	---	---	---	
RGPD1	400966	broad.mit.edu	37	2	88091357	88091357	+	Intron	DEL	A	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88091357delA	uc010fhc.1	-						RGPD1_uc002ssm.1_Intron	NM_001024457	NP_001019628	Q68DN6	RGPD1_HUMAN	RANBP2-like and GRIP domain containing 1						intracellular transport		binding				0						accctgtcttaaaaaaaaaaa	0.194													9	7	---	---	---	---	
TMEM37	140738	broad.mit.edu	37	2	120195182	120195183	+	3'UTR	INS	-	G	G	rs2278565	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120195182_120195183insG	uc002tly.2	+	2						NM_183240	NP_899063	Q8WXS4	CCGL_HUMAN	transmembrane protein 37							integral to membrane	calcium channel activity|voltage-gated ion channel activity			breast(1)	1						AGAAATGGCCCGGGGGCCTCTG	0.584													5	3	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	133636255	133636256	+	Intron	DEL	CA	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133636255_133636256delCA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						acacaccgcccacacacacaca	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232509782	232509785	+	IGR	DEL	CTTT	-	-	rs144976269		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232509782_232509785delCTTT								C2orf57 (50790 upstream) : PTMA (63450 downstream)																							ccctccctccctttctttcttttt	0.152													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	103257382	103257382	+	IGR	DEL	T	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103257382delT								None (None upstream) : None (None downstream)																							TTTACACAGCTTTTTTTTTTT	0.348													3	3	---	---	---	---	
C3orf52	79669	broad.mit.edu	37	3	111824387	111824390	+	Intron	DEL	GTGT	-	-	rs143779896		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111824387_111824390delGTGT	uc003dyq.3	+						C3orf52_uc011bhs.1_Intron|C3orf52_uc011bht.1_Intron	NM_024616	NP_078892	Q5BVD1	TTMP_HUMAN	TPA-induced transmembrane protein							endoplasmic reticulum membrane|integral to membrane					0						ttctttggccgtgtgtgtgtgtgt	0.093													4	2	---	---	---	---	
BOD1L	259282	broad.mit.edu	37	4	13581618	13581619	+	Intron	DEL	AA	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13581618_13581619delAA	uc003gmz.1	-							NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division								DNA binding			ovary(5)|breast(1)	6						ATAAACAAACAAAAAAAAATTT	0.322													4	2	---	---	---	---	
TMEM156	80008	broad.mit.edu	37	4	39000163	39000164	+	Intron	INS	-	AAA	AAA			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39000163_39000164insAAA	uc003gto.2	-						TMEM156_uc010ifj.2_Intron	NM_024943	NP_079219	Q8N614	TM156_HUMAN	transmembrane protein 156							integral to membrane				skin(1)	1						gactccatctcaaaaaaaaaaa	0.094													4	2	---	---	---	---	
LIMCH1	22998	broad.mit.edu	37	4	41421714	41421714	+	Intron	DEL	T	-	-	rs140812988		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41421714delT	uc003gvu.3	+						LIMCH1_uc003gvt.1_Intron|LIMCH1_uc003gvv.3_Intron|LIMCH1_uc003gvw.3_Intron|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Intron|LIMCH1_uc003gvy.3_Intron	NM_014988	NP_055803	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4						ccttccttccttccttccttc	0.000													6	3	---	---	---	---	
HERC5	51191	broad.mit.edu	37	4	89414077	89414077	+	Intron	DEL	T	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89414077delT	uc003hrt.2	+						HERC5_uc011cdm.1_Intron	NM_016323	NP_057407	Q9UII4	HERC5_HUMAN	hect domain and RLD 5						innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		acaattaatgttagctattta	0.144													43	24	---	---	---	---	
NHEDC1	150159	broad.mit.edu	37	4	103869482	103869483	+	Intron	INS	-	AC	AC			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103869482_103869483insAC	uc003hww.2	-						NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1							integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		ggcaaagccatacacacacaca	0.000													4	3	---	---	---	---	
MAML3	55534	broad.mit.edu	37	4	140750130	140750133	+	Intron	DEL	AGGA	-	-	rs35172258		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140750130_140750133delAGGA	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187	Q96JK9	MAML3_HUMAN	mastermind-like 3						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)					ctgtTGAAAGaggaaggaaggaag	0.034													2	4	---	---	---	---	
TRIM2	23321	broad.mit.edu	37	4	154098798	154098799	+	Intron	INS	-	A	A	rs61641662		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154098798_154098799insA	uc003ing.2	+							NM_001130067	NP_001123539	Q9C040	TRIM2_HUMAN	tripartite motif-containing 2 isoform 2							cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		actccttctccaaaaaaaaaaa	0.020													6	3	---	---	---	---	
SPOCK3	50859	broad.mit.edu	37	4	167663386	167663389	+	Intron	DEL	ATCT	-	-	rs35160494		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167663386_167663389delATCT	uc003iri.1	-						SPOCK3_uc011cjp.1_Intron|SPOCK3_uc011cjq.1_Intron|SPOCK3_uc011cjr.1_Intron|SPOCK3_uc003irj.1_Intron|SPOCK3_uc011cjs.1_Intron|SPOCK3_uc011cjt.1_Intron|SPOCK3_uc011cju.1_Intron|SPOCK3_uc011cjv.1_Intron	NM_016950	NP_058646	Q9BQ16	TICN3_HUMAN	testican 3 isoform 2						signal transduction	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase inhibitor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		tctatctatcatctatctatctat	0.211													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1649912	1649913	+	IGR	DEL	TC	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1649912_1649913delTC								LOC728613 (15792 upstream) : MRPL36 (148587 downstream)																							tttctctctttctctctctctc	0.000													3	3	---	---	---	---	
ADAMTS16	170690	broad.mit.edu	37	5	5232302	5232302	+	Intron	DEL	A	-	-	rs10713189		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5232302delA	uc003jdl.2	+						ADAMTS16_uc003jdk.1_Intron|ADAMTS16_uc010itk.1_5'Flank	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						TTGGGTAAGGAAAAAAAAAAC	0.363													6	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	90475765	90475772	+	IGR	DEL	GAAGGAAG	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90475765_90475772delGAAGGAAG								GPR98 (15733 upstream) : ARRDC3 (188769 downstream)																							aaggaaggaagaaggaaggaaggaagga	0.029													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116217510	116217513	+	IGR	DEL	GGAA	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116217510_116217513delGGAA								SEMA6A (306959 upstream) : None (None downstream)																							ATGAATGAGTGgaaggaaggaagg	0.059													6	3	---	---	---	---	
FAM13B	51306	broad.mit.edu	37	5	137295680	137295680	+	Intron	DEL	A	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137295680delA	uc003lbz.2	-						FAM13B_uc003lcb.2_Intron|FAM13B_uc003lca.2_Intron	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN	hypothetical protein LOC51306 isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0						GTGTTTTCACAACCAAGTCTC	0.313													5	3	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155935513	155935513	+	Intron	DEL	A	-	-	rs111768881		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155935513delA	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTCAAAAATTAAAAAAAAAAA	0.303													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	9661051	9661052	+	IGR	DEL	AA	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9661051_9661052delAA								None (None upstream) : TFAP2A (735865 downstream)																							GTGTTACAGCAAAAAAAAAAAA	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	15144681	15144684	+	IGR	DEL	AAAC	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15144681_15144684delAAAC								None (None upstream) : JARID2 (101050 downstream)																							agaaagaaagaaacaaacaaagaa	0.000													6	7	---	---	---	---	
STK19	8859	broad.mit.edu	37	6	31948381	31948382	+	Intron	DEL	CC	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31948381_31948382delCC	uc003nyv.2	+						STK19_uc003nyt.2_Intron|STK19_uc011dox.1_Intron|STK19_uc003nyw.2_Intron|STK19_uc010jtn.1_Intron|C4A_uc011doy.1_5'Flank|C4A_uc011doz.1_5'Flank|C4A_uc011dpa.1_5'Flank	NM_032454	NP_115830	P49842	STK19_HUMAN	serine/threonine kinase 19 isoform 2							nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			skin(4)	4						GCTCCTCAGGCCTCTAGGCCTT	0.550													87	41	---	---	---	---	
CYP39A1	51302	broad.mit.edu	37	6	46607082	46607082	+	Intron	DEL	T	-	-	rs145394714		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46607082delT	uc003oyf.1	-						CYP39A1_uc011dwa.1_Intron|CYP39A1_uc010jzd.1_Intron	NM_016593	NP_057677	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A,						bile acid biosynthetic process|bile acid catabolic process|digestion|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	24-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(1)	1						caaaaaaaaaTAATTTAAAAG	0.219													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	47798995	47798996	+	IGR	DEL	TC	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47798995_47798996delTC								OPN5 (4881 upstream) : C6orf138 (47044 downstream)																							tttccttctttctctttctttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50864684	50864687	+	IGR	DEL	CTTC	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50864684_50864687delCTTC								TFAP2B (49359 upstream) : PKHD1 (615458 downstream)																							tccttcctttcttccttccttcct	0.025													4	2	---	---	---	---	
IL17F	112744	broad.mit.edu	37	6	52109409	52109409	+	5'Flank	DEL	T	-	-	rs3215541		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52109409delT	uc003pam.1	-							NM_052872	NP_443104	Q96PD4	IL17F_HUMAN	interleukin 17F precursor						cartilage development|inflammatory response|lymphotoxin A biosynthetic process|negative regulation of angiogenesis|proteoglycan metabolic process|regulation of granulocyte macrophage colony-stimulating factor biosynthetic process|regulation of interleukin-2 biosynthetic process|regulation of interleukin-6 biosynthetic process|regulation of interleukin-8 biosynthetic process|regulation of transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|cytokine binding|protein homodimerization activity			ovary(1)	1	Lung NSC(77;0.116)					AATGCAGGGGTTTTTTTTTTT	0.418													1	7	---	---	---	---	
LRRC1	55227	broad.mit.edu	37	6	53787794	53787794	+	3'UTR	DEL	T	-	-	rs67155925		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53787794delT	uc003pcd.1	+	14						NM_018214	NP_060684	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1							cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		CCCGGTGTGATTTTTTTTTTT	0.458													5	3	---	---	---	---	
C6orf165	154313	broad.mit.edu	37	6	88123761	88123762	+	Intron	INS	-	AAT	AAT	rs140289881	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88123761_88123762insAAT	uc003plv.2	+						C6orf165_uc003plw.2_Intron|C6orf165_uc010kbv.1_Intron|C6orf165_uc003plu.1_Intron	NM_001031743	NP_001026913	Q8IYR0	CF165_HUMAN	hypothetical protein LOC154313 isoform 1											central_nervous_system(1)	1		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		AGGAATACAACGTTAGAAATGC	0.302													7	5	---	---	---	---	
AKD1	221264	broad.mit.edu	37	6	109818530	109818531	+	Intron	DEL	CA	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109818530_109818531delCA	uc003ptn.2	-						AKD1_uc011eas.1_Intron	NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1						agtgcttgttcacacacacaca	0.000													6	3	---	---	---	---	
LAMA4	3910	broad.mit.edu	37	6	112463694	112463695	+	Intron	INS	-	A	A	rs141758766	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112463694_112463695insA	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TGAAAGAAAGCAAAAAAAAAGT	0.391													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	55659699	55659699	+	IGR	DEL	C	-	-	rs140374894		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55659699delC								VOPP1 (19499 upstream) : LOC442308 (53613 downstream)																							CTCAGCTGCACCCCCCCTCTT	0.587													5	4	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	70786929	70786930	+	Intron	INS	-	CCTT	CCTT	rs150369774	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70786929_70786930insCCTT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				ctccctccctcccttccttcct	0.000													7	5	---	---	---	---	
CCDC146	57639	broad.mit.edu	37	7	76796901	76796901	+	Intron	DEL	A	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76796901delA	uc003uga.2	+						CCDC146_uc003ufz.1_Intron	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				GTTTATTTTTATTATTTTCCA	0.264													4	2	---	---	---	---	
MCPH1	79648	broad.mit.edu	37	8	6390140	6390141	+	Intron	INS	-	C	C	rs141106218	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6390140_6390141insC	uc003wqi.2	+						ANGPT2_uc003wqj.3_Intron|ANGPT2_uc003wqk.3_Intron|ANGPT2_uc010lri.2_Intron|ANGPT2_uc003wql.3_Intron	NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin							microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		TACCTTGCCTTCCTTTTGGAAT	0.312													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	21329938	21329938	+	IGR	DEL	G	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21329938delG								None (None upstream) : GFRA2 (219592 downstream)																							gagggaaggagggaaggGGAA	0.204													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101438774	101438776	+	IGR	DEL	ATT	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101438774_101438776delATT								RNF19A (116447 upstream) : ANKRD46 (83211 downstream)																							caccgccatcattaccaccacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42383711	42383712	+	IGR	INS	-	C	C			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42383711_42383712insC								None (None upstream) : LOC441666 (443603 downstream)																							tcaaatggaatcaaaataacca	0.000													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	59302920	59302921	+	IGR	INS	-	G	G			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59302920_59302921insG								None (None upstream) : IPMK (652697 downstream)																							gaaggaaggaaggaaggaagga	0.000													3	3	---	---	---	---	
DNA2	1763	broad.mit.edu	37	10	70184845	70184845	+	Intron	DEL	C	-	-	rs75564385		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70184845delC	uc001jof.2	-						DNA2_uc001jog.1_Intron|DNA2_uc001joh.1_Intron	NM_001080449	NP_001073918	P51530	DNA2L_HUMAN	DNA replication helicase 2 homolog						base-excision repair|DNA replication, removal of RNA primer|mitochondrial DNA repair|mitochondrial DNA replication|positive regulation of DNA replication|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	mitochondrial nucleoid|nucleoplasm	5'-flap endonuclease activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|site-specific endodeoxyribonuclease activity, specific for altered base				0						TGGAACAtttctttttttttt	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81340488	81340491	+	IGR	DEL	AAGG	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81340488_81340491delAAGG								SFTPA2 (20325 upstream) : SFTPA1 (30221 downstream)																							ggaaggaagtaaggaaggaaggaa	0.010													3	3	---	---	---	---	
PKD2L1	9033	broad.mit.edu	37	10	102058696	102058701	+	Intron	DEL	TTATTA	-	-	rs72108775		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102058696_102058701delTTATTA	uc001kqx.1	-						PKD2L1_uc009xwm.1_Intron	NM_016112	NP_057196	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1						signal transduction	integral to membrane	calcium activated cation channel activity|calcium ion binding|cytoskeletal protein binding			ovary(4)	4		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		AAAattattgttattattattattat	0.238													4	2	---	---	---	---	
VAX1	11023	broad.mit.edu	37	10	118897632	118897632	+	5'UTR	DEL	C	-	-	rs56950787		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118897632delC	uc009xyx.2	-	1					VAX1_uc001ldb.1_5'UTR	NM_001112704	NP_001106175	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1 isoform a							nucleus	sequence-specific DNA binding			ovary(2)	2				all cancers(201;0.0108)		GGGGGGGGGGCGGAGAAGGAA	0.438													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69610156	69610159	+	IGR	DEL	TTTC	-	-	rs148354284		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69610156_69610159delTTTC								FGF4 (19985 upstream) : FGF3 (14578 downstream)																							tttctttctttttctctttctttt	0.029													4	4	---	---	---	---	
RNF169	254225	broad.mit.edu	37	11	74460517	74460518	+	Intron	INS	-	A	A	rs138072056	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74460517_74460518insA	uc001ovl.3	+							NM_001098638	NP_001092108	Q8NCN4	RN169_HUMAN	ring finger protein 169								zinc ion binding			ovary(1)	1						TCCCGGGCCCTACTCGGGCGGG	0.644													8	5	---	---	---	---	
MANSC1	54682	broad.mit.edu	37	12	12482821	12482821	+	3'UTR	DEL	A	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12482821delA	uc001rai.1	-	4					MANSC1_uc010shm.1_3'UTR|MANSC1_uc001raj.1_3'UTR|MANSC1_uc009zht.1_3'UTR	NM_018050	NP_060520	Q9H8J5	MANS1_HUMAN	MANSC domain containing 1 precursor							integral to membrane					0		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		ctctgtctccaaaaaaaaaaa	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68946696	68946696	+	IGR	DEL	T	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68946696delT								MDM1 (220535 upstream) : RAP1B (57956 downstream)																							caaattattcttttttTTTTT	0.179													4	2	---	---	---	---	
TDG	6996	broad.mit.edu	37	12	104378858	104378859	+	Intron	INS	-	AC	AC	rs61937634		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104378858_104378859insAC	uc001tkg.2	+						TDG_uc009zuk.2_Intron|TDG_uc010swi.1_Intron|TDG_uc010swj.1_Intron	NM_003211	NP_003202	Q13569	TDG_HUMAN	thymine-DNA glycosylase						depyrimidination|mismatch repair	nucleoplasm	damaged DNA binding|mismatched DNA binding|protein binding|pyrimidine-specific mismatch base pair DNA N-glycosylase activity			ovary(3)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(302;0.00114)		tatacatatatacacataagta	0.069								BER_DNA_glycosylases					6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	105775874	105775875	+	IGR	DEL	GT	-	-	rs113016921		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105775874_105775875delGT								C12orf75 (10579 upstream) : NUAK1 (681250 downstream)																							ctcaaaaaaagtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119145988	119145993	+	IGR	DEL	TGGTGA	-	-	rs146473069		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119145988_119145993delTGGTGA								SUDS3 (290149 upstream) : SRRM4 (273403 downstream)																							gtgatggtggtggtgatggtggtggt	0.000													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73153055	73153056	+	IGR	DEL	AC	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73153055_73153056delAC								DACH1 (711725 upstream) : C13orf37 (129439 downstream)																							acacacacagacacacacacac	0.218													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20081407	20081408	+	IGR	DEL	AC	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20081407_20081408delAC								P704P (61135 upstream) : OR4Q3 (134179 downstream)																							ATATATGTGGacacacacacac	0.257													4	3	---	---	---	---	
C14orf37	145407	broad.mit.edu	37	14	58699122	58699123	+	Intron	INS	-	T	T	rs5808963		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58699122_58699123insT	uc010tro.1	-						ACTR10_uc001xdf.2_Intron|ACTR10_uc001xdg.2_Intron|ACTR10_uc001xdh.2_Intron|ACTR10_uc010trp.1_Intron|ACTR10_uc010apc.2_Intron	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor							integral to membrane	binding				0						CTGACtttttcttttttttttt	0.144													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	85281016	85281023	+	IGR	DEL	CCTCCCTC	-	-	rs76839618		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85281016_85281023delCCTCCCTC								None (None upstream) : FLRT2 (715465 downstream)																							tcccttccttcctccctccctccctccc	0.125													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106016171	106016171	+	Intron	DEL	T	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106016171delT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						Ggccggaaggttttttttttt	0.353													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	36749321	36749324	+	IGR	DEL	ACAT	-	-	rs66473257		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36749321_36749324delACAT								ATPBD4 (910917 upstream) : C15orf41 (122488 downstream)																							acacacacacacatacacacacac	0.338													6	4	---	---	---	---	
RAD51	5888	broad.mit.edu	37	15	40993575	40993575	+	Intron	DEL	T	-	-	rs67977099		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40993575delT	uc001zmi.3	+						RAD51_uc010bbw.2_Intron|RAD51_uc010bbx.2_Intron|RAD51_uc001zmk.3_Intron|RAD51_uc001zml.3_Intron|RAD51_uc001zmm.1_Intron|RAD51_uc001zmn.1_Intron	NM_002875	NP_002866	Q06609	RAD51_HUMAN	RAD51 homolog protein isoform 1						DNA recombinase assembly|DNA unwinding involved in replication|mitotic recombination|positive regulation of DNA ligation|protein homooligomerization|reciprocal meiotic recombination	mitochondrial matrix|nucleus|perinuclear region of cytoplasm|PML body	ATP binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|protein C-terminus binding|single-stranded DNA binding|single-stranded DNA-dependent ATPase activity				0		all_cancers(109;1.19e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.45e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000421)|COAD - Colon adenocarcinoma(120;0.163)		tttttctttcttttttttttt	0.124								Homologous_recombination					5	5	---	---	---	---	
ATP8B4	79895	broad.mit.edu	37	15	50152132	50152132	+	3'UTR	DEL	A	-	-	rs34981519		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50152132delA	uc001zxu.2	-	28					ATP8B4_uc010ber.2_3'UTR|ATP8B4_uc010ufd.1_3'UTR|ATP8B4_uc010ufe.1_RNA|ATP8B4_uc001zxt.2_3'UTR	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		AGGTTGATTTAAAAAAAAAAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	60085738	60085739	+	IGR	DEL	CA	-	-	rs10566064		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60085738_60085739delCA								BNIP2 (104096 upstream) : FOXB1 (210682 downstream)																							TTTCTAATACcacacacacaca	0.252													4	2	---	---	---	---	
DAPK2	23604	broad.mit.edu	37	15	64325525	64325526	+	Intron	INS	-	AGG	AGG	rs150809859	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64325525_64325526insAGG	uc002amr.2	-						DAPK2_uc010uim.1_Intron|DAPK2_uc010bgu.1_Intron	NM_014326	NP_055141	Q9UIK4	DAPK2_HUMAN	death-associated kinase 2						apoptosis|induction of apoptosis|intracellular protein kinase cascade	cytoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2				LUAD - Lung adenocarcinoma(2;0.215)		ggaaggaaggaaAAAAAAAATA	0.015													5	3	---	---	---	---	
C16orf71	146562	broad.mit.edu	37	16	4794635	4794636	+	Intron	INS	-	TTCA	TTCA	rs144683946	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4794635_4794636insTTCA	uc002cxn.2	+							NM_139170	NP_631909	Q8IYS4	CP071_HUMAN	hypothetical protein LOC146562											central_nervous_system(1)	1						GTCACTCCTACTTCACCAAGCC	0.500													4	3	---	---	---	---	
PARN	5073	broad.mit.edu	37	16	14700252	14700252	+	Intron	DEL	G	-	-	rs62037478		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14700252delG	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						aagaccctgagggaaaaaaaa	0.139													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21409629	21409630	+	IGR	DEL	AC	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21409629_21409630delAC								NCRNA00169 (79717 upstream) : NPIPL3 (3821 downstream)																							tctataTTAAacacacacacac	0.153													4	2	---	---	---	---	
ZCCHC14	23174	broad.mit.edu	37	16	87500652	87500652	+	Intron	DEL	T	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87500652delT	uc002fjz.1	-						ZCCHC14_uc002fka.1_Intron	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14						cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AAAAAAATTGTtttttttttt	0.229													3	4	---	---	---	---	
GLOD4	51031	broad.mit.edu	37	17	673936	673936	+	Intron	DEL	T	-	-	rs72295826		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:673936delT	uc002frv.2	-						GLOD4_uc002frt.2_Intron|GLOD4_uc002fru.2_Intron|GLOD4_uc010vqc.1_Intron	NM_016080	NP_057164	Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4							mitochondrion					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		cgcatctatgttttttttttt	0.000													5	6	---	---	---	---	
RPA1	6117	broad.mit.edu	37	17	1779217	1779217	+	Intron	DEL	T	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1779217delT	uc002fto.2	+							NM_002945	NP_002936	P27694	RFA1_HUMAN	replication protein A1						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	actin cytoskeleton|cytoplasm|DNA replication factor A complex|PML body	metal ion binding|protein binding|single-stranded DNA binding				0						GGGTTTACTCTTTTTTTTTTT	0.358								NER					4	4	---	---	---	---	
NCOR1	9611	broad.mit.edu	37	17	15948314	15948314	+	Intron	DEL	A	-	-	rs112069615		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15948314delA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpl.2_Intron|NCOR1_uc002gpm.2_Intron|NCOR1_uc010vwb.1_Intron|NCOR1_uc010coy.2_Intron	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TGAACTTAAGAAAAAAAAAAA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	26744464	26744465	+	IGR	INS	-	A	A			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26744464_26744465insA								SLC46A1 (11236 upstream) : SLC13A2 (56199 downstream)																							ACAACTATGCCAAAAGACATCC	0.431											OREG0024274	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68974725	68974726	+	IGR	INS	-	GGGA	GGGA			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68974725_68974726insGGGA								KCNJ2 (798544 upstream) : None (None downstream)																							aggaaaagaaggggagggaggg	0.084													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	77876983	77876984	+	IGR	INS	-	CTTC	CTTC	rs12943230	by1000genomes	TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77876983_77876984insCTTC								CBX4 (63770 upstream) : TBC1D16 (36837 downstream)																							ttccttccttcctttctttctt	0.000													6	3	---	---	---	---	
NRTN	4902	broad.mit.edu	37	19	5824421	5824422	+	Intron	DEL	GT	-	-	rs141994814		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5824421_5824422delGT	uc002mde.2	+							NM_004558	NP_004549	Q99748	NRTN_HUMAN	neurturin preproprotein						axon guidance|MAPKKK cascade|neural crest cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region	growth factor activity				0						GTGGGAGGTGGTGGGGGGGTGT	0.530													3	3	---	---	---	---	
MAP4K1	11184	broad.mit.edu	37	19	39096415	39096415	+	Intron	DEL	T	-	-			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39096415delT	uc002oix.1	-						MAP4K1_uc002oiw.1_Intron|MAP4K1_uc002oiy.1_Intron|MAP4K1_uc010xug.1_Intron	NM_007181	NP_009112	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|peptidyl-serine phosphorylation		ATP binding|MAP kinase kinase kinase kinase activity|protein binding|small GTPase regulator activity			skin(4)|lung(3)|ovary(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TCAGATGATCTCAGAGAGGGC	0.413													15	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20151890	20151891	+	IGR	INS	-	ACCATC	ACCATC	rs11280728		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20151890_20151891insACCATC								ZDHHC8 (16361 upstream) : LOC150197 (41964 downstream)																							tcaccatcgttaccatcaccat	0.025													5	3	---	---	---	---	
IL3RA	3563	broad.mit.edu	37	X	1501563	1501564	+	3'UTR	INS	-	T	T			TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1501563_1501564insT	uc004cps.2	+	12					IL3RA_uc011mhd.1_3'UTR	NM_002183	NP_002174	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	TGATAAAGTGATTTTTTTTTTT	0.426													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	64672722	64672723	+	IGR	DEL	AC	-	-	rs138713712		TCGA-CJ-4905-01A-02D-1429-08	TCGA-CJ-4905-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64672722_64672723delAC								ZC4H2 (418129 upstream) : ZC3H12B (35983 downstream)																							ctccatctAAacacacacacac	0.000													2	4	---	---	---	---	
